Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities

Plant-phytopathogen interactions: bacterial responses to environmental and plant stimuli

(2017) Simon Leonard et al.   ENVIRONMENTAL MICROBIOLOGY

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture

(2017) Gao Chen et al.   ENVIRONMENTAL MICROBIOLOGY

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes

(2017) Emily B. Graham et al.   ENVIRONMENTAL MICROBIOLOGY

Abundant carbon substrates drive extremely high sulfate reduction rates and methane fluxes in Prairie Pothole Wetlands

(2017) Paula Dalcin Martins et al.   GLOBAL CHANGE BIOLOGY

Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains

(2017) V.L. Bailey et al.   SOIL BIOLOGY & BIOCHEMISTRY

Community structure follows simple assembly rules in microbial microcosms

(2017) Jonathan Friedman et al.   Nature Ecology & Evolution

Spatial scale drives patterns in soil bacterial diversity

(2016) Sarah L. O'Brien et al.   ENVIRONMENTAL MICROBIOLOGY

Engineering microbial consortia for controllable outputs

(2016) Stephen R Lindemann et al.   ISME Journal

The ecology and biogeochemistry of stream biofilms

(2016) Tom J. Battin et al.   NATURE REVIEWS MICROBIOLOGY

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

(2016) Man Jae Kwon et al.   PLoS One

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

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

A new view of the tree of life

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

Deciphering microbial community robustness through synthetic ecology and molecular systems synecology

(2015) Ben Stenuit et al.   CURRENT OPINION IN BIOTECHNOLOGY

Aquifer environment selects for microbial species cohorts in sediment and groundwater

(2015) Laura A Hug et al.   ISME Journal

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

(2015) James I. Prosser   NATURE REVIEWS MICROBIOLOGY

Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation

(2015) Nora B. Sutton et al.   PLoS One

Solute Concentrations Influence Microbial Methanogenesis in Coal-bearing Strata of the Cherokee Basin, USA

(2015) Matthew F. Kirk et al.   Frontiers in Microbiology

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

(2015) Lydia H. Zeglin   Frontiers in Microbiology

Removal of Pharmaceuticals and Personal Care Products during Water Recycling: Microbial Community Structure and Effects of Substrate Concentration

(2014) Kathryn M. Onesios-Barry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metatranscriptome of an Anaerobic Benzene-Degrading, Nitrate-Reducing Enrichment Culture Reveals Involvement of Carboxylation in Benzene Ring Activation

(2014) Fei Luo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Application of the Biolog EcoPlate Approach in Ecotoxicological Evaluation of Dairy Sewage Sludge

(2014) Agata Gryta et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Rapid succession of uncultured marine bacterial and archaeal populations in a denitrifying continuous culture

(2014) Beate Kraft et al.   ENVIRONMENTAL MICROBIOLOGY

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points

(2014) Kim M. Handley et al.   ENVIRONMENTAL MICROBIOLOGY

Dynamics in microbial communities: unraveling mechanisms to identify principles

(2014) Allan Konopka et al.   ISME Journal

Functional Diversity of the Microbial Community in Healthy Subjects and Periodontitis Patients Based on Sole Carbon Source Utilization

(2014) Yifei Zhang et al.   PLoS One

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Syntrophic exchange in synthetic microbial communities

(2014) M. T. Mee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages

(2014) E. A. Ottesen et al.   SCIENCE

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Functional microbial diversity explains groundwater chemistry in a pristine aquifer

(2013) Theodore M Flynn et al.   BMC MICROBIOLOGY

A direct test of nitrogen and phosphorus limitation to net primary productivity in a lowland tropical wet forest

(2013) S. Alvarez-Clare et al.   ECOLOGY

Genus-wide acid tolerance accounts for the biogeographical distribution of soilBurkholderiapopulations

(2013) Nejc Stopnisek et al.   ENVIRONMENTAL MICROBIOLOGY

Differentiation between sediment and hypolimnion methanogen communities in humic lakes

(2013) Nicholas D. Youngblut et al.   ENVIRONMENTAL MICROBIOLOGY

CO2-induced shift in microbial activity affects carbon trapping and water quality in anoxic bioreactors

(2013) Matthew F. Kirk et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Effects of dissimilatory sulfate reduction on FeIII (hydr)oxide reduction and microbial community development

(2013) Man Jae Kwon et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Micrometer-scale physical structure and microbial composition of soil macroaggregates

(2013) Vanessa L. Bailey et al.   SOIL BIOLOGY & BIOCHEMISTRY

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Biodegradation of aged diesel in diverse soil matrixes: impact of environmental conditions and bioavailability on microbial remediation capacity

(2012) Nora B. Sutton et al.   BIODEGRADATION

Culturing captures members of the soil rare biosphere

(2012) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

Metabolic specialization and the assembly of microbial communities

(2012) David R Johnson 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

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Disentangling the importance of ecological niches from stochastic processes across scales

(2011) J. M. Chase et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Microbial Community Structure and Denitrification in a Wetland Mitigation Bank

(2010) A. L. Peralta et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Examining the global distribution of dominant archaeal populations in soil

(2010) Scott T Bates et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso 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

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

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

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

One-dimensional metric for tracking bacterial community divergence using sole carbon source utilization patterns

(2009) Kela P. Weber et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Nitrous oxide production kinetics during nitrate reduction in river sediments

(2009) Anniet M. Laverman et al.   WATER RESEARCH

Defined spatial structure stabilizes a synthetic multispecies bacterial community

(2008) H. J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA