Transferring concepts from plant to microbial ecology: A framework proposal to identify relevant bacterial functional traits

Trait dimensions in bacteria and archaea compared to vascular plants

(2021) Mark Westoby et al.   ECOLOGY LETTERS

Cell size, genome size, and maximum growth rate are near‐independent dimensions of ecological variation across bacteria and archaea

(2021) Mark Westoby et al.   Ecology and Evolution

Exploring the functional composition of the human microbiome using a hand-curated microbial trait database

(2021) Jake L. Weissman et al.   BMC BIOINFORMATICS

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil

(2020) Steven J. Blazewicz et al.   ISME Journal

Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives

(2020) Haiyan Chu et al.   mSystems

Predictive genomic traits for bacterial growth in culture versus actual growth in soil

(2019) Junhui Li et al.   ISME Journal

Soil microbial communities with greater investment in resource acquisition have lower growth yield

(2019) Ashish A. Malik et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fast and accurate average genome size and 16S rRNA gene average copy number computation in metagenomic data

(2019) Emiliano Pereira-Flores et al.   BMC BIOINFORMATICS

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

(2019) Ashish A. Malik et al.   ISME Journal

The fitness of chemotrophs increases when their catabolic by‐products are consumed by other species

(2019) Mayumi Seto et al.   ECOLOGY LETTERS

Functional diversity enhances, but exploitative traits reduce tree mixture effects on microbial biomass

(2019) Chen Chen et al.   FUNCTIONAL ECOLOGY

Unlinked rRNA genes are widespread among bacteria and archaea

(2019) Tess E. Brewer et al.   ISME Journal

Microbial functional diversity: From concepts to applications

(2019) Arthur Escalas et al.   Ecology and Evolution

Linking high GC content to the repair of double strand breaks in prokaryotic genomes

(2019) Jake L. Weissman et al.   PLoS Genetics

Mechanisms of soil bacterial and fungal community assembly differ among and within islands

(2019) Pandeng Wang et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial Tradeoffs in Growth Rate and Extracellular Enzymes

(2019) Kelly I. Ramin et al.   Frontiers in Microbiology

Mechanisms and ecological implications of the movement of bacteria in soil

(2018) Pu Yang et al.   APPLIED SOIL ECOLOGY

Variation in range size and dispersal capabilities of microbial taxa

(2018) Mallory J. Choudoir et al.   ECOLOGY

Delivering the promises of trait-based approaches to the needs of demographic approaches, and vice versa

(2018) Roberto Salguero-Gómez et al.   FUNCTIONAL ECOLOGY

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession

(2018) Rüdiger Ortiz-Álvarez et al.   ISME Journal

Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession

(2018) Patrick J. Kearns et al.   ISME Journal

High dispersal ability is related to fast life-history strategies

(2018) Noelle G. Beckman et al.   JOURNAL OF ECOLOGY

What makes trait-abundance relationships when both environmental filtering and stochastic neutral dynamics are at play?

(2018) Jessy Loranger et al.   OIKOS

The biomass distribution on Earth

(2018) Yinon M. Bar-On et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating taxon-specific population dynamics in diverse microbial communities

(2018) Benjamin J. Koch et al.   Ecosphere

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin

(2018) Min Ren et al.   Frontiers in Microbiology

Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology

(2018) Jennifer L. Wood et al.   Frontiers in Microbiology

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

Life in Dry Soils: Effects of Drought on Soil Microbial Communities and Processes

(2018) Joshua P. Schimel   Annual Review of Ecology Evolution and Systematics

Plant drought resistance is mediated by soil microbial community structure and soil-plant feedbacks in a savanna tree species

(2018) Nianxun Xi et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

Soil microbial communities alter conspecific and congeneric competition consistent with patterns of field coexistence in three Trifolium congeners

(2018) Andrew Siefert et al.   JOURNAL OF ECOLOGY

BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis

(2018) Lorenz Christian Reimer et al.   NUCLEIC ACIDS RESEARCH

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

(2018) Philippe C. Baveye et al.   Frontiers in Microbiology

Understanding how microbiomes influence the systems they inhabit

(2018) Ed K. Hall et al.   Nature Microbiology

Fire modulates ecosystem functioning through the phylogenetic structure of soil bacterial communities

(2018) Eduardo Pérez-Valera et al.   SOIL BIOLOGY & BIOCHEMISTRY

The Biokinetic Spectrum for Temperature and optimal Darwinian fitness

(2018) Ross Corkrey et al.   JOURNAL OF THEORETICAL BIOLOGY

Where less may be more: how the rare biosphere pulls ecosystems strings

(2017) Alexandre Jousset et al.   ISME Journal

The microbial habitat in soil: Scale, heterogeneity and functional consequences

(2017) Naoise Nunan   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

Defining Disturbance for Microbial Ecology

(2017) Craig J. Plante   MICROBIAL ECOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

How to design trait-based analyses of community assembly mechanisms: Insights and guidelines from a literature review

(2017) Rémi Perronne et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Response and effect traits of arable weeds in agro-ecosystems: a review of current knowledge

(2017) S Gaba et al.   WEED RESEARCH

Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information

(2017) Albert Barberán et al.   mSphere

Growth Rates of Microbes in the Oceans

(2016) David L. Kirchman   Annual Review of Marine Science

Reinoculation elucidates mechanisms of bacterial community assembly in soil and reveals undetected microbes

(2016) Davide Francioli et al.   BIOLOGY AND FERTILITY OF SOILS

A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

(2016) Jason M. Peters et al.   CELL

Modularity of nitrogen-oxide reducing soil bacteria: linking phenotype to genotype

(2016) Constance A. Roco et al.   ENVIRONMENTAL MICROBIOLOGY

A global method for calculating plant CSR ecological strategies applied across biomes world-wide

(2016) Simon Pierce et al.   FUNCTIONAL ECOLOGY

Genetic and life-history traits associated with the distribution of prophages in bacteria

(2016) Marie Touchon et al.   ISME Journal

The effect of extrinsic mortality on genome size evolution in prokaryotes

(2016) Piotr Bentkowski et al.   ISME Journal

Beneficial role of bacterial endophytes in heavy metal phytoremediation

(2016) Ying Ma et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Methodologies for probing the metatranscriptome of grassland soil

(2016) Aaron Garoutte et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Constraints, Trade-offs and the Currency of Fitness

(2016) Luis Acerenza   JOURNAL OF MOLECULAR EVOLUTION

Indispensability of Horizontally Transferred Genes and Its Impact on Bacterial Genome Streamlining

(2016) Ildikó Karcagi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reinforcing loose foundation stones in trait-based plant ecology

(2016) Bill Shipley et al.   OECOLOGIA

Global biogeography of microbial nitrogen-cycling traits in soil

(2016) Michaeline B. Nelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments

(2016) Mohamed Faraj Edbeib et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge

(2016) Aline Frossard et al.   Frontiers in Microbiology

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

(2016) Aaron Weimann et al.   mSystems

Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems

(2016) Rubén López-Mondéjar et al.   Scientific Reports

Quantitative Microbial Ecology through Stable Isotope Probing

(2015) Bruce A. Hungate et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Model of Extracellular Enzymes in Free-Living Microbes: Which Strategy Pays Off?

(2015) Sachia J. Traving et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Decreases in average bacterial community rRNA operon copy number during succession

(2015) Diana R Nemergut et al.   ISME Journal

Shelter in a Swarm

(2015) Rasika M. Harshey et al.   JOURNAL OF MOLECULAR BIOLOGY

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages

(2015) Haiwei Luo et al.   MOLECULAR BIOLOGY AND EVOLUTION

The global spectrum of plant form and function

(2015) Sandra Díaz et al.   NATURE

Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

(2015) James I. Prosser   NATURE REVIEWS MICROBIOLOGY

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Microbial hotspots and hot moments in soil: Concept & review

(2015) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fitness of multidimensional phenotypes in dynamic adaptive landscapes

(2015) Daniel C. Laughlin et al.   TRENDS IN ECOLOGY & EVOLUTION

Effects of Genic Base Composition on Growth Rate in G+C-rich Genomes

(2015) Y. D. Kelkar et al.   G3-Genes Genomes Genetics

The complex relationship between microbial growth rate and yield and its implications for ecosystem processes

(2015) David A. Lipson   Frontiers in Microbiology

Microbial resource utilization traits and trade-offs: implications for community structure, functioning, and biogeochemical impacts at present and in the future

(2015) Elena Litchman et al.   Frontiers in Microbiology

Long-term forest soil warming alters microbial communities in temperate forest soils

(2015) Kristen M. DeAngelis et al.   Frontiers in Microbiology

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape

(2015) Florentin Constancias et al.   MicrobiologyOpen

Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula

(2015) Jeff S. Bowman et al.   PLoS One

What Are Species Pools and When Are They Important?

(2014) Howard V. Cornell et al.   Annual Review of Ecology Evolution and Systematics

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Effects of herbivory on leaf life span in woody plants: a meta-analysis

(2014) Elena L. Zvereva et al.   JOURNAL OF ECOLOGY

The world-wide ‘fast-slow’ plant economics spectrum: a traits manifesto

(2014) Peter B. Reich   JOURNAL OF ECOLOGY

The evolution of bacterial DNA base composition

(2014) Deepa Agashe et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Leaf trait variation captures climate differences but differs with species irrespective of functional group

(2014) Guohong Wang et al.   Journal of Plant Ecology

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Niche and host-associated functional signatures of the root surface microbiome

(2014) Maya Ofek-Lalzar et al.   Nature Communications

Systematic Perturbation of Cytoskeletal Function Reveals a Linear Scaling Relationship between Cell Geometry and Fitness

(2014) Russell D. Monds et al.   Cell Reports

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

(2014) Sascha Krause et al.   Frontiers in Microbiology

Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities

(2014) Noah Fierer et al.   Frontiers in Microbiology

The microbial contribution to macroecology

(2014) Albert Barberán   Frontiers in Microbiology

The use of microbial gene abundance in the development of fuel remediation guidelines in polar soils

(2014) Elizabeth L Richardson et al.   Integrated Environmental Assessment and Management

CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction

(2014) Florent E Angly et al.   Microbiome

Cell Size Distributions of Soil Bacterial and Archaeal Taxa

(2013) Maria C. Portillo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic potential of endophytic bacteria

(2013) Günter Brader et al.   CURRENT OPINION IN BIOTECHNOLOGY

Carbon use efficiency of microbial communities: stoichiometry, methodology and modelling

(2013) Robert L. Sinsabaugh et al.   ECOLOGY LETTERS

Allocating CSR plant functional types: the use of leaf economics and size traits to classify woody and herbaceous vascular plants

(2013) Simon Pierce et al.   FUNCTIONAL ECOLOGY

Growth Temperature and Genome Size in Bacteria Are Negatively Correlated, Suggesting Genomic Streamlining During Thermal Adaptation

(2013) Niv Sabath et al.   Genome Biology and Evolution

Community assembly along a soil depth gradient: contrasting patterns of plant trait convergence and divergence in a Mediterranean rangeland

(2013) Maud Bernard-Verdier et al.   JOURNAL OF ECOLOGY

Bacterial motility confers fitness advantage in the presence of phages

(2013) T. B. Taylor et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Habitat species pools for phylogenetic structure in microbes

(2013) Jianjun Wang et al.   Environmental Microbiology Reports

Soil development and microbial functional diversity: Proposal for a methodological approach

(2012) S. Marinari et al.   GEODERMA

Density-dependent fitness benefits in quorum-sensing bacterial populations

(2012) S. E. Darch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community specificity: life and afterlife effects of genes

(2012) Thomas G. Whitham et al.   TRENDS IN PLANT SCIENCE

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

A trait-based framework for predicting when and where microbial adaptation to climate change will affect ecosystem functioning

(2011) Matthew D. Wallenstein et al.   BIOGEOCHEMISTRY

Evidence for a three-way trade-off between nitrogen and phosphorus competitive abilities and cell size in phytoplankton

(2011) Kyle F. Edwards et al.   ECOLOGY

Functional diversity indices reveal the impacts of land use intensification on plant community assembly

(2011) Robin J. Pakeman   JOURNAL OF ECOLOGY

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

CWM and Rao’s quadratic diversity: a unified framework for functional ecology

(2011) Carlo Ricotta et al.   OECOLOGIA

Investment in rapid growth shapes the evolutionary rates of essential proteins

(2011) S. Vieira-Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Local and regional factors influencing bacterial community assembly

(2011) Eva S. Lindström et al.   Environmental Microbiology Reports

Competition and Dispersal in Pseudomonas aeruginosa

(2010) Tiffany B. Taylor et al.   AMERICAN NATURALIST

Species Turnover along Abiotic and Biotic Gradients: Patterns in Space Equal Patterns in Time?

(2010) Janne Soininen   BIOSCIENCE

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

A user's guide to functional diversity indices

(2010) D. Schleuter et al.   ECOLOGICAL MONOGRAPHS

A distance-based framework for measuring functional diversity from multiple traits

(2010) Etienne Laliberté et al.   ECOLOGY

A structured and dynamic framework to advance traits-based theory and prediction in ecology

(2010) Colleen T. Webb et al.   ECOLOGY LETTERS

Escherichia coli rpoB Mutants Have Increased Evolvability in Proportion to Their Fitness Defects

(2010) J. E. Barrick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Changes through time: integrating microorganisms into the study of succession

(2010) Noah Fierer et al.   RESEARCH IN MICROBIOLOGY

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

Is There a Latitudinal Gradient in the Importance of Biotic Interactions?

(2009) Douglas W. Schemske et al.   Annual Review of Ecology Evolution and Systematics

Environmental stress and evolvability in microbial systems

(2009) F. Baquero   CLINICAL MICROBIOLOGY AND INFECTION

Towards a worldwide wood economics spectrum

(2009) Jerome Chave et al.   ECOLOGY LETTERS

Mapping field-scale spatial patterns of size and activity of the denitrifier community

(2009) Laurent Philippot et al.   ENVIRONMENTAL MICROBIOLOGY

How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis

(2009) C. R. Woese et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Bacterial competition: surviving and thriving in the microbial jungle

(2009) Michael E. Hibbing et al.   NATURE REVIEWS MICROBIOLOGY

Causes and consequences of variation in leaf mass per area (LMA): a meta-analysis

(2009) Hendrik Poorter et al.   NEW PHYTOLOGIST

Suites of plant traits in species from different stages of a Mediterranean secondary succession

(2009) M.-L. Navas et al.   PLANT BIOLOGY

Genome streamlining and the elemental costs of growth

(2009) Dag O. Hessen et al.   TRENDS IN ECOLOGY & EVOLUTION

NEW MULTIDIMENSIONAL FUNCTIONAL DIVERSITY INDICES FOR A MULTIFACETED FRAMEWORK IN FUNCTIONAL ECOLOGY

(2008) Sébastien Villéger et al.   ECOLOGY

Plant species traits are the predominant control on litter decomposition rates within biomes worldwide

(2008) William K. Cornwell et al.   ECOLOGY LETTERS

Scaling environmental change through the community-level: a trait-based response-and-effect framework for plants

(2008) KATHARINE N. SUDING et al.   GLOBAL CHANGE BIOLOGY

Functional identity is more important than diversity in influencing ecosystem processes in a temperate native grassland

(2008) Karel Mokany et al.   JOURNAL OF ECOLOGY

Plant response traits mediate the effects of subalpine grasslands on soil moisture

(2008) N. Gross et al.   NEW PHYTOLOGIST

Microbial Biogeography: From Taxonomy to Traits

(2008) J. L. Green et al.   SCIENCE

Microcolony and biofilm formation as a survival strategy for bacteria

(2007) Leah R. Johnson   JOURNAL OF THEORETICAL BIOLOGY