20140612 Edanz Kyushu Session 2

Jeffrey Robens, PhD Senior Research Consultant

Education Group Leader

Kyushu University Department of Agriculture

Session 2 – Reviewing the literature

Kyushu University

12 June 2014

Seminar series

June 5 Effective presentations

June 12 Reviewing the literature

June 19 Academic publishing

June 26 Research and publication ethics

July 3 Effective writing

July 10 Manuscript structure

July 17 Communicating with journals

July 24 Peer review and revisions

Searching for literature

Section 1

Coverage and Staffing Plan Searching for

literature Reading improves manuscript writing

Read often!

Learn how native English speakers write

Learn proper argument structure

Learn manuscript structure and style

Get new ideas, identify problems

Discuss with colleagues


literature How to choose an article

Where can you find it?

Databases

Journal websites

Review articles



– Review articles



– Review articles

PubMed

Abstract

Link

Related citations




Databases

Journal websites

Review articles



– Online databases




Databases

Journal websites

Review articles


literature Sign up for alerts

Email alerts

Follow on social network sites


literature Social networks

Facebook Twitter

LinkedIn

Activity 1

You read an interesting article called “Transgene × environment interactions in genetically modified wheat” (Zeller et al. PLoS One. 2010; 5: e11405). You would like to find more articles like this one. Using the Internet resources we discussed earlier, please find: 1. one more article similar to this one that is also published in

PLOS ONE.

2. two review articles related to this article

Activity 1

1) Article

2) Reviews

Reading strategies

Section 2

Reading strategies How to read an article

From start to finish?

Section by

section?

Not efficient!

What do you want to know?


Reading strategies

Read Figures and then Results

Read Discussion for interpretation

Self-assess knowledge of topic

Read Title and Abstract first

Refer to Introduction and Methods if necessary

Strategies for reading

Read last paragraph of introduction for hypothesis/objectives

Reading strategies

What are you looking for?

Where is it found?

What are the key words?

Key points

Aims, key findings, implications

Introduction, Results, and Discussion

Reading strategies

Background

Aims

Methods

Results

Conclusions

What are the 5 parts of an abstract?

Reading abstracts

Why the study was done

Objectives/hypothesis

Approach/methodology

Most important findings

Implications for the field

Reading strategies

Five-year outcomes in living donor kidney transplants with a positive crossmatch

Renal transplant candidates with high levels of donor-specific anti-HLA antibodies have low transplantation rates and high mortality rates on dialysis. Using desensitization protocols, good short-term outcomes are possible in “positive crossmatch kidney transplants (+XMKTx)”, but long-term outcome data are lacking. The aim of the current study was to determine actual 5-year graft outcomes of +XMKTx. We compared graft survival and the functional and histologic status of 102 +XMKTx to 204 −XMKTx matched for age and sex. Actual 5-year death-censored graft survival was lower in the +XMKTx group (70.7% vs. 88.0%, p < 0.01) and chronic injury (glomerulopathy) was present in 54.5% of surviving grafts. Graft survival was higher in recipients with antibody against donor class I only compared with antibody against class II (either alone or in combination with class I) (85.3% vs. 62.6%, p = 0.05) and was similar to −XMKTx (85.3 vs. 88.0%, p = 0.64). Renal function and proteinuria ranged across a wide spectrum in all groups reflecting the different histological findings at 5 years. We conclude that when compared to −XMKTx, +XMKTx have inferior outcomes at 5 years, however, almost half of the surviving grafts do not have glomerulopathy and avoiding antibodies against donor class II may improve outcomes.

Bentall et al. Am J Transplant. 2013;13:76–85.

Finding information in abstracts

Reading strategies



Bentall et al. Am J Transplant. 2013;13:76–85.

Aims

Methods

Conclusions

Background

Results

Finding information in abstracts

Reading strategies

Key words - objectives: aim, examined, explored, studied, investigated, but, however

Key words – results: showed, compared, identified, found, stronger, higher, lower



Key words – conclusions: conclusion, summary

Key words in abstracts

Reading strategies Introduction

General introduction

Specific aims Aims

Current state of the field

Problem in the field

Reading strategies Introduction – flow of information

Lung cancer is the leading cause of cancer mortality for men and women. Despite smoking prevention and cessation programs and advances in early detection, the 5-year survival rate for lung cancer is only 16% with current therapies. Although lung cancer incidence rates have recently declined in the United States, more lung cancer is now diagnosed when considered together in former- and never-smokers than in current smokers. Thus, even if all of the national anti-smoking campaign goals are met, lung cancer will remain a major public health problem for decades. New ways to treat or prevent lung cancer are therefore needed. One potential therapeutic target for lung cancer is the Wnt signaling pathway. The canonical Wnt signaling pathway in mammals consists of a family of secreted lipid-modified Wnt protein ligands that bind to a family of 7-pass transmembrane Frizzled (Fzd) receptors, as reviewed. In brief, in the absence of ligand, glycogen synthase kinase-3 (GSK3), in complex with axin and adenomatous polyposis coli (APC), constitutively phosphorylates β-catenin, the primary Wnt signaling effector, targeting it for ubiquitination and proteasomal destruction. Ligand binding engages a pathway involving Dishevelled (Dvl) that inhibits GSK3, allowing β-catenin to accumulate in a hypophosphorylated form. This stabilized form of β-catenin can translocate to the nucleus, where it activates target gene transcription by complexing with T cell factor (TCF) and lymphoid enhancer-binding factor (LEF). In addition to key mediators of embryonic development, these target genes include critical growth-regulators such as myc and cyclin D1. Aberrant Wnt signaling due to mutations in β-catenin or APC drives deregulated growth in both familial and non-hereditary colorectal cancers. However, non-small cell lung cancers (NSCLC), the most common type of lung cancer, rarely harbor APC or β-catenin mutations. Rather, aberrant Wnt activity in lung cancer is linked to increased expression of upstream Wnt signaling effectors such as Dvl or decreased expression of Wnt antagonists such as Wnt-inhibitory factor 1 (Wif-1). Effective pharmacological inhibitors of the Wnt pathway have only recently become available. Screens for small-molecule antagonists of the Wnt pathway found two enzymes to be key mediators of Wnt signaling. These are poly-ADP-ribose polymerase (PARP) enzymes, tankyrase (TNKS) 1 and TNKS2, which attach poly-ADP-ribose (PAR) onto substrate proteins. Their roles in regulating telomerase function and mitotic spindle formation are known, but their role in PARsylating axin so as to maintain the optimal level for canonical Wnt signaling has only recently been recognized. The compounds identified in these screens, XAV939, IWR-1 exo, and IWR-1 endo, act by specifically inhibiting the PARP activity of TNKS1 and TNKS2. IWR-exo is a stereoisomer of IWR-1 endo with ~14-fold lower EC50. PARP inhibition is a tractable pharmacological target in vivo, as antagonists of other PARP homologs exert antineoplastic responses in breast and ovarian cancer, as reviewed. This study explored the hypothesis that inhibition of TNKS by pharmacological or genetic means would inhibit lung cancer growth in vitro and in vivo in clinically-relevant transgenic mouse models of lung cancer that were previously developed, as reviewed.

Busch et al. BMC Cancer. 2012;13:211.

Objectives

Current state

Background

Reading strategies Introduction – flow of information

Lung cancer is the leading cause of cancer mortality for men and women. Despite smoking prevention and cessation programs and advances in early detection, the 5-year survival rate for lung cancer is only 16% with current therapies. Although lung cancer incidence rates have recently declined in the United States, more lung cancer is now diagnosed when considered together in former- and never-smokers than in current smokers. Thus, even if all of the national anti-smoking campaign goals are met, lung cancer will remain a major public health problem for decades. New ways to treat or prevent lung cancer are therefore needed. One potential therapeutic target for lung cancer is the Wnt signaling pathway. The canonical Wnt signaling pathway in mammals consists of a family of secreted lipid-modified Wnt protein ligands that bind to a family of 7-pass transmembrane Frizzled (Fzd) receptors, as reviewed. In brief, in the absence of ligand, glycogen synthase kinase-3 (GSK3), in complex with axin and adenomatous polyposis coli (APC), constitutively phosphorylates β-catenin, the primary Wnt signaling effector, targeting it for ubiquitination and proteasomal destruction. Ligand binding engages a pathway involving Dishevelled (Dvl) that inhibits GSK3, allowing β-catenin to accumulate in a hypophosphorylated form. This stabilized form of β-catenin can translocate to the nucleus, where it activates target gene transcription by complexing with T cell factor (TCF) and lymphoid enhancer-binding factor (LEF). In addition to key mediators of embryonic development, these target genes include critical growth-regulators such as myc and cyclin D1. Aberrant Wnt signaling due to mutations in β-catenin or APC drives deregulated growth in both familial and non-hereditary colorectal cancers. However, non-small cell lung cancers (NSCLC), the most common type of lung cancer, rarely harbor APC or β-catenin mutations. Rather, aberrant Wnt activity in lung cancer is linked to increased expression of upstream Wnt signaling effectors such as Dvl or decreased expression of Wnt antagonists such as Wnt-inhibitory factor 1 (Wif-1). Effective pharmacological inhibitors of the Wnt pathway have only recently become available. Screens for small-molecule antagonists of the Wnt pathway found two enzymes to be key mediators of Wnt signaling. These are poly-ADP-ribose polymerase (PARP) enzymes, tankyrase (TNKS) 1 and TNKS2, which attach poly-ADP-ribose (PAR) onto substrate proteins. Their roles in regulating telomerase function and mitotic spindle formation are known, but their role in PARsylating axin so as to maintain the optimal level for canonical Wnt signaling has only recently been recognized. The compounds identified in these screens, XAV939, IWR-1 exo, and IWR-1 endo, act by specifically inhibiting the PARP activity of TNKS1 and TNKS2. IWR-exo is a stereoisomer of IWR-1 endo with ~14-fold lower EC50. PARP inhibition is a tractable pharmacological target in vivo, as antagonists of other PARP homologs exert antineoplastic responses in breast and ovarian cancer, as reviewed. This study explored the hypothesis that inhibition of TNKS by pharmacological or genetic means would inhibit lung cancer growth in vitro and in vivo in clinically-relevant transgenic mouse models of lung cancer that were previously developed, as reviewed.

Busch et al. BMC Cancer. 2012;13:211.

This study explored the hypothesis that inhibition of TNKS…would inhibit lung cancer growth…

Key words - objectives: aim, examined, explored, studied, investigated

Objectives

Current state

Background

Reading strategies Results

What they found

Order of results is logical, tells a story

Each subsection often corresponds to one figure

1. Initial observation 2. Characterization 3. Application

Reading strategies

Jang et al. BMC Cell Biology. 2010;11:25.

Results

Reading strategies Results

Figure 1: Isolation of the stem cells

Figure 2: Differentiate into fat, bone, and cartilage cells

Figure 3: Brain cell differentiation

Figure 4: Brain cell activity

Subsection 1: Isolation of the

stem cells

Subsection 2: Differentiation into different cell types

Subsection 3: Differentiation into

brain cells

Reading strategies

Figure 1: Isolation of the stem cells

Figure 2: Differentiate into fat, bone, and cartilage cells

Figure 3: Brain cell differentiation

Figure 4: Brain cell activity

Subsection 1: Isolation of the

stem cells

Subsection 2: Differentiation into different cell types

Subsection 3: Differentiation into

brain cells

Keyword: Figure 3

Results

Reading strategies Discussion

Summary of findings

Relevance of findings

Implications for the field

Reading strategies

We report that 3D acini undergo rotational motion during the first 4 d of morphogenesis. Whereas our observation is consistent with recent studies on rotational motions , we find an unexpected role for rotational motion during assembly of basement membrane matrix. Interestingly, assembly of fibronectin matrix did not require the rotational motion. Thus, we report a unique mechanophysical property associated with basement membrane assemble during 3D acinar morphogenesis. In addition, we find that both cell polarity and microtubule dynamics are required for the rotational motion. Whereas inhibition of actomyosin contractility blocked both rotational and random cell movement, disruption of microtubules inhibited rotational motion without affecting random movement. We are intrigued by the specificity of the role played by microtubules because of the intimate relationship between the microtubule cytoskeleton and polarized cellular processes such as migration and vesicle trafficking . In polarized epithelia, microtubules align along the lateral membrane with minus ends facing the apical and plus ends facing the basal domains . Consistent with this notion, we find that the overall organization of microtubules was disrupted in 3D structures derived from cancer cell lines that failed to rotate. Whereas we observe defects in organization of Rab5a early endosome and basal localization of alpha6 integrin, the mechanisms may also involve orientation of centrosomes, or Golgi or directed vesicle transport. It is also possible to establish polarity by regulating orientation of the apical pole by positioning organelles such as the Golgi or centrosomes along the axis of polarity. Golgi elements directly interact with microtubule motors, dynein and kinesin. The interaction of the Golgi with the dynein1 complex is critical for both compaction of the Golgi and maintenance of Golgi stacks. Disruption of directional Golgi orientation by loss of golgins, golgin-160 and GMAP210, impairs directional cell migration and wound healing, demonstrating a direct relationship between polarization of Golgi stacks and directional migration. It is likely that the relationship between Golgi orientation (apical pole) and rotational motion involves similar mechanisms, highlighting the need to understand how cells establish and coordinate directionality during rotation. We document an unexpected relationship between rotational motion and assembly of basement membrane. We observed loss of basement membrane by electron microscopy and loss of laminin-111, laminin-332, and collagen IV components of basement membrane. In addition to collagen IV and laminin, basement membranes contain nidogens, perlecan, and agrin. Whereas the process of basement membrane assembly is not well understood, it is thought that interaction of laminin with cell surface receptors integrin and dystroglycans initiate the process of basement membrane assembly. The laminin matrix is linked to the collagen IV by the action of the linking proteins, nidogen, perlecan, and agrin during the maturation of the basement membrane lattice. The role rotational motion plays during this process is not known. Consistent with our observations, a recent study identifies a role for tissue revolutions playing a role during ECM assembly in developing Drosophila eggs. Together these studies suggest a hitherto unexpected, evolutionarily conserved role for rotational motion during assembly of basement membrane. Properly assembled basement membrane plays a critical role during establishment of cell polarity and epithelial morphogenesis. Defects in ECM assembly will also affect the ability of cancer cells to invade during metastasis. Thus, our observations identify a unique aspect of morphogenesis that can impact both normal morphogenesis and carcinoma. Our results also highlight the need to place more emphasis on understanding the mechanisms that regulate plasticity and dynamics of cellular interactions where cell–cell and cell–matrix interactions are in a state of constant flux.

Conclusion/Summary of the findings

Relevance

Conclusion/Implications

Wang et al. PNAS. 2013;110:163–168.

Finding information in the Discussion

Reading strategies

Properly assembled basement membrane plays a critical role during establishment of cell polarity and epithelial morphogenesis. Defects in ECM assembly will also affect the ability of cancer cells to invade during metastasis. Thus, our observations identify a unique aspect of morphogenesis that can impact both normal morphogenesis and carcinoma. Our results also highlight the need to place more emphasis on understanding the mechanisms that regulate plasticity and dynamics of cellular interactions where cell–cell and cell–matrix interactions are in a state of constant flux.

Wang et al. PNAS. 2013;110:163–168.

Why implications are important

Thus, our observations identify a unique aspect of morphogenesis that can impact both normal morphogenesis and carcinoma.

Our results also highlight the need to place more emphasis on understanding the mechanisms that regulate plasticity…

Why is this study important for you?

What are the next steps?

Activity 2

From the abstract below, please answer the following questions. 1. What is the objective of the study? Please circle it in the

abstract.

2. Which intercrop design had the greatest increase in yield?

3. What is the major conclusion? Which cropping design is the most effective system?

4. When was the study conducted?

Food security has become a global issue, seriously threatening developing countries owing to fast-growing human populations and declining availability of land for agriculture. Increasing crop yields could be achieved by intensive systems, but these usually need higher energy and emit more carbon (C). Here, we studied crop productivity, energy yields, and C emissions of intercropping versus sole cropping. We tested maize–wheat, maize–rape, maize–pea, and soybean–wheat intercropping, and sole crops as controls in field experiments at Wuwei experimental station in from 2009 to 2011 in a randomized block design with three replicates. We used an evaluation index integrating yield and environmental factors. Results showed a yield increase of 27 % for maize–wheat, 41 % for maize–rape, and 42 % for maize–pea versus sole crops. Water use efficiency increased by 25 % for maize–wheat intercropping over sole wheat, 152 % for maize–rape over sole rape, and 95 % for maize–pea over sole pea. The three maize–crop intercrops produced 68, 308, and 256 % more energy yield than did the sole wheat, sole rape, and sole pea crops, respectively. They emitted 42, 52, and 45 % less C per unit of water in 2009, 2010, and 2011, respectively, compared with the sole maize crop. The maize-based intercropping received a the highest evaluation index (0.82 out of 1.0) among the systems evaluated, clearly showing that the maize-based intercropping is the most effective and sustainable cropping system for arid irrigation areas.

Activity 2

Chai et al. Agron Sustain Dev. 2014; 34: 535–543.


Activity 2


Background

Aims

Methods

Results

Conclusion

Activity 2



1) Objectives

2) Maize–pea

3) Maize-based intercropping

4) 2009–2011

Activity 3

You have 3 Introductions and 3 beginnings of the associated Discussions. After identifying the key information in each Introduction (circle the research problem and objectives and conclusions), match which Discussion is most appropriate.

Activity 3 – Introduction 1

The spread of non-native earthworms into previously earthworm-free temperate hardwood forests in North America can have significant ecosystem effects. Earthworms can dramatically modify soil structure through reduction of the leaf litter layer and the top soil floor, redistribution of organic material, and changes in soil compaction and water flow, leading to changes in nutrient cycling, fine root distribution, microbial activity and reductions in litter-dependent biota. Furthermore, earthworms can affect plant community assembly, plant survival and germination, both in Europe and North America, suggesting earthworms are important ecosystem engineers. Observational evidence often indicates a correlation between earthworm presence and abundance of different plant species. However, growth, survival, recruitment and demography of plant species interact with earthworms in multiple and complex ways, suggesting idiosyncratic species-specific relationships that can be highly dependent on habitat characteristics and the influence of other associated stressors. For example, a study conducted in an aspen forest in the Rocky Mountains indicated that individual plant species presence, but not total plant biomass and cover, correlated with Lumbricus terrestris L. abundance, and that responses varied by plant species: Vicia americana Muhl. ex Willd. cover was negatively correlated, while Viola canadensis L. cover was positively correlated with L. terrestris abundance. Several mechanisms have been proposed to explain patterns observed in the field. Plant species that may benefit from earthworm presence include species that expand vegetatively, produce small seeds, have high chemical protection, or do not form mycorrhizal associations. Further, taxonomic and ecological characteristics of earthworms and plant species may also affect the outcome of their interactions. Notably, life form and developmental stage may affect the importance of these different mechanisms. For example, seeds may be affected by direct consumption, while seedlings may be affected by desiccation of fine roots after leaf litter disappearance. In addition, earthworm relative abundance and their associated impacts are also affected by land use history and grazing regimes, facilitation between earthworms and non-native plant species, and alterations of predator–prey interactions. Furthermore, earthworms and abundant white-tailed deer (Odocoileus virginiana Zimmermann) in North America may interact and affect plants in multiple yet poorly understood ways. For example, earthworms benefit from high deer abundance by utilizing fecal pellets as a food resource, and earthworm invasion followed by the demise of vulnerable plants may also increase deer feeding pressure on remaining plants further reducing forest plant diversity. While field studies have provided evidence for earthworm effects and generated plausible mechanisms for their impacts, a multitude of potentially confounding factors make it difficult to gauge the true extent of the earthworm effect. Predictions about detrimental or beneficial effects of earthworm invasion on different plant species appear difficult to make, and experimental studies are needed to identify and quantify the contribution of different mechanisms to the patterns reported from the field. While different venues clearly have effects on the outcome of ecological experiments and may even generate contradictory evidence, only through rigorous examination of multiple stressors and potential mechanisms in the same experimental framework can we advance our ecological understanding and gain an improved ability to manage ecological stressors. Here we evaluate, through a greenhouse mesocosm experiment, the effect of L. terrestris on seedlings of species typical of forest plant communities of central New York, USA. Our focal earthworm species L. terrestris was introduced by early European settlers and the species is now widely distributed across temperate North America. Impacts on plant communities by L. terrestris are believed to be mainly indirect, through changes in leaf litter abundance, humus and soil characteristics. For example removal of established humus and litter layers in forests that were previously earthworm-free, and subsequent mixing of topsoil, may lead to uprooting, desiccation and increased plant mortality. However, L. terrestris can also produce significant direct effects via selective consumption of seeds and seedlings in both cotyledon and radical stages, especially of legumes. In fact, seedling vulnerability to earthworm activities may be an Achilles heel for many native plant species. If the collapse of the leaf litter and humus layers is associated with widespread mortality of individuals, recruitment from the seed bank or dispersal by propagules from outside could rescue remaining populations from extinction or genetic bottlenecks. Such rescue effects, through natural processes or assisted restoration, will only be successful if seedlings are able to survive and grow after the initial earthworm invasion has changed local abiotic and biotic conditions. Our goal was to evaluate whether seedlings of native forest understory plant species are able to survive and grow after initial earthworm impacts have occurred – i.e., in areas with no humus layer, but with annual leaf-litter inputs. We used large experimental units (tree pots) to allow proper burrowing of L. terrestris and to provide enough space to grow multiple plant species as earthworm and plants would naturally encounter in the field. We focused on the seedling stage and therefore planted seedlings rather than seed, to avoid confounding different mechanisms (such as direct consumption) operating at different developmental stages. While direct consumption or burial of seed is clearly an important mechanism, seed predation is unlikely to remove 100% of propagules, so we were interested in the performance of surviving individuals.

Background


Objectives

Observational evidence often indicates a correlation between earthworm presence and abundance of different plant species. However, growth, survival, recruitment and demography of plant species interact with earthworms in multiple and complex ways, suggesting idiosyncratic species-specific relationships that can be highly dependent on habitat characteristics and the influence of other associated stressors. For example, a study conducted in an aspen forest in the Rocky Mountains indicated that individual plant species presence, but not total plant biomass and cover, correlated with Lumbricus terrestris L. abundance, and that responses varied by plant species: Vicia americana Muhl. ex Willd. cover was negatively correlated, while Viola canadensis L. cover was positively correlated with L. terrestris abundance. Several mechanisms have been proposed to explain patterns observed in the field. Plant species that may benefit from earthworm presence include species that expand vegetatively, produce small seeds, have high chemical protection, or do not form mycorrhizal associations. Further, taxonomic and ecological characteristics of earthworms and plant species may also affect the outcome of their interactions. Notably, life form and developmental stage may affect the importance of these different mechanisms. For example, seeds may be affected by direct consumption, while seedlings may be affected by desiccation of fine roots after leaf litter disappearance. In addition, earthworm relative abundance and their associated impacts are also affected by land use history and grazing regimes, facilitation between earthworms and non-native plant species, and alterations of predator–prey interactions. Furthermore, earthworms and abundant white-tailed deer (Odocoileus virginiana Zimmermann) in North America may interact and affect plants in multiple yet poorly understood ways. For example, earthworms benefit from high deer abundance by utilizing fecal pellets as a food resource, and earthworm invasion followed by the demise of vulnerable plants may also increase deer feeding pressure on remaining plants further reducing forest plant diversity. While field studies have provided evidence for earthworm effects and generated plausible mechanisms for their impacts, a multitude of potentially confounding factors make it difficult to gauge the true extent of the earthworm effect. Predictions about detrimental or beneficial effects of earthworm invasion on different plant species appear difficult to make, and experimental studies are needed to identify and quantify the contribution of different mechanisms to the patterns reported from the field. While different venues clearly have effects on the outcome of ecological experiments and may even generate contradictory evidence, only through rigorous examination of multiple stressors and potential mechanisms in the same experimental framework can we advance our ecological understanding and gain an improved ability to manage ecological stressors. Here we evaluate, through a greenhouse mesocosm experiment, the effect of L. terrestris on seedlings of species typical of forest plant communities of central New York, USA. Our focal earthworm species L. terrestris was introduced by early European settlers and the species is now widely distributed across temperate North America. Impacts on plant communities by L. terrestris are believed to be mainly indirect, through changes in leaf litter abundance, humus and soil characteristics. For example removal of established humus and litter layers in forests that were previously earthworm-free, and subsequent mixing of topsoil, may lead to uprooting, desiccation and increased plant mortality. However, L. terrestris can also produce significant direct effects via selective consumption of seeds and seedlings in both cotyledon and radical stages, especially of legumes. In fact, seedling vulnerability to earthworm activities may be an Achilles heel for many native plant species. If the collapse of the leaf litter and humus layers is associated with widespread mortality of individuals, recruitment from the seed bank or dispersal by propagules from outside could rescue remaining populations from extinction or genetic bottlenecks. Such rescue effects, through natural processes or assisted restoration, will only be successful if seedlings are able to survive and grow after the initial earthworm invasion has changed local abiotic and biotic conditions.

“…a multitude of potentially confounding factors make it difficult to gauge the true extent of the earthworm effect.”


How do earthworms affect plant species?


Background


Objectives



Objectives


Our goal was to evaluate whether seedlings of native forest understory plant species are able to survive and grow after initial earthworm impacts have occurred – i.e., in areas with no humus layer, but with annual leaf-litter inputs. We used large experimental units (tree pots) to allow proper burrowing of L. terrestris and to provide enough space to grow multiple plant species as earthworm and plants would naturally encounter in the field. We focused on the seedling stage and therefore planted seedlings rather than seed, to avoid confounding different mechanisms (such as direct consumption) operating at different developmental stages. While direct consumption or burial of seed is clearly an important mechanism, seed predation is unlikely to remove 100% of propagules, so we were interested in the performance of surviving individuals.


Research problem

Determine if earthworms affect the survival and growth of these plant seedlings

Objectives



Despite the importance of these tropical ecosystems, it is still unclear how local differences in aboveground communities, or anthropogenic disturbances to them, can impact the functioning of the nutrient cycle systems. The great diversity and complex interactions assumed to occur between above- and belowground communities especially within in tropical ecosystems, make it difficult to evaluate how communities affect each other and ecosystem processes. Most work has been done in these disturbed systems rather than on naturally occurring plant species within undisturbed forests to determine if naturally occurring plants can have such influences on microbial communities and ecosystem functions. Although this plant has had practical and beneficial uses for humans, the ecological role of this bromeliad is unclear.


Despite the importance of these tropical ecosystems, it is still unclear how local differences in aboveground communities, or anthropogenic disturbances to them, can impact the functioning of the nutrient cycle systems. The great diversity and complex interactions assumed to occur between above- and belowground communities especially within in tropical ecosystems, make it difficult to evaluate how communities affect each other and ecosystem processes. Most work has been done in these disturbed systems rather than on naturally occurring plant species within undisturbed forests to determine if naturally occurring plants can have such influences on microbial communities and ecosystem functions. Although this plant has had practical and beneficial uses for humans, the ecological role of this bromeliad is unclear.

As a naturally occurring aboveground species, how do bromeliads affect belowground microbial communities?

Research question

How do aboveground communities affect belowground communities?

How do these communities affect each other?

Do naturally occurring species influence microbial communities?

What is the ecological role of bromeliads?


We hypothesized that these bromeliad-associated soils would have lower rates of C and N biomass development and less diversity and richness of fungi…we also hypothesized there to be less phenol oxidase activity associated with the bromeliad soils, as a result of the potential anti-fungal activity of the plants.

Objectives


Research question


With a relative wealth of data available describing patterns of land use associated change in overall abundance (at least for well-studied taxa) and also studies that link soil community characteristics to ecological metrics e.g., quantifying these community effects and establishing their functional links to soil processes is potentially achievable.

Research question

How does land-use management affect soil processes?

?

Objectives


National monitoring programmes have often identified that soils under different land use and land management regimes harbour differing soil communities. In a limited number of cases the primary drivers of this variation have been identified, such as the strong influence of soil pH on bacterial communities. When augmented by the results of smaller scale experimental and monitoring studies, which have frequently shown similar effects, these observations suggest a strong forcing effect of incumbent land use on overall soil community size and composition. Such community changes can have implications for soil functioning. In particular, the activities of specific groups of the soil biota (e.g. microorganisms, ecosystem engineers) are considered important to many soil functions that underpin the provision of ecosystem goods and services. These functionally relevant groups have become, therefore, an established focus for soil community and ecosystem process research. With a relative wealth of data available describing patterns of land use associated change in overall abundance (at least for well-studied taxa) and also studies that link soil community characteristics to ecological metrics e.g., quantifying these community effects and establishing their functional links to soil processes is potentially achievable. Here we have sought to summarise how some of the best-studied changes in land use and management affect community metrics for two key functional components of the soil biota, namely earthworms and soil fungi. We focus on transitions of extensification in land use that may benefit these taxa. Further, we relate community size changes for these two groups to influences on soil structural properties, thereby attempting to quantify implications of land use changes to functional linkages in the soil ecosystem. The approach we have chosen for the assessment was based on a systematic review and meta-analysis of the published literature. For earthworms, the analysis focused on assessing the effects of land use and land management changes on overall community size. This focus on total abundance was chosen because in published studies, detailed community characteristics, such as species identity, were often not reported; and this would have limited the size of the available data-set. For soil fungi, both overall abundance measures and community structural indicators were considered. This reflects the wider variety of metrics reported in the literature for this group. For both taxa, we sought to quantify the magnitude of community change occurring when land management practices or land use convert from more intensive to less intensive conditions. Three such scenarios were considered 1) implementation of reduced tillage regimes to previously intensively tilled lands; 2) conversion of managed arable land to natural or managed grassland; 3) successional conversion or afforestation of grassland to woodland.

Background?

Current state of the field?

Objectives?


National monitoring programmes have often identified that soils under different land use and land management regimes harbour differing soil communities. In a limited number of cases the primary drivers of this variation have been identified, such as the strong influence of soil pH on bacterial communities. When augmented by the results of smaller scale experimental and monitoring studies, which have frequently shown similar effects, these observations suggest a strong forcing effect of incumbent land use on overall soil community size and composition. Such community changes can have implications for soil functioning. In particular, the activities of specific groups of the soil biota (e.g. microorganisms, ecosystem engineers) are considered important to many soil functions that underpin the provision of ecosystem goods and services. These functionally relevant groups have become, therefore, an established focus for soil community and ecosystem process research. With a relative wealth of data available describing patterns of land use associated change in overall abundance (at least for well-studied taxa) and also studies that link soil community characteristics to ecological metrics e.g., quantifying these community effects and establishing their functional links to soil processes is potentially achievable. Here we have sought to summarise how some of the best-studied changes in land use and management affect community metrics for two key functional components of the soil biota, namely earthworms and soil fungi. We focus on transitions of extensification in land use that may benefit these taxa. Further, we relate community size changes for these two groups to influences on soil structural properties, thereby attempting to quantify implications of land use changes to functional linkages in the soil ecosystem. The approach we have chosen for the assessment was based on a systematic review and meta-analysis of the published literature. For earthworms, the analysis focused on assessing the effects of land use and land management changes on overall community size. This focus on total abundance was chosen because in published studies, detailed community characteristics, such as species identity, were often not reported; and this would have limited the size of the available data-set. For soil fungi, both overall abundance measures and community structural indicators were considered. This reflects the wider variety of metrics reported in the literature for this group. For both taxa, we sought to quantify the magnitude of community change occurring when land management practices or land use convert from more intensive to less intensive conditions. Three such scenarios were considered 1) implementation of reduced tillage regimes to previously intensively tilled lands; 2) conversion of managed arable land to natural or managed grassland; 3) successional conversion or afforestation of grassland to woodland.

Methodology!

Objectives!

Activity 3 – Matching

Match each of the 3 partial Discussions with the appropriate Introduction.


Discussion 1: Our meta-analyses for land-use transition effects on community metrics highlighted a consistent trend across the two studied taxa. This pattern relates declining land use intensity with positive effects on community parameters, especially in agricultural lands.

Introduction 3

Research question

How does land-use management affect soil processes?


Discussion 2: This study suggests that a naturally occurring plant can have biologically important effects on belowground ecosystems in established tropical forests.

Introduction 2


Research question


Discussion 3: Our results indicate no effects of earthworms on seedling survival, biomass or fertility of 12 of the 14 plant species tested when grown in experimental mesocosms.

Introduction 1


Research problem

Activity 3 – Conclusion

What do you notice about the conclusion in the Discussion?

Usually answers the research problem

Paper management tools

Section 3

Paper management

Why use paper management tools?

Avoid trying to find an article like this!

Paper management Papers

Search by keywords, authors, journals, etc.

Sort articles by authors, titles, journals, or year

Read full screen, Email, or print your articles

Organize your articles in folders and “smart folders”

Paper management Mendeley

Paper management

Reference management software

Why should you use it?

Keeps your references organized Simplifies in-text citations Prepares the reference list in the ‘correct’ format Allows you change reference style easily if you

change journals

Paper management


EndNote Most established Styles easy to find on journal websites

Which one to use?

RefWorks Web-based Widely used

Mendeley Newer (and free!) Allows collaborations

Papers Easy-to-use interface (iTunes) Great for paper management

Paper management


Where to find ‘styles’?

Most have the journal styles pre-installed

Can often download up-to-date styles

But always double-check for formatting accuracy

ChemPhysChem

Thank you!

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Jeffrey Robens: [email protected]

20140612 Edanz Kyushu Session 2

Education

Transcript of 20140612 Edanz Kyushu Session 2