Chapter 24

Nutrient Cycles, Bioremediation, and Symbioses

I. The Carbon and Oxygen Cycles

24.1 The Carbon Cycle

24.2 Syntrophy and Methanogenesis

24.1 The Carbon Cycle

Carbon is cycled through all of Earth’s major carbon

reservoirs

i.e., atmosphere, land, oceans, sediments, rocks, and

biomass

Figure 24.1

Reservoir size and turnover time are important

parameters in understanding the cycling of elements

Major Carbon Reservoirs on Earth

CO2 in the atmosphere is the most rapidly transferred carbon

reservoir

- CO2 is fixed primarily by photosynthetic land plants and

marine microbes

- CO2 is returned to the atmosphere by respiration of

animals and chemoorganotrophic microbes as well as

anthropogenic activities

Microbial decomposition is the largest source of CO2 released

to the atmosphere

The carbon and oxygen cycles are intimately linked

Phototrophic organisms are the foundation of the carbon

cycle

Oxygenic phototrophic organisms can be divided into two

groups: Plants and microorganisms

- Plants dominant phototrophic organisms of terrestrial

environments

- Phototrophic microbes dominate aquatic environments

Photosynthesis and respiration are reverse reactions

- Photosynthesis

CO2 + H2O (CH2O) + O2

- Respiration

(CH2O) + O2 CO2 + H2O

Redox Cycle for Carbon

Figure 24.2

The two major end products of decomposition of

carbon-containing materials are CH4 and CO2

24.2 Syntrophy and Methanogenesis

Methanogenesis is central to carbon cycling in anoxic

environments

- Most methanogens reduce CO2 to CH4 with H2 as an

electron donor; some can reduce other substrates to

CH4 (e.g., acetate)

- Methanogens team up with partners (syntrophs) that

supply them with necessary substrates

Anoxic Decomposition

Figure 24.3

Rxns of Anoxic Conversion of Organic Compounds to CH4

Methanogenic symbionts can be found in some protists

(e.g. protozoa)

- Believed that endosymbiotic methanogens benefit

protists by consuming H2 generated from glucose

fermentation

Termites and Their Carbon Metabolism

Figure 24.4

Hindgut and termite larva

Methanogens in symbiotic protozoa in hindgut

Fluoresces due to F420

On a global basis, biotic processes release more CH4

than abiotic processes (Table 24.3)

Estimates of CH4 Released into the Atmosphere

Acetogenesis is a competing H2-consuming process to

methanogenesis in some environments

e.g., termite hindgut, permafrost soils

- Methanogenesis from H2 (-131 kJ) is energetically more

favorable than acetogenesis (-105 kJ)

- Acetogens position themselves in the termite gut nearer to the

source of H2 produced from cellulose fermentation (by protozoa)

than methanogens

- Acetogens can ferment glucose and methoxylated aromatic

compounds from lignin whereas methanogens cannot

Sulfate-reducing bacteria outcompete methanogens and

acetogens in marine environments

II. Nitrogen, Sulfur, and Iron Cycles

24.3 The Nitrogen Cycle

24.4 The Sulfur Cycle

24.5 The Iron Cycle

24.3 The Nitrogen Cycle

Nitrogen

A key constituent of cells

Exists in a number of oxidation states

Redox Cycle for Nitrogen

Figure 24.5

N2 is the most stable form of nitrogen and is a major

reservoir

The ability to use N2 as a cellular nitrogen source (nitrogen

fixation) is limited to only a few prokaryotes

Denitrification is the reduction of nitrate to gaseous nitrogen

products and is the primary mechanism by which N2 is

produced biologically

Ammonia produced by nitrogen fixation or ammonification

can be assimilated into organic matter or oxidized to nitrate

Anammox is the anaerobic oxidation of ammonia to N2

gas (NH4+ + NO2

- → N2 + 2 H2O)

Denitrification and anammox result in losses of nitrogen

from the biosphere

24.4 The Sulfur Cycle

Sulfur transformations by microbes are complex

The bulk of sulfur on Earth is in sediments and rocks as

sulfate and sulfide minerals (e.g., gypsum, pyrite)

The oceans represent the most significant reservoir of

sulfur (as sulfate) in the biosphere

Redox Cycle for Sulfur

Figure 24.6

Hydrogen sulfide is a major volatile sulfur gas that is

produced by bacteria via sulfate reduction or emitted

from geochemical sources

- Sulfide is toxic to many plants and animals and reacts

with numerous metals

Sulfur-oxidizing chemolithotrophs can oxidize sulfide

and elemental sulfur at oxic/anoxic interfaces

Organic sulfur compounds can also be metabolized by

microbes

- The most abundant organic sulfur compound in nature is

dimethyl sulfide (DMS)

Produced primarily in marine environments as a degradation

product of dimethylsulfoniopropionate (an algal osmolyte)

- DMS can be transformed via a number of microbial

processes

24.5 The Iron Cycle

Iron is one of the most abundant elements in the

Earth’s crust

- On the Earth’s surface, iron exists naturally in two

oxidation states

Ferrous (Fe2+)

Ferric (Fe3+)

e.g. Fe + CuSO4 FeSO4 + Cu (Fe + Cu2+ Fe2+ + Cu)

Redox Cycle of Iron

Figure 24.7

Fe3+ can be used by some microbes as electron

acceptors in anaerobic respiration

In aerobic acidic pH environments, acidophilic

chemolithotrophs can oxidize Fe2+ (e.g.,

Acidithiobacillus)

Oxidation of Ferrous Iron (Fe2+)

Figure 24.8a

A Microbial Mat Containing High Levels of Ferrous Iron (Fe2+)

Figure 24.8b

Pyrite (FeS2)

One of the most common forms of iron in nature

Its oxidation by bacteria can result in acidic conditions in

coal-mining operations

Pyrite and Coal

Figure 24.9

Role of Iron-Oxidizing Bacteria in Oxidation of Pyrite

Figure 24.10a

Acid Mine Drainage

An environmental problem in coal-mining regions

Occurs when acidic mine waters are mixed with natural

waters in rivers and lakes

Bacterial oxidation of sulfide minerals is a major factor in

its formation

Acid Mine Drainage from a Bituminous Coal Region

Figure 24.11

Ferroplasma acidarmanus

Figure 24.12

Streamers of F. acidarmanus, an extremely acidophilic iron-oxidizing archaeon

Ferroplasma acidarmanus

Figure 24.12

Scanning electron micrograph of F. acidarmanus

III. Microbial Bioremediation

24.6 Microbial Leaching of Ores

24.7 Mercury and Heavy Metal Transformations

24.8 Petroleum Biodegradation

24.9 Biodegradation of Xenobiotics

Bioremediation

Refers to the cleanup of oil, toxic chemicals, or other

pollutants from the environment by microorganisms

Often a cost-effective and practical method for pollutant

cleanup

Microbial Leaching

The removal of valuable metals, such as copper, from

sulfide ores by microbial activities

Particularly useful for copper ores

24.6 Microbial Leaching of Ores

Effect of the Acidithiobacillus ferrooxidans on Covellite

Figure 24.13

CuS

In microbial leaching, low-grade ore is dumped in a large

pile (the leach dump) and sulfuric acid is added to maintain

a low pH

The liquid emerging from the bottom of the pile is enriched in

dissolved metals and is transported to a precipitation plant

Bacterial oxidation of Fe2+ is critical in microbial leaching as

Fe3+ itself can oxidize metals in the ores

The Microbial Leaching of Low-Grade Copper Ores

Figure 24.14a

A Typical Leaching Dump Effluent from a Copper Leaching Dump

Figure 24.14c

Recovery of Copper as a Metallic Copper Small Pile of Metallic Copper Removed from the Flume

Arrangement of a Leaching Pile and Reactions

Figure 24.15

Microbes are also used in the leaching of uranium and

gold ores

Gold Bioleaching tanks in Ghana

24.7 Mercury and Heavy Metal Transformations

Mercury is of environmental importance because of its

tendency to concentrate in living tissues and its high toxicity

The major form of mercury in the atmosphere is elemental

mercury (Hgo) which is volatile and oxidized to mercuric ion

(Hg2+) photochemically

Most mercury enters aquatic environments as Hg2+

Biogeochemical Cycling of Mercury

Figure 24.17

Hg2+ readily absorbs to particulate matter where it can

be metabolized by microbes

- Microbes form methylmercury (CH3Hg+), an extremely

soluble and toxic compound

- Several bacteria can also transform toxic mercury to

nontoxic forms

Bacterial resistance to heavy metal toxicity is often

linked to specific plasmids that encode enzymes

capable of detoxifying or pumping out the metals

- Transform CH3Hg+ to Hg2+ and Hg2+ to Hg0

Mechanism of Hg2+ Reduction to Hgo in P. aeruginosa

Figure 24.18a

The mer operon

Transport and Reduction of Hg2+

24.8 Petroleum Biodegradation

Prokaryotes have been used in bioremediation of

several major crude oil spills

Environmental Consequences of Large Oil Spills

Figure 24.19a

Contaminated Beach in Alaska containing oil from the Exxon Valdez spill of 1989

Figure 24.19c

Oil Spilled into the Mediterranean Sea from a Power Plant

Figure 24.19b

Center rectangular plot (arrow) was treated with inorganic nutrients to stimulate bioremediation

Taean Oil Spills

Taean Oil Spills

Taean Oil Spills

Taean Oil Spills

Diverse bacteria, fungi, and some cyanobacteria and green

algae can oxidize petroleum products aerobically

Oil-oxidizing activity is best if temperature and inorganic

nutrient concentrations are optimal

Hydrocarbon-degrading bacteria attach to oil droplets and

decompose the oil and dispense the slick

Hydrocarbon-Oxidizing Bacteria in Association with Oil

Figure 24.20

Gasoline and crude oil storage tanks are potential

habitats for hydrocarbon-oxidizing microbes

- If sufficient sulfate is present, sulfate-reducing bacteria can

grow and consume hydrocarbons

Some microbes can produce petroleum

Particularly certain green algae

Botryococcus braunii excreting oil droplets

24.9 Biodegradation of Xenobiotics

Xenobiotic Compound

Synthetic chemicals that are not naturally occurring

e.g., pesticides, polychlorinated biphenyls, munitions,

dyes, and chlorinated solvents

Many degrade extremely slowly

Pesticides

Common components of toxic wastes

Include herbicides, insecticides, and fungicides

Represent a wide variety of chemistries

Some of which can be used as carbon sources and

electron donors by microbes

Examples of Xenobiotic Compounds

Figure 24.23

Persistence of Herbicides and Insecticides in Soils

Table 24.4

Table 24.4

Some xenobiotics can be degraded partially or

completely if another organic material is present as a

primary energy source (cometabolism)

Chlorinated xenobiotics can be degraded anaerobically

(reductive dechlorination) or aerobically (aerobic

dechlorination)

- Reductive dechlorination is usually a more important

process as anoxic conditions develop quickly in polluted

environments

Biodegradation of the Herbicide 2,4,5-T

Figure 24.24a

Growth of Burkoholderia cepacia on 2,4,5,-trichlorophenoxyacetic acid

Pathway of Aerobic Herbicide 2,4,5-T Biodegradation

Figure 24.24b

Plastics of various types are xenobiotics that are not

readily degraded by microbes

Chemistry of Synthetic Polymers

Figure 24.25

The recalcitrance of plastics has fueled research efforts

into a biodegradable alternative (biopolymers)

Bacterial Plastics

Figure 24.26a

Poly-β-hydroxyvalerate and poly-β-hydroxybutyrate

Bacterial Plastics

Figure 24.26bShampoo Bottle Made of the PHB/PHV Copolymer

IV. Animal–Microbia Symbioses

24.10 The Rumen and Ruminant Animals

24.11 Hydrothermal Vent Microbial Ecosystems

24.12 Squid-Alvibrio Symbiosis

24.10 The Rumen and Ruminant Animals

Microbes form intimate symbiotic relationships with

higher organisms

Ruminants

Herbivorous mammals (e.g., cows, sheep, goats)

Possess a special digestive organ (rumen) within which

cellulose and other plant polysaccharides are digested

with the help of microbes

Diagram of the Rumen and Gastrointestinal System of a Cow

Figure 24.27a

Photo of Fistulated Holstein Cow

Figure 24.27b

The rumen contains 1010-1011microbes/g of rumen

constituents

Microbial fermentation in the rumen is mediated by

celluloytic microbes that hydrolyze cellulose to free glucose

that is then fermented, producing volatile fatty acids (e.g.,

acetic, propionic, butyric) and the CH4 and CO2

Fatty acids pass through rumen wall into bloodstream and

are utilized by the animal as its main energy source

Biochemical Reactions in the Rumen

Figure 24.28

Rumen microbes also synthesize amino acids and

vitamins for their animal host

- Rumen microbes themselves can serve as a source of

protein to their host when they are directly digested

- Anaerobic bacteria dominate in the rumen

Characteristics of Some Rumen Prokaryotes

Abrupt changes in an animal’s diet can result in

changes in the rumen flora

- Rumen acidification (acidosis) is one consequence of

such a change

Anaerobic protists and fungi are also abundant in the

rumen

- Many perform similar metabolisms as their prokaryotic

counterparts

Cecal Animals

Herbivorous animals that possess a cecum

A cecum is

An organ for celluloytic digestion

Located posterior to the small intestine and anterior

to the large intestine

24.11 Hydrothermal Vent Microbial Ecosystems

Deep-sea hot springs (hydrothermal vents) support

thriving animal communities that are fueled by

chemolithotrophic microbes

Hydrothermal Vents

Figure 24.29

Diverse invertebrate communities develop near

hydrothermal vents, including large tube worms, clams,

and mussels

Invertebrates Living Near Deep-Sea Thermal Vents

Figure 24.30a

Tube Worms (Family Pogonophora)

Figure 24.30b

Close-up Photograph Showing Worm Plume

Figure 24.30c

Mussel Bed in Vicinity of Warm Vent

Chemolithotrophic prokaryotes that utilize reduced

inorganic materials emitting from the vents form

endosymbiotic relationships with vent invertebrates

- Vent tube worms harbor several features that facilitate

the growth of their endosymbionts (e.g., trophosome,

specialized hemoglobins, high blood CO2 content)

* Trophosome: spongy tissue filled with sulfur granule and large

populations of sulfur-oxidizing procaryotes

Chemolithotrophic Sulfur-Oxidizing Bacterial Symbionts

Figure 24.31a

SEM of Trophosome Tissue TEM of Bacteria in Sectioned Trophosome Tissue

Black Smokers

Thermal vents that emit mineral-rich hot water (up to

350°C) forming a dark cloud of precipitated material on

mixing with cold seawater

Thermophilic and hyperthermophilic microbes live in

gradients that form as hot water mixes with cold

seawater

Phylogenetic FISH Staining of Black Smoker Chimneys

Figure 24.33

Bacteria

Archaea

24.12 Squid-Aliivibrio Symbiosis

A mutualistic symbiosis between the marine bacterium

Aliivibrio fischeri and the Hawaiian bobtail squid Euprymna

scolopes is a model for how animal–bacterial symbioses are

established

The squid harbors large populations of the bioluminescent

A. fischeri in a specialized structure (light organ)

Bacteria emit light that resembles moonlight penetrating

marine waters, which camouflages the squid from predators

Squid-Aliivibrio Symbiosis

Figure 24.34a

Hawaiian bobtail squid, Euprymna scolopes

Figure 24.34b

Thin-sectioned TEM through the E. scolopes light organ

The symbiotic relationship is highly specific and benefits

both partners

Transmission of bacterial cells is horizontal

The light organ is colonized by A. fischeri from surrounding

seawater shortly after juvenile squid hatch

Bioluminscence is controlled quorum sensing

A. fischeri is supplied with nutrients by the squid

V. Plant–Microbial Symbioses

21.13 Lichens and Mycorrhizae

24.14 Agrobacterium and Crown Gall Disease

24.15 The Legume–Root Nodule Symbiosis

24.13 Lichens and Mycorrhizae

Lichens

Leafy or encrusting microbial symbiosis

Often found growing on bare rocks, tree trunks, house roofs,

and the surfaces of bare soils

Consist of a mutalistic relationship between a fungus and an

alga (or cyanobacterium)

Alga is photosynthetic and produces organic matter for the

fungus

The fungus provides a structure within which the phototrophic

partner can grow protected from erosion by rain or wind

Lichens

Figure 24.35

Lichen Structure

Figure 24.36

Mycorrhizae

Mutalistic associations of plant roots and fungi

Two classes

Ectomycorrhizae

Endomycorrhizae

Ectomycorrhizae

Fungal cells form an extensive sheath around the

outside of the root with only a little penetration into the

root tissue

Found primarily in forest trees, particularly boreal and

temperate forests

Mycorrhizae: Typical Ectomycorrhizal Root of Pinus Rigida

Figure 24.37a

Mycorrhizae

Figure 24.37b

Endomycorrhizae

Fungal mycelium becomes deeply embedded within the

root tissue

Are more common than ectomycorrhizae

Found in >80% of terrestrial plant species

Mycorrhizal fungi assist plants by

Improving nutrient absorption

This is due to the greater surface area provided by the

fungal mycelium

Helping to promote plant diversity

Effect of Mycorrhizal Fungi on Plant Growth

Figure 24.38

24.14 Agrobacterium and Crown Gall Disease

Agrobacterium tumefaciens forms a parasitic symbiosis

with plants causing crown gall disease

- Crown galls: Plant tumors induced by A. tumefaciens

cells harboring a large plasmid, the Ti (tumor induction)

plasmid

Crown Gall Tumors on a Tobacco Plant

Figure 24.39

Structure of the Ti Plasmid of Agrobacterium

Figure 24.40

T-DNA: Transferred DNA; integrated into plant’s genome.vir genes: Encode proteins that are essential for T-DNA transfer.ops genes: Encode proteins that produce opines (e.g. octopine, noplaine) in plant cells transformed by T-DNA. Opines are used as a source of carbon, nitrogen, and phosphate for the parasitic agrobacteria. Transmissability genes: Involved in the transfer of Ti-plasmid by conjugation from agrobacteria to another.

200 kbp

To initiate tumor formation, A. tumefaciens cells must

attach to the wound site on the plant

- Attached cells synthesize cellulose microfibrils and

transfer a portion of the Ti plasmid to plant cells

DNA transfer is mediated by Vir proteins

Mechanism of Transfer of T-DNA to the Plant Cell

Figure 24.41

(a) Phenolic compounds are induced by metabolites synthesized by wounded plant tissues and induce the transcription of vir genes.

(b) VirD is an endonuclease.

(c) VirB functions as a conjugation bridge.

VirE is a single-strand binding protein that assists in T-DNA transfer.

The Ti plasmid has been used in the genetic

engineering of plants

24.15 The Legume–Root Nodule Symbiosis

The mutalistic relationship between leguminous plants

and nitrogen-fixing bacteria is one of the most important

symbioses known

- Examples of legumes include soybeans, clover, alfalfa,

beans, and peas

- Rhizobia are the most well-known nitrogen-fixing

bacteria engaging in these symbioses

Infection of legume roots by nitrogen-fixing bacteria

leads to the formation of root nodules that fix nitrogen

Leads to significant increases in combined nitrogen in soil

- Nodulated legumes grow well in areas where other

plants would not

Soybean Root Nodules

Figure 24.42

Effect of Nodulation on Plant Growth

Figure 24.43

Nitrogen-fixing bacteria need O2 to generate energy for

N2 fixation, but nitrogenases are inactivated by O2

In the nodule, O2 levels are controlled by the O2-binding

protein leghemoglobin

Root Nodule Structure

Figure 24.44

Cross-Inoculation Group

Group of related legumes that can be infected by a

particular species of rhizobia

Major Cross-Inoculation Groups of Leguminous Plants

The critical steps in root nodule formation are as follows:

Step 1: Recognition and attachment of bacterium to root hairs

Step 2: Excretion of nod factors by the bacterium

Step 3: Bacterial invasion of the root hair

Step 4: Travel to the main root via the infection thread

Step 5: Formation of bacteroid state within plant cells

Step 6: Continued plant and bacterial division, forming the

mature root nodule

Steps in the Formation of a Root Nodule in a Legume

Figure 24.45

( ∵ Nod factors)

( ∵ Nod factors)

The Infection Thread and Formation of Root Nodules

Figure 24.46a

Bacteria

Figure 24.46b

Figure 24.46e

Bacterial nod genes direct the steps in nodulation

nodABC gene encode proteins that produce

oligosaccharides called nod factors

Nod factors

Induce root hair curling

Trigger plant cell division

Nod Factors: General Structure and Structural Differences

Figure 24.47

General structure

Structural differences

NodD is a positive regulator that is induced by plant

flavonoids

Plant Flavonoids and Nodulation

Figure 24.48b

A flavonoid molecule that is an inhibitor of nod gene expression in Rhizobium leguminosarum biovar viciae

A flavonoid molecule that is an inducer of nod gene expressionin Rhizobium leguminosarum biovar viciae

The legume–bacterial symbiosis is characterized by

several metabolic reactions and nutrient exchange

The Root Nodule Bacteriod

Figure 24.49

A few legume species form nodules on their stems

Nonlegume nitrogen-fixing symbiosis also occurs

- The water fern Azolla contains a species of

heterocystous nitrogen-fixing cyanobacteria known as

Anabaena

- The alder tree (genus Alnus) has nitrogen-fixing root

nodules that harbor the nitrogen-fixing bacterium

Frankia

Root nodules of the common alder Alnus Glutinosa

Frankia culture purified from nodules of Comptonia peregri