Selection imposed by local environmental conditions drives differences in microbial community composition across geographically distinct groundwater aquifers

Factors influencing aquatic and terrestrial bacterial community assembly

(2019) Silke Langenheder et al.   Environmental Microbiology Reports

Spring Water of an Alpine Karst Aquifer Is Dominated by a Taxonomically Stable but Discharge-Responsive Bacterial Community

(2019) Domenico Savio et al.   Frontiers in Microbiology

Soil parameters, land use, and geographical distance drive soil bacterial communities along a European transect

(2019) Pierre Plassart et al.   Scientific Reports

Inoculation history affects community composition in experimental freshwater bacterioplankton communities

(2018) Koen Rummens et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa

(2018) Mallory J. Choudoir et al.   ISME Journal

Why do microbes exhibit weak biogeographic patterns?

(2018) Kyle M. Meyer et al.   ISME Journal

Microbial biogeography of 925 geothermal springs in New Zealand

(2018) Jean F. Power et al.   Nature Communications

Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology

(2018) James C. Stegen et al.   Nature Communications

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain

(2018) Yu Shi et al.   Microbiome

Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers

(2018) Robert E. Danczak et al.   mSystems

Temporal and spatial dynamics in microbial community composition within a temperate stream network

(2018) Norman Hassell et al.   ENVIRONMENTAL MICROBIOLOGY

The biomass and biodiversity of the continental subsurface

(2018) C. Magnabosco et al.   Nature Geoscience

IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences

(2018) Adithya Murali et al.   Microbiome

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes

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

Dispersal timing determines the importance of priority effects in bacterial communities

(2017) Pavel Svoboda et al.   ISME Journal

Towards an integrated understanding of how micro scale processes shape groundwater ecosystem functions

(2017) Susanne I. Schmidt et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Microdiversity shapes the traits, niche space, and biogeography of microbial taxa

(2017) Alyse A. Larkin et al.   Environmental Microbiology Reports

Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China

(2017) Bin Ma et al.   mSystems

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

(2017) et al.   Processes

Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse

(2017) Chi Liu et al.   Scientific Reports

Spatial scale drives patterns in soil bacterial diversity

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

Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences

(2016) Martin W Hahn et al.   ISME Journal

Quantification of aquatic sediment prokaryotes—A multiple-steps optimization testing sands from pristine and contaminated aquifers

(2016) Anne Bayer et al.   LIMNOLOGICA

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Metacommunity ecology meets biogeography: effects of geographical region, spatial dynamics and environmental filtering on community structure in aquatic organisms

(2016) Jani Heino et al.   OECOLOGIA

Environmental conditions shape soil bacterial community structure in a fragmented landscape

(2016) Romina Almasia et al.   SOIL BIOLOGY & BIOCHEMISTRY

Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

(2016) James C. Stegen et al.   Nature Communications

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

Coupling among Microbial Communities, Biogeochemistry and Mineralogy across Biogeochemical Facies

(2016) James C. Stegen et al.   Scientific Reports

Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation

(2016) E. D. Beaton et al.   Frontiers in Microbiology

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

(2016) Emily B. Graham 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

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment

(2015) Erik S. Wright   BMC BIOINFORMATICS

Microbial biogeography of permafrost thaw ponds across the changing northern landscape

(2015) Jérôme Comte et al.   ECOGRAPHY

Assembly mechanisms determining high species turnover in aquatic communities over regional and continental scales

(2015) Duarte S. Viana et al.   ECOGRAPHY

Environmental rather than spatial factors structure bacterioplankton communities in shallow lakes along a > 6000 km latitudinal gradient in South America

(2015) Caroline Souffreau et al.   ENVIRONMENTAL MICROBIOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

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

Hydrologic linkages drive spatial structuring of bacterial assemblages and functioning in alpine floodplains

(2015) Remo Freimann et al.   Frontiers in Microbiology

Estimating and mapping ecological processes influencing microbial community assembly

(2015) James C. Stegen et al.   Frontiers in Microbiology

The spatial structure of bacterial communities is influenced by historical environmental conditions

(2014) Martin G. I. Andersson et al.   ECOLOGY

Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools

(2014) Tanja Shabarova et al.   FEMS MICROBIOLOGY ECOLOGY

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

(2014) Jizhong Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Weighing the deep continental biosphere

(2013) Sean McMahon et al.   FEMS MICROBIOLOGY ECOLOGY

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Changes in assembly processes in soil bacterial communities following a wildfire disturbance

(2013) Scott Ferrenberg et al.   ISME Journal

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

(2013) Jianjun Wang et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

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

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

Beyond biogeographic patterns: processes shaping the microbial landscape

(2012) China A. Hanson et al.   NATURE REVIEWS MICROBIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Testing the Limits of 454 Pyrotag Sequencing: Reproducibility, Quantitative Assessment and Comparison to T-RFLP Fingerprinting of Aquifer Microbes

(2012) Giovanni Pilloni et al.   PLoS One

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

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

Local and regional factors influencing bacterial community assembly

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

Picante: R tools for integrating phylogenies and ecology

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

Scale dependency of processes structuring metacommunities of cladocerans in temporary pools of High-Andes wetlands

(2010) Steven A. J. Declerck et al.   ECOGRAPHY

Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities

(2010) Paul V. A. Fine et al.   ECOGRAPHY

Metacommunity phylogenetics: separating the roles of environmental filters and historical biogeography

(2010) Mathew A. Leibold et al.   ECOLOGY LETTERS

Conceptual Synthesis in Community Ecology

(2010) Mark Vellend   QUARTERLY REVIEW OF BIOLOGY

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Disintegration of the Ecological Community

(2008) Robert E. Ricklefs   AMERICAN NATURALIST

FORWARD SELECTION OF EXPLANATORY VARIABLES

(2008) F. Guillaume Blanchet et al.   ECOLOGY

Microbial biodiversity in groundwater ecosystems

(2008) C. GRIEBLER et al.   FRESHWATER BIOLOGY