Subsurface Groundwater Dependent Ecosystems

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NATIONAL WATER COMMISSION—WATERLINES I

Subsurface Groundwater

Dependent Ecosystems:a review of their biodiversity,

ecological processes andecosystem services

Moya Tomlinson and Andrew BoultonUniversity of New England

Waterlines Occasional Paper No 8, October 2008



Waterlines

This paper is part of a series of works commissioned by the National Water Commission onkey water issues. This work has been undertaken by the University of New England on behalf of the National Water Commission.



©Commonwealth of Australia 2008

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Requests and enquiries concerning reproduction and rights should be addressed to theCommonwealth Copyright Administration, Attorney General’s Department, Robert GarranOffices, National Circuit, Barton ACT 2600 or posted at www.ag.gov.au/cca.

Online: ISBN 978-1-921107-67-2

Subsurface groundwater dependent ecosystems: a review of their biodiversity, ecologicalprocesses and ecosystem services, October 2008

Authors: Moya Tomlinson and Andrew Boulton

Published by the National Water Commission

95 Northbourne Avenue

Canberra ACT 2600

Tel: 02 6102 6088

Email: [email protected]

Date of publication: October 2008

Cover design by: AngelInk

Cover photo courtesy of Moya Tomlinson

Disclaimer

This paper is presented by the National Water Commission for the purpose of informingdiscussion and does not necessarily reflect the views or opinions of the Commission.

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Contents National Water Commission position statement........................................................................ iii Acknowledgements ....................................................................................................................v Executive summary...................................................................................................................vi1 Introduction............................................................................................................................ 1

1.1 Aims and scope of this review........................................................................................ 1 1.2 What are SGDEs?.......................................................................................................... 2 1.3 Brief description of the main occurrences of SGDEs..................................................... 51.4 A fundamental property of SGDEs: connection to other ecosystems............................ 8 1.5 Characteristics of SGDEs and their fauna ..................................................................... 9 1.6 Drivers of groundwater ecology ................................................................................... 10

2 Biodiversity values of SGDEs.............................................................................................. 12 2.1 Defining biodiversity ..................................................................................................... 12 2.2 The value of biodiversity .............................................................................................. 12 2.3 Subterranean biodiversity ............................................................................................ 13 2.4 Characteristics of stygobitic fauna ............................................................................... 14 2.5 Australian stygobitic biodiversity .................................................................................. 15

3 Subsurface ecological processes........................................................................................ 19 4 Provision of goods and services.......................................................................................... 21

4.1 Provisioning services ................................................................................................... 21 4.2 Supporting services...................................................................................................... 21 4.3 Regulating services...................................................................................................... 23 4.4 Cultural services........................................................................................................... 24

5 Management of SGDEs....................................................................................................... 26 5.1 Conservation ................................................................................................................ 26 5.2 Threatening processes and SGDEs............................................................................. 27

5.3 The potential impact of climate change ....................................................................... 28 5.4 Current policy setting in Australia................................................................................. 30 5.5 International groundwater policy: Europe .................................................................... 38 5.6 International groundwater policy: South Africa ............................................................ 39

6 Knowledge needs and research directions ......................................................................... 40 6.1 What is the appropriate management scale for SGDEs? ............................................ 43 6.2 A proposed typology of SGDEs ................................................................................... 44 6.3 Investigations of functional groups............................................................................... 49 6.4 What level of taxonomic identification is necessary?................................................... 51 6.5 Measuring biodiversity and monitoring management action........................................ 51 6.6 Priority research directions........................................................................................... 52

7 Conclusion........................................................................................................................... 55 8 References .......................................................................................................................... 56Glossary................................................................................................................................... 75

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List of tables Table 1: Characteristics of groundwater environments and implications for groundwater

biodiversity and ecology.................................................................................................... 9 Table 2: Stygobitic biodiversity in Australia ............................................................................. 16 Table 3: Ecosystem services provided by groundwater.......................................................... 21 Table 4: Legislation and policy addressing NWI requirements regarding environmental water

........................................................................................................................................ 30 Table 5: NWI objectives and actions relevant to environmental management of groundwater,

and actions reported in jurisdictional NWI implementation plans ................................... 33 Table 6: Knowledge needed to address NWI objectives, and suggested research questions 41 Table 7: Suggested SGDE typology........................................................................................ 47

List of figuresFigure 1: Conceptual model of factors influencing the biotic composition of SGDEs ............... 1 Figure 2: Location of regions and places referred to in the text................................................ 5 Figure 3: SGDEs (centre) are linked through ecotones (speckled area) to other ecosystems

(outer circle) ...................................................................................................................... 8 Figure 4: A classification of groundwater species based on their affinity to groundwater

habitats............................................................................................................................ 13 Figure 5: A new genus of bathynellid syncarid........................................................................ 15 Figure 6: Conceptual model of anthropogenic impacts on groundwater bodies..................... 39 Figure 7: The extremely coarse scale of identification of GDEs within groundwater

management units in the Australian Water Resources 2005 assessment..................... 43 Figure 8: Classification of major climate types in Australia ..................................................... 48 Figure 9: Response curves...................................................................................................... 50

List of boxesBox 1: A functional definition of groundwater............................................................................ 3 Box 2: Attributes of the groundwater water regime (GWR) (SKM 2001)................................... 3 Box 3: Classes of GDE (Eamus et al. 2006) ............................................................................. 3 Box 4: Subsurface groundwater dependent ecosystem............................................................ 4 Box 5: Resistance and resilience .............................................................................................. 7 Box 6: Values served by biodiversity conservation ................................................................. 12 Box 8: Adaptations to subsurface groundwater habitats......................................................... 14 Box 9: Nitrogen processes in groundwater ............................................................................. 19 Box 10: Case study 1 – J ewel Cave Western Australia .......................................................... 25 Box 11: EPBC Act listing of stygofaunal species and groundwater-dependent ecological

communities.................................................................................................................... 26 Box 12: Threatening processes in SGDEs.............................................................................. 27 Box 13: Symptoms of hydroschizophrenia .............................................................................. 31 Box 15: Necessary policy actions............................................................................................ 40 Box 16: Case study 2: An alluvial aquifer in temperate Australia – The Peel alluvium, NSW 45 Box 17: Case Study 2: An alluvial aquifer in arid Australia – Alice Springs Town Basin, NT . 46 Box 18: Understanding the groundwater resource.................................................................. 53

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National Water Commission positionWater-dependent ecosystems

Water-dependent ecosystems in Australia

Water-dependent ecosystems include wetlands, floodplains, riparian areas, estuaries andsprings. They provide many important services including provision of good quality water forirrigation and domestic use, habitat for fish and other aquatic fauna and flora, removal ofwastes and contaminants, and aesthetic, cultural and recreational benefits. Withoutadequate and timely water these ecosystems lose their capacity to provide such services. Insome cases, the losses may be irreversible; in others, they may be difficult and costly toreverse. Under current conditions, many significant water-dependent ecosystems are underthreat.

Commitments under the National Water Initiative to water-dependent ecosystems

Striking a balance between water for consumptive uses and water for ecosystem health—sothat environmental, social and economic outcomes are optimised—is integral to the NationalWater Initiative Agreement. Water planning is the fundamental means for achieving thisbalance. Overallocated water systems need to be restored to environmentally sustainablelevels of extraction; in other systems, crucial environmental assets and ecosystem servicesneed to be protected.

The National Water Initiative calls for:

• environmental water to enjoy the same security as water for consumptive uses

• environmental water managers to be established and equipped with the necessaryauthority and resources

• water market and trading arrangements to protect the needs of the environment• environmental water to be included in water accounts and audited

• periodic assessments of river and wetland health to be conducted so that adaptivemanagement can be undertaken on an evidence basis.

Progress on water-dependent ecosystems

The National Water Commission’s 2007 First Biennial Assessment of Progress in theImplementation of the National Water Initiative found that all states had made statutoryprovision for water to meet environmental and public benefit outcomes within water plans,however:

• over-allocated systems were not always adequately identified

• environmentally sustainable levels of extraction were poorly defined

•there was considerable variability in the quality of the science underpinning waterplans

• in many cases the trade-offs between environmental and consumptive uses werenot transparent

• there was often a lack of specificity in the environmental outcomes.The Commission considers that the protection of threatened water-dependent ecosystems,including the recovery of overallocated systems, continues to be a major challenge inimplementing the National Water Initiative Agreement.

The Commission’s water-dependent ecosystems activities

Over the past three years, the focus of Commission activities has been on filling knowledgegaps and promoting science to support good decisions about environmental water. Theseactivities have included:

• commissioning the synthesis of existing knowledge about specific aspects of water-dependent ecosystems and their management

NATIONAL WA TER COMMISSION — WATERLINES ii i



• commissioning scoping studies to identify critical knowledge gaps and provideguidance on research priorities

• providing grants to research programs addressing issues such as the formation ofacid sulfate sediments, water requirements for native fish populations and the use ofaerial surveys of waterbirds as indications for wetland health

• supporting environmental water managers by establishing a ‘community of practice’

where they can share experiences• undertaking trials of a national framework for assessing river and wetland health

(FARWH), with the intention that an agreed framework will be delivered in 2011.

Future directions for water-dependent ecosystems

The Commission will continue to build on these activities. However improved knowledgealone will not ensure that environmental outcomes are achieved. The Commission hastherefore adopted the following six priorities to guide future work involving the managementof water-dependent ecosystems:

1. Help develop and implement national guidelines and procedures for determiningenvironmentally sustainable levels of extraction of water. A nationally agreed methodwill expedite the formulation of water plans that protect water-dependentecosystems and include a pathway to recover overallocated systems. The methodswill include guidelines for establishing clear environmental outcomes.

2. Pursue an agreed national inventory of over-allocated water systems together withcommitments by governments to return them to sustainable levels of extraction.Identifying overallocated systems and recording agreed actions to recover the waterneeded to restore sustainability is central to achieving environmental outcomescontained in the NWI.

3. Improve the security of environmental water. In spite of the legislation now passed inall jurisdictions, environmental water allocations often lack specificity and there isuncertainty around the status and security of environmental water holdings.

4. Support more effective management of environmental water. There are manyshortcomings in the governance and operations of environmental water managers.Statutory empowerment, funding, skills and access to science, data and best

practice guidelines all require urgent attention. The development of a nationalcommunity of practice in environmental water management is an important initiativethat will support these water managers.

5. Strengthen the role of adaptive management of environmental water. Recent workcommissioned by the Commission1 showed there is a deficiency in monitoring andreporting on plan implementation. This is a significant weakness when coupled withgaps in ecological knowledge and the occurrence of climatic conditions outside theplanned-for circumstances. More systematic monitoring and reporting is essential toenable the water management regime to be adapted intelligently in the light ofexperience.

6. Implement the Framework for the Assessment of River and Wetland Health. While theCommission will continue to support the implementation of the Framework for the Assessment of River and Wetland Health, its successful adoption rests with the

parties to the National Water Initiative Agreement.

By pursuing these priorities, the Commission will play its part in promoting the enduringobjective of the National Water Initiative to manage water–dependent ecosystems to besteffect. We urge the parties to the National Water Initiative Agreement to do likewise.

National Water Commission

1 September 2008

1 Hamstead M., Baldwin, C. and O’Keefe, V. (2008) Water allocation planning in Australia –current practices and lessons learned. Waterline Occassional Paper No. 6, April 2008.National Water Commission.

iv NATIONAL WATER COMMISSION — WATERLINES



Acknowledgements For valuable discussion, additional references and helpful comments on drafts we thankAndy Austin (University of Adelaide), Steve Cooper (South Australian Museum), RussellCrosbie (CSIRO), Stefan Eberhard (Subterranean Ecology), Graham Fenwick (NationalInstitute of Water and Atmospheric Research, New Zealand), Hans J ürgen Hahn (Universityof Koblenz-Landau, Germany), Peter Hancock (University of New England), Stuart Halse(Bennelongia Pty. Ltd.), Bill Humphreys (Western Australian Museum), David Le Maitre(Council for Scientific and Industrial Research, South Africa), Sarah Mika (University of NewEngland), Dean Olsen (Cawthron Institute, New Zealand) and Ian Smith (Department of Natural Resources, Environment and the Arts, Northern Territory Government).

Support is gratefully acknowledged from the Australian Research Council and the ARC-funded Environmental Futures Network, and from the Wentworth Group of ConcernedScientists for MT to attend the XXXV Congress of the International Association of Hydrogeologists in Lisbon in September 2007.

The authors

Moya Tomlinson has a background in science communication and practical experience inwater policy and planning with the Northern Territory government. She is currently completingan ARC-funded PhD at the University of New England assessing the environmental waterrequirements of a subterranean ecosystem, with a focus on ecological requirements of invertebrates in groundwaters and the ecosystem goods and services that they supply.

Professor Andrew Boulton has worked on SGDEs since 1990, and has published papers ontheir ecological processes (for example, (Boulton et al. 1992, Boulton 1993, Boulton andStanley 1996, Boulton et al. 1998, Boulton and Hancock 2006), Boulton et al. 2002) andgoods and services ((Boulton 2000a, Boulton et al. 2003, Boulton 2005), Boulton et al. 2008)as well as presented invited addresses on SGDEs and processes threatening their ecology

(SIL, Dublin 1998, Fenner conference 2001). He has been on several expert panelsassessing ecological demands for SGDEs in Western Australia, South Australia, NSW andQueensland, and had considerable input into the NSW GDE policy document. He has cowritten two textbooks and over 100 research papers on aquatic ecology, and is internationallyknown for his work on GDEs, especially river baseflow systems and the hyporheic zone.

NATIONAL WATER COMMISSION — WATERLINES v



Executive summary This Waterlines report is part of a series of papers commissioned on issues relating toAustralian aquatic ecosystems. These Waterlines reports will contribute to improved

environmental water management by stimulating discussion, synthesising current thinking,identifying knowledge gaps and highlighting areas that warrant further investigation.

The papers draw together and synthesise the current knowledge and thinking on topics tostimulate ongoing discussion, debate and learning, highlight areas for further work, andimprove general knowledge and understanding of the environmental water requirements. Insome cases, guidelines and frameworks have been proposed to assist policy makers,planners and water managers in considering the issues. A part of each paper is theidentification of whether further work would be beneficial in each area, and where these areidentified, suggest directions for future investment.

This project aimed to:

• review knowledge of the biodiversity, ecological processes and ecosystem services of

subsurface groundwater dependent ecosystems (SGDEs) in Australia• identify research directions that will provide accessible information and tools to help

environmental water managers make informed contributions to the water planningprocess in relation to the needs of SGDEs in Australia.

We suggest that the sequestered location of SGDEs underground has led not only to thesehabitats being overlooked in favour of more accessible GDEs, but has also masked theirdiversity, ecosystem services and the close interconnections between SGDEs and otherecosystems.

Recognition of the variety of subsurface groundwater habitats and of the key habitatcharacteristics of living space and resource supply will aid understanding of the drivers of SGDE ecology and the ecological significance of SGDEs. To assist this understanding, weoutline a proposed typology of SGDEs that reflects a more ecologically-relevant scale for

management than the current groundwater management unit does.

Our overview of the biodiversity in SGDEs identifies extensive gaps in our knowledge of thedistribution, composition and biodiversity value of Australian stygofauna (groundwateranimals).

Despite this incomplete inventory, it is apparent that stygofauna are present across a varietyof Australian subsurface environments and are generally characterised by high diversity andlocal-scale endemicity. They are also often of high scientific interest, for example, theoccurrence of the only known southern hemisphere representatives of several phyletic relictlineages.

Microbes are a key component of SGDEs, forming the basis of the food chain and mediatingthe metabolism of carbon and other nutrients. Microbial activity degrades contaminants and

delivers energy and nutrients to aquifer food webs and to biota in connected ecosystems.Microbially-mediated bioremediation and metabolism are examples of ecosystem servicesprovided by SGDEs.

Other goods and services include providing water for a range of consumptive uses, regulatingthe effects of floods, supplying ecological and evolutionary refugia, supporting othergroundwater dependent ecosystems, and serving cultural values including those of science,Indigenous culture and recreation.

The interconnections between SGDEs and other ecosystems, both terrestrial and aquatic(including marine), indicate that threatening processes in SGDEs typically threatenecosystems connected to SGDEs.

Anthropogenic disturbance (for example, pollution or overextraction) or managementinterventions either in SGDEs or their connected systems have flow-on effects, often with timelags, so that impacts might not be evident for decades. Disturbances to the groundwaterregime result in a range of threats, including salinisation, pollution, eutrophication and land

NATIONAL WATER COMMISSION — WATERLINESvi



subsidence. We give some examples of these in this review, and we also consider the likelyimpact of climate change on SGDEs in Australia.

The interconnections between surface and subsurface ecosystems demonstrate that thewater needs of SGDEs must be considered in truly holistic water planning; and ecosystemfunctions of SGDEs must be maintained if only to meet desired environmental outcomes forsome surface waters.

The National Water Quality Management Strategy guidelines (ANZECC/ARMCANZ 2000)state in Box 1.1 on page 2 of the Introduction that ‘groundwater should be managed in such away that when it comes to the surface, whether from natural seepages or from bores, it willnot cause the established water quality objectives for these waters to be exceeded, norcompromise their designated environmental values’ and that ‘little is known of the lifecyclesand environmental requirements of [underground aquatic ecosystems and their novel fauna],and given their high conservation value, the groundwater upon which they depend should begiven the highest level of protection’.

National water reforms outlined in the National Water Initiative (NWI) require that water plansinclude an environmental allocation for the purpose of meeting environmental objectives,which are defined as maintaining ecosystem function (for example, through periodicinundation of floodplain wetlands), biodiversity, water quality; and river health targets.

In its first assessment of jurisdictional implementation of the NWI, the National WaterCommission found that progress towards environmental management of groundwater had notbeen achieved as envisaged. This lack of progress is unsurprising given the knowledge,technical and policy gaps identified in this review.

We argue there is an overriding imperative for groundwater management to undergo aparadigm shift, even though there are uncertainties about the distribution, taxonomy andecology of groundwater fauna, a lack of standard sampling protocols, no coordinated nationalrecording of survey data, and no established tools for assessing SGDE ecological condition orpredicting the magnitude and direction of change in condition following disturbance.

The tools and techniques that will enable water managers to achieve NWI objectives can bestbe developed by research and management that take an ecological perspective. This means

investigating key differences in habitat and resource supply between SGDE types,acknowledging the scale at which ecological processes occur, taking account of linkagesbetween SGDEs and other ecosystems, and managing SGDEs on a scale that is informed bythis ecological understanding.

The European experience of integrating management of surface water and groundwaterthrough the Water Framework Directive provides useful examples that merit closer attentionin Australia.

There are actions that can be taken without delay to improve cross-disciplinary working, takemaximum benefit from existing data and knowledge, and target research effort mostproductively. The key research directions are:

• more precise identification of SGDE types as a framework for investigations of ecosystem

responses to disturbance in the groundwater regime• confirmation that stygofauna provide useful indicators of the condition of SGDEs, and if

they are

• determination of the level of taxonomic identification required for faunal indicators of ecosystem condition.

Progress in these inquiries will help identify priorities for management action, and alsogenerate tools for water managers, so that knowledge and policy translates into watermanagement arrangements that meet policy goals.

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History of natural andClimate anthropogenic disturbance Geology Geomorphology

rate and volume

of infiltration porosity

Vegetation Aquifer material

Groundwater regime:

flux/flow, level/pressure and water quality

Abundance, richness anddistribution of subsurface

fauna and microbes

Biogeography, lifehistory strategies,

biotic interactions

permeability

Useable void space

Rate and volume of recharge

gradients of

environmental

conditions

1 Introduction

1.1 Aims and scope of this review

The purpose of this review is twofold.

Firstly, we summarise what is known about biodiversity in groundwater, the ecologicalprocesses in groundwater environments, and the ecosystem goods and services provided bysubsurface groundwater dependent ecosystems (SGDEs). The focus is on Australia.

Secondly, we match current knowledge with the knowledge needs of national policy on theenvironmental management of groundwater and its associated surface waters.

From the gaps between existing knowledge and knowledge needs, we identify directions forresearch that will produce accessible information and tools to help environmental watermanagers to make informed contributions to the water planning process regarding the needsof SGDEs.

The three main subject areas of this review – (1) biodiversity and taxonomy, (2) ecologicalprocesses and (3) ecosystem goods and services – are presented with reference to likelyhabitat types based on factors that influence subsurface biota and ecological processes(Figure 1).

Figure 1: Conceptual model of factors influencing the biotic composition of SGDEs

Notes: This diagram is taken from and modified substantially from a diagram of variables known to influence thehyporheos (Brunke and Gonser, 1997)

NATIONAL WATER COMMISSION — WATERLINES 1



1.2 What are SGDEs?

The need for careful definit ion

Our collective understanding of the ecology of SGDEs has lagged severely behind that of

surface waters; this has hampered effective management. An equal hindrance to sustainablemanagement of SGDEs is that the paradigm shift required for groundwater managers to fullyembrace ecological principles such as ecological sustainability and resilience/resistance todisturbance has only just begun.

Integral to such a paradigm shift is the consideration of new understandings of key conceptsand agreement on conceptual models to encapsulate these definitions and convey a sharedunderstanding and knowledge structure (after Benda et al. 2002).

The concepts and definitions of hydrogeology ably serve the purpose of managingunderground water for consumptive use. This goal of hydrogeology is demonstrated in theaccepted disciplinary definitions of its basic materials:

• groundwater is all water beneath the watertable in soils and geologic formations that are

fully saturated (Freeze and Cherry 1979)• an aquifer is a geologic unit that can store and transmit water at rates fast enough to

supply reasonable amounts of water to wells (bores) (Fetter 2001).

From an ecological point of view, these definitions are inadequate for sustainablemanagement of groundwater.

Ecology is the study of the relationships between living things and their environment.Ecologists study processes and interactions between and among the living and inanimatecomponents of ecosystems. From an ecological point of view, it is not useful to designatewater as groundwater simply on the basis of its subsurface location.

Consider the case of a stream soon after draining into a cave in a karstic area. Although it isnow technically groundwater, as it stands in a pool at the cave entrance, and as it flows

through subsurface conduits and voids, it retains the physical and chemical characteristics of the surface stream for varying periods of time depending on rate of flow, interactions with thesubstrate or subsurface matrix, and degree of mixing with water from subsurface sources.

Another example is a subsurface stream reach below large boulders and root mats (Collins etal. 2007) in which the biota and water chemistry (temperature, specific conductivity, dissolvedoxygen, and dissolved organic carbon concentrations) of subsurface water are similar tothose of the surface water. Similarly in the hyporheic zone – the zone of mixing betweensurface and groundwater below the bed of a stream (White 1993) – water is considered to beadvected surface water until it undergoes physico-chemical changes due to interactions withgroundwater and the sediment matrix (Fraser and Williams 1998). Groundwater is defined aswater that has not yet been influenced by channel processes (White 1993).

From an ecological perspective, aquifers are not simply containers of accessible and useable

water: the flow of water towards a bore in economically useful amounts is not alwaysecologically meaningful.

An ecological definition of an aquifer should consider its habitat characteristics: availability of food, shelter, and suitable conditions for respiration, reproduction and dispersal; and theaccompanying biogeochemical transformations of energy and matter (compare this with theidentification of streams as ecosystems by Triska et al. (1989)).

An ecological perspective is apparent in the definition of an aquifer in the European WaterFramework Directive (see later). This European definition requires two criteria to beconsidered in determining whether geological strata qualify as aquifers: (1) a significant flowof groundwater, and (2) that removal of groundwater would result in a significant diminution inthe ecological quality of a surface water body or a directly dependent terrestrial ecosystem(Scheidleder et al. 2008).

These ecological considerations frame our treatment of SGDEs, and point to the need for afunctional definition of groundwater for this review (Box 1).

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Box 1: A functional definition of groundwater

Water that has been present in pores and cracks of the saturated zone of soil or rock forsufficient time to undergo physical and chemical changes resulting from interactions with theaquifer environment.

This functional definition extends the hydrogeological definition (all water beneath the

watertable in soils and geologic formations that are fully saturated) to one that is ecologicallyrelevant. It is not proposed as a replacement for other definitions of groundwater, but it issuggested to help promote an ecological perspective.

The temporal component of this ecological definition of groundwater recognises the role thatchanges in water chemistry play in determining the characteristics and function of groundwater. These physical and chemical changes have likely repercussions for subsurfacemicrobes and invertebrates as well as for human consumption of groundwater.

The growing recognition that groundwaters are integral to many surface water systems andare ecosystems in their own right is reflected in at least two decades’ awareness of groundwater dependent ecosystems (GDEs), largely initiated in Australia by Hatton andEvans (1998).

These authors identified four main types of GDEs: terrestrial vegetation, river base flowsystems, aquifer and cave systems, and wetlands. The degree of dependency of theseecosystems on groundwater varies from complete dependency in the case of aquiferecosystems, to opportunistic use of groundwater by some terrestrial vegetation.

SKM (2001) extended their consideration of ecosystem dependency to include two moretypes – terrestrial fauna, and estuarine and nearshore marine systems. They also suggestedthree key attributes of groundwater on which ecosystem dependency is based (Box 2).

Box 2: Attributes of the groundwater water regime (GWR) (SKM 2001)

• flow or flux, or the rate and volume of supply of groundwater

• water level in unconfined aquifers and pressure in confined aquifers

• the chemical quality of groundwater expressed in terms of pH, salinity and/or otherpotential constituents, including nutrients and contaminants.

The attributes on which ecosystem dependency is based comprise the environmental waterrequirements of that ecosystem. Changes in these attributes could be deleterious todependent ecosystems.

For example, reduced groundwater flow can affect the rate of discharge to dependentecosystems such as cave or estuarine environments; lowered water levels can fall below therooting depth of groundwater-dependent terrestrial vegetation; and changes in water qualitycan exceed the tolerance ranges of aquifer fauna.

Most recently, Eamus et al. (2006) grouped GDEs into three classes (Box 3):

Box 3: Classes of GDE (Eamus et al. 2006)

• aquifer and cave ecosystems

• ecosystems dependent on the surface expression of groundwater, for example moundsprings, baseflow rivers, and estuarine seagrass beds

• ecosystems dependent on the subsurface presence of groundwater, for example wherevegetation has roots accessing groundwater.

This classification identified ecosystems associated with a common groundwater resource. Itspurpose was to assist managers to identify appropriate tools for assessing groundwaterdependency; for example, for the first class, microbial plating or faunal sampling; for thesecond, stable isotopes or tracers; and for the third, physiological measurements of plantwater use.

The advantage of this classification is that it goes some way towards helping us seek parallelsand contrasts in the behaviour of functionally-similar GDEs.




This review focuses on aquifer ecosystems, here termed SGDEs (Box 4), and the aquaticfauna that inhabits these ecosystems.

Box 4: Subsurface groundwater dependent ecosystem

An ecosystem occurring below the surface of the ground that would be significantly altered bya change in the chemistry, volume and/or temporal distribution of its groundwater supply.

Adapted from Parsons and Wentzel (2007)

These systems are the least known GDEs, partly because of their sequestered nature, butalso because research into terrestrial GDEs has been prioritised following therecommendation of Hatton and Evans (1998) that there not be a large investment ininvestigations of aquifer ecosystems.

Subsequent research has focused on the water needs of terrestrial GDEs, and a recent‘toolbox’ of techniques (Clifton et al. 2007) for assessing the environmental waterrequirements of GDEs addresses only terrestrial vegetation, wetlands and river systems.

Despite the shared characteristic of being subterranean, there is a great variety of aquifersystems in karstic, calcrete, alluvial and fractured rock environments. Not all subterraneanecosystems and species are groundwater dependent.

Caves and other subsurface voids can harbour terrestrial fauna (troglofauna (Humphreys2000a)) that do not rely directly on groundwater, although groundwater provides a humidenvironment and carries food from the surface. Troglofauna have been recorded from cavesin karstified carbonate rocks in the Kimberley, Cape Range, Barrow Island, Perth Basin (forexample, Eneabba, J urien, Yanchep), the Leeuwin-Naturaliste Ridge and the Nullarbor Plain(Eberhard 2007) and in voids of pisolite in the Pilbara (Biota Environmental Services 2006).Figure 2 shows regions and places mentioned in this report.

Due to their dependence on high relative humidity, troglofauna might be affected by aquiferdewatering and other changes to the groundwater regime and so could have somegroundwater dependence. Where terrestrial fauna are found in association with particulargroundwater habitats, such as fauna on cave walls permanently wetted by seepinggroundwater (Sket 2004), they are clearly groundwater dependent. For example, Sket (2004)

describes leptodirine beetles in the film of seeping groundwater on the walls of karstic cavesfrom north-eastern Italy to Montenegro. These beetles walk in the film, dipping theirmouthparts into the water to collect food particles. Their morphological adaptations to thisenvironment include thickened femora, large, curved claws, and mouthparts specialised forfilter feeding.

Anchialine habitats illustrate the variety and complexity of many SGDEs. These habitats arebodies of saline water with subterranean connections to the sea and restricted openings tothe open air, showing marine and terrestrial influences (Iliffe 2000).

Anchialine pools and sinkholes are stratified, with fresher groundwater overlying deepersaline water. Water in anchialine pools or sinkholes reflects tidal movements to a varyingextent, depending on distance from the sea. Typically, anchialine fauna occur at depthswhere the salinity is equivalent to that of seawater (Humphreys 1999b).




Figure 2: Location of regions and places referred to in this report

Ngalia Basin

Alice

Springs

Cape

Range

Pilbara

Kimberley

Yilgarn

Nullarbor

Peelalluvium

Great Artesian Basin

Yanchep

BarrowIsland

Christmas

Island (2300 km NW

of Perth)

Perth

Murchisonregion

Leeuwin-

NaturalisteJewel

Caveridge

1.3 Brief description of the main occurrences of SGDEs

Unconsolidated aquifers

Unconsolidated aquifers consist of particles of gravel, sand, silt or clay that are not bound bymineral cement, by pressure or by thermal alteration of the grains (Freeze and Cherry 1979).Deposition can be by wind (aeolian aquifers, for example in sand dunes), flowing water(alluvial aquifers), or by settlement of sediment in lakes (lacustrine aquifers).

Stanford and Ward (1993) proposed that alluvial aquifers are a component of a continuum inwhich the aquifer-river complex can be conceptualised as a network of active channels and a

series of hydrogeological units linked dynamically by the ‘hyporheic corridor’. Zones andpathways of differential permeability follow palaeochannels laid down by variable flows.

On a larger scale, alluvial aquifers represent an interstitial highway linking spatiallydiscontinuous subterranean ecosystems with surface waters (Ward and Palmer 1994).

Stygofaunal surveys have concentrated on unconsolidated alluvial habitats because thesehigh-yielding aquifers are the focus of groundwater extraction and the associated network of monitoring bores allows ready access for sampling (Hancock and Boulton in press).

Fractured rock aquifers

Fractured rock aquifers occur in rocks of sedimentary, igneous or metamorphic origin.

Fissures or cracks develop along bedding planes or in zones of stress caused by pressurechanges due to tectonic movement, glaciation, erosion of overburden, or rapid temperaturechanges (Fetter 2001).




Groundwater flow follows the fractures, but in sedimentary rock, the flow might also permeatethe rock matrix: depending on the geology there can be a complex and spatially variable dual-porosity environment. Fissures and joints can become enlarged solution cavities thateventually form large voids.

Fractured rock aquifers are undersampled, but stygofauna have been recorded from thishabitat type in the Pilbara region of Australia (Eberhard et al. 2005).

Karst

Karst is a term describing a landscape rather than an aquifer type (Fetter 2001). It is a terraincharacterised by sinkholes, caves and springs developed most commonly in carbonate rockswhere significant solution of the rock has occurred due to flowing water. The distinctlandforms of karst are due to the action of subterranean drainage. Karstic terrain can alsodevelop by other processes – weathering, hydraulic action, tectonic movements, melt waterand the evacuation of molten rock (lava). Because the dominant process in these cases is notsolution, this suite of landforms is termed pseudokarst (Halliday 2007). An example is theUndara Lava Tubes in north Queensland.

Karst in Australia occurs in scattered outcrops in the highlands from north Queensland to Tasmania, with a concentration in south-east Australia; in dunal limestones along southwesterly facing shores from Cape Range, Western Australia to Victoria; extensively in marinelimestones on the Nullarbor; in the Kimberley, and across northern Australia to the Barkly Tableland in Queensland (Finlayson and Hamilton-Smith 2003).

The karstic caves in the Swan Coastal Plain and the Leeuwin-Naturaliste Ridge contain rootmat communities (J asinska et al. 1996), which are listed as threatened ecologicalcommunities under Commonwealth endangered species legislation (see later section).

Karstic systems provide a wide variety of habitats characterised by periodicity of saturation,climatic influences and degrees of connection to streams and groundwater systems. They arealso highly heterogeneous due to spatial differences in groundwater flow rates because of thevariable occurrence of conduits and fissures (Bakalowicz 2005).

Calcrete aquifers

Calcretes are carbonate deposits that form in the soil or in the vicinity of the watertable as aresult of evaporation of soil water or groundwater respectively. Calcretes may develop alongpalaeochannel systems in a succession of chemical precipitations associated with increasingsalinity. Episodic recharge and fluctuating groundwater levels create solution cavities alonglow-gradient drainage lines.

Calcrete aquifers are technically karstic because the cavities are formed by solution, but it isuseful to treat them here as a separate habitat type. Groundwater calcretes (Mann andHorowitz 1979) occur in Australia north of about latitude 30° South in an area where meanannual rainfall is less than 200 millimetres and potential annual evaporation exceeds 3000

millimetres. These provided refugia for relict lineages following the onset of aridity(Humphreys 2001).

Calcrete aquifers are widespread in the Australian arid zone and many of those alreadysampled have yielded a rich and diverse invertebrate fauna (Humphreys 2001, Watts andHumphreys 2006) in which the species are largely endemic to a single calcrete body (Leys etal. 2003, Cooper et al. in press, Guzik et al. 2008).

Pisolite

Another type of chemically-precipitated aquifer occurs in pisolote mesas or channel irondeposits in the Pilbara. These are highly permeable due to tertiary porosity and are apotentially rich but little investigated faunal habitat (Biota Environmental Services 2006).




Ecotones: the hyporheic and vadose zones

The definition of groundwater ecosystems has broadened to include the hyporheic zone(Hancock et al. 2005). The hyporheic zone is the zone in a stream bed where surface waterand groundwater mix (White 1993).

It can be defined more specifically as ‘a spatially fluctuating ecotone between the surfacestream and the deep groundwater where important ecological processes and theirrequirements and products are influenced at a number of scales by water movement,permeability, substrate particle size, resident biota, and the physicochemical features of theoverlying stream and adjacent aquifers’ (Boulton et al. 1998).

Upwelling groundwater creates zones of low dissolved oxygen and organic matter, the veryconditions favourable to stygobites. In the arid zone, the hyporheos of ephemeral streams isgroundwater-dependent for most of the time, many species relying entirely on subsurfacewater after surface pools have dried (Boulton et al. 1992, Cooling and Boulton 1993).

The vadose zone is the unsaturated zone above the watertable in which the spaces betweenparticles are only partially filled with water. Water in the vadose zone can be percolatingrainwater or discharging groundwater. In the arid zone, where rainfall is low but groundwater

tables are close enough to the surface to support terrestrial vegetation (O'Grady et al. 2006a),fauna in the vadose zone can be considered groundwater dependent because vadose zonemoisture is discharging groundwater.

In karstic aquifers, the vadose zone is a complex rock–soil interface termed epikarst or ‘skinof karst’ (Bakalowicz 2004). The epikarst in Europe (Pipan and Culver 2007) and NorthAmerica (Pipan et al. 2006) has been found to hold a diverse stygofauna distinct from thefauna found in the saturated zone. Sampling of epikarst in southwestern Western Australia, Tasmania and New South Wales indicates that epikarst is likely to support stygofauna(Eberhard 2004).

Aquitards

Another largely uninvestigated subterranean habitat can be found in aquitards, or compactaquifers (after Hahn and Fuchs (submitted)) comprising aquifers with a reduced pore size anda very low hydraulic conductivity (less than 10–6 m/s), such as clay, loess and very fine sands,and also compact rock formations.

A survey of 16 bores (sampled twice) in ‘compact aquifers’ in Germany yielded stygofauna inmore than half of the bores, although the fauna was depauperate compared with that of nearby alluvial, karstic and fractured rock aquifers.

These compact formations, which are not technically classified as aquifers, are SGDEs andmight play a role in the resilience of other groundwater ecosystems (Box 5), for example bycontributing to habitat heterogeneity.

We are not suggesting here that each of these habitat types necessarily harbours a distinctive

fauna. Where connections between habitats exist, there might be a broad overlap of taxa,although richness and abundances differ. Eberhard et al. (2005) state that, with the exceptionof large taxa such as fish, which require large voids and are restricted to karstic aquifers,stygofauna from the Pilbara and adjacent areas are found wherever groundwaterenvironments provide suitable habitat, including in porous, karstic, and fractured-rock aquifersas well as the hyporheic zone and springs.

Box 5: Resistance and resilience

Resistance is the capacity to withstand a disturbance, for example through desiccation-resistant eggs or life stages.

Resilience is the ability to recover from a disturbance, for example, by occupying refugia

offered by fine scale microhabitat differences.(Fritz and Dodds 2004)




This tendency to habitat generality by many taxa indicates that conclusions about habitataffinity and consequent faunal distribution based on limited sampling should be drawn withcaution. But it is also true that some taxa are restricted in range, sometimes to within a singlecalcrete body (Cooper et al. in press).

Rather than enabling prediction of faunal distribution, the suggested habitat types offers anapproach to understanding the main aspects of groundwater regime and living space, thehabitat traits most relevant to stygofaunal community composition.

These habitat aspects are likely to be hierarchically important, rather like a series of filterscontrolling faunal distribution (Poff 1997). For example, Reeves et al. (2007) found thatsubregional differentiation in ostracod genera in the Pilbara, Western Australia, wasdetermined primarily by altitude, then surface drainage basin, and finally aquifer.

1.4 A fundamental property of SGDEs:connection to other ecosystems

SGDEs are connected to terrestrial and aquatic surface ecosystems through transition zones

including the hyporheic zone, the vadose zone, marine upwelling and intrusion zones and thepsammolittoral (Figure 3). There can also be direct connections between SGDEs, forexample, where an alluvial aquifer overlies or is interdigitated with another aquifer type.

The interfaces between habitats are usually characterised by spatially and temporallydynamic gradients in environmental conditions that make precise delineation of ecosystemboundaries difficult. These dynamic ecotones (Vervier et al. 1992) are zones of exchange of materials and energy and potential pathways for faunal dispersal and transmission of contaminants.

The interconnections between SGDEs and surface aquatic systems are most well-known inalluvial aquifers that are hydraulically interactive with rivers and floodplains over extensivereaches. In these environments, the hyporheic zone often extends not only longitudinallyalong the river but also laterally for several kilometres, suggesting that alluvial aquifers can be

conceptualised as the core of an ‘interstitial highway’ (Ward and Palmer 1994).

Figure 3: SGDEs (centre) are linked through ecotones (speckled area) to other ecosystems(outer circle)

SGDEs

Freshwater

psammo-

littoral

Hyporheic

zone

Marine

psammo

littoral

Riparian

vegetation

Marine and

estuarineSurface

waters

Terrestrial

vegetation

Vadose

zone

Marine

upwelling

and intrus ion

(Springs, rivers,

wetlands)




Characteristics o f groundwater environments

Implications for fauna Implications for biodiversity,ecological processes andecosystem services

Relatively stableenvironmental conditionscompared with surfaceaquatic environments

Buffering from environmentalchange taking place at thesurface

Fauna are morphologicallyconservative

Selective pressure towards

delayed breeding, longer lifecycles, larger size and feweryoung

Reduced habitatheterogeneity (Sket 1999)

Persistent habitat for relictlineages

Fauna are potentiallyvulnerable to changes ingroundwater regime

Morphological similarity and

cryptic speciation requiresthat taxonomic approachescombine morphological andmolecular investigations

Lightless No primary producers;herbivores represented onlyby root-mat feeders; fewerpredators; a trophic shifttowards omnivory; food webtruncated and dominated by

detritivores (Gibert andDeharveng 2002)

A low number of lineageshave passed through theecological filter of lightlessness

Microbes rather than plantsare the basis of the foodchain and therefore have keyroles in supportingbiodiversity and ecosystemfunction

Typically restricted inputs of energy; low productivity

Fauna have slower metabolicrates (Danielopol et al. 1994),longer life cycles, lowerfecundity (Dole-Olivier et al.2000) than surfacecounterparts

Overall densities are usually

very low due to lack of food

Some species have restrictedability to respond rapidly toenvironmental change or torecolonise readily after localextinction; low resilience andresistance

Some species are able to

respond rapidly to prolongedincreases in food availability

Close monitoring is requiredto detect population declinebut response time can bedecades

May be spatially discrete orpatchy

Restricted dispersal andrecruitment

High potential for speciationand short range endemism

Vulnerable to habitat changeresulting in local or totalextinction of species

1.5 Characteristics of SGDEs and their fauna

Despite the variety of SGDEs, there are parallels in the contrasts between lightlesssubsurface environments and those of most surface environments (see Table 1).

Table 1: Characteristics of groundwater environments and implications for groundwater

biodiversity and ecology




Although not exclusive to groundwater environments, in combination these characteristicsform a suite of powerful drivers of faunal biodiversity, predominant subsurface ecologicalprocesses, and the ecosystem services provided by SGDEs.

Heterotrophy rather than photosynthesis is the basis of the food chain (Gibert and Deharveng2002), and it is largely carried out by biofilms coating surfaces and sediment particles.Biofilms are consortia of bacteria and fungi in a mucilaginous polysaccharide matrix secretedby the microorganisms (Brunke and Gonser 1997, Mauclaire et al. 2000).

Primary producers are not entirely absent from aquifers, although lightlessness precludesphotosynthesis; Kuehn et al. (1992) document 21 species of soil algae in groundwaterassociated with recharge zones, and suggest that algal populations are likely to supplementthe diet of aquifer fauna. Ellis et al. (1998) recorded 24 genera of algae some four kilometresfrom the river in a highly transmissive alluvial aquifer.

Groundwater environments are dynamic systems in which biological and geochemicalinteractions and transformations take place at a range of scales. Shifting patterns of physicochemical, oxygen and nutrient gradients (see later) create a patchy mosaic of microenvironments (Pospisil 1994, Coineau 2000) constituting a set of functionalmesohabitats that can be distinguished by hydraulic and physical characteristics (Brunke etal. 2001).

Absence of light and widespread perceptions of reduced habitat heterogeneity, lowproductivity, and unfavourable but stable and predictable environmental conditions belie thetrue diversity of aquifer habitats and the habitat differences that are key to appreciating thesubtle complexities of subterranean ecology.

Features of ecological relevance in particular aquifers could be small-scale exchangeprocesses between surface and groundwater (Sophocleous 2002), and patchily-occurringpatterns of recharge, or zones of higher transmissivity due to palaeochannels (Ward et al.1994), which drive spatial and temporal variability in biogeochemical processes and faunaldistribution, abundance and richness.

An ecological perspective that recognises these small-scale differences within habitats, aswell as the differences between habitat types, is more likely to identify knowledge gaps that

translate into carefully planned and targeted research questions.

1.6 Drivers of groundwater ecology

Dissolved oxygen is a key environmental parameter in interstitial environments (Danielopol etal. 1994, Ward et al. 1998), although Malard and Hervant (1999) state that dissolved oxygenis not a limiting resource for all animals in groundwater, as faunal distribution in many studiesdoes not match oxygen gradients, and further, not all groundwater habitats have lowdissolved oxygen. However, Hahn (2006) found oxygen concentrations of one milligram perlitre to be a critical limit for subsurface fauna.

Although a correlation between an easily-measured variable, such as dissolved oxygen, and

a measure of community condition, such as species richness, would be ideal for the purposeof management, such a relationship is seldom apparent or consistent.

Some studies show weak correlations between individual water quality variables andstygofaunal community composition or species distribution (Dumas et al. 2001, Hahn 2006,Castellarini et al. 2007b).

Others show contrasting results. For example, Mauclaire et al. (2000), working in aglaciofluvial aquifer some 20 kilometres east of Lyon, France, found that, while bacterialactivity and abundance were correlated with dissolved organic carbon (DOC) concentrations,faunal abundance was relatively homogeneous and only weakly correlated with DOC.

However, in the same aquifer, but at sites closer to the Rhône River, Datry et al. (2005)reported that groundwater invertebrate assemblages were more abundant and diverse in sitesartificially recharged with storm water compared with reference sites recharged by rainfall

infiltration. Concentrations of dissolved organic carbon (DOC) were significantly higher in therecharge sites than in reference sites, where the thickness of the vadose zone was less than




10 metres in all sites, although mean concentrations of DOC were no greater than onemilligram per litre at any site.

In contrast, Masciopinto et al. (2006) reported that, in wells affected by artificial recharge of waste water in southern Italy, increased DOC at similar concentrations to the Datry study wasassociated with a decline in faunal biodiversity. DOC concentration in bedrock zonegroundwater is typically quite low; Wetzel (2001) cites a median DOC content of groundwateras 0.65 milligrams per litre. This is comparable to a median value of 0.7 milligrams per litrerecorded in a survey of 100 bores and springs in 27 states of the US (Kaplan and Newbold2000).

These results might indicate differences in the quality rather than quantity of DOC (Sobczakand Findlay 2002). The bioavailability of DOC varies, and depends on its source and chemicalcomposition. DOC consists of an extremely complex mix of organic compounds of varyingstructure and molecular weight. The more labile, simpler compounds are metabolized morerapidly by bacteria, although there is some evidence that more complex compounds supporthigher bacterial numbers over longer time periods (McDonald et al. 2007).

Although organic matter supply may be necessary to sustain life, species richness, faunalcommunity composition and spatial patterning are likely to be determined by multipleinteracting factors: transmissivity, oxygen, dissolved organic carbon, redox and pH accountedfor 52 per cent of the variability in faunal abundance in two French alluvial riverbank aquifers(Mauclaire and Gibert 2001).

The conflicting results could also be due to the limitations of measuring water quality variablesfrom pumped groundwater in which mixing effects mask small-scale heterogeneity in aquiferconditions (Strayer 1994).

Physico-chemical variables are also unlikely to be the sole determinants of speciesdistributions and community assemblages. Dispersal constraints (Belyea and Lancaster1999), such as hydrological disconnection (Sheldon and Thoms 2006), could isolate parentpopulations from which populations observed at any particular sampling time are derived.

Lag effects are likely, so that the species presence and abundance data collected at anysampling time could result from previous rather than current physico-chemical conditions.

There might also be multiple points of population or community stability due to varyinginfluences of different combinations of driving variables as environmental conditions change.




2 Biodiversity values of SGDEs

2.1 Defining biodiversity

The Convention of Biological Diversity (1992) defined biodiversity as ‘the variability amongliving organisms from all sources, including terrestrial, marine and other aquatic ecosystems,and the ecological complexes of which they are part; this includes diversity within species,between species and of ecosystems’.

Biodiversity thus has genetic, species, community and landscape components, all of whichrelate to each other and should not be considered in isolation. The spatial components of biodiversity at the species level can be differentiated as the number of species at a location,the number of species in the regional species pool, and the variability in numbers of speciesbetween localities within a region (Thompson and Starzomski 2007). Thus the biodiversity of SGDEs encompasses both the fauna and the habitats. The term biodiversity ‘hotspot’ is commonly used to denote areas with high species richnessand endemism (Reid 1998), but it is defined more usefully for management by Myers et al.

(2000) as ‘areas featuring exceptional concentrations of endemic species and experiencingexceptional loss of habitat’. The term was applied arbitrarily by Culver and Sket (2000) tocave and karst well sites with 20 or more obligate subterranean species of troglofauna orstygofauna. Using this criterion, many Australian sites would qualify as hotspots. Forexample, one bore in the Pilbara has yielded at least 32 stygobitic taxa (Eberhard et al. inpress).

2.2 The value of biodiversity

Biodiversity conservation serves a number of values (Box 6).

Box 6: Values served by biodiversity conservation

• preservation of genetic diversity and therefore of species’ ability to adapt toenvironmental change

• protection of threatened species or ecosystems

• maintenance of ecosystem functions such as provision of goods and services

• maintenance of ecosystem resistance and resilience, or the ability to resist or recoverfrom disturbance

• intangible human social and cultural benefits.

(Thompson and Starzomski 2007)

It is a social and political decision whether these values justify conservation action; for

example, does the protection of a ‘tiny, blind cannibal’ take precedence over the mining of $12.5 billion of iron ore (see The West Australian, 30 March 2007)? Prioritisation of thesevalues is usually implicit rather than explicit in biodiversity management. Funds could beallocated more readily for the protection of rare and endemic fauna than to a community of microbes, yet the loss of ecosystem services not only has economic repercussions but couldbe accompanied by a greater loss of biodiversity.




c

2.3 Subterranean biodiversity

Patterns of subterranean biodiversity are the product of four particular characteristics (Gibertand Deharveng 2002):

• low number of lineages due to the ecological filter of the transition to lightless

environments

• high endemism due to fragmentation of habitat

• high level of relict taxa due to persistence of environmental conditions over longgeological periods of unfavourable surface conditions, for example during the onset of aridity

• truncated food webs with few predators and herbivores and no primary producers. Theabsence or reduction in importance of predators is a result of a shift towards omnivoryimposed by scarcity or irregularity of food supply.

Terminology for subterranean fauna varies in the literature. An initial distinction can be madebetween aquatic and terrestrial subterranean fauna, termed stygofauna and troglofauna

respectively. Although collectively termed stygofauna (Hancock et al. 2005), groundwaterspecies are often classified according to their affinity to groundwater habitats (Gibert et al.1994) (Figure 4).

Figure 4: A classification of groundwater species based on their affinity to groundwaterhabitats

a

b

c

Sediment

Surface waterlifecycle

Species can be(a) stygoxene, accidentally orfacultatively present in groundwaterhabitats(b) stygophile, completing part of thelife cycle in groundwater habitats

(c) stygobite, obligate inhabitants of groundwater habitats throughout thelife cycle.

Adapted from Gibert et al. (1994)

Species that complete their entire life cycles in groundwater and are seldom found in surfacewaters are termed stygobites.

In spring discharge sites and in alluvial aquifers with strong hydrological connections tosurface water bodies, there could be stygophilic species that spend part of their life cycle ingroundwater, and stygoxenes, species that are accidental or facultative visitors togroundwater habitats.

In parallel terminology for the hyporheos (the fauna of the hyporheic zone) Williams andHynes (1974) distinguished the occasional hyporheos, taxa that spend part of their life cyclesin the hyporheic zone, from the permanent hyporheos, taxa that complete their life cycles inthe hyporheic zone.

The trap for the unwary reader is that, in some groundwater habitats, the entire stygofaunalassemblage will be stygobitic, but in others will variously comprise stygobites, stygophiles andstygoxenes. Readers should be aware of differences in usage of the term stygofauna forgroundwater fauna in caves and karsts (Thurgate et al. 2001), alluvial (Dole-Olivier et al.

1993) or calcrete (Watts and Humphreys 2006) aquifers, or an array of groundwaterenvironments both subsurface and surface (Eberhard et al. 2005). In this review, we use the




term stygofauna to encompass all groundwater fauna, but where necessary, use theclassification by Gibert et al. (1994) to distinguish stygoxenes, stygophiles, and stygobites.

2.4 Characteristics of stygobitic fauna

Obligate groundwater invertebrates have morphological, physiological, behavioural and lifehistory adaptations (Box 7). Morphological adaptations (Figure 5) include loss of pigmentation, small size, eye reduction or loss, elongate or attenuated body shape, andhypertrophy of some sensory organs, but development of sensory setae (Gibert et al. 1994).

Physiological and behavioural adaptations to suboxia (dissolved oxygen concentration (DO)less than 3.0 milligrams per litre) or limited food supply (Malard and Hervant 1999, Hervantand Renault 2002, Datry et al. 2003) include lower energetic requirements compared withsurface water forms; high storage of fermentable fuels, providing a more sustained supply foranaerobic metabolism; low metabolic rate in normoxia (DO less than 3.0 milligrams per litre)and a further reduction by reducing locomotion and ventilation in hypoxia (DO less than 0.01milligrams per litre); and the ability to rapidly resynthesise glycogen stores during posthypoxic recovery.

Box 7: Adaptations to subsurface groundwater habitats

• eye loss or reduction

• small size

• loss of pigmentation

• attenuated body shape

• development of sensory setae

• fewer but larger eggs

• longer time for egg development

• longer life cycles

• lower metabolic rates

• reduced locomotory and physiological activity in response to environmental stress.

(Gibert et al. 1994, Hervant et al. 1999, Eberhard 2005, J arvis et al. 2005)

These adaptations confer greater tolerance of starvation and low oxygen levels on stygobitescompared with surface water fauna (Hervant et al. 1995, Hervant et al. 1999). The Europeangroundwater amphipod Niphargus sp. survived for two months in hypoxic water, but a surfacewater amphipod Gammarus sp. survived for only two days (Danielopol 1989). Hypoxia isnevertheless a stressor for stygobites, and heavy nutrient contamination and subsequentoxygen depletion can result in high mortality (Sinton 1984).

The higher tolerance of suboxia in stygobites might confer a competitive advantage overstygophilic taxa, but if oxygen supply is adequate in nutrient-enriched environments, thehigher metabolic rates of stygophiles might enable these taxa to out-compete stygobites(Wilhelm et al. 2006). Danielopol et al. (1994) describes the subsurface isopod Proasellusslavus as euryoxic (tolerant of a wide range in oxygen concentration), but having aphysiological optimum at higher oxygen concentrations.

Oxygen availability can account for differences in interstitial faunal composition (Boulton et al.1997, Marmonier et al. 2000). Redox gradients that influence local oxidation pathways arepartly determined by porosity, which can influence entrainment of allochthonous organicmatter (Gibert et al. 1994).

Despite a tolerance of suboxia, fauna in unconfined aquifers preferentially occupy the zone just below the watertable where dissolved oxygen and nutrient concentrations are highest

(Pospisil 1994, Edler and Dodds 1996, Sarkka and Makela 1999). Thus fauna in unconfinedaquifers are potentially vulnerable to stranding if the amplitude and frequency of watertablefluctuations are increased by groundwater extraction. Microcosm experiments on stygofauna




from bores near Tamworth, NSW, indicate that small-bodied fauna such as copepods areable to follow declining water levels, or perhaps become entrained, but larger bodied speciessuch as amphipods become stranded (Tomlinson et al. 2007b).

Life history adaptations by stygofauna to the relatively more stable aquifer environment aresummarised by Dole-Olivier et al. (2000). These include fewer but larger eggs; a longer timefor egg development (Rouch and Danielopol 1999) and longer life cycles. For example theEuropean amphipod Niphargus sp. lives 10 years (Mauclaire et al. 2000) and the isopodStenasellus virei boui takes 10 years to develop from egg to adult (Rouch and Danielopol1999), compared with a mean life span of six months for the benthic amphipod Gammaruschevreuxi (Subida et al. 2005).

Figure 5: A new genus of bathynellid syncarid

This new genus of bathynellid syncarid illustrates morphological adaptations to the groundwater environment: smallsize, loss of eyes and pigment, attenuated body shape and development of sensory setae. Photo: Peter Hancock

These data are all from studies of European fauna. Although equivalent physiologicaladaptations and life histories may be assumed for Australian stygofauna, research is neededto confirm this assumption so that European results may be extrapolated with confidence. These life history adaptations to the relatively stable aquifer environment would not beadvantageous in a situation of environmental change such as anthropogenic water levelfluctuations. Fauna in seasonally unfavourable or unpredictable environments either migrateor become dormant during adverse conditions (Gyllstrom and Hansson 2004). Dormancy is astate of suppressed development presenting as either quiescence (a short-term response to a

limiting factor) or diapause (an obligate period of arrested development triggered byenvironmental factors) (Dahms 1995). Diapause in unfavourable environmental conditions isknown for surface water species of taxa that include groundwater forms, for example,copepods (Hairston et al. 1995, Hairston and Caceres 1996) and tardigrades (Rebecchi et al.2006), but has not yet been recorded in groundwater forms.

2.5 Australian stygobitic biodiversity

Table 2 summarises Australian stygobitic biodiversity as records of taxa in a variety of groundwater environments. Following Sket (1999), surface water taxa and inhabitants of wetsoil were excluded. The groundwater environments are listed as reported in the literature, butare not mutually exclusive; for example calcrete aquifers might or might not be karstified, and

calcrete deposits are often inter-fingered with alluvium resulting in heterogeneousenvironments.




Survey effort in Australia is patchy and incomplete; but it has rapidly improved in recent years,with many exploratory baseline surveys being conducted, particularly in Western Australia aspart of the environmental impact assessment for mining developments. Existing survey workcovers some coastal and inland alluvial, fractured rock and arid zone karstic and calcreteaquifers and caves in the Northern Territory, New South Wales, Queensland, Tasmania,Western Australia and Christmas Island. In Europe the number of endemic stygofauna is

greater in karstic systems than in alluvial aquifers, perhaps because the greater isolation of karstic habitats facilitates speciation (Danielopol et al. 2000). Because much of easternAustralian karst is sparsely surveyed (Thurgate et al. 2001), it is likely that much stygobiticdiversity remains undocumented. The apparent patterns of biodiversity probably reflectavailable taxonomic interest and expertise; unexplored groups could be equally diverse.

Table 2: Stygobitic biodiversity in Australia

Taxa Calc-rete

Al luv-ial

Anchia-line

Karst:freshwater

Fractur-ed rock

Protista ? 9 ? ? ?

Platyhelminthes Turbellaria 9 9 ? 9

Aschelminthes Nematoda ? 9 ?

Rotatoria

Tardigrada 9

Annelida Oligochaeta 9 9 9 9

Polychaeta 9

Mollusca Gastropoda Hydrobiidae 9 9 9

Glacidorbidae 9

Arachnida Acarina 9 9

Crustacea Ostracoda Myodocopida 9

Podocopida 9 9 9

Halocyprida 9

unidentified 9 9 9 9 9

Copepoda Cyclopoida 9 9 9

Harpacticoida 9 9 9

Calanoida 9 9

Misophrioida 9

unidentified 9 9 9 9 9

Remipedia Nectiopoda 9

Syncarida Psammaspididae

9 9

Koonungidae 9

Anaspidae 9

Bathynellidae 9 9 9

Parabathynellidae

9 9 9 9 9

Undescribedfamily

9

Decapoda Atyidae 9 9 9 9

Isopoda Phreatoicidae 9 9 9 9

J aniridae 9




Taxa Calc-rete

Al luv-ial

Anchia-line

Karst:freshwater

Fractur-ed rock

Flabellifera 9

Tainisopidea 9 9 9

Amphisopidae 9

Oniscidea 9

Cirolanidae 9 9

Amphipoda Paramelitidae 9 9

Neo-niphargidae 9

Melitidae 9 9

Bogidiellidae 9

Hadziidae 9

Crangonyctidae 9

Chiltoniidae9 9

Spelaeogriphacea

9

Thermosbaenacea

9 9 9

Insecta* Coleoptera Dytiscidae 9 9

Elmidae 9

Vertebrata Pisces 9 9

After Poore and Humphreys (1998), Humphreys (2000b, 2001), J aume et al. (2001), Thurgate et al. (2001), Eberhardet al. (2005), Humphreys pers. comm., Humphreys (2006b), Pinder et al. (2006), Tomlinson, unpublished data). Ticksindicate a record for the taxon. Question marks indicate that occurrence is likely but unrecorded to date

*Hyporheic fauna recorded from alluvial habitats in Australia also include stygophile taxa:– Coleoptera (Scirtidae); Diptera (Ceratopogonidae, Chironomidae, Muscidae, Simuliidae, Stratiomyidae);Ephemeroptera (Baetidae, Caenidae, Leptophlebiidae); Megaloptera (Corydalidae); Odonata; Plecoptera(Gripopterygidae); Trichoptera (Calamoceratidae, Calocidae, Ecnomidae, Hydrobiosidae, Hydroptilidae,Leptoceridae, Philopotamidae) – (see Cooling and Boulton 1993, Boulton and Foster 1998, Hancock 2006, Boultonet al. 2007).

Table 2 is incomplete and unsatisfactory for a number of reasons: much of Australia’sstygofaunal biodiversity remains unsurveyed, there is a serious lack of taxonomic capacitydespite the efforts of the last decade (Humphreys 2008), much information is not readilyaccessible because it resides in consultancy or government reports and other grey literatureor in individual researcher’s records; definitions of stygofauna are not always clear in thepublished literature, or the degree of groundwater dependency of the specimen was unknown

to the authors, so that reported biodiversity variously includes stygobites, other taxa that usegroundwater habitats for part of their lifecycle, or facultative visitors; reports of stygofaunaldistribution do not always indicate the habitat type; and the records are sometimesincompatible because of taxonomic revision and re-assignment over time.

These issues demonstrate the urgent need for a central register or database of stygofaunaltaxa conforming to a standard, nationally-agreed terminology and including metadata such assampling method, frequency of sampling, details of aquifer type and other location data, andassociated details of water quality (for example, conductivity and dissolved oxygen).

European groundwater faunal populations are dominated by crustaceans, with stygobiticspecies making up 40 per cent of the total European crustacean fauna (Danielopol et al.2000). Crustaceans – including amphipods, copepods, ostracods and isopods – are also themajority of Australian stygofauna. Surveys to date, largely focused on Western Australia,

have revealed a new genus of isopod (Wilson 2003), 41 species of copepod (Karanovic 2006)and over 110 species of ostracod (Reeves et al. 2007) in the Pilbara region alone, and 31




species of copepod from the Murchison area of the Yilgarn Craton (Karanovic 2004). Of thecrustacean superorder Syncarida, anaspids are restricted to southern Australia (Hobbs 2000). The bathynellids are well-represented and largely undescribed, although the WesternAustralian fauna have received some attention (Cho 2005, Cho et al. 2005, Cho et al. 2006a,Cho et al. 2006b). A wide range of other taxa are represented in Australia, including morethan 80 new species of dytiscid diving beetles (Watts and Humphreys 2006, Watts et al.

2007) and two species of fish (Humphreys 1999a). Priority groups for taxonomic work are theamphipods, isopods and bathynellids (Professor Andrew Austin, University of Adelaide andDr. Steve Cooper, South Australian Museum, pers. comm.). The diversity of subsurfacemicrobial (Kimura et al. 2005, Goldscheider et al. 2006), fungal and protozoan (Novarino et al.1997, Ellis et al. 1998, Andrushchyshyn et al. 2007) communities is virtually unexplored inAustralia. Some biochemically novel, chemoautrophic communities consisting of mucoidsheets or tongues and dependent on nitrite oxidation have been described from karst of theNullarbor Plain (Holmes et al. 2001, Subterranean Ecology 2007).

Characteristic of the Australian stygofauna are taxa that are relicts of ancient lineages andhave very limited distributions. The anchialine fauna of Cape Range are an example of thepersistence of phyletic relict fauna buffered from climatic and other environmental change. The Cape Range fauna are hypothesized to derive from populations that were alreadyinhabiting subterranean habitats before the breakup of Gondwana (Humphreys 2000b). Theyinclude the only Southern Hemisphere representatives of the copepod order Misophrioida(J aume et al. 2001), another crustacean order Thermosbaenacea (Poore and Humphreys1992) and the class Remipedia (Lasionectes exleyi (Yager and Humphreys 1996), knownfrom a single water-filled cave at Cape Range). The only Australian records of the peracaridcrustacean order Spelaeogriphacea are two species (of only four globally) from the Fortescuevalley in the Pilbara (Poore and Humphreys 1998, 2003).

Harvey (2002) defined short-range endemic species as those with a range of less than 10,000square kilometres, and noted that the majority of short-range endemic species possesscharacteristics such as limited dispersal ability and confinement to discontinuous habitats.Eberhard et al. (in press) suggested that 1000 square kilometres may be a more satisfactorythreshold for short-range endemism. The high diversity of short-range endemic dytiscid divingbeetles in calcrete aquifers in the Pilbara has been ascribed to multiple independent

colonisations of aquifers that subsequently became subterranean ‘islands’ isolated by theonset of aridity (Cooper et al. 2002, Leys et al. 2003). Studies of the mitochondrial DNA of amphipods (Cooper et al. 2007), oniscidean isopods (Cooper et al. in press) andparabathynellids (Guzik et al. 2008) from these calcretes support this interpretation.




3 Subsurface ecological processes Energy – the capacity to do work – is ultimately derived from the sun. It flows through foodwebs as chemical bonds in organic compounds, and it is dissipated through respiration or

stored in sediments.Chemical elements cycle through organisms and their abiotic environment in a series of reactions termed biogeochemical cycles (Clapham 1973, Brewer 1988) of which the carbon,nitrogen and phosphorus cycles are most pertinent from the perspective of this review.

As most subterranean food webs are heterotrophic, transfer of carbon from particulate anddissolved organic matter to invertebrates is mediated by biofilms coating sediment particlesand rock surfaces (Bärlocher and Murdoch 1989, Chafiq and Gibert 1996, Claret et al. 1998,Findlay and Sinsabaugh 1999). Biofilms transduce nutrients and energy (Battin et al. 2003)through processes including abiotic adsorption of molecules to the biofilm matrix andbiological uptake by enzymatic hydrolysis.

The bacterial uptake and repackaging of carbon and nutrients constitutes a microbial loop(Sherr and Sherr 1988) through which dissolved and particulate organic matter is madeavailable to grazing protozoans and invertebrates. Carbon and nitrogen cycles are linkedbecause most nitrogen in aquatic systems is bound in organic matter and is unavailable untilit is mineralised to ammonium (NH4

+) by the breakdown of organic matter (Duff and Triska2000).

Microbially-mediated geochemical cycles involve the transfer of electrons betweencompounds. The rate and direction of geochemical cycling depends on the availability of electron donors and acceptors. Under aerobic conditions, oxygen acts as an electronacceptor, but under anaerobic conditions other compounds are used as donors in a reductionsequence of nitrate, manganese, iron, sulphate and carbon dioxide (Wetzel 2001).

Different reactions occur in oxic and anoxic conditions, and the co-occurrence over smallspatial scales of coupled processes contributes to the characteristic patchiness of SGDEs.

Microbially-mediated nitrogen cycling (Box 8) can occur as coupled nitrification-denitrificationreactions along gradients of oxygenation (Baldwin and Mitchell 2000).

Phosphorus dynamics are closely related to the cycling of iron, and therefore requireanaerobiosis (Baldwin and Mitchell 2000). Rates of biogeochemical transformations areaffected by factors such as temperature, pH or the presence of heavy metals.

Box 8: Nitrogen processes in groundwater

Nitrification is the bacterial oxidation of ammonium (NH4+). Ammonium is produced by

excretion or the decomposition of organic matter. Denitrification is the bacterial reduction of nitrites and nitrates (NOx) either back to ammonium, or to nitrogen gas, which is then lostfrom the system.

(Wetzel 2001)

The spatial availability of electron donors is determined by patterns of water flow, which inturn, are driven by hydrologic connectivity and hydraulic conductivity (Baker et al. 2000a), keyfactors in our proposed typology. Water is a transport agent (Bakalowicz 1994) thatpercolates through the vadose zone, or pulses through the hyporheic zone, to deliverdissolved and particulate organic matter and dissolved oxygen to biofilms.

Microbial activity is typically highest near the source of recharge and declines along agradient with distance from it (Kaplan and Newbold 2000). In aquifers connected to surfacewaters, the hyporheic zone is a crucial interface for fluxes of nutrients (Boulton et al. 1998,Dahm et al. 1998, Fischer et al. 2005).

Flood pulse inundation in a semiarid catchment in New Mexico altered rates of nutrientretention and organic matter processing in floodplain groundwater (Baker et al. 2000b). Local

lateral exchange processes such as cycles of bank discharge and recharge can also play animportant role in the timing and direction of nutrient processing in floodplains (Lamontagne etal. 2005b).




In unconfined alluvial aquifers with fluctuating watertables, a significant portion of organiccarbon metabolism can occur in oxic–anoxic cycles in the zone of intermittent saturation(Vinson et al. 2007).

Hydraulic conductivity also determines the availability of electron donors for biogeochemicalprocesses. Interstitial storage of dissolved organic matter and the availability of dissolvedoxygen are influenced by particle size and pore size (Maridet et al. 1996). Larger particle sizeand high porosity allow higher flows and higher availability of oxygen but reduce entrapmentand retention of nutrients.

In fractured rock and karstic aquifers, uneven porosity due to the distribution of fissures,fractures and solutional conduits creates preferential flow paths, which create spatialheterogeneity in biogeochemical cycling (Ayraud et al. 2006). Spatial and temporal variabilityin groundwater flow paths is also influenced by surface microtopography (Pfeiffer et al. 2006)and by stream channel morphology (Dahm et al. 1998).

The functional diversity of subsurface ecological processes is thus determined by shiftinggradients in oxygen, nutrients and physico-chemical conditions, which create pockets of oxiaand anoxia, nitrification and denitrification.

As in other ecosystems, heterogeneity in subsurface environments is a critical determinant of

ecosystem function (McCarty et al. 2007). Disturbance to the groundwater regime, includingdisruption of patterns of hydrological connectivity (Baker et al. 2000b) and sediment wetting-drying cycles (Baldwin and Mitchell 2000), might potentially alter spatial and temporal patternsof groundwater flow, flux and quality, with implications for rates of organic mattermineralisation and nutrient cycling.

Pumping from a fractured rock aquifer in north-west France caused physical disturbance towater flux in the aquifer, reduced groundwater residence time and subsequent drasticmodification to the water chemistry resulting in less active biogeochemical processes (Ayraudet al. 2006).

Prolonged desiccation of sediments caused by watertable drawdown is likely to alter thebalance between aerobic and anaerobic processes and change the composition of microbialpopulations, reducing the incidence or rate of anaerobic metabolism.

Fischer et al. (2005) concluded that carbon and nitrogen cycling in hyporheic sediments werecentral to the metabolism of a large lowland river in Germany, and designated the hyporheiczone as the ‘river’s liver’.

Disturbance to the groundwater regime can alter the rate and nature of subsurface ecologicalprocesses, resulting in reduced availability of carbon, nitrogen and phosphorus, with flow-oneffects for biodiversity and ecosystem services, not only within the aquifer, but also inconnected ecosystems including rivers, riparian zones and estuaries.




4 Provision of goods and services Ecosystem goods and services are the conditions and processes through which naturalecosystems, and the species that are part of them, help sustain and fulfill human life (Daily et

al. 1997). Goods are tangible, direct benefits. Services are ecological functions that benefithumans. While goods can often be assigned a value, services are less tangible and far moredifficult to value.

As surface waters deteriorate in quality and quantity, and demands on groundwater increase,the goods and services provided by groundwater will gain value; but there is a risk that thedemands for consumptive use of groundwater will prioritise the use of ecosystem goods overthe maintenance of ecosystem services. This risk is exacerbated by the high probability of accelerating change in deterioration of ecosystem services. Further, irreparable damagemight occur to ecosystem service providers (ESPs) if excessive water is removed or otherimpacts, not readily detectable, take place. The use of groundwater could continue in excessof recharge for some time before the escalating impacts of extraction become apparent.

The main categories of ecosystem services (Millennium Ecosystem Assessment 2005)

provided by groundwater (Table 3) are as follows: Table 3: Ecosystem services provided by groundwater

Type of service Examples

Provisioning Water for drinking, irrigation, stock and industrial uses

Supporting Bioremediation, ecosystem engineering, nutrient cycling, sustaininglinked ecosystems, providing refugia

Regulating Flood control and erosion prevention

Cultural Religious and scientific values, tourism

4.1 Provisioning services

Goods provided by subsurface ecosystems include drinking water, water for irrigation andstock watering, and water for industrial uses (National Research Council 1997). Totalconsumptive water use in Australia was 24,058 gigalitres in 1996–97 (Ball et al. 2001), 21,703gigalitres in 2000–01 and 18,767 gigalitres in 2004–05 (National Water Commission 2006).About 20 per cent of total consumptive water use is from groundwater, with 10 per cent of thissourced from the Great Artesian Basin (Commonwealth of Australia 2007b). The quantity of groundwater extracted for stock and domestic use in Australia is largely unlicensed andunmetered. Adoption under the NWI of consistent metering and measuring of all water access

entitlements, and the development of national metering specifications and standards, willimprove the accuracy of water extraction data and provide better understanding of the extentof consumption of groundwater goods.

4.2 Supporting services

Bioremediation

Bioremediation is the process, either spontaneous or managed, of degradation ortransformation of contaminants by living organisms, mostly bacteria, into non-toxic or lesstoxic products (Chapelle 2000, Andreoni and Gianfreda 2007). Common contaminants inaquifers are anthropogenic chemicals such as chlorinated solvents, polycyclic aromatic

hydrocarbons (PAHs: naphthalene, phenanthrene, anthracene) resulting from the incompletecombustion of coal, oil, petrol, and wood (Bamforth and Singleton 2005), and volatilearomatics collectively designated as BTEX (benzene, toluene, ethylbenzene and xylene)




derived from chemical industries, industrial wastes and hydrocarbon storage and spillage(Andreoni and Gianfreda 2007).

Bacterial bioremediation has been the subject of detailed studies (Meckenstock et al. 1999).Bioremediation of contaminants by aquifer bacteria occurs both aerobically and anaerobically(Andreoni and Gianfreda 2007), often at the edge of contaminant plumes (Griebler et al.2007), where electron donors from the plume mix with electron acceptors from thesurrounding groundwater across a steep physico-chemical gradient (Griebler et al. 2007). Therate of groundwater flow is critical to effective bioremediation. Faster flow reduces interactionsbetween water, the matrix and its biofilm, thus limiting the potential for contaminant removalor attenuation (Malard et al. 1997), but low flows can facilitate clogging (Mauclaire et al.2006). The rate of movement of a contaminant also varies according to its solubility. PAHshave low water solubility, resist biodegradation and are highly persistent; BTEX are highlysoluble and volatile and are more readily biodegradable (Bamforth and Singleton 2005,Andreoni and Gianfreda 2007).

The role of other aquifer biota in bioremediation is not well understood, although protozoangrazing promotes biodegradation by stimulating bacterial activity (Mattison et al. 2005), and asimilar role seems likely for stygofauna. European researchers are investigating thecontribution of stygofauna to bioremediation in a mesoscale experiment (Schmidt et al.

2007a), in which groundwater will be run through heterogeneous aquifer material with itsnatural faunal community. A contaminant plume will be established, and the microbial andinvertebrate contributions to biodegradation studied under conditions of varying permeabilityand therefore flow rate.

Stygofaunal crustaceans were implicated in the remediation of groundwater contaminated bybacteria from an effluent disposal area on the Canterbury Plains, South Island, New Zealand(Sinton 1984, Boulton et al. 2008). High numbers of crustaceans, particularly large-bodiedisopods, occurred along a gradient downstream of the disposal site. The dominant species,an isopod, was found to ingest and digest live bacteria.

Biogeochemical processes

Processing of organic matter in alluvial aquifers and delivery of nutrients to streams through

groundwater discharge contributes to surface GDEs by maintaining water quality for riparian,floodplain and instream vegetation (Baker et al. 2000b) and providing nutrients and dissolvedorganic matter to macrophytes (Hayashi and Rosenberry 2002). Many groundwaterheterotrophic bacteria are able to reduce nitrate and also play an important role in themineralisation of organic matter and other biogeochemical processes (Baldwin and Mitchell2000, Mermillod-Blondin et al. 2005b). Ecosystem services of alluvial aquifers include theattenuation of high nitrogen inputs from anthropogenic sources, reducing nitrogen loading inthe river. Denitrification (the reduction of nitrates) in groundwaters is important in regulatingthe export of nutrients into surface waters (Lamontagne et al. 2005b).

Microbial involvement in the biogeochemical cycling of carbon has also contributed to theproduction of fossil fuels. Several methanogenic microbial communities have been identifiedin the deep subsurface, each adapted to particular salinity conditions and with preferential

substrate use, and each inducing distinct geochemical groundwater signatures (Waldron et al.2007).

Support to groundwater dependent ecosystems

Groundwater discharge contributes to river flow (Wood et al. 2005, Cook et al. 2006),supports instream and riparian communities (Boulton and Hancock 2006), wetlands(McCarthy 2006), aquatic communities in caves (Eberhard 2004), springs and springbrooks(Meyer et al. 2003), terrestrial vegetation (Wischusen et al. 2004, Lamontagne et al. 2005a,O'Grady et al. 2006b), and it supports estuarine and marine ecosystems. Groundwater is asignificant component of summer flow in the Swan-Canning Estuary in Western Australia(Linderfelt and Turner 2001). Thermal and salinity anomalies due to seeping intertidalgroundwater in coastal Delaware, USA, create habitat differences equivalent to a northward

latitudinal shift of 250 kilometres in summer and a southward 380-kilometre shift in winter,




with implications for biological productivity, faunal distribution and community composition of benthic biota (Dale and Miller 2007).

Ecosystem engineering

Grazing of biofilm by stygofauna is postulated to prevent overgrowth of biofilm andconsequent sediment clogging, as demonstrated for a soil flagellate by Mattison (2002).Stygofaunal grazing may also stimulate biofilm activity, thus maintaining biofilm function(Edler and Dodds 1996). Bacterial activity also affects the physical and hydraulic properties of aquifers through the production or dissolution of intergranular cements (Chapelle 2000).

Benthic and hyporheic fauna alter the physical and hydraulic attributes of their habitat throughmechanical bioturbation and pelletisation (Mermillod-Blondin et al. 2003, Mermillod-Blondin etal. 2004a, Mermillod-Blondin et al. 2004c, Nogaro et al. 2006), helping to maintain flow bypreventing sediment clogging (Mattison et al. 2002, Hancock et al. 2005, Mauclaire et al.2006), and thereby contributing to the sustainability of water supply for a range of consumptive and non-consumptive uses (Caliman et al. 2007). A similar role for stygofaunahas been suggested (Boulton et al. 2008) but not yet tested experimentally.

Refugia

Some surface aquatic taxa resist water loss and desiccation by migration into moist orsaturated refugia including SGDEs. Boulton et al. (1992) suggested that the dry channelhyporheic biotope provides a crucial refuge from drought for some surface-dwellinginvertebrates in temporary streams with sandy or gravel substrates. For example, surfacewater amphipods (Harris et al. 2002) and hyporheic invertebrates (Clinton et al. 1996) survivethe drying of ponds by migrating into deeper sediments with the falling watertable. Crayfishburrows full of water provide refugia for some stream insects (Boulton and Lake in press) andfor the syncarid Allanaspides hickmani, which lives in seasonally ephemeral pools in buttongrass moorland in Tasmania (Driessen and Mallick 2007). Fish in floodplains of the eastKimberley retreat to karst sinkholes during the dry season (Humphreys 1995).

The eskers of Finland are identified by Sarkka and Makela (1999) as refugia and possiblepathways for faunal dispersal between alpine and arctic areas. Groundwater discharge intoestuaries can provide refuge zones for saline-sensitive species during periods of hypersalineconditions associated with reduced river discharge during droughts (Taylor et al. 2006).

On an evolutionary scale, aquifers have provided refugia from changing environmentalconditions on the surface, including the onset of aridity in Australia (Cooper et al. 2002,Cooper et al. 2007, Finston et al. 2007).

4.3 Regulating services

Flood control and erosion prevention

As receptors, storages, and transmitters of recharge, aquifers regulate parts of thehydrological cycle, absorbing runoff and mitigating the impact of storm events. Aquifer storageof runoff and streamflow is particularly significant in zones of strong groundwater–surfacewater connections such as riverbanks and floodplains (Brunke and Gonser 1997,Sophocleous 2002). During flooding, rivers lose water to the riverbanks or, if the banks areover-topped, to the floodplain. During dry periods, these aquifer storages release water backto the river, helping to compensate for reduced river flow. This ‘buffering effect’ reduces therate of change (or ‘flashinesss’) of stream discharge, with important hydrologicalrepercussions for surface fauna and processes (Bunn and Arthington 2002).




4.4 Cultural services

Ecological indicators

Stygofauna have the potential to offer a service as indicators of ecosystem condition and the

integrity of some of the fundamental ecological processes occurring in groundwaters. The useof aquatic macroinvertebrates as indicators of river health is well-established (see discussionof the river health concept in Boulton (2000b)), but currently, river health assessment doesnot include an examination of the ‘health’ or condition of hyporheic zones (Boulton 2000b,Hancock 2002) or aquifers. Application of the river continuum concept suggests that inclusionof these components would enhance the robustness of river health assessment (Reid andBrooks 2000), especially in ephemeral arid zone rivers with subsurface flow.

For aquifers, Gibert et al (1994) indicate that the relative stability of systems and high degreeof specialisation of fauna suggests that stygofauna will be sensitive to environmental change. The relative abundance of surface water and groundwater forms can be related to the flowpatterns of pollutants (Malard et al. 1994, Malard et al. 1996). Dumas et al. (2001),investigating the impacts of agricultural pollutants in the Ariège alluvial aquifer in the French

Pyrénées found that macrocrustaceans constitute natural indicators of aquiferhydrodynamics; a dominance of stygobites indicates low surface water inputs, and so couldindicate the absence of nitrate-enriched surface water in aquifers (Claret et al. 1999a).Organic pollution from surface waters allows invasion by surface water forms, forcingstygobites into oligotrophic refugia. Surface water cladocerans (water fleas) predominate inthe hyporheos of polluted reaches of the Rhône (Schmidt 1994). No syncarids were found ingroundwater below a sewage bed in New Zealand (Scarsbrook and Fenwick 2003), indicatingthat syncarids might be sensitive to high levels of nutrients. These responses could well betaxa-specific as Dumas and Lescher-Moutoue (2001) found little apparent effect of nitrates oncyclopoids in the Ariège aquifer, with acute toxicity occurring only at levels greater than 200milligrams per litre. (For comparison, the maximum limit for nitrates in drinking water is 45milligrams per litre in the USA (Manassaram et al. 2006) and 50 milligrams per litre inAustralia (National Health and Medical Research Council 2004)).

If stygofauna are more sensitive than surface water fauna to chemical pollutants (Mosslacher2000), groundwater quality criteria based on responses of surface water organisms could beinsufficient to be used to protect groundwater systems (Hose 2005). The use of stygofauna asbiomonitors of heavy metal contamination has been explored in several studies in Europe(Plénet and Gibert 1994, Plénet et al. 1996, Canivet et al. 2001, Canivet and Gibert 2002), butthere is no equivalent work in Australia. Plénet (1999), working under laboratory conditionswith fauna collected from the Rhône River catchment, found that a stygobitic amphipod wasless sensitive than a surface water amphipod to zinc and copper concentrations, perhaps thiswas due to differences in metabolic rates. Nevertheless, the lower metabolic rates of stygobites could mean that longer exposure might be required before toxic effects are evident(Hose 2007).

Indigenous cultural valuesGroundwater has strong cultural values in Indigenous Australia. Stories associated withgroundwater-related sites such as springs, mound springs, caves and native wells played arole in traditional law and protocols (Moggridge 2007). In the Australian arid zone, wherestream flow is ephemeral, groundwater in streambeds supplied drinking water, and diffusedischarge supports important food species such as the EPBC-listed Ipomoea sp. Stirling(Department of the Environment, Water, Heritage and the Arts 2008). The Indigenousrelationship with aquatic systems can be understood as a socio-ecological relationship that isequivalent to kinship relations of obligation and care (J ackson 2006), suggesting thatcontemporary Indigenous communities are likely to have cultural reasons for involvement ingroundwater management.




Tourism and recreation

Cave tours began in Australia in the 19th century and continue as a major tourism activitytoday (Finlayson and Hamilton-Smith 2003). J enolan Caves is the most visited cave system inAustralia, with more than 250,000 visitors annually. This is a significant proportion of the750,000 paid visits to caves every year (Spate 1989). An unknown number of ‘wild’ cave visitsis made by individuals and members of caving organisations; the Australian SpeleologicalFederation Inc. has about 1000 members and 32 constituent bodies (Finlayson and Hamilton-Smith 2003). Western Australia’s largest tourism cave, J ewel Cave (Box 9), presents aninteresting case study of the challenges of managing SGDEs.

Box 9: Case study 1 – J ewel Cave Western Australia

Location: 34° 17’ S, 115° 07’ E

The J ewel Cave karst system in southwest Western Australia houses a stygofaunalcommunity associated with submerged eucalypt tree roots. This aquatic root mat communityis one of four listed as threatened under the Commonwealth Environment Protection andBiodiversity Conservation Act 1999 because of declining groundwater levels. A multidisciplinary investigation of this SGDE found that groundwater abstraction was not

contributing to the water decline as had been previously suggested. Besides a majordecrease in rainfall over several decades, the declining water levels were possibly alsoinfluenced by a changed fire regime within the catchment. Fire management practiceschanged from regular hazard reduction burns undertaken every year or so over manydecades, to no hazard reduction burns. The absence of fire allowed dense growth of understorey vegetation and an accumulation of ground litter that contributed to reducedgroundwater recharge through interception of rainfall and increased evapotranspiration.

The study concluded that conservation actions for this threatened SGDE need to be focusedat the most appropriate spatial scale, which is the karst drainage system and catchment area.Since this study, rainfall in southwest Western Australia has continued to decline markedly,and long-term climate modelling suggests this trend will continue, possibly exacerbated byanthropogenic climate change. The groundwater levels in the J ewel Cave are presently at a

critically low level, with virtually all known habitat and occurrences of the aquatic root matcommunity having dried up or likely to disappear in the near future.

(Eberhard 2004, Eberhard 2005)




5 Management of SGDEs

5.1 Conservation

In Australia there are obligations to conserve subterranean fauna and communities if theprovisions of the Commonwealth Environment Protection and Biodiversity Conservation Act1999 (EPBC Act) are triggered (Box 10). Under this Act, environmental assessment istriggered by an action that is likely to have a significant impact on matters of nationalenvironmental significance protected under Part 3 of the Act. These matters includethreatened species and ecological communities listed in accordance with Schedule 1 of theAct. Lists maintained under territory and state law have no bearing in this context.

There are numerous obstacles to effective conservation of stygofaunal biodiversity, including:shortage of taxonomists, lack of knowledge of reference conditions, lack of knowledge aboutmicrobial assemblages, lack of data from replicated surveys, incomplete coverage of habitattypes, lack of standardised protocols for sample collection and processing, lack of identification keys, a need for centralised repository of reference material, and a need for a

central database adhering to nationally-agreed standards (Tomlinson et al 2007a). Further,groundwater management in Australia to date has seldom involved ecologists, so datacollection and assessments have not been done with an ecological perspective thatrecognises small-scale differences within habitats, or differences between habitat types. These challenges limit the application of stygofaunal research in management, yet it is onlyby continued strategic research, including targeted surveys (Tomlinson et al. 2007a), thatmanagement applications will be developed.

Box 10: EPBC Act listing of stygofaunal species and groundwater-dependent ecologicalcommunities

Species listed under the EPBC Act are:

• Three stygofaunal species from Western Australia:

– the remiped crustacean Lasionectes exleyi

– the Blind Cave Eel Ophisternon candidum

– the Blind Gudgeon Milyeringa veritas.

• Five subsurface groundwater dependent communities in Western Australia (four rootmat communities in caves of the Leeuwin-Naturaliste Ridge and one root matcommunity in caves on the Swan Coastal Plain).

• At least four communities with some dependence on groundwater:

– temperate highland peat swamps on sandstone

– the thrombolite (microbial) community of coastal freshwater lakes of the SwanCoastal Plain (Lake Richmond)

– the community of native species dependent on natural discharge of groundwaterfrom the Great Artesian Basin

– assemblages of plants and invertebrate animals of tumulus (organic mound) springsof the Swan Coastal Plain.

(http://www.environment.gov.au/cgi-bin/sprat/public/publiclookupcommunities.pl )


http://www.environment.gov.au/cgi-bin/sprat/public/publiclookupcommunities.pl

http://www.environment.gov.au/cgi-bin/sprat/public/publiclookupcommunities.pl



5.2 Threatening processes and SGDEs

A threatening process (Box 11) is defined in the EPBC Act as a process that threatens orcould threaten the survival, abundance or evolutionary development of a native species orecological community. The intimate hydrological and functional connections between SGDEs

and other ecosystems indicate their reciprocal vulnerability to threatening processes at thesurface and in the groundwater.

Box 11: Threatening processes in SGDEs

Disturbance to the groundwater regime can result in:

• increases in salinity

• pollutants (for example, heavy metals) in discharging groundwater

• increased nitrates causing eutrophication in receiving waters

• reduced connectivity to dependent ecosystems

• land subsidence

• loss of groundwater habitat.

Changes in the quantity and quality of recharge impact on the key groundwater attributes of flux or flow, level (in unconfined aquifers) or pressure (in confined aquifers), and quality.

Impairment of groundwater flow, quantity or quality can potentially affect the resilience of connected systems, not only by direct effects such as input of contaminants but also indirectlyby altering the pathways for resource capture and energy flow (Brookes et al. 2005).

The magnitude of impacts could be exacerbated by the inertia of many groundwater bodies.Slow groundwater flow rates and the thickness of the saturated zone result in time lags beforethe impacts of pressures such as extraction are apparent, and parallel time lags beforemanagement improvements take effect. For example, nitrate concentrations in an Iowawatershed in the 1990s were still influenced by heavy application of nitrogen fertiliser 30

years previously (Tomer and Burkart 2003). Without careful monitoring, tolerance thresholdscould be crossed and goods and services lost before the impacts of intensifying threats areevident.

The mechanism and extent of dryland salinity in Australia is well-known (for example, seeClarke et al. 2002in relation to Western Australia). Groundwater recharge has increased dueto widespread land clearing, the replacement of deep-rooted native vegetation with shallow-rooted pasture or crops, and responses to irrigation and river regulation (J olly et al. 1993).Rising water levels intercept salt stored in the former unsaturated zone, or bring naturallysaline water to the surface, resulting in salinisation of soils and streams. Deep, marine-sourced aquifers can also be sources of salinity where seepages originate from fracturedbedrock (Morgan et al. 2006). Input of saline groundwater is a substantial threat to thebiodiversity of surface wetlands and rivers (Halse et al. 2003), and can drive shifts in faunal

assemblage towards more salt-tolerant taxa, with an associated shift in feeding groupcomposition which has implications for trophic linkages in the receiving waters (Boulton et al.2007).

Salinisation may also occur due to seawater intrusion into coastal aquifers under pressurefrom extraction. For example, considerable seawater intrusion has already occurred in coastalaquifers near Bundaberg, Queensland, where groundwater has been extracted since 1958 forirrigation, industrial use and urban water supply. Salinisation was first detected during a dryperiod in the 1960s. During succeeding years of below-average rainfall, groundwater levelswere drawn below sea level by more than three metres for a period of more than 15 months,inducing further seawater intrusion (Zhang et al. 2004).

Discharging groundwater can be a source of metals derived from leachate from landfill,pollution by earlier mining and ore processing (Coynel et al. 2007), or from solution of metals

in fresh fractures caused by mining-induced subsidence (J ankowski and Spies 2007).Elevated concentrations of nitrates leached from agricultural fertilisers and from urban and




industrial point sources occur widely in groundwater in many parts of the world, includingAustralia (Burkart and Stoner 2002, Scanlon et al. 2007). Increased nitrate levels in drinkingwater threaten human health (Manassaram et al. 2006), and together with increases inphosphate levels in discharging groundwater, likely contribute to eutrophication in freshwater,estuarine and marine discharge zones (Valiela et al. 1990, Linderfelt and Turner 2001, Slompand Van Cappellen 2004, Rasiah et al. 2005). Eutrophication causes a loss in the ecosystem

goods and services, including recreational and potable uses of the receiving waters (Rast and Thornton 1996).

Human disturbance to the hydrological cycle often results in a cascade of effects in aquaticand terrestrial systems. These include habitat loss, degradation or fragmentation, alteredwater quality and reduction or cessation of baseflow and spring discharge (Pringle 2001).Reduced groundwater discharge threatens the ecology and biodiversity of many wetlands andrivers by limiting connectivity, affecting stream metabolism and failing to support dry seasonrefugia (Boulton and Hancock 2006). By 2000, groundwater exploitation had causedcessation of flow in one third of the 3000 natural springs of the Great Artesian Basin (Wilmerand Wilcox 2007), resulting in the listing of mound springs communities under Commonwealthendangered species legislation.

Increasing demand for groundwater extraction resulting in decreased storage volumes or

deterioration in quality also potentially impacts groundwater-dependent terrestrial vegetationand associated fauna. Groom et al. (2000) investigated the effect of lowered water levels dueto extraction combined with poor recharge following low rainfall on the Banksia woodlandoverlying the Gnangara Mound, a shallow, unconfined aquifer near Perth. Extensive death of overstorey and understorey species coincided with a lowering of groundwater level by 2.2metres, with no significant decreases in the abundance of overstorey or understorey speciesrecorded in a monitored site not influenced by groundwater extraction. Monitoring data from a20 to 30 year period indicated that changes in species distribution and vigour were primarilycaused by long-term declines in groundwater levels resulting from the cumulative effects of extraction and below average annual rainfall (Groom et al. 2001). Impaired surface vegetationbiomass and land cover can trigger a cascade of impacts, including reduced subsurfacesupply of organic matter and changes in runoff and recharge.

Groundwater extraction can result in land subsidence due to loss of pressure in the aquiferand surface soil compaction. Large-scale pumping of groundwater from aquifers in the PortAdelaide region during the last 50 years is associated with ground subsidence of 2.5millimetres per year, with a maximum subsidence of 10 millimetres per year wheregroundwater withdrawal coincides with wetland reclamation (Belperio 1993). Loss of storagevolume and lowering of water levels through overextraction necessarily reduces habitat forstygofauna.

5.3 The potential impact of climate change

The projected changes in Australia’s climate due to global warming that are summarised inthis report are based on simulations by nine different climate models (Commonwealth of

Australia 2003). Changes in annual average rainfall by 2030 are predicted to be in the rangeof –20 to +5 per cent in southwest Australia and –10 to +5 per cent in south-eastern Australia.By 2070, changes in the range of –60 to +10 per cent are predicted in south-western Australiaand –35 to +10 per cent in south east Australia. Annual average temperature is predicted toincrease by 0.4 to 2° C by 2030 and by 1 to 6° C by 2070. Projections for northern and inlandAustralia are indefinite, but the impacts of climate change are likely to vary from locality tolocality. Increased evaporative stress is expected with increased temperatures. There is alsoa predicted increase in frequency in extreme weather events with associated increasedincidence and severity of flooding and erosion. Climate models suggest that drought could beas much as 20 per cent more common by 2030 over much of Australia and up to 80 per centmore common in south-western Australia by 2070. Finally, a sea level rise of between nineand 88 centimetres is predicted by 2100.

The vulnerability of SGDEs to climate change can be expected to vary with habitat type.

Highly transmissive, unconfined aquifers near the coast will be more sensitive to changes inrecharge, surface water temperatures and sea level rise than deep inland aquifers with low




rates of recharge and throughflow. Although the ability to predict the effect of climate changeon groundwater is limited by uncertainties between models (Crosbie 2007), the most directimpact will be on recharge, with a change in recharge in the same direction as a change inprecipitation.

Potential changes in recharge versus rainfall are highly nonlinear and vary with soil type andvegetation (Green et al. 2007). In general, decreasing rainfall and increasing temperaturessuggest a decrease in runoff and recharge. Projected reductions in runoff vary from seven to35 per cent in Melbourne, 10 to 25 per cent in the Murray-Darling Basin and 31 per cent in theStirling catchment (Western Australia) (Commonwealth of Australia 2007a). Since the late1960s, mean annual rainfall in southwest Western Australia has declined dramatically, andriver flows have reduced by almost three times the reduction in mean rainfall. That is, anaverage rainfall decline of 10 to 20 per cent caused a 40 to 60 per cent decline in dam inflow(Commonwealth of Australia 2007a). Groundwater storage volumes can be expected todecrease due to loss of recharge, with a parallel decrease in capillary rise to vegetation and aloss of discharge to springs and streams. Lowered groundwater input to streams could alterhydraulic gradients between the stream and connected aquifers. Sustained reduction inrecharge and increased evapotranspiration will result in groundwater drought, with complexand diverse consequences (Peters et al. 2003). Drought attenuates the flushing of nitratesand dissolved organic carbon into groundwater, limiting microbial metabolism and reducingthe supply of energy and nutrients to streams (Dahm et al. 2003). Greater frequency of drought will exacerbate demand on groundwater resources and intensify competition betweenconsumptive and non-consumptive uses of groundwater.

Reduced streamflow and higher surface water temperatures will potentially be associated withincreased eutrophication of surface waters, with implications for changed rates of benthicprocesses. Effects of surface warming can be expected to be particularly strong in summer ingroundwater-fed streams, with increases in mean annual oxygen consumption, rates of mineralisation and higher bacterial biomass (Sand-J ensen et al. 2007). Surface warming ingroundwater recharge areas could elevate subsurface temperatures, with likely impacts onrates and dominance by different biogeochemical processes and on subterranean microbesand fauna adapted to narrow zones of thermal stability. Higher surface water temperatureswill result in reduced levels of dissolved oxygen, with probable impairment of suitable

conditions for the hyporheos in downwelling zones. Higher groundwater temperatures will beassociated with a decrease in viscosity and a resulting increase in hydraulic conductivity(Freeze and Cherry 1979), with implications for enhanced transport of solutes andcontaminants.

In areas where rainfall and the severity of storms is expected to increase, higher rates of recharge will result in increases in flux in aquifers and potentially elevated rates of nitrateleaching; erosion will increase leading to higher sediment loads in streams, perhapshampering groundwater–surface water exchange; and increases in storage may exacerbatedryland salinity. It is also possible that increased rainfall in arid and semi-arid regions willstimulate biomass productivity, resulting in no nett increase to groundwater recharge (Scanlonet al. 2006).

Sea level rise will result in increased salinisation of surface and ground waters in coastal and

island regions, a rise in coastal groundwater levels and inland movement of the underlyingsaline lens resulting in reduced water quality, possibly threatening GDEs associated withcoastal aquifers. Salt-water intrusion will be exacerbated by lowered level or pressure due togroundwater drought, particularly in aquifers under pressure of extraction.

Both Crosbie (2007) for Australia and Puri (2006) speaking globally suggest that the directimpact of climate change on groundwater will be less significant than the impacts of associated pressures such as increasing consumptive demand, land clearing, urbanisationand other factors impacting on hydrological cycles. McMahon and Finlayson (2003) considerthat even if the most extreme predicted climate change scenarios for Australia were toeventuate, their impact and rate of onset, at least for surface waters, would be on a lesserscale than the changes that have already occurred as a result of river regulation.




5.4 Current policy setting in Australia

Australian states and territories are constitutionally responsible for natural resourcemanagement. The Commonwealth drives the co-ordination of natural resource managementby linking National Competition Council payments with jurisdictional progress towards

institutional reforms agreed by the Council of Australian Governments (COAG), and throughstrategic investment under the $2 billion Australian Government Water Fund administered bythe NWC and the Commonwealth Department of the Environment, Water, Heritage and theArts.

The water reforms agreed in 1994 require that water must be allocated for environmental usefirst, having regard for nationally-agreed principles (ARMCANZ/ANZECC 1996) and based onbest available science.

By April 2006, all Australian jurisdictions had signed the Intergovernmental Agreement on aNational Water Initiative (NWI), under which the COAG reforms are to be carried forward. TheNWI commits participating jurisdictions to a number of actions, including the development of water plans that include a specific provision for water to meet environmental and other publicbenefit outcomes, and a definition of the appropriate water management arrangements to

achieve those outcomes. Implementation of the NWI is now underway across Australia.All jurisdictions have now made legal provision for environmental water (Table 4) and aredeveloping water plans to meet environmental outcomes. The NWI states (in Schedule B(ii))that environmental outcomes can include: maintaining ecosystem function (for example,through periodic inundation of floodplain wetlands) and targets for biodiversity, water quality;and river health. These are congruent with the main subject areas of this review: biodiversity,subsurface ecological processes, and ecosystem goods and services.

Table 4: Legislation and policy addressing NWI requirements regarding environmental water

Jurisdiction Legislation relating to water planning

Policy documents relating toenvironmental provision

New South Wales Water Management Act 2000 State Water ManagementOutcomes Plan 2002NSW StateGDE Policy

Queensland Water Act 2000 Qld Water Plan 2005–2010

Tasmania Water Management Act 1999 Water for Ecosystems Policy2001

Western Australia Rights in Water and Irrigation Act 1914

State Water Plan 2007Statewide Policy No. 5

South Australia Natural Resources Management Act 2004

State Natural ResourcesManagement Plan 2006

Victoria Water Act 1989 Our Water, Our Future

Northern Territory Water Act 1992 No specific policy document;policy approach outlined inindividual water resource plans

Australian Capital Territory Water Resources Act 2007 Water Resources ManagementPlan 2004Environmental Flow Guidelines2006

States and territories have prepared NWI implementation plans (National Water Commission

2007b) in accordance with guidelines provided by the NWC. The basic framework forintegrated and sustainable groundwater management is being established through extraction




licensing, bore metering, and arrangements for data storage. Actions taken to implement NWIobjectives relating to environmental management of groundwater address legislative changesand other administrative matters that establish the foundation for groundwater management,but there are few indications of actions to identify GDEs, let alone to assess theirenvironmental water requirements. This is unsurprising given the paucity of basic data ongroundwater extraction, the historical separation of surface water and groundwater

management (a symptom of ‘hydroschizophrenia’ (Box 12)), the knowledge gaps relating toGDEs and the scant scientific guidance on assessment of environmental water requirements.

Box 12: Symptoms of hydroschizophrenia

• separate management of surface and groundwater

• playing down the role of groundwater

• poor and uncoordinated transboundary groundwater management.

(J arvis et al. 2005, Llamas and Martinez-Santos 2005)

The inability to specify rules for managing environmental groundwater flows or to specifysuitable indicators for monitoring responses to aquifer management had already beenidentified (National Groundwater Committee 2004). Australian research effort concerned withGDEs has focused on assessing groundwater dependency of terrestrial GDEs (Zencich et al.2002, Lamontagne et al. 2005a, Cook and O'Grady 2006, O'Grady et al. 2006b).

The only guidance documents in Australia regarding SGDEs are the NSW GDE policy(Department of Land and Water Conservation 2002) and a Western Australian document andtechnical appendix providing guidance for consideration of subterranean fauna duringenvironmental impact assessments (Environmental Protection Authority 2003, 2007). TheNSW policy sets out principles and a general framework for GDE management but lacks adetailed work plan, which would deliver tools and guidelines for effective implementation. TheWestern Australian guidance document addresses the specific situation of environmentalimpact assessment, and although useful in describing sampling methods and survey design,is not directly applicable to the needs of statutory water planning.

The first biennial assessment of progress in implementation of the NWI (National WaterCommission 2007a) found that arrangements for the management of environmental waterhad not yet emerged as envisaged by the NWC, that environmental water sustainabilitydeserved renewed attention, and that a more harmonised and rigorous national approach tomonitoring river health and groundwater is required. It was recommended that action be takento ‘improve understanding of groundwater and management of groundwater-surface waterinteraction’ and to ‘improve and harmonise river health and groundwater ecosystemmonitoring and assessment to enable states to incorporate information from this monitoringinto their adaptive management frameworks’.

A key process in defining the water needs of GDEs is the identification of environmental waterrequirements (EWRs), analogous to the concept of environmental flows for surface water. The EWR is the water regime needed to maintain ecological values and ecosystem servicesof water dependent ecosystems at a low level of risk (SKM 2001). EWRs are determined on

the basis of the best scientific information available and are the primary consideration in thedetermination of environmental water provisions (EWPs), which are the water regimesprovided as a result of the water allocation decision-making process taking into accountecological, social and economic impacts. The EWPs can meet the EWRs in part or in full.Development of approaches to providing environmental flows or EWRs in aquifers associatedwith GDEs is at an early stage in Australia, and no research to date has focused on the waterrequirements of stygofauna (although see Box 17).

The starting points in estimation of EWRs for GDEs are assessing the key attributes of flux,level or pressure, and water quality, and explicitly describing their roles in relation to theprocesses that drive the structure and function of dependent ecosystems. In the conceptualframework of SKM (2001), thresholds are determined for responses to change in waterregime. The EWR is the water regime that maintains responses within ‘limits of acceptable

change’. For SGDEs, there is a lack of baseline environmental and faunal data as well asknowledge gaps on community resilience to environmental change such as altered recharge,the impacts of groundwater extraction, tolerances to ranges of driving variables (dissolved




oxygen, nutrients, electrical conductivity, salinity, water level fluctuations), and tolerance tocontaminants (see Figure 1). In the absence of these data, the limits to acceptable changemust be set conservatively and perhaps by proxy through the EWRs for connected terrestrialwater-dependent habitats. The multiplicity of connections between SGDEs and other systemsdescribed above (see the section on threatening processes) argues for consideration of SGDEs, if only to prevent harm to other systems.

Table 5 lists the four (out of ten) NWI objectives concerned most directly with environmentalmanagement of groundwater (Box 14), the consequent NWI outcomes and NWI actions, andactions reported in the State and Territory Implementation Plans to address these. Objectiveiii) is in two parts: statutory provision for environmental and other public benefit outcomes,and improved environmental management practices. Action to address the first part involvesreform of existing water legislation or the introduction of new legislation (Table 4).

Box 14. NWI requirements most relevant to groundwater management

• make statutory provision for water plans and improve adaptive management

• address overallocation

• identify high conservation value systems

• recognise connectivity with surface water

Action to improve environmental management practices is less straightforward, beingpredicated not only on the identification of environmental outcomes, including maintenance of ecosystem function, biodiversity, and water quality, but also on an understanding of the watermanagement practices that support these outcomes. However, some actions to identify GDEsand assess their water needs are reported by the jurisdictions. These projects will besupported by actions to return previously overallocated and/or overdrawn surface andgroundwater systems to environmentally-sustainable levels of extraction (objective iv),arrangements for data collection and storage to improve water accounting (objective vii), andassessments of groundwater-surface water interconnection (objective x). Although the level of detail of GDE investigations is perhaps sufficient to meet broad reporting requirements, it isinadequate to assess their scale and scope at an ecologically relevant level. More detailed

reporting at workshops and in publications including websites would provide a more reliableand useful picture of the status of GDE investigations, facilitate sharing of methods,techniques and experiences, and help indicate knowledge gaps and priority areas forresearch effort.




NWI objecti ve NWI outcome NWI action Actions reported in NWI Implementatio

Tas: Currently trialing an extraction licensrelation to the protection of groundwater d

management plans. Ongoing consideratiothrough Conservation of Freshwater Ecos

Vic: Review groundwater activities and reof extraction for commercial or irrigation u

Qld: Water resource plans (WRPs) and Rhave been or are currently being developsystems, including areas with high levels

Groundwater resources are included in onthis stage. In the Pioneer, Lockyer valley,groundwater areas, groundwater managefor integration with water resource plans. groundwater and surface water is being cenvironment are being included to the ext

Ecological outcomes are stated in each Wflow strategies. The associated ROP requecological outcomes be monitored, asses

The approach used to estimate the risk toinvolves ranking the groundwater systemcompared with recharge, vulnerability to twatertables, threats to groundwater depeas local pumping effects, development pr

WA: investigations and assessments includependent ecosystems is underway.

Water to meet environmental and other pplans to be defined, provided and manage

Actions already taken: identification of grofeatures and ecological processes regardeIndigenous communities as part of studieWest Yarragadee aquifer, including how iaffected by changes in water level




NWI objecti ve NWI outcome NWI action Actions reported in NWI Implementatio

Revise current water allocation plans to fubetween surface and groundwater, by J u

In comparison to other jurisdictions, the vinteraction between surface water and gro The prime areas where there is interactioClare Valley and the Flinders Ranges, whflow. Most of these baseflows are ephemepools that sustain water dependent ecosy

Following the prescription of Mount Lofty conducted to identify this interaction as pathe water resources, including the impactsubsequent development of the water alloensure the maintenance groundwater dis

Tas: The Australian Government Water Fresults – enhancing water planning in Tas

interrelation between key groundwater – development of models of groundwater-s2008.

Vic: Ongoing investigations to determine between surface water and groundwater.integrated groundwater and streamflow m

WA: Connection between surface water ainvestigated as part of the development oon the level of modelling and assessmentCommission 2000) groundwater integration the hydraulic circumstances.

NATIONAL WA



5.5 International groundwater pol icy: Europe

For this review, we thought it would be useful to provide some brief outlines of thegroundwater policies currently underway in other parts of the world – partly for context butalso to indicate potential sources of information or guidance for Australian work on SGDEs

and to take some lessons from overseas experiences.The European Union (EU) Water Framework Directive (WFD) came into force in 2000(2000/60/EC). Its aim is to achieve ‘good ecological and chemical status’ for water across the27 EU member states by 2015. The WFD is based on the concept of river basinmanagement. A river basin management plan to protect and improve water quality will bedeveloped for each river basin, some of which transcend national borders. The WFD requiresclassification of water bodies into five quality classes using an Ecological Quality Ratio: theratio between a reference condition and the measured status of a waterbody (see<http://ec.europa.eu/environment/water/water-framework/info/intro_en.htm >).

A daughter direct ive to the WFD dealing with groundwater quality was adopted in 2006(2006/118/EC). This establishes criteria for evaluation of good groundwater chemical andquantitative (water level) status, and aims to harmonise the monitoring and evaluation of

groundwater quality across the EU. The WFD defines groundwater bodies as distinct volumesof groundwater within an aquifer or aquifers. Although the ecological status of groundwaterbodies is not considered directly (Danielopol et al. 2004), assessment of groundwaterchemical status requires assessment of the interactions between groundwater and surfacewaters, and analysis of the impact of groundwater bodies on the ecological status of surfacewater bodies and terrestrial GDEs. Further, the groundwater directive states (paragraph 20 of the recital): ‘Research should be conducted in order to provide better criteria for ensuringgroundwater ecosystem quality and protection. Where necessary, the findings obtainedshould be taken into account when implementing or revising this Directive. Such research, aswell as dissemination of knowledge, experience and research findings, needs to beencouraged and funded’ (see <http://ec.europa.eu/environment/water/waterframework/groundwater/policy/current_framework/index_en.htm>).

The objectives of the WFD that relate to groundwater are as follows:

• achievement of good groundwater quantitative and chemical status by 2015

• prevention of deterioration from one status class to another (for example, prevention of pollution)

• reversal of any significant and sustained upward trends in pollutant concentrations andprevention or limitation of input of pollutants to groundwater

• achievement of water-related objectives and standards for protected areas.

Lessons from the European experienceCommon conceptual models and terminology

Conceptual models have been developed for processes in groundwater bodies using asource-pathway-receptor paradigm (Figure 6). For each groundwater body, anthropogenicactivities are identified that could exert an environmental effect or pressure. This is analogousto the concept of threatening processes. The risk for each groundwater body is assessed byidentifying the pathways between pressure and receptors such as an aquatic ecosystem or awater user. The level of vulnerability is determined from the horizontal and vertical distancebetween pressure and receptor, and characteristics of the groundwater body such asresidence times, porosity, transmissivity and hydraulic gradient. Krause et al. (2007) applythis approach in developing an ecohydrogeological framework to assess the risk of significantdamage to groundwater dependent terrestrial ecosystems in the United Kingdom and theRepublic of Ireland.


http://ec.europa.eu/environment/water/water-framework/info/intro_en.htm

http://ec.europa.eu/environment/water/water

http://ec.europa.eu/environment/water/water-framework/info/intro_en.htm

http://ec.europa.eu/environment/water/water



water

pollution source user

aquatic ecosystemreceptor

receptor

direction of groundwater flow

Figure 6: Conceptual model of anthropogenic impacts on groundwater bodies

An anthropogenic impact produces a pressure that is transmitted along a groundwater pathway to receptors. The

pressure is diluted or attenuated (reducing size of arrows) along the pathway. Properties of the aquifer determine theextent of dilution or attenuation. Adapted from Quevauviller (2004).

Groundwater bodies are categorised in the EU approach as being at significant risk, probablyat significant risk but more information is needed, probably not at significant risk, and not atsignificant risk. This risk assessment determines the research, monitoring and managementpriorities. The effects of climate change on water quality parameters could oblige reevaluation of reference conditions and restoration targets (Noges et al. 2007).

As well as helping guide risk assessment and management, these models ensure that thereis shared understanding and agreement on pollutant pathways and processes withingroundwater bodies. Use of common terminology based on the shared conceptual modelsgreatly assists communication and development of useful knowledge structures (Benda et al.

2002).

5.6 International groundwater policy: South Africa

South Africa’s National Water Act 1998 provides for a reserve to be set aside for essentialhuman use and to protect aquatic systems before water is allocated to other uses. Waterresources are defined in the Act as including watercourses, surface water, estuaries andaquifers, so ostensibly groundwater and surface water are afforded the same provisions.Nevertheless, like Australia, omission of explicit inclusion of groundwater in the ecologicalreserve allows it to be disregarded (for example the exclusive attention to rivers by van Wyk

et al. (2006)), lack of procedural clarity hampers implementation of ecological protection forGDEs (MacKay 2006), and investigations of groundwater dependence have focussed onterrestrial ecosystems (Le Maitre et al. 1999). A recent report (Colvin et al. 2007) summarisesknowledge of GDEs in South Africa, identifies knowledge gaps, and makes recommendationsfor further research to meet the requirements of the relevant legislation.




6 Knowledge needs and researchdirections The knowledge needed to meet the agreed objectives of the NWI and specific researchquestions to provide these data are outlined in Table 6. Accompanying policy actions (Box 13)are needed to support these research directions.

The greatest benefit of groundwater ecology to groundwater management derives from theidentification of ecosystem and habitat types, with application to conservation planning,design of monitoring programs and sustainable use (Danielopol et al. 2008). Because manysurface water ecosystems are interdependent with SGDEs, the water needs of SGDEs mustbe considered in water planning. Similarly, ecosystem functions of SGDEs must bemaintained, if only to meet desired environmental outcomes for surface waters.

Specific research directions are discussed in the following sections.

Box 13: Necessary policy actions

Necessary policy actions are as follows:

• revise the National Principles for the Provision for Water to Ecosystems(ARMCANZ/ANZECC 1996) to take account of groundwater

• agree on nationally-consistent sampling, monitoring and reporting protocols for SGDEs

• improve frequency and extent of groundwater level and water quality monitoring

• establish mechanisms to facilitate sharing of information, case studies and methods, forexample, through workshops, publications and websites such as the Bureau of RuralSciences ‘Connected Waters’ website

• support regular workshops for water managers, consultants, and taxonomists to developrapid assessment tools, identify priorities for research and develop funding proposals

• require lodgement of specimens in a centralised register or ‘Stygobase’ that conforms toa standard, nationally-agreed terminology and including metadata such as samplingmethod, frequency of sampling, details of aquifer type and other location data includingassociated water quality data such as dissolved oxygen and conductivity

• establish coordinated data management and storage procedures

• require that determination of EWRs and EWPs for groundwater consider theenvironmental values and water quality objectives established under the National WaterQuality Monitoring Standards for connected surface waters.




NWI objecti ve Broad knowledge needs Specific research questions

iii) statutory provision for Improved ecological Can the proposed typology of groundwater habitats be incorpenvironmental and other understanding of SGDEs and of groundwater management units to develop biologically relevapublic benefit outcomes, andimproved environmentalmanagement practices

the relationship betweenbiodiversity and ecosystemfunction and the provision of

What are the drivers of SGDE ecosystem function? How confunctional units in our typology and across time?

groundwater ecosystem goodsand services

What are the faunal or environmental variables or suites of vapredict trends in ecosystem function? What is their reliability?

Water management arrangementswill maintain ecosystem function,water quality, and biodiversity

What are the threshold values in indicators that trigger manag

Do changes in wetting and drying cycles affect the functioning

values Does stygofauna have a role in maintaining hydraulic conducfunction, and in bioremediation? Are rates of decomposition of organic matter similar in SGDEgroundwater reserves? What level of taxonomic identification is sufficient for monitor

Conservation priorities Undertake targeted surveys to fill knowledge gaps regarding:rare species, key species of particular evolutionary significancservice providers; representative communities; identification ecology and ecological processes.

What are the indicators and predictors of high conservation vsites?

Investigate methods such as phylogenetic diversity (Forest etconservation priorities.

Take account of climate change Use the typological approach to identify which SGDEs are at

Consider strategies to protect vulnerable SGDEs, especially services.

Table 6: Knowledge needed to address NWI objectives, and suggested research questions

NATIONAL WA



NWI objecti ve Broad knowledge needs Specific research questions

iv) complete the return of allcurrently overallocated or

overused systems toenvironmentally-sustainablelevels of extraction

Determination of environmentallysustainable extraction

Processes of recovery forgroundwater systems

Restoration strategies for SGDEs,including effects of restoration of adjacent terrestrial and surfaceaquatic ecosystems

Monitor faunal community and water quality variables in areaAnalyse correlations and generate hypotheses for field testing

Test definitions of sustainability of groundwater extraction bywater quality indicators. Determine acceptable limits of change in groundwater regime

Monitor capacity for stygofauna recovery after overextraction

vii) water accounting which isable to meet the informationneeds of different watersystems in respect toplanning, monitoring, trading,environmental management

and on-farm management

Methods for measuring indicatorsof biodiversity, ecologicalprocesses and ecosystemservices in SGDEs

Protocols for data recording,storage, analysis and reporting

Establishment of database thatmeshes with databases onsurface biota and environmentalvariables

Compare methods of data collection, storage and analysis.

Look overseas for current approaches to data base manageproposed ‘Stygobase’ with existing GDE register.

x) recognition of theconnectivity between surfaceand groundwater resourcesand connected systemsmanaged as a singleresource

Identification of indicators of significant interconnectionbetween groundwater and surfacewater for the functional units in ourtypology

Compare indicators of interconnection between groundwater tracers, temperature, fauna, water quality variables).

How are aquifer processes linked with quality and quantity ofecosystems?

Coordinate studies investigating processes and impacts in SG

How does management action, including EWPs, in connecte

responses confined only to the ‘highly connected’ systems in




6.1 What is the appropriate management scalefor SGDEs?

An ecological view of groundwater as habitat and as providing ecosystem goods and services

raises the question of appropriate management scale. Until the water reforms of the lastdecade, groundwater management in Australia was not concerned with ecologicalconsiderations such as the water needs of GDEs. To accommodate the requirement of thewater reforms that water planning provide for environmental outcomes including themaintenance of ecosystem function, a smaller, ecologically-relevant scale of managementunit is needed. Yet, although effective management must focus at the ecosystem scale, thenational groundwater management unit is far larger.

The Australian Water Resources 2005 (National Water Commission 2006) uses thegroundwater management units designated by the National Land and Water Audit (Figure 7). The groundwater management unit is a hydrogeological unit defined as an area withappropriate scale for groundwater management practices dealing with resource issues andintensity of use (National Water Commission 2006). Although we recognise that the Australian

Water Resources 2005 was a first step and we acknowledge that the authors wereconstrained by the existing planning framework, the information presented in Appendix C andMap 45 (reproduced here as Figure 7) of the AWR 2005 Baseline Assessment Level 1 KeyFindings Report has little practical application for planning due to its extremely coarse scale.

Figure 7: The extremely coarse scale of identification of GDEs within groundwatermanagement units in the Australian Water Resources 2005 assessment

In practice, groundwater is not managed at the scale of the groundwater management unit butat smaller-scale planning units variously termed water control districts (Northern Territory),regional groundwater management areas (Western Australia), water resource management

areas (Victoria), water resource plan areas (Queensland), water management areas(Australian Capital Territory, Tasmania), and prescribed wells areas (South Australia).




In South Africa, a groundwater management unit is defined as ‘an area of a catchment thatrequires consistent management actions to maintain the desired level of use or protection of groundwater’ (Parsons and Wentzel 2007). This seems to be a good way forward.

6.2 A proposed typology of SGDEs

For the purpose of ecologically-relevant groundwater management in Australia, we proposethe development of a classification or typology of SGDEs based on descriptors of habitat.

This typology would help to simplify a diverse array of habitats and might even generatepredictions of the ecological traits that might characterise the fauna in these types. Forexample, Claret et al. (1999b) classified subsurface faunal communities using species traitsderived from research in Europe, sorting subsurface invertebrates according to their degree of affinity to the subsurface habitat, and showing that the proportions of these categorieschanged with different habitat conditions. In an analogous approach, Timms and Boulton(2001) derived a typology for central Australian arid zone floodplain wetlands based oncorrelations between invertebrate composition and the driving variables of water regime,salinity and turbidity within and among wetland types.

The main abiotic controls on animal distributions are ecological factors determining theavailability of resources such as food (energy) and living space (habitat). In SGDEs, resourceavailability is determined broadly by groundwater environment type; geology determines theporosity and contributes to the hydraulic conductivity of the aquifer matrix. But aquifer typealone is insufficient. A hydrogeological typology would place two aquifer systems in the samecategory, but differences in climate and hydrologic connection (Box 14 and 18) are likely todrive major differences in ecosystem metabolism and faunal community characteristics. Asanother example, Schmidt et al. (2007b) found that stygofaunal assemblage composition didnot reflect geological, chemical or topographical features in an alluvial aquifer in the MarblingBrook catchment near Perth, Western Australia, but was better characterised by a range of finer-scale abiotic features including dissolved oxygen and temperature.

It is accepted that flow regimes in surface waters determine physical habitat and are a majordeterminant of biotic composition (Poff et al. 1997, Puckridge et al. 1998, Bunn andArthington 2002). Similarly, the physical structure of an aquifer and the movement of waterand allochthonous (externally sourced) materials through it largely govern the composition of its stygofauna (Strayer 1994). Groundwater upwelling zones in streams are characterised bylow levels of dissolved oxygen (Malcolm et al. 2005); upwelling and downwelling zones areoften dominated by different groups of fauna, with stygofauna and benthic speciespreferentially occupying groundwater and surface water respectively (Dole-Olivier andMarmonier 1992, Dole-Olivier et al. 1994, Malard et al. 2003, Sliva and Williams 2005).

Porosity also determines the distribution of fauna by shaping the available physical spaces; ina fractured rock aquifer, fauna were distributed throughout the dendritic system of interconnected joints and fissures (Malard et al. 1996). Thus geomorphology, in particularinterstitial space, is a driver of distribution and abundance of groundwater fauna (Dole-Olivierand Marmonier 1992, Rouch 1992, Ward et al. 1994, Rouch and Danielopol 1999), not only

because it imposes spatial constraints (Creuzé des Châtelliers et al. 1994), but also becauseit influences the availability of nutrients and oxygen. Dominantly intergranular flow,intergranular/fracture flow, dominantly fracture flow or conduit flow determine whether flow isundifferentiated, through preferential pathways, or channelled through discrete pathways. This, in turn, determines the rate of transport of solutes and particulate matter, the rate of interchange of gases, and the spatial distribution of loci of biogeochemical activity therebycreating resource patches that drive the spatial distribution of fauna.

Clearly, an ecologically-relevant classification of stygofaunal habitat would require a muchfiner spatial scale than that of the groundwater management unit to take account of small-scale differences in recharge and hydraulic conductivity. These local-scale effects influencethe supply of organic material, which is the basis of many subsurface food webs (Datry et al.2005, Hancock et al. 2005). Therefore, a spatial and temporal perspective that matches the

tenets of modern groundwater ecology is needed. In a management context, a typologybased on an ecological perspective could potentially help predict stygofaunal biodiversity,abundance and community structure (Hahn and Fuchs submitted) and would therefore be




useful in determining priorities for stygofaunal surveys and other management applicationssuch as predicting species distributions, assessing vulnerability to risks, and identifyingconservation priorities (Castellarini et al. 2007a, Castellarini et al. 2007b). Given our currentlack of knowledge of Australian stygofauna, this typology could also reveal potential hot spotsof biodiversity that need protection during groundwater resource development.

Box 14: Case study 2: An alluvial aquifer in temperate Australia – The Peel alluvium, NSW

Location: 31° 18’ S, 151° 09’ EArea: 196 square kilometres Composition: mainly sands and gravelsMaximum thickness of alluvium: 15–20 metres Estimated porosity: 10 per cent

The Peel River, north-eastern NSW, is a 320-kilometre-long inland-flowing river. It joins the NamoiRiver, a major tributary of the Barwon-Darling system, west of Tamworth. Its width is restricted in theupper part of the valley, but below Tamworth the river flats reach their maximum width of more thanthree kilometres (Water Conservation and Irrigation Commission NSW 1970, Water ResourcesCommission 1986). Alluvium beneath the river flats contain an estimated 10 to 20 megalitres of groundwater per hectare (Peel and Upper Namoi Valley Irrigation Project Team 1989). The economy of the valley is supported by water from the Peel River and its alluvium. Chaffey Dam (capacity 62,000megalitres, 43 kilometres upstream of Tamworth) provides water for irrigation and Tamworth city watersupply (Peel and Upper Namoi Valley Irrigation Project Team 1989).

Water in the Peel alluvium generally contains less than 1000 milligrams per litre total salts, attributableto ready recharge by rainfall and streamflow. Hydrological connectivity between the river and thealluvium is inferred from correlations between rainfall, streamflow and variations in water levels and boreyields (Water Resources Commission 1986).

Before regulation, flows in the Peel River varied widely from periods of no flow to periods of overbankflooding. In the 45 years between 1923 and 1968, flows varied from about five to 450 per cent of recorded annual average flow (Water Conservation and Irrigation Commission NSW 1970). Streamflowrecords indicate that all streams in the valley have ceased to flow for extended periods of time duringdroughts; the longest period without flow was 223 days from J anuary to August 1966 for the Peel Riverat Piallamore (Water Conservation and Irrigation Commission NSW 1970). Considerable declines in thewatertable were experienced during drought periods, necessitating the deepening of some wells (WaterConservation and Irrigation Commission NSW 1970). The frequency of no-flow conditions was a major

restriction on farming development in the Peel Valley, prompting the construction of Chaffey Dam(Water Conservation and Irrigation Commission NSW 1970).

Since 1925, about 40 floods have exceeded the trigger level for flood warnings at Tamworth (Bureau of Transport Economics 2001). The longest interval without floods of this magnitude was 1925 to 1931. The most severe sequence of floods occurred from 1950 to 1956, when there were twelve floods thatexceeded the trigger level (Water Conservation and Irrigation Commission NSW 1970). Regularinundation of river flats would have provided nutrients as well as connectivity to the aquifer, and it isclear from the stream gauge records that water level fluctuations in the hydrologically-connected Peelalluvium were an ecosystem characteristic.

The NSW Department of Land and Water Conservation’s Stressed Rivers Report (1998b) listed theUpper Peel River as a category S3 (high) in overall stress classification, a high hydrology stress ratingand a medium environmental stress rating, indicating that water extraction is likely to be contributing toenvironmental stress and that the river was a high priority for the preparation of a river management

plan. In a similar assessment of stressed aquifers, the Peel Valley alluvium was identified as being athigh risk of over-extraction and a high priority for the development of a management plan (NSWDepartment of Land and Water Conservation 1998a).

Regular quarterly surveys from September 2005 to October 2007 (Tomlinson, unpubl.) revealed anabundant and diverse stygofaunal community widespread throughout the Peel alluvium. Lack of datafrom before dam construction prevents assessment of how these patterns are modified from a referencestate. This research is investigating relationships between water quality variables, water levelfluctuations and temporal and spatial patterns of stygofaunal species distributions and communitycomposition.

The management challenge in the Peel valley is to provide for the consumptive uses of water from theregulated river and its alluvium while providing for the environmental water requirements of the aquiferecosystem in which hydrological conditions are highly modified from the natural state.




Box 15: Case Study 2: An alluvial aquifer in arid Australia – Alice Springs Town Basin, NT

Location: 23° 41’ S, 133° 52’ EArea: 7.7 square kilometres Composition: a mixture of gravel, sand, silt and clayMaximum thickness of alluvium: 25 metres Estimated porosity: 20 per cent

The Alice Springs Town Basin is a small alluvial basin associated with the Todd River on which the town

of Alice Springs is now situated (Northern Territory Government 2007). Until recently, it was rechargedprimarily from ephemeral flows in the Todd River. The Town Basin supports culturally important riverbedvegetation, including mature river red gums that have traditional significance to the local Arrerntepeople. Groundwater flows both underneath the Todd River and along buried former channel beds.Before the 1970s, water levels in the Basin fluctuated widely in response to episodic river flow.

For some 50 years, the Town Basin was the main water supply to Alice Springs. Extraction virtuallyceased in the 1970s following the development of a borefield accessing deeper sedimentary aquifers of the underlying Amadeus Basin. Subsequent high rainfall years and high recharge from irrigation of lawns resulted in sustained high water levels in the Town Basin, with levels remaining four to sevenmetres higher than those recorded before the establishment of the Amadeus borefield. These high waterlevels mobilised salts from fringing bedrock, resulting in dramatic increases in salinity of up to 7000milligrams per litre total dissolved salts (Read 2003). The salinisation is also due to evaporationassociated with recharge from lawn overwatering.

Town Basin water is no longer potable, and although the Town Basin now supplies water for irrigation of lawns and the golf course, the quality in some parts of the Town Basin is now too poor even for this use.As well as higher salinity, water quality is affected by the urban and industrial activity (Read 2003).

The Town Basin presents an interesting management challenge. It is a shallow, alluvial aquifer that,despite hydrological disturbance, salinisation and poor quality, continues to supply consumptive andnon-consumptive uses, including groundwater dependent ecosystems. The Alice Springs WaterResource Strategy recommends that to maintain the health of the river red gums, groundwater levels inthe river corridor must not decline beyond eight metres below ground level. An open research questionis whether this imperative to protect the culturally-significant river red gums will also provide for thewater needs of other groundwater dependent species. It is likely that there is a stygofaunal communityof scientific interest in the Town Basin. The presence of stygofauna in the Town Basin was confirmed bypreliminary sampling of three monitoring bores in September 2006, which revealed a parabathynellidsyncarid (Tomlinson, unpublished data).

The necessity for a revised aquifer typology has been driven in Europe by the implementationof the Water Framework Directive (WFD). This involves characterising water bodies andtypes, identifying pressures and impacts on these waterbodies, assessing risks towaterbodies, and developing criteria to assess ecological and chemical status. Theinadequacy of defined groundwater management units that might contain more than oneaquifer and are not on a scale appropriate for ecological management had already beennoted by Gibert et al. (1994).

In response to the management requirements of the WFD, Dahl et al. (2007) proposed amulti-scale typology of groundwater-surface water interaction based on geomorphic,geological and hydrological concepts reflecting functional linkages and controlling flowprocesses at successively finer spatial scales. On a catchment scale (more than fivekilometres), groundwater flow is classified by regional geomorphology: on an intermediate orreach scale (one to five kilometres), the groundwater-riparian interactions are classified byhydrogeology; and at the local scale of 10 to 1000 metres, classification is based on the typeof local flow path, classified as either diffuse, overland, directly connected to groundwater, orthrough drainage ditches. Flow regime is important in delineating groundwater bodies andassessing their vulnerability to pollution. Vulnerability assessment involves considering thetravel time of infiltrating water, the effectiveness of hydrological connection between surfaceand groundwater, and the hydrogeological attributes of the aquifer materials (Quevauviller2008).

These considerations are readily applicable to an ecologically-focused typology. Hahn(submitted) develops a scale-based, ecologically-focussed hierarchical typology of groundwater habitats. In this approach, communities are defined at a macroscale

(continental) by biogeography, at the mesoscale (landscape) by the aquifer type, and at alocal scale by the degree of hydrological exchange with surface water. The degree of




hydrological exchange determines the nutrient supply, rated as poor, moderate or good (Hahn2006). Hahn and Fuchs (submitted) applied this approach to the identification of groundwaterhabitats in the south-western German state of Baden-Württemberg (an area of 37,750 squarekilometres). The state was separated into regional geological units, which were subdividedinto geohydrological groups (aquifer types). Stygofaunal community structure was found to beshaped broadly by the geohydrological type, and more finely by sub-types characterised by

differences in porosity and hydraulic conductivity, which influenced hydrological exchangeand the amount of living space.

A typological approach is taken by Colvin et al. (2007) in their classification of ‘aquiferdependent ecosystems’ in different type-settings in South Africa. The type-settings arepresented as a matrix of six aquifer types based on lithology and seven habitat types similarto the Australian GDE classes. This simplified type-setting enables a national-scale overviewof the main aquifer types and assists identification of possible locations for aquifer dependentecosystems. The authors use the term ‘aquifer dependent’ to avoid the confusion that can begenerated by definitions of groundwater that include all water below the ground, rather thanwater within the saturated zone. Thus, they define aquifer dependent ecosystems asecosystems that depend on groundwater in, or discharging from, an aquifer.

A typology of SGDEs has not been developed for Australia. The European approach of

hierarchical classification incorporating ecological factors is potentially useful, although itsapplication must take account of differences between Europe and Australia, including thegreater range and variability in environmental conditions in Australia. An ecohydrogeologicalapproach to an Australian SGDE typology is suggested in Table 7. This classification is basedon the amount of living space for stygofauna and resource supply, and it is intentionallyfocused on invertebrates; different classifications might be needed for microbial or otherecological components of SGDEs.

Degrees of primary, secondary and tertiary porosity determine available living space andplace physical constraints on faunal size and food particles (for example, organic matter). Thetype of porosity also affects the spatial distribution of fauna and influences the surface areaavailable for bacterial colonisation. Permeability affects hydraulic conductivity and thereforethe delivery rate of oxygen, particulate organic matter and solutes.

Table 7: Suggested SGDE typology

Living space

Between sediment

particles (primary

porosity)

In fractures, cracks

along bedding

planes, and solution

cavities (secondary

porosity)

In large voids

(tertiary porosity)

Some karsts,

sedimentary

rocks, basalt,

carbonates

Some karsts,

limestones,

some calcretes,

lava tubes

Deep caves

High connectivity High connectivity

Some

sandstones and

other

sedimentary

rocks

Hyporheic zone,

vadose zone in

discharge areas

in the arid zone

Stable GWR Variable GWR

Resource supply

Unconsolidated

aoelian, alluvial

and/or lacustrine

clays, sands and

gravels

Low connectivity

Deep

sedimentary

aquifers

Outcropping

fractured

aquifers, some

calcretes in arid

zone

Deep, fractured

aquifers

Stable GWR

Adapted from Fetter (2001), Wendland (2007), Hahn and Fuchs (submitted) and Hahn (submitted). SGDE type isdetermined by attributes of the groundwater regime, which are driven by patterns of recharge and discharge,hydraulic conductivity and hydrologic connection to recharge. Disturbance may alter the groundwater regime orconnectivity and cause shifts in SGDE type, for example, a stable groundwater regime, low connectivity SGDE mayshift to variable groundwater regime, low connectivity under the pressure of unsustainable extraction.

Resource supply is determined by the groundwater regime and the degree of hydrologicconnection to recharge. The groundwater regime is composed of the three attributes of flow




or flux, level or pressure, and water quality (Box 2), with the addition of temperature to thelatter attribute. The groundwater regime is affected by patterns of recharge and discharge,which in turn are driven by climate. The range of climatic types across Australia (Figure 8)and the high variability of rainfall and streamflow (Finlayson and McMahon 1998) are likely tobe strong drivers of spatial and temporal differences in aquifer hydrology where connectivityto the surface is high.

Figure 8: Classification of major climate types in Australia

Source: 2005 Bureau of Meteorology data

Seasonality and variability in rainfall and temperature in zones of groundwater rechargedetermine the frequency and volume of recharge, fluctuations in groundwater level orpressure, and water quality variations. Inputs of allochthonous organic matter, the mainenergy source for most SGDEs, are governed by the nature of the hydrological connectionwith surface waters or recharge area. Exchanges with the surface, and hence the timing and

quantity of food supply, are affected by longitudinal, lateral and vertical dimensions of connection as well as the dimension of time (Ward 1989, Humphreys 2006a). Lateral andvertical connection can be through the hyporheic zone to surface waters, longitudinal linkagesto recharge zones upstream, diffuse catchment inputs by percolation, or through conduits orother pathways of preferential flow through the aquifer.

Linear distance to the nearest surface waterbody is seldom a reliable measure of longitudinalor lateral connection due to the probable presence of preferential subsurface flow paths orimpermeable layers. The vertical connectedness can be inferred from the depth belowsurface in the case of infiltration through the unsaturated zone, but similarly this depth is notalways indicative of connection if overlying formations are of low permeability. These factors,which control lateral and vertical connectivity, vary on a fine scale. For each aquifer type ineach climatic region, the inputs of allochthonous resources depend not only on factors of catchment size and subsurface porosity, but also on how fine-scale surface morphology

directs drainage (Humphreys 2000b).




This proposed typology assumes heterotrophic metabolism based on allochthonous nutrientsources. An allochthonous base for the food chain is prevalent in subterranean habitats(Gibert and Deharveng 2002) although chemoautotrophy is significant in particular systems,such as the anchialine Bundera Sinkhole on the Cape Range peninsula in Western Australia(Humphreys 1999b), cave lakes on the Nullarbor (Subterranean Ecology 2007) and deepsubsurface environments such as the Great Artesian Basin aquifers (Kimura et al. 2005). Por

(2007) suggests that a deep subterranean chemoautotrophic biome continuous withanchialine systems and marine hot vents and cold seeps could provide an ecologicalexplanation for the high taxonomic diversity of subterranean fauna; however, this isspeculative. Because rates of chemoautotrophic production are slow (Chapelle and Lovley1990), it is assumed here that autotrophy makes an insignificant contribution to mostsubterranean food webs.

Continuing research effort will generate faunal and environmental data to test the usefulnessof the suggested typology and further elucidate the variables that drive faunal communitycomposition and that are related to the void characteristics, connectivity, and variability of groundwater regimes. As more data accumulate on the environmental conditions andcommunity characteristics of groundwater fauna across a range of SGDEs, it could bepossible to plot species response curves (Figure 9) and therefore identify key drivingvariables and the tolerance levels of stygofauna to changes in groundwater regime as a resultof groundwater extraction or other disturbance. It is likely that faunal community responses togradients in environmental variables are influenced by a number of these variables, and sofurther research is also required to identify associations between combinations of environmental and faunal community variables at a range of scales, and to develop stressorgradients for these combined variables. It should also be considered that the magnitude andrate of change in responses could vary with small shifts in critical variables, and might not beconsistent over time (Bressler et al. 2006, Hering et al. 2006, J ohnson et al. 2006). Thesedata and analyses would assist in developing an ecologically-based SGDE typology, enablingmanagers to estimate the likely distribution and composition of groundwater communities andhelping to identify and prioritise knowledge gaps.

The European approach of categorising groundwater bodies is similar to that of our proposedtypology in which aquifer type and resource supply, determined by climate and degree of

hydrological connection, determine SGDE type.

6.3 Investigations of functional groups

A currently-active research area centres on the relationship between biodiversity andecosystem function, and involves the concept of the ‘functional group’, which is a set of species having a similar role in ecosystem processes (Chapin et al. 1992). Proceeding fromthis is the question of functional redundancy (Schwartz et al. 2000), if several species play asimilar role, does loss of one or more of these species alter ecosystem function?

Investigations of functional groups of benthic and hyporheic invertebrates in freshwater and

marine environments (Mermillod-Blondin et al. 2001, Mermillod-Blondin et al. 2002, Gerino etal. 2003, Mermillod-Blondin et al. 2003, Mermillod-Blondin et al. 2004b, Mermillod-Blondin etal. 2005a) show the variability of species effects and interspecific effects within functionalgroups (Michaud et al. 2005, Norling et al. 2007). Caliman et al. (2007), working withsediment and benthic invertebrates collected from a shallow freshwater lagoon in Brazil,observed a significant positive effect of benthic bioturbator diversity on flux of total dissolvedphosphorus in experimental microcosms.

Boulton et al. (2008) characterised functional groups of stygofauna in alluvial aquifers as‘ecosystem service providers’, which are collectively responsible for services such asbioturbation, stimulating microbial activity through grazing, and organic matter decomposition.Localised loss of common or species-diverse taxa within each group of ecosystem serviceproviders might be readily compensated for, but loss of rarer taxa might not be so easily

accommodated, potentially leading to an impairment of ecosystem services.




For any biologically-relevant abiotic variable there is a range over which biological responses

occur (Figure 9a)

Figure 9a Response curve for a typical animal, showing the tolerance range of a biologicalindicator, in this case metabolic rate, and maximum and minimum temperature tolerance(Clapham 1973)

Tolerance range

M e t a b o l i c r a t e

Minimum Maximum Temperature

Within the response curve there is a range for which the response is optimum (Figure 9b).

Figure 9b Response curves with a broad optimum (a) and narrow optimum (b) (Clapham1973)

a b

Field observations of species responses might reflect responses to gradients in singleenvironmental variables, but in many cases do not (Figure 9c) due to the effects of responsesto other environmental variables or to biotic factors such as inter-specific competition.

Figure 9c Observed (field) species response and the experimentally-derived response curve(dashed) for an environmental variable. Points represent the observed response of thespecies at different locations (Clapham 1973).

S p e c i e s

r e s p o n s e

Gradient of environmental variable

Figure 9: Response curves




6.4 What level of taxonomic identification isnecessary?

The level of taxonomic identification required for some management decisions (Marshall et al.2006) has not yet been assessed for subsurface fauna: for example, is family levelidentification sufficient to assess a community response to changes in groundwater regime, orare there ecologically-relevant differences in the responses of species? These questions donot negate the necessity for species-level identification for biodiversity conservation. Due toconvergent evolution and the development in multiple lines of phreatomorphies, there mightbe no readily-apparent morphological differences between taxa (Proudlove and Wood 2003)so DNA analyses are frequently necessary (Finston et al. 2004, Finston et al. 2007) butshould be carried out in tandem with morphological descriptions to help non-experts identifytaxa where possible.

In parts of Europe, the stygofauna are well known; for example most of the Germancrustacean stygofauna have probably been described (Dr Hans J ürgen Hahn, UniversityKoblenz-Landau, Germany, pers. comm.). A centralised database developed as part of thePASCALIS project (Gibert et al. 2005) contains distributional and other details of groundwater

biodiversity drawn from published records of stygobitic taxa from six European countries. Acomplete species inventory for Australia is unrealistic in the short term as the time, expertiseand resources are not available in the immediate future (the next five years) to conductcomprehensive surveys and identify samples; but improvements can be made in the currentpiecemeal and reactive approach. Data from stygofaunal surveys are not centrally stored andmany surveys are conducted to answer immediate, local questions related to resource userather than the integrated and multidisciplinary research questions necessary to assistmanagement decisions about conservation and sustainable use. Spot surveys that take ascattergun approach to sampling and omit environmental data do not provide anunderstanding of the drivers of patterns of species distributions, abundance and communitycomposition. Given our current poor knowledge of stygofaunal species occurrence anddistributions, data are needed in order to identify appropriate criteria and indicators of biodiversity in SGDEs and to develop monitoring programs. Co-ordinated, well-planned and

targeted research is needed to generate the data and analyses with predictive capacity thatare meaningful for managers, and will also help the community understand the trade-offsimplicit in water management decisions.

6.5 Measuring biodiversity and monitoringmanagement action

A key management question is how to measure biodiversity and thus monitor the effects of management actions. There are two broad approaches to estimating biodiversity: use of taxon-based indicators, such as particular indicator species, and use of spatial or otherfeatures of community structure, such as habitat heterogeneity or species composition

(Lindenmayer et al. 2000). Indicators are more than a means of estimating or monitoringbiological diversity; they are most useful as tools to guide decision-making in policy.Identification of appropriate indicators is crucial to the application of basic science to naturalresources management (Failing and Gregory 2003). A promising approach is the use of phylogenetic diversity (Forest et al. 2007). This is a biodiversity index that measures thelength of evolutionary pathways that connect a given set of taxa and may be more useful thantaxon richness in guiding conservation effort.

Selecting the appropriate indicators enables managers to detect changes due to disturbance;using indicator response curves that have been derived experimentally or from field recordsgives managers some predictive capacity. The challenge in many groundwater environmentsis that the long residence time of groundwater creates a hydraulic time lag betweendisturbance and impact, and this can be exacerbated by an ecological time lag before change

is detectable in species with longer life cycles and lower fecundity (Table 1). Presently, wehave little idea of the shape of these species response curves for any groundwater taxon inthe world, severely restricting the utility of any individual stygofauna species as an indicator.




6.6 Priority research directions

Our knowledge gaps about groundwater and SGDEs suggest broad questions (Box 16),which are addressed by specific research directions:

• determine the minimum level of taxonomic identification required to distinguish

ecologically-relevant morphotaxa for management needs

• undertake surveys to investigate correlations between individual and suites of environmental variables (water quality variables, water level or pressure) with stygofaunalcommunity composition and abundance, in different aquifer types (Henry and Danielopol1998, Datry et al. 2005, Hahn 2006, Schmidt et al. 2007b) to derive species responsecurves that will build predictive capacity and help in conservation planning (Ferreira et al.2007) such as formulating restoration actions

• apply survey results to extending our ecohydrogeological typology of stygofaunal habitatsto enable identification of SGDE habitat types within groundwater management units at ascale appropriate for management

• compare species response curves within and between habitat types (Masciopinto et al.

2006) to derive type-specific stressor tolerance values (Bressler et al. 2006) and toidentify tipping points (Nina Bate, EPA Victoria, pers. comm.)

• identify the key ecosystem service providers either at species, higher taxonomic group orfunctional group level and characterise their functional relationships and functionalstructure, assess how aspects of the community structure of ecosystem service providersand its changes affect provision of services, identify how key environmental factors affectecosystem service providers and their provision of services, and measure the spatiotemporal scales over which ecosystem service providers and their services operate(Boulton et al. 2008)

• focus taxonomic attention on developing molecular and morphological phylogenies forkey groups that have potential as indicator taxa or key ecosystem service providers

• improve understanding of the effects of water quality changes (especially in electricalconductivity, temperature, and concentrations of nutrients and dissolved oxygen) onecological processes to generate hypotheses of ecosystem processes and functions tobe tested in field and laboratory experiments

• develop conceptual models of SGDE function to help identify indicators, design researchand monitoring programs, assess resilience of SGDEs and identify, assess and managerisk, particularly the risk of a shift in SGDE type, for example a shift from a stablegroundwater regime to a variable groundwater regime

• identify SGDEs at greatest risk from threats including climate change

• evaluate the 14 tools in Land and Water Australia’s toolbox (Clifton et al. 2007) forapplicability in assessing the environmental water requirements of SGDEs. For example,

tool 14 is ‘analysis of aquatic ecology’ or the use of ecological survey techniques toidentify aquatic species with reproductive behaviour or habitat requirements that indicategroundwater dependency. An indicator identified for this tool is the presence of obligategroundwater fauna in the hyporheic zone. By extending sampling to bores in theconnected alluvium, this tool can readily be applied to assessment of SGDEs and wouldprovide valuable data to assist in management of the linked systems

• improve understanding of groundwater–surface water linkages and link aquifer processeswith quality and quantity of groundwater discharges to dependent ecosystems

• develop approaches to rescaling models of aquifer processes from the hydrogeologic toan appropriate ecological scale (similar to the challenge of downscaling global climatedata for regional applications); investigate how fine scale patterns of discharge and ratesof salinisation vary with topography (Doble et al. 2006)




• develop a definition of ecosystem health in SGDE types based on type-specific indicatorsof biodiversity and water quality, and including limits of acceptable change in theseindicators and triggers for management actions

• develop a framework for identifying high conservation value in SGDE types, identify areaswith high biodiversity value, areas that are most heavily impacted, and areas that arevulnerable to loss of biodiversity value

• derive priorities for protection or restoration effort by identifying areas already impacted orunder pressure which would most reward conservation or restoration effort (Linke andNorris 2003) using an approach that considers irreplaceability, condition and vulnerability(Linke et al. 2007)

• develop management practices that optimise consumptive use of SGDE goods in thecontext of climate change and maintenance of ecosystem services

• revise threshold values for limits on contaminant levels in groundwater (Hose 2005,2007).

Box 16: Understanding the groundwater resource

What are the characteristics of the groundwater regime (flow/flux, level/pressure, water quality)? What is the water balance (location, rate and volume of recharge and discharge)? What are the water access entitlements and when are they exercised? What SGDEs are present? What are the characteristics of subsurface biodiversity and ecosystem services? How are they related? What are the environmental water requirements? What are the indicators of ecosystem condition and what are the acceptable levels of change in these indicators? What are the risks to the resource, including land uses, extraction, climate change, and threats from connected ecosystems?

What is the sustainable level of extraction? How does it change over time? What actions are necessary to protect biodiversity and ecosystem services including provision of goods? Adapted from Cullen (2006)Presently reference condition data are scanty because surveys are constrained to the existingbore network, which was established to monitor the impacts of groundwater extraction. A risk-based approach will identify aquifer habitats that are under pressure and have not beensampled adequately: so far the effort has focused on some calcrete, alluvial and karstichabitats and aquifers in mineraliferous rocks subject to mining. Sampling other habitat typescould elucidate ecological questions such as the function of ecotones and the role of less

porous aquifers as faunal habitat. Within-habitat sampling should be stratified (Castellarini etal. 2007a).

Consideration should be given to evaluating existing aquatic research projects foropportunities to collect and synthesise data that may be relevant to SGDE management.Examples include projects determining the environmental water requirements of linked GDEs,assessing the impact of regulation, surface water extraction and environmental flow releasesin rivers with hydraulically connected alluvium, and projects where opportunities exist forstygofaunal and water quality monitoring during aquifer injection and artificial recharge,groundwater bypass during mining or construction projects, assessments of aquifer waterbalances or economic valuation of aquifer goods and services.

For sustainable management of groundwaters and connected surface waters there must becross-disciplinary research and management. Coordinated analysis of physico-chemical,

faunal and hydrological factors will assist the development of practical, on-the-groundsolutions to management needs.




Agencies and research groups should be encouraged to identify challenges to integration,develop and share strategies to address these challenges, and promote joint work, by:

• supporting and publishing case studies of projects in which hydrogeological andecological research questions were integrated explicitly in the study design

• holding joint workshops between hydrogeologists and both terrestrial and aquatic

ecologists in which disciplinary axioms and conceptual models are shared, assumptionsare identified, research questions are explored and formulated jointly, and the barriers toeffective cross-working are worked through

• encouraging joint or cross-publication, especially between hydrogeologists and ecologists

• maintaining up-to-date websites that report on work in progress, minimise duplication of effort and ensure ready availability of data.




7 Conclusion This review demonstrates extensive knowledge gaps about the distribution, composition andbiodiversity value of Australian stygofauna, and the rudimentary level of our understanding of

the drivers of subsurface ecological processes. It also demonstrates that many SGDEsdeliver a range of goods and services, and through their connections with other systems,impact on and are impacted by them. Surface and groundwater systems are interconnected,although this interconnection may be intermittent or pulsed, depending on the groundwaterregime and the volume and degree of connection to recharge. Disturbance such as pollutionor management interventions either in SGDEs or connected systems has flow-on effects,often with time lags.

We propose an ecologically-oriented typology of SGDE habitats that will assist in developingresearch projects that are most likely to meet the environmental water objectives of the NWI. The research directions identified here aim to produce decision tools and develop standardmethods and protocols for monitoring and assessing indicators of SGDE health andidentifying high conservation value ecosystems, and to provide guidance on SGDE-specificmanagement actions to maintain biodiversity, ecosystem function and water quality.




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Glossary Aeolian Relating to or arising from the action of wind

Allochthonous Originating outside the ecosystem under discussion (Boulton andBrock 1999)

Anchialine habitats Bodies of saline water with subterranean connections to the sea andrestricted openings to the open air, showing marine and terrestrialinfluences (Iliffe 2000)

Anthropogenic Derived from human activities

Aquifer A geologic unit that can store and transmit water at rates fast enoughto supply reasonable amounts of water to wells (Fetter 2001)

Aquitard A geological layer of low permeability than can store groundwater andalso transmit it slowly from one aquifer to another (Fetter 2001)

Biodiversity The variability among living organisms from all sources, includingterrestrial, marine and other aquatic ecosystems and the ecologicalcomplexes of which they are part; this includes diversity withinspecies (genetic), between species, and of ecosystems

Biodiversity hotspot An area featuring exceptional concentrations of endemic species andexperiencing exceptional loss of habitat (Myers et al. 2000)

Calcrete Carbonate deposits that form in soil or in the vicinity of the watertableas a result of evaporation of soil water or groundwater respectively

Carbonate rocks Rocks consisting primarily of a carbonate mineral such as calcite(CaCO3) or dolomite (CaMg(CO3)

2), the chief minerals in limestoneand dolostone respectively

Discharge The loss of water from groundwater to surface water, the atmosphereand the ocean. Includes springs, diffuse seepage into drainagesystems (both natural and anthropogenic) and lakes, diffuse andlocalised discharge through the seafloor, evaporation of soil moisturethat is replenished by seepage (dry salt lakes) and transpiration byphreatophytic vegetation that draws its water from the watertable(UNESCO/IHP 2006)

Ecotone A transition zone between two ecosystems (Brewer 1988)

Environmental water The water regimes provided as a result of the water allocationprovisions (EWPs) decision-making process taking into account ecological, social and

economic impacts

Environmental water The water regime needed to maintain ecological values andrequirements ecosystem services of water dependent ecosystems at a low level of (EWRs) risk (SKM 2001)

Epikarst The heterogeneous interface between unconsolidated material andsolutionally altered carbonate rock, which is partially saturated andcapable of delaying or storing and locally rerouting vertical infiltration

to the underlying karst aquifer (J ones et al. 2004)




Eutrophication The enrichment of water bodies with excess nutrients, typicallynitrogen and phosphorus, and the subsequent effects on water qualityand biological structure and function. It is a process rather than astate (Rast and Thornton 1996)

Flux (in Rate of groundwater flow per unit width of aquiferhydrogeologicalterms)

Groundwater The subsurface water that occurs beneath the watertable in soils and(hydrogeological geologic formations that are fully saturated (Freeze and Cherry 1979)definition)

Groundwater, Water that has been present in pores and cracks of the saturated(ecological zone of soil or rock for sufficient periods of time to undergo physicaldefinition) and chemical changes due to interactions with the aquifer

environment

Groundwater An ecosystem that would be significantly altered by a change in thedependent chemistry, volume and/or temporal distribution of its groundwaterecosystem (GDE) supply (Parsons and Wentzel 2007). The degree of ecosystem

dependence on groundwater is proportional to the fraction of theannual water budget that ecosystem derives from groundwater(Hatton and Evans 1998).

Groundwater flow The underground pathway by which ground water moves from areassystem of recharge to areas of discharge

Groundwater A hydraulically connected groundwater system that is defined andmanagement unit recognised by Australian State and Territory agencies. This definition(GMU) allows for management of the groundwater resource at an appropriate

scale at which resources issues and intensity of use can beincorporated into groundwater management practices.

In South Africa a GMU is an area of a catchment that requiresconsistent management actions to maintain the desired level of use orprotection of groundwater; delineation is based on managementconsiderations rather than geohydrological criteria (Parsons andWentzel 2007)

Groundwater regime The three broad attributes of groundwater that are ecologically(GWR) significant to dependent ecosystems: flow or flux, level or pressure,

and water quality

Groundwater The period of time from when a groundwater parcel percolates into anresidence time aquifer at a certain site to its outflow into surface water (river, lake,

sea)

Hydraulic A rate of flow indicating the ease with which water will pass throughconductivity aquifer material

Hydrologic The water-mediated transfer of matter, energy, and/or organismsconnectivity within or between elements of the hydrologic cycle

Hyporheic zone The saturated interstitial areas beneath the stream bed and into thestream banks that contain some proportion of channel water or thathave been altered by channel water infiltration (White 1993)

Hyporheos The fauna occupying the hyporheic zone




Karst A Slovenian word describing a terrain characterised by sinkholes,caves and springs developed most commonly in carbonate rockswhere significant solution of the rock has occurred due to flowingwater (J ennings 1985, ‘Culver et al. 1995, ‘Fetter 2001)

Palaeochannels Strips of buried sand and gravel laid down by former water courses

Permeability The property of porous materials which determines the flow of fluidunder pressure; it is a function of porosity and the interconnectednessof the pore spaces

Phreatomorphies The convergent morphological, behavioural and physiological featuresof stygobites (Humphreys 2000a)

Porosity The percentage of the aquifer matrix that is taken up by space,comprising pores between grains (primary porosity), fractures(secondary porosity) and enlarged cavities (tertiary porosity)

Psammolittoral The sandy zone on the shore of a surface water body between thehighest water level and the lower limits of submersed rootedvegetation (Wetzel 2001)

Pseudokarst Landforms which resemble karst but are not produced by solution of rock but by processes such as wave action, earth movements or theevacuation of lava (Halliday 2007)

Recharge Any influx of water entering a groundwater system at any of itsdefined boundaries. Includes natural recharge by diffuse infiltration,subsurface preferential flow and inflow from streams and lakes, andartificial recharge from intentional aquifer storage and excessirrigation (UNESCO/IHP 2006)

Stygobite Aquatic animal which completes its life cycle in groundwater

Stygofauna Aquatic animals found in groundwater; sometimes used as a synonymof stygobite

Stygophile Animals which spend part of their life cycle in groundwater

Stygoxene Animals which occur accidentally in groundwater but have no affinitywith groundwater habitats

Subsurface An ecosystem occurring below the surface of the ground that wouldgroundwater be significantly altered by a change in the chemistry, volume and/or

dependent temporal distribution of its groundwater supply (Adapted from Parsonsecosystem (SGDE) and Wentzel (2007))

Subsurface Groundwater Dependent Ecosystems

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