Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland

Deterministic Assembly and Diversity Gradient Altered the Biofilm Community Performances of Bioreactors

(2019) Zhaojing Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland

(2019) Manoeli Lupatini et al.   MICROBIAL ECOLOGY

Factors influencing aquatic and terrestrial bacterial community assembly

(2019) Silke Langenheder et al.   Environmental Microbiology Reports

Unraveling spatio‐temporal variability of arbuscular mycorrhiza fungi in a temperate grassland plot

(2019) Kezia Goldmann et al.   ENVIRONMENTAL MICROBIOLOGY

Experimental Evidence that Stochasticity Contributes to Bacterial Composition and Functioning in a Decomposer Community

(2019) Michaeline B. N. Albright et al.   mBio

Functional Traits and Spatio-Temporal Structure of a Major Group of Soil Protists (Rhizaria: Cercozoa) in a Temperate Grassland

(2019) Anna Maria Fiore-Donno et al.   Frontiers in Microbiology

Environmental filtering: A case of bacterial community assembly in soil

(2019) Yan Yan et al.   SOIL BIOLOGY & BIOCHEMISTRY

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands

(2019) Selma Vieira et al.   ISME Journal

Interactions of Microhabitat and Time Control Grassland Bacterial and Fungal Composition

(2019) Michaeline B. N. Albright et al.   Frontiers in Ecology and Evolution

Disentangling good from bad practices in the selection of spatial or phylogenetic eigenvectors

(2018) David Bauman et al.   ECOGRAPHY

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

(2018) Binu M. Tripathi et al.   ISME Journal

Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes

(2018) Yuanyuan Mo et al.   ISME Journal

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

(2018) Dinka Mandakovic et al.   Scientific Reports

Bacterial diversity is positively correlated with soil heterogeneity

(2018) Emily E. Curd et al.   Ecosphere

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

(2018) Anthony Diego Muller Barboza et al.   PeerJ

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

Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures

(2018) Daniel R. Lammel et al.   Microbiome

Biogeography of soil bacteria and archaea across France

(2018) Battle Karimi et al.   Science Advances

Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers

(2018) Robert E. Danczak et al.   mSystems

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

Two key features influencing community assembly processes at regional scale: Initial state and degree of change in environmental conditions

(2018) Youzhi Feng et al.   MOLECULAR ECOLOGY

Body size determines soil community assembly in a tropical forest

(2018) Lucie Zinger et al.   MOLECULAR ECOLOGY

Dispersal alters bacterial diversity and composition in a natural community

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

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

(2017) Alexandre Jousset et al.   ISME Journal

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere

(2017) Sadaf Kalam et al.   JOURNAL OF BASIC MICROBIOLOGY

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Soil pH is a major driver of soil diazotrophic community assembly in Qinghai-Tibet alpine meadows

(2017) Yansu Wang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Priming of soil organic matter: Chemical structure of added compounds is more important than the energy content

(2017) D.P. Di Lonardo et al.   SOIL BIOLOGY & BIOCHEMISTRY

Spatial and temporal dynamics of nitrogen fixing, nitrifying and denitrifying microbes in an unfertilized grassland soil

(2017) Kathleen Regan et al.   SOIL BIOLOGY & BIOCHEMISTRY

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

(2017) et al.   Processes

Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria

(2016) Anna M. Kielak et al.   ARCHIVES OF MICROBIOLOGY

Spatial scale drives patterns in soil bacterial diversity

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

Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem

(2016) Allison M. Veach et al.   MOLECULAR ECOLOGY

Temporal and small-scale spatial variation in grassland productivity, biomass quality, and nutrient limitation

(2016) Valentin H. Klaus et al.   PLANT ECOLOGY

Carbon transfer from maize roots and litter into bacteria and fungi depends on soil depth and time

(2016) Karolin Müller et al.   SOIL BIOLOGY & BIOCHEMISTRY

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

(2016) Cheryl P. Andam et al.   mBio

History Leaves Its Mark on Soil Bacterial Diversity

(2016) Jennifer B. H. Martiny   mBio

Spatial Interaction of Archaeal Ammonia-Oxidizers and Nitrite-Oxidizing Bacteria in an Unfertilized Grassland Soil

(2016) Barbara Stempfhuber et al.   Frontiers in Microbiology

Myxobacteria: Moving, Killing, Feeding, and Surviving Together

(2016) José Muñoz-Dorado 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

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest

(2016) Stephanie N Kivlin et al.   PLoS One

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

(2015) Sebastián Fuentes et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Controlling false discoveries in high-dimensional situations: boosting with stability selection

(2015) Benjamin Hofner et al.   BMC BIOINFORMATICS

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure

(2015) Richard Hill et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter

(2015) Lucia Žifčáková et al.   ENVIRONMENTAL MICROBIOLOGY

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment

(2015) Mohammad Bahram et al.   ISME Journal

Differentiating between niche and neutral assembly in metacommunities using null models of β-diversity

(2015) Caroline M. Tucker et al.   OIKOS

Increasing aridity reduces soil microbial diversity and abundance in global drylands

(2015) Fernando T. Maestre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The bacterial community inhabiting temperate deciduous forests is vertically stratified and undergoes seasonal dynamics

(2015) Rubén López-Mondéjar et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial hotspots and hot moments in soil: Concept & review

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

Temporal patterns of rarity provide a more complete view of microbial diversity

(2015) Ashley Shade et al.   TRENDS IN MICROBIOLOGY

Deterministic processes vary during community assembly for ecologically dissimilar taxa

(2015) Jeff R. Powell et al.   Nature Communications

Estimating and mapping ecological processes influencing microbial community assembly

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

Key Edaphic Properties Largely Explain Temporal and Geographic Variation in Soil Microbial Communities across Four Biomes

(2015) Kathryn M. Docherty et al.   PLoS One

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability

(2014) Ruth Henneberger et al.   ENVIRONMENTAL MICROBIOLOGY

Dynamics in microbial communities: unraveling mechanisms to identify principles

(2014) Allan Konopka et al.   ISME Journal

Spatial patterns of microbial diversity and activity in an aged creosote-contaminated site

(2014) Shinjini Mukherjee 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

Spatial scale resolves the niche versus neutral theory debate

(2014) Jonathan M. Chase   JOURNAL OF VEGETATION SCIENCE

Spatial Ecology of Bacteria at the Microscale in Soil

(2014) Xavier Raynaud et al.   PLoS One

Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

(2014) Xiangzhen Li et al.   PLoS One

Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization

(2014) Nikolina Udikovic-Kolic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Seasonal controls on grassland microbial biogeography: Are they governed by plants, abiotic properties or both?

(2014) Kathleen M. Regan et al.   SOIL BIOLOGY & BIOCHEMISTRY

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

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

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Beta diversity as the variance of community data: dissimilarity coefficients and partitioning

(2013) Pierre Legendre et al.   ECOLOGY LETTERS

The importance of species sorting differs between habitat generalists and specialists in bacterial communities

(2013) Anna J. Székely et al.   FEMS MICROBIOLOGY ECOLOGY

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

(2013) Steven J Blazewicz et al.   ISME Journal

Temporal variability in soil microbial communities across land-use types

(2013) Christian L Lauber et al.   ISME Journal

A meta-analysis of changes in bacterial and archaeal communities with time

(2013) Ashley Shade et al.   ISME Journal

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

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

(2013) Romain L Barnard et al.   ISME Journal

Evidence from the real world:15N natural abundances reveal enhanced nitrogen use at high plant diversity in Central European grasslands

(2013) Till Kleinebecker et al.   JOURNAL OF ECOLOGY

Active microorganisms in soil: Critical review of estimation criteria and approaches

(2013) Evgenia Blagodatskaya et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial community assembly, theory and rare functions

(2013) Mujalin K. Pholchan et al.   Frontiers in Microbiology

General and rare bacterial taxa demonstrating different temporal dynamic patterns in an activated sludge bioreactor

(2012) Taek-Seung Kim et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Model-based boosting in R: a hands-on tutorial using the R package mboost

(2012) Benjamin Hofner et al.   COMPUTATIONAL STATISTICS

Variable selection with error control: another look at stability selection

(2012) Rajen D. Shah et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Generalized additive models for location, scale and shape for high dimensional data-a flexible approach based on boosting

(2012) Andreas Mayr et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS

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

Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil

(2012) Kathryn G. Eilers et al.   SOIL BIOLOGY & BIOCHEMISTRY

Spatial Patterns of Iron- and Methane-Oxidizing Bacterial Communities in an Irregularly Flooded, Riparian Wetland

(2012) Juanjuan Wang et al.   Frontiers in Microbiology

Fundamentals of Microbial Community Resistance and Resilience

(2012) Ashley Shade et al.   Frontiers in Microbiology

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Abundance and activity of nitrate reducers in an arable soil are more affected by temporal variation and soil depth than by elevated atmospheric [CO2]

(2011) Sven Marhan et al.   FEMS MICROBIOLOGY ECOLOGY

Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils

(2011) Daniel Keil et al.   FEMS MICROBIOLOGY ECOLOGY

Species sorting and neutral processes are both important during the initial assembly of bacterial communities

(2011) Silke Langenheder et al.   ISME Journal

Diversity and dynamics of rare and of resident bacterial populations in coastal sands

(2011) Angélique Gobet et al.   ISME Journal

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

(2011) Noah Fierer et al.   ISME Journal

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

(2011) Petr Baldrian 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

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

Activity of abundant and rare bacteria in a coastal ocean

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

Soil moisture is the major factor influencing microbial community structure and enzyme activities across seven biogeoclimatic zones in western Canada

(2011) Beth F.T. Brockett et al.   SOIL BIOLOGY & BIOCHEMISTRY

Implementing large-scale and long-term functional biodiversity research: The Biodiversity Exploratories

(2010) Markus Fischer et al.   BASIC AND APPLIED ECOLOGY

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

A Robust Procedure for Comparing Multiple Means under Heteroscedasticity in Unbalanced Designs

(2010) Esther Herberich et al.   PLoS One

Long-term impacts of high-input annual cropping and unfertilized perennial grass production on soil properties and belowground food webs in Kansas, USA

(2009) S.W. Culman et al.   AGRICULTURE ECOSYSTEMS & ENVIRONMENT

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

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

Partitioning the turnover and nestedness components of beta diversity

(2009) Andrés Baselga   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Simultaneous Inference in General Parametric Models

(2008) Torsten Hothorn et al.   BIOMETRICAL JOURNAL

Variable Selection and Model Choice in Geoadditive Regression Models

(2008) Thomas Kneib et al.   BIOMETRICS

Boosting additive models using component-wise P-Splines

(2008) Matthias Schmid et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

FORWARD SELECTION OF EXPLANATORY VARIABLES

(2008) F. Guillaume Blanchet et al.   ECOLOGY