Microbial functional diversity: From concepts to applications
Abstract
Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realizemore »
- Authors:
-
[1];
- MARBEC CNRS Ifremer IRD University of Montpellier Montpellier Cedex 5 France, Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA
- Water Management Research Unit SJVASC USDA‐ARS Parlier CA USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control School of Environment Tsinghua University Beijing China
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
- Department of Civil and Environmental Engineering University of California Berkeley CA USA
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology University of Oklahoma Norman OK USA, State Key Joint Laboratory of Environment Simulation and Pollution Control School of Environment Tsinghua University Beijing China, Earth and Environmental Sciences Lawrence Berkeley National Laboratory Berkeley CA USA
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1568935
- Alternate Identifier(s):
- OSTI ID: 1568938; OSTI ID: 1580942
- Grant/Contract Number:
- AC02‐05CH11231; AC02-05CH11231; SC0004601; SC0010570; CBET‐1336709; P42ES004705
- Resource Type:
- Published Article
- Journal Name:
- Ecology and Evolution
- Additional Journal Information:
- Journal Name: Ecology and Evolution Journal Volume: 9 Journal Issue: 20; Journal ID: ISSN 2045-7758
- Publisher:
- Wiley
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; functional diversity; functional traits; microbial communities; theoretical frameworks of diversity; trait‐based ecology
Citation Formats
Escalas, Arthur, Hale, Lauren, Voordeckers, James W., Yang, Yunfeng, Firestone, Mary K., Alvarez‐Cohen, Lisa, and Zhou, Jizhong. Microbial functional diversity: From concepts to applications. United Kingdom: N. p., 2019.
Web. doi:10.1002/ece3.5670.
Escalas, Arthur, Hale, Lauren, Voordeckers, James W., Yang, Yunfeng, Firestone, Mary K., Alvarez‐Cohen, Lisa, & Zhou, Jizhong. Microbial functional diversity: From concepts to applications. United Kingdom. https://doi.org/10.1002/ece3.5670
Escalas, Arthur, Hale, Lauren, Voordeckers, James W., Yang, Yunfeng, Firestone, Mary K., Alvarez‐Cohen, Lisa, and Zhou, Jizhong. Fri .
"Microbial functional diversity: From concepts to applications". United Kingdom. https://doi.org/10.1002/ece3.5670.
@article{osti_1568935,
title = {Microbial functional diversity: From concepts to applications},
author = {Escalas, Arthur and Hale, Lauren and Voordeckers, James W. and Yang, Yunfeng and Firestone, Mary K. and Alvarez‐Cohen, Lisa and Zhou, Jizhong},
abstractNote = {Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.},
doi = {10.1002/ece3.5670},
journal = {Ecology and Evolution},
number = 20,
volume = 9,
place = {United Kingdom},
year = {2019},
month = {9}
}
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Works referenced in this record:
Interactions in the microbiome: communities of organisms and communities of genes
journal, January 2014
- Boon, Eva; Meehan, Conor J.; Whidden, Chris
- FEMS Microbiology Reviews, Vol. 38, Issue 1
Phytoplankton traits predict ecosystem function in a global set of lakes
journal, August 2015
- Zwart, Jacob A.; Solomon, Christopher T.; Jones, Stuart E.
- Ecology, Vol. 96, Issue 8
Fundamentals of Microbial Community Resistance and Resilience
journal, January 2012
- Shade, Ashley; Peter, Hannes; Allison, Steven D.
- Frontiers in Microbiology, Vol. 3
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
journal, August 2013
- Langille, Morgan G. I.; Zaneveld, Jesse; Caporaso, J. Gregory
- Nature Biotechnology, Vol. 31, Issue 9
Defining Disturbance for Microbial Ecology
journal, March 2017
- Plante, Craig J.
- Microbial Ecology, Vol. 74, Issue 2
Beyond the Venn diagram: the hunt for a core microbiome: The hunt for a core microbiome
journal, October 2011
- Shade, Ashley; Handelsman, Jo
- Environmental Microbiology, Vol. 14, Issue 1
How fundamental plant functional trait relationships scale-up to trade-offs and synergies in ecosystem services: Plant traits scale to ecosystem services trade-offs
journal, December 2011
- Lavorel, Sandra; Grigulis, Karl
- Journal of Ecology, Vol. 100, Issue 1
A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning
journal, September 2011
- Wallenstein, Matthew D.; Hall, Edward K.
- Biogeochemistry, Vol. 109, Issue 1-3
Concluding Remarks
journal, January 1957
- Hutchinson, G. E.
- Cold Spring Harbor Symposia on Quantitative Biology, Vol. 22, Issue 0
Cultivation of unculturable soil bacteria
journal, September 2012
- Pham, Van H. T.; Kim, Jaisoo
- Trends in Biotechnology, Vol. 30, Issue 9
Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China
journal, November 2014
- Huang, Qiuyuan; Briggs, Brandon R.; Dong, Hailiang
- PLoS ONE, Vol. 9, Issue 11
Responses of Methanogen mcrA Genes and Their Transcripts to an Alternate Dry/Wet Cycle of Paddy Field Soil
journal, November 2011
- Ma, Ke; Conrad, Ralf; Lu, Yahai
- Applied and Environmental Microbiology, Vol. 78, Issue 2
Disentangling biodiversity effects on ecosystem functioning: deriving solutions to a seemingly insurmountable problem
journal, June 2003
- Naeem, Shahid; Wright, Justin P.
- Ecology Letters, Vol. 6, Issue 6
Alpine soil carbon is vulnerable to rapid microbial decomposition under climate cooling
journal, May 2017
- Wu, Linwei; Yang, Yunfeng; Wang, Shiping
- The ISME Journal, Vol. 11, Issue 9
Explaining microbial phenotypes on a genomic scale: GWAS for microbes
journal, April 2013
- Dutilh, B. E.; Backus, L.; Edwards, R. A.
- Briefings in Functional Genomics, Vol. 12, Issue 4
Microbiomes in light of traits: A phylogenetic perspective
journal, November 2015
- Martiny, J. B. H.; Jones, S. E.; Lennon, J. T.
- Science, Vol. 350, Issue 6261
Partitioning of functional and taxonomic diversity in surface-associated microbial communities: Partitioning of microbial diversity
journal, May 2016
- Roth-Schulze, Alexandra J.; Zozaya-Valdés, Enrique; Steinberg, Peter D.
- Environmental Microbiology, Vol. 18, Issue 12
In Nature, There Is Only Diversity
journal, January 2018
- McLaren, Michael R.; Callahan, Benjamin J.
- mBio, Vol. 9, Issue 1
Loss in microbial diversity affects nitrogen cycling in soil
journal, March 2013
- Philippot, Laurent; Spor, Aymé; Hénault, Catherine
- The ISME Journal, Vol. 7, Issue 8
Re-evaluating prokaryotic species
journal, August 2005
- Gevers, Dirk; Cohan, Frederick M.; Lawrence, Jeffrey G.
- Nature Reviews Microbiology, Vol. 3, Issue 9
Belowground biodiversity and ecosystem functioning
journal, November 2014
- Bardgett, Richard D.; van der Putten, Wim H.
- Nature, Vol. 515, Issue 7528
Biodiversity and ecosystem productivity in a fluctuating environment: The insurance hypothesis
journal, February 1999
- Yachi, S.; Loreau, M.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 4
Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils
journal, August 2015
- Eichorst, Stephanie A.; Strasser, Florian; Woyke, Tanja
- FEMS Microbiology Ecology, Vol. 91, Issue 10
Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets
journal, February 2016
- Nagpal, Sunil; Haque, Mohammed Monzoorul; Mande, Sharmila S.
- PLOS ONE, Vol. 11, Issue 2
Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information
journal, August 2017
- Barberán, Albert; Caceres Velazquez, Hildamarie; Jones, Stuart
- mSphere, Vol. 2, Issue 4
Which is more important for classifying microbial communities: who’s there or what they can do?
journal, August 2014
- Xu, Zhenjiang; Malmer, Daniel; Langille, Morgan G. I.
- The ISME Journal, Vol. 8, Issue 12
High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved
journal, June 2016
- Turaev, Dmitrij; Rattei, Thomas
- Current Opinion in Biotechnology, Vol. 39
Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy
journal, February 2014
- Miki, Takeshi; Yokokawa, Taichi; Matsui, Kazuaki
- Proceedings of the Royal Society B: Biological Sciences, Vol. 281, Issue 1776
Molecular biology and regulation of methane monooxygenase
journal, April 2000
- Murrell, J. Colin; Gilbert, Bettina; McDonald, Ian R.
- Archives of Microbiology, Vol. 173, Issue 5-6
Microbial resource utilization traits and trade-offs: implications for community structure, functioning, and biogeochemical impacts at present and in the future
journal, April 2015
- Litchman, Elena; Edwards, Kyle F.; Klausmeier, Christopher A.
- Frontiers in Microbiology, Vol. 06
Patterns and Processes of Microbial Community Assembly
journal, September 2013
- Nemergut, D. R.; Schmidt, S. K.; Fukami, T.
- Microbiology and Molecular Biology Reviews, Vol. 77, Issue 3
Unifying Species Diversity, Phylogenetic Diversity, Functional Diversity, and Related Similarity and Differentiation Measures Through Hill Numbers
journal, November 2014
- Chao, Anne; Chiu, Chun-Huo; Jost, Lou
- Annual Review of Ecology, Evolution, and Systematics, Vol. 45, Issue 1
Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints
journal, December 2011
- Mouchet, Maud A.; Bouvier, Corinne; Bouvier, Thierry
- FEMS Microbiology Ecology, Vol. 79, Issue 3
Functional trait space and the latitudinal diversity gradient
journal, September 2014
- Lamanna, C.; Blonder, B.; Violle, C.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 38
Functional diversity: back to basics and looking forward
journal, June 2006
- Petchey, Owen L.; Gaston, Kevin J.
- Ecology Letters, Vol. 9, Issue 6
Biodiversity Loss Threatens Human Well-Being
journal, August 2006
- Díaz, Sandra; Fargione, Joseph; Chapin, F. Stuart
- PLoS Biology, Vol. 4, Issue 8
Probing the active fraction of soil microbiomes using BONCAT-FACS
journal, June 2019
- Couradeau, Estelle; Sasse, Joelle; Goudeau, Danielle
- Nature Communications, Vol. 10, Issue 1
Effects of biodiversity on the functioning of trophic groups and ecosystems
journal, October 2006
- Cardinale, Bradley J.; Srivastava, Diane S.; Emmett Duffy, J.
- Nature, Vol. 443, Issue 7114
Functional diversity measures: an overview of their redundancy and their ability to discriminate community assembly rules: Functional diversity measures
journal, March 2010
- Mouchet, Maud A.; Villéger, Sébastien; Mason, Norman W. H.
- Functional Ecology, Vol. 24, Issue 4
GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves
journal, November 2012
- Bai, Shijie; Li, Jiangwei; He, Zhili
- Applied Microbiology and Biotechnology, Vol. 97, Issue 15
Biodiversity effects on ecosystem functioning: emerging issues and their experimental test in aquatic environments
journal, March 2004
- S. Giller, Paul; Hillebrand, Helmut; Berninger, Ulrike-G.
- Oikos, Vol. 104, Issue 3
Function and functional redundancy in microbial systems
journal, April 2018
- Louca, Stilianos; Polz, Martin F.; Mazel, Florent
- Nature Ecology & Evolution, Vol. 2, Issue 6
A trait-based approach for modelling microbial litter decomposition
journal, May 2012
- Allison, S. D.
- Ecology Letters, Vol. 15, Issue 9
VAMPS: a website for visualization and analysis of microbial population structures
journal, February 2014
- Huse, Susan M.; Mark Welch, David B.; Voorhis, Andy
- BMC Bioinformatics, Vol. 15, Issue 1
Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology
journal, June 2015
- Prosser, James I.
- Nature Reviews Microbiology, Vol. 13, Issue 7
Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes
journal, November 2016
- Iwai, Shoko; Weinmaier, Thomas; Schmidt, Brian L.
- PLOS ONE, Vol. 11, Issue 11
Application of metatranscriptomics to soil environments
journal, November 2012
- Carvalhais, Lilia C.; Dennis, Paul G.; Tyson, Gene W.
- Journal of Microbiological Methods, Vol. 91, Issue 2
Linking microbial community structure and microbial processes: an empirical and conceptual overview
journal, September 2015
- Bier, Raven L.; Bernhardt, Emily S.; Boot, Claudia M.
- FEMS Microbiology Ecology, Vol. 91, Issue 10
Binning metagenomic contigs by coverage and composition
journal, September 2014
- Alneberg, Johannes; Bjarnason, Brynjar Smári; de Bruijn, Ino
- Nature Methods, Vol. 11, Issue 11
Trait-based approaches for understanding microbial biodiversity and ecosystem functioning
journal, May 2014
- Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A.
- Frontiers in Microbiology, Vol. 5
Bacterial community assembly based on functional genes rather than species
journal, August 2011
- Burke, C.; Steinberg, P.; Rusch, D.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 34
Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes
journal, October 2006
- Polz, Martin F.; Hunt, Dana E.; Preheim, Sarah P.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1475
Emergent simplicity in microbial community assembly
journal, August 2018
- Goldford, Joshua E.; Lu, Nanxi; Bajić, Djordje
- Science, Vol. 361, Issue 6401
Bacteria Are Smartphones and Mobile Genes Are Apps
journal, December 2016
- Young, J. Peter W.
- Trends in Microbiology, Vol. 24, Issue 12
GroopM: an automated tool for the recovery of population genomes from related metagenomes
journal, January 2014
- Imelfort, Michael; Parks, Donovan; Woodcroft, Ben J.
- PeerJ, Vol. 2
Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota
journal, December 2016
- Raguideau, Sébastien; Plancade, Sandra; Pons, Nicolas
- PLOS Computational Biology, Vol. 12, Issue 12
A functional evenness index for microbial ecology
journal, December 1981
- Troussellier, Marc; Legendre, Pierre
- Microbial Ecology, Vol. 7, Issue 4
Defining and measuring ecological specialization
journal, February 2010
- Devictor, Vincent; Clavel, Joanne; Julliard, Romain
- Journal of Applied Ecology, Vol. 47, Issue 1
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
journal, July 2017
- Callahan, Benjamin J.; McMurdie, Paul J.; Holmes, Susan P.
- The ISME Journal, Vol. 11, Issue 12
Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria
journal, April 2014
- Barberán, Albert; Ramirez, Kelly S.; Leff, Jonathan W.
- Ecology Letters, Vol. 17, Issue 7
Biodiversity as spatial insurance in heterogeneous landscapes
journal, October 2003
- Loreau, M.; Mouquet, N.; Gonzalez, A.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 22
Reinforcing loose foundation stones in trait-based plant ecology
journal, January 2016
- Shipley, Bill; De Bello, Francesco; Cornelissen, J. Hans C.
- Oecologia, Vol. 180, Issue 4
Microbial services: challenges for microbial ecologists in a changing world
journal, September 2008
- Ducklow, H.
- Aquatic Microbial Ecology, Vol. 53
Not all traits are ‘functional’: insights from taxonomy and biodiversity-ecosystem functioning research
journal, January 2014
- Mlambo, Musa C.
- Biodiversity and Conservation, Vol. 23, Issue 3
Bergey's Manual of Determinative Bacteriology
journal, May 1975
- S., F. A.; Buchanan, R. E. T.; Gibbons, N. E.
- Taxon, Vol. 24, Issue 2/3
Biodiversity in a complex world: consolidation and progress in functional biodiversity research: Consolidation and progress in BDEF research
journal, October 2009
- Hillebrand, Helmut; Matthiessen, Birte
- Ecology Letters, Vol. 12, Issue 12
Toward Understanding, Managing, and Protecting Microbial Ecosystems
journal, January 2011
- Bodelier, Paul L. E.
- Frontiers in Microbiology, Vol. 2
What is microbial community ecology?
journal, August 2009
- Konopka, Allan
- The ISME Journal, Vol. 3, Issue 11
Microdiversity shapes the traits, niche space, and biogeography of microbial taxa: The ecological function of microdiversity
journal, March 2017
- Larkin, Alyse A.; Martiny, Adam C.
- Environmental Microbiology Reports, Vol. 9, Issue 2
Plant trait-based models identify direct and indirect effects of climate change on bundles of grassland ecosystem services
journal, September 2014
- Lamarque, P.; Lavorel, S.; Mouchet, M.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 38
Benefits of plant diversity to ecosystems: immediate, filter and founder effects
journal, December 1998
- Grime, J. P.
- Journal of Ecology, Vol. 86, Issue 6
Metagenomic analysis reveals microbial functional redundancies and specificities in a soil under different tillage and crop-management regimes
journal, February 2015
- Souza, Renata Carolini; Hungria, Mariangela; Cantão, Maurício Egídio
- Applied Soil Ecology, Vol. 86
GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater
journal, November 2014
- Bayer, Kristina; Moitinho-Silva, Lucas; Brümmer, Franz
- FEMS Microbiology Ecology, Vol. 90, Issue 3
The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands
journal, February 2015
- Yue, Haowei; Wang, Mengmeng; Wang, Shiping
- The ISME Journal, Vol. 9, Issue 9
Resistance, resilience, and redundancy in microbial communities
journal, August 2008
- Allison, S. D.; Martiny, J. B. H.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue Supplement 1
Measuring the biodiversity of microbial communities by flow cytometry
journal, July 2016
- Props, Ruben; Monsieurs, Pieter; Mysara, Mohamed
- Methods in Ecology and Evolution, Vol. 7, Issue 11
The generation and maintenance of diversity in microbial communities
journal, March 2011
- Fierer, Noah; Lennon, Jay T.
- American Journal of Botany, Vol. 98, Issue 3
Let the concept of trait be functional!
journal, May 2007
- Violle, Cyrille; Navas, Marie-Laure; Vile, Denis
- Oikos, Vol. 116, Issue 5
Giving microbes their due - animal life in a microbially dominant world
journal, June 2015
- McFall-Ngai, M. J.
- Journal of Experimental Biology, Vol. 218, Issue 12
Mapping the niche space of soil microorganisms using taxonomy and traits
journal, August 2012
- Lennon, Jay T.; Aanderud, Zachary T.; Lehmkuhl, B. K.
- Ecology, Vol. 93, Issue 8
Topographic diversity of fungal and bacterial communities in human skin
journal, May 2013
- Findley, Keisha; Oh, Julia; Yang, Joy
- Nature, Vol. 498, Issue 7454
Microbial Biogeography: From Taxonomy to Traits
journal, May 2008
- Green, J. L.; Bohannan, B. J. M.; Whitaker, R. J.
- Science, Vol. 320, Issue 5879
Theoretical microbial ecology without species
journal, September 2017
- Tikhonov, Mikhail
- Physical Review E, Vol. 96, Issue 3
Experimental evidence for strong stabilizing forces at high functional diversity of aquatic microbial communities
journal, May 2015
- Carrara, Francesco; Giometto, Andrea; Seymour, Mathew
- Ecology, Vol. 96, Issue 5
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.
journal, May 2015
- Aßhauer, Kathrin P.; Wemheuer, Bernd; Daniel, Rolf
- Bioinformatics, Vol. 31, Issue 17
Functional metagenomic profiling of nine biomes
journal, March 2008
- Dinsdale, Elizabeth A.; Edwards, Robert A.; Hall, Dana
- Nature, Vol. 452, Issue 7187
Exploration of community traits as ecological markers in microbial metagenomes: METAGENOMIC COMMUNITY TRAITS
journal, November 2011
- BarberÁN, Albert; FernÁNdez-Guerra, Antoni; Bohannan, Brendan J. M.
- Molecular Ecology, Vol. 21, Issue 8
Decoupling function and taxonomy in the global ocean microbiome
journal, September 2016
- Louca, S.; Parfrey, L. W.; Doebeli, M.
- Science, Vol. 353, Issue 6305
A Common Toolbox to Understand, Monitor or Manage Rarity? A Response to Carmona et al.
journal, December 2017
- Violle, Cyrille; Thuiller, Wilfried; Mouquet, Nicolas
- Trends in Ecology & Evolution, Vol. 32, Issue 12
The Niche-Relationships of the California Thrasher
journal, October 1917
- Grinnell, Joseph
- The Auk, Vol. 34, Issue 4
Response diversity determines the resilience of ecosystems to environmental change: Response diversity and ecosystem resilience
journal, December 2012
- Mori, Akira S.; Furukawa, Takuya; Sasaki, Takehiro
- Biological Reviews, Vol. 88, Issue 2
Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis
journal, March 2011
- Schloss, Patrick D.; Westcott, Sarah L.
- Applied and Environmental Microbiology, Vol. 77, Issue 10
Predicting microbial traits with phylogenies
journal, September 2015
- Goberna, Marta; Verdú, Miguel
- The ISME Journal, Vol. 10, Issue 4
Traits Without Borders: Integrating Functional Diversity Across Scales
journal, May 2016
- Carmona, Carlos P.; de Bello, Francesco; Mason, Norman W. H.
- Trends in Ecology & Evolution, Vol. 31, Issue 5
Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities
journal, November 2014
- Fierer, Noah; Barberán, Albert; Laughlin, Daniel C.
- Frontiers in Microbiology, Vol. 5
Consequences of changing biodiversity
journal, May 2000
- Chapin III, F. Stuart; Zavaleta, Erika S.; Eviner, Valerie T.
- Nature, Vol. 405, Issue 6783
Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient
journal, May 2018
- Cheaib, Bachar; Le Boulch, Malo; Mercier, Pierre-Luc
- Frontiers in Microbiology, Vol. 9
The emergence and promise of functional biogeography
journal, September 2014
- Violle, C.; Reich, P. B.; Pacala, S. W.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 38
Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties
journal, July 2015
- Powell, Jeff R.; Welsh, Allana; Hallin, Sara
- Ecology, Vol. 96, Issue 7
Functional Structure of Biological Communities Predicts Ecosystem Multifunctionality
journal, March 2011
- Mouillot, David; Villéger, Sébastien; Scherer-Lorenzen, Michael
- PLoS ONE, Vol. 6, Issue 3
Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units
journal, July 2018
- Glassman, Sydney I.; Martiny, Jennifer B. H.
- mSphere, Vol. 3, Issue 4
Community niche predicts the functioning of denitrifying bacterial assemblages
journal, December 2009
- Salles, Joana F.; Poly, Franck; Schmid, Bernhard
- Ecology, Vol. 90, Issue 12
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
journal, October 2016
- Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A.
- Nature Communications, Vol. 7, Issue 1
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
journal, September 2008
- Meyer, F.; Paarmann, D.; D'Souza, M.
- BMC Bioinformatics, Vol. 9, Issue 1
Biodiversity and Ecosystem Functioning: Current Knowledge and Future Challenges
journal, October 2001
- Loreau, M.
- Science, Vol. 294, Issue 5543
A unified initiative to harness Earth's microbiomes
journal, October 2015
- Alivisatos, A. P.; Blaser, M. J.; Brodie, E. L.
- Science, Vol. 350, Issue 6260
The microbiome beyond the horizon of ecological and evolutionary theory
journal, October 2017
- Koskella, Britt; Hall, Lindsay J.; Metcalf, C. Jessica E.
- Nature Ecology & Evolution, Vol. 1, Issue 11
New Multidimensional Functional Diversity Indices for a Multifaceted Framework in Functional Ecology
journal, August 2008
- Villéger, Sébastien; Mason, Norman W. H.; Mouillot, David
- Ecology, Vol. 89, Issue 8
Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease
journal, August 2019
- Mourkas, Evangelos; Florez‐Cuadrado, Diego; Pascoe, Ben
- Environmental Microbiology, Vol. 21, Issue 12
Microbial genotype–phenotype mapping by class association rule mining
journal, May 2008
- Tamura, Makio; D'haeseleer, Patrik
- Bioinformatics, Vol. 24, Issue 13
The Microbial Engines That Drive Earth's Biogeochemical Cycles
journal, May 2008
- Falkowski, P. G.; Fenchel, T.; Delong, E. F.
- Science, Vol. 320, Issue 5879
Sizing up metatranscriptomics
journal, August 2012
- Moran, Mary Ann; Satinsky, Brandon; Gifford, Scott M.
- The ISME Journal, Vol. 7, Issue 2
Integrating microbial ecology into ecosystem models: challenges and priorities
journal, September 2011
- Treseder, Kathleen K.; Balser, Teri C.; Bradford, Mark A.
- Biogeochemistry, Vol. 109, Issue 1-3
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
journal, December 2009
- Schnoes, Alexandra M.; Brown, Shoshana D.; Dodevski, Igor
- PLoS Computational Biology, Vol. 5, Issue 12