Function and functional redundancy in microbial systems

Taxonomic variability and functional stability in microbial communities infected by phages

(2017) Stilianos Louca et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial nutrient niches in the gut

(2017) Fátima C. Pereira et al.   ENVIRONMENTAL MICROBIOLOGY

Dispersal alters bacterial diversity and composition in a natural community

(2017) Michaeline B N Albright et al.   ISME Journal

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

(2017) Benjamin J Tully et al.   ISME Journal

Biofilm community succession: a neutral perspective

(2017) Stephen Woodcock et al.   MICROBIOLOGY-SGM

Geochemical and Temporal Influences on the Enrichment of Acidophilic Iron-Oxidizing Bacterial Communities

(2016) Yizhi Sheng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion

(2016) Inka Vanwonterghem et al.   ENVIRONMENTAL MICROBIOLOGY

Integrating biogeochemistry with multiomic sequence information in a model oxygen minimum zone

(2016) Stilianos Louca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

(2016) Jan-Hendrik Hehemann et al.   Nature Communications

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

(2016) Damian Rafal Plichta et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Microbial Communities Are Well Adapted to Disturbances in Energy Input

(2016) Nuria Fernandez-Gonzalez et al.   mSystems

High taxonomic variability despite stable functional structure across microbial communities

(2016) Stilianos Louca et al.   Nature Ecology & Evolution

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents

(2015) Daniel C Reed et al.   ISME Journal

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

(2015) Adam R Burns et al.   ISME Journal

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

(2015) Francisco Dini-Andreote 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

Rapid evolution of adaptive niche construction in experimental microbial populations

(2014) Benjamin J. Callahan et al.   EVOLUTION

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

(2014) Inka Vanwonterghem et al.   ISME Journal

Dynamics in microbial communities: unraveling mechanisms to identify principles

(2014) Allan Konopka et al.   ISME Journal

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

Gene-centric approach to integrating environmental genomics and biogeochemical models

(2014) Daniel C. Reed et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations

(2014) Y. Yawata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

(2014) A. K. Hawley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Processes and patterns of oceanic nutrient limitation

(2013) C. M. Moore et al.   Nature Geoscience

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

(2013) Matthew D. Herron et al.   PLOS BIOLOGY

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

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

(2012) J. J. Morris et al.   mBio

Bacteriophage ecology in environmental biotechnology processes

(2011) Orr H Shapiro et al.   CURRENT OPINION IN BIOTECHNOLOGY

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors

(2011) Aline Frossard et al.   ISME Journal

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

Drivers of bacterial  -diversity depend on spatial scale

(2011) J. B. H. Martiny et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anaerobic Digestion of Renewable Biomass: Thermophilic Temperature Governs Methanogen Population Dynamics

(2010) N. Krakat et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial community dynamics in a functionally stable pilot-scale wastewater treatment plant

(2010) Xiaohui Wang et al.   BIORESOURCE TECHNOLOGY

Function-specific response to depletion of microbial diversity

(2010) Hannes Peter et al.   ISME Journal

Balance of Neutral and Deterministic Components in the Dynamics of Activated Sludge Floc Assembly

(2010) Joaquín M. Ayarza et al.   MICROBIAL ECOLOGY

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

Combined niche and neutral effects in a microbial wastewater treatment community

(2010) I. D. Ofiteru et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conceptual Synthesis in Community Ecology

(2010) Mark Vellend   QUARTERLY REVIEW OF BIOLOGY

Ammonia-oxidizing communities in a highly aerated full-scale activated sludge bioreactor: betaproteobacterial dynamics and low relative abundance of Crenarchaea

(2009) George F. Wells et al.   ENVIRONMENTAL MICROBIOLOGY

Towards a consistent classification scheme for geochemical environments, or, why we wish the term ‘suboxic’ would go away

(2009) D. E. CANFIELD et al.   Geobiology

Relative roles of niche and neutral processes in structuring a soil microbial community

(2009) Alex J Dumbrell et al.   ISME Journal

Explaining microbial population genomics through phage predation

(2009) Francisco Rodriguez-Valera et al.   NATURE REVIEWS MICROBIOLOGY

Bacterial competition: surviving and thriving in the microbial jungle

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

The interaction between predation and competition

(2008) Peter Chesson et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE