Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities

Responses of soil microbial functional genes to global changes are indirectly influenced by aboveground plant biomass variation

(2017) Hui Li et al.   SOIL BIOLOGY & BIOCHEMISTRY

Ecological effects of extreme drought on Californian herbaceous plant communities

(2016) Stella M. Copeland et al.   ECOLOGICAL MONOGRAPHS

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass

(2016) Erin E. Nuccio et al.   ECOLOGY

A trait-based approach to bacterial biofilms in soil

(2016) Jay T. Lennon et al.   ENVIRONMENTAL MICROBIOLOGY

Do shifts in life strategies explain microbial community responses to increasing nitrogen in tundra soil?

(2016) Minna Männistö et al.   SOIL BIOLOGY & BIOCHEMISTRY

Modeling coupled pesticide degradation and organic matter turnover: From gene abundance to process rates

(2016) Holger Pagel et al.   SOIL BIOLOGY & BIOCHEMISTRY

Predicting the Responses of Soil Nitrite-Oxidizers to Multi-Factorial Global Change: A Trait-Based Approach

(2016) Xavier Le Roux et al.   Frontiers in Microbiology

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

(2016) Emily B. Graham et al.   Frontiers in Microbiology

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

(2016) Paul Carini et al.   Nature Microbiology

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

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

Biotic context and soil properties modulate native plant responses to enhanced rainfall

(2015) A. Eskelinen et al.   ANNALS OF BOTANY

Nitrogen addition changes grassland soil organic matter decomposition

(2015) Charlotte E. Riggs et al.   BIOGEOCHEMISTRY

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

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties

(2015) Jeff R. Powell et al.   ECOLOGY

Coupled Carbon and Nitrogen Inputs Increase Microbial Biomass and Activity in Prairie Bioenergy Systems

(2015) Elizabeth M. Bach et al.   ECOSYSTEMS

A time for every season: soil aggregate turnover stimulates decomposition and reduces carbon loss in grasslands managed for bioenergy

(2015) Elizabeth M. Bach et al.   Global Change Biology Bioenergy

Temporal variation overshadows the response of leaf litter microbial communities to simulated global change

(2015) Kristin L Matulich et al.   ISME Journal

Microbial response to simulated global change is phylogenetically conserved and linked with functional potential

(2015) Anthony S Amend et al.   ISME Journal

Predicting microbial traits with phylogenies

(2015) Marta Goberna et al.   ISME Journal

Decreases in average bacterial community rRNA operon copy number during succession

(2015) Diana R Nemergut et al.   ISME Journal

Erosion of beta diversity under interacting global change impacts in a semi-arid grassland

(2015) Anu Eskelinen et al.   JOURNAL OF ECOLOGY

Fungal Traits That Drive Ecosystem Dynamics on Land

(2015) Kathleen K. Treseder et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Resource colimitation governs plant community responses to altered precipitation

(2015) Anu Eskelinen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

(2015) Jonathan W. Leff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiomes in light of traits: A phylogenetic perspective

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

Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons

(2015) Shengjing Shi et al.   mBio

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

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

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities

(2014) Marta Goberna et al.   ECOLOGY LETTERS

Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria

(2014) Albert Barberán et al.   ECOLOGY LETTERS

Disturbance and temporal partitioning of the activated sludge metacommunity

(2014) David C Vuono et al.   ISME Journal

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Changing precipitation pattern alters soil microbial community response to wet-up under a Mediterranean-type climate

(2014) Romain L Barnard et al.   ISME Journal

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

Is bacterial moisture niche a good predictor of shifts in community composition under long-term drought?

(2013) Sarah E. Evans et al.   ECOLOGY

Exotic plant invasions under enhanced rainfall are constrained by soil nutrients and competition

(2013) Anu Eskelinen et al.   ECOLOGY

Climate change alters ecological strategies of soil bacteria

(2013) Sarah E. Evans et al.   ECOLOGY LETTERS

Response of microbial communities to long-term fertilization depends on their microhabitat

(2013) Dominik Neumann et al.   FEMS MICROBIOLOGY ECOLOGY

Responses of soil bacterial and fungal communities to extreme desiccation and rewetting

(2013) Romain L Barnard et al.   ISME Journal

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

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

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Sequential extraction of denitrifying organisms from soils; strongly attached cells produce less N2O than loosely attached cells

(2013) Shahid Nadeem et al.   SOIL BIOLOGY & BIOCHEMISTRY

Effect of Rainfall-Induced Soil Geochemistry Dynamics on Grassland Soil Microbial Communities

(2012) Karelyn Cruz-Martínez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Scout Hypothesis, Stochastic Exit from Dormancy, and the Nature of Slow Growers

(2012) S. Buerger et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolically versatile large-genome prokaryotes

(2012) Benoit Guieysse et al.   CURRENT OPINION IN BIOTECHNOLOGY

Mapping the niche space of soil microorganisms using taxonomy and traits

(2012) Jay T. Lennon et al.   ECOLOGY

Lineage-dependent ecological coherence in bacteria

(2012) Alexander F. Koeppel et al.   FEMS MICROBIOLOGY ECOLOGY

Microbial communities and their responses to simulated global change fluctuate greatly over multiple years

(2012) Jessica L. M. Gutknecht et al.   GLOBAL CHANGE BIOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups

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

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition

(2012) Nicholas J. Bouskill et al.   Frontiers in Microbiology

Integrating microbial ecology into ecosystem models: challenges and priorities

(2011) Kathleen K. Treseder et al.   BIOGEOCHEMISTRY

Microbial seed banks: the ecological and evolutionary implications of dormancy

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

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition

(2011) Marko Davinic et al.   SOIL BIOLOGY & BIOCHEMISTRY

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

(2011) Katherine C. Goldfarb et al.   Frontiers in Microbiology

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Selectivity in Mammalian Extinction Risk and Threat Types: a New Measure of Phylogenetic Signal Strength in Binary Traits

(2010) SUSANNE A. FRITZ et al.   CONSERVATION BIOLOGY

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

(2010) Etienne Laliberté et al.   ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Microbial biogeography at the soil pore scale

(2010) Léo Simon Ruamps et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

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

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland

(2009) Karelyn Cruz-Martínez et al.   ISME Journal

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous Inference in General Parametric Models

(2008) Torsten Hothorn et al.   BIOMETRICAL JOURNAL

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

Microbial Biogeography: From Taxonomy to Traits

(2008) J. L. Green et al.   SCIENCE