Metagenomic Sequencing Reveals that the Assembly of Functional Genes and Taxa Varied Highly and Lacked Redundancy in the Earthworm Gut Compared with Soil under Vanadium Stress

Metagenomic sequencing reveals detoxifying and tolerant functional genes in predominant bacteria assist Metaphire guillelmi adapt to soil vanadium exposure

(2021) Xinwei Wang et al.   JOURNAL OF HAZARDOUS MATERIALS

Laboratory versus field soil aging: Impacts on cadmium distribution, release, and bioavailability

(2021) Quan-Ying Wang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics

(2020) Cheng Gao et al.   Nature Communications

Soil vanadium(V)-reducing related bacteria drive community response to vanadium pollution from a smelting plant over multiple gradients

(2020) Song Wang et al.   ENVIRONMENT INTERNATIONAL

The effect of biochar on soil-plant-earthworm-bacteria system in metal(loid) contaminated soil

(2020) Hong-Tao Wang et al.   ENVIRONMENTAL POLLUTION

The prevalence of ampicillin-resistant opportunistic pathogenic bacteria undergoing selective stress of heavy metal pollutants in the Xiangjiang River, China

(2020) Qing Wang et al.   ENVIRONMENTAL POLLUTION

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

Geometry and evolution of the ecological niche in plant-associated microbes

(2020) Thomas M. Chaloner et al.   Nature Communications

Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles

(2020) Lu Luan et al.   mSystems

Rare taxa maintain the stability of crop mycobiomes and ecosystem functions

(2020) Chao Xiong et al.   ENVIRONMENTAL MICROBIOLOGY

Responses of soil and earthworm gut bacterial communities to heavy metal contamination

(2020) Peng Liu et al.   ENVIRONMENTAL POLLUTION

Nitrate application decreased microbial biodiversity but stimulated denitrifiers in epiphytic biofilms on Ceratophyllum demersum

(2020) Ziqiu Zhang et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Hill-based dissimilarity indices and null models for analysis of microbial community assembly

(2020) Oskar Modin et al.   Microbiome

Press Disturbance Alters Community Structure and Assembly Mechanisms of Bacterial Taxa and Functional Genes in Mesocosm-Scale Bioreactors

(2020) Ezequiel Santillan et al.   mSystems

Toxicity of soil antimony to earthworm Eisenia fetida (Savingy) before and after the aging process

(2020) Zhinan Xu et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Deciphering functional redundancy in the human microbiome

(2020) Liang Tian et al.   Nature Communications

Environmental risk characterization and ecological process determination of bacterial antibiotic resistome in lake sediments

(2020) Haiyang Chen et al.   ENVIRONMENT INTERNATIONAL

Stochasticity versus determinism: Microbial community assembly patterns under specific conditions in petrochemical activated sludge

(2020) Yiming Jiang et al.   JOURNAL OF HAZARDOUS MATERIALS

Profiling microbial community structures and functions in bioremediation strategies for treating 1,4-dioxane-contaminated groundwater

(2020) Yu Miao et al.   JOURNAL OF HAZARDOUS MATERIALS

Spatiotemporal successions of shrimp gut microbial colonization: high consistency despite distinct species pool

(2019) Jinbo Xiong et al.   ENVIRONMENTAL MICROBIOLOGY

Health risk assessment of potentially toxic elements in soils along the Central Elbe River, Germany

(2019) Jörg Rinklebe et al.   ENVIRONMENT INTERNATIONAL

A Randomized Trait Community Clustering approach to unveil consistent environmental thresholds in community assembly

(2019) Xavier Triadó-Margarit et al.   ISME Journal

Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions

(2019) Emilie E. L. Muller   mSystems

Drivers of human gut microbial community assembly: coadaptation, determinism and stochasticity

(2019) Kaitlyn Oliphant et al.   ISME Journal

Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

(2019) Shuo Jiao et al.   ISME Journal

Co-regulation map of the human proteome enables identification of protein functions

(2019) Georg Kustatscher et al.   NATURE BIOTECHNOLOGY

Soil fungal assemblage complexity is dependent on soil fertility and dominated by deterministic processes

(2019) Junjie Guo et al.   NEW PHYTOLOGIST

Diversity-triggered deterministic bacterial assembly constrains community functions

(2019) Weibing Xun et al.   Nature Communications

Stochastic processes shape microeukaryotic community assembly in a subtropical river across wet and dry seasons

(2019) Weidong Chen et al.   Microbiome

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes

(2018) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure

(2018) Sonya Erlandson et al.   MOLECULAR ECOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Liming does not counteract the influence of long-term fertilization on soil bacterial community structure and its co-occurrence pattern

(2018) Bin Ma et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

Competitive lottery-based assembly of selected clades in the human gut microbiome

(2018) Adrian J. Verster et al.   Microbiome

Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits

(2017) Juan E Pérez-Jaramillo et al.   ISME Journal

Contrasting the relative importance of species sorting and dispersal limitation in shaping marine bacterial versus protist communities

(2017) Wenxue Wu et al.   ISME Journal

Biogeography and ecological diversity patterns of rare and abundant bacteria in oil-contaminated soils

(2017) Shuo Jiao et al.   MOLECULAR ECOLOGY

Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments

(2017) Xiao Xiao et al.   MOLECULAR ECOLOGY

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Upscaling species richness and abundances in tropical forests

(2017) Anna Tovo et al.   Science Advances

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

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

Vanadium and proteins: Uptake, transport, structure, activity and function

(2015) João Costa Pessoa et al.   COORDINATION CHEMISTRY REVIEWS

Microbiomes in light of traits: A phylogenetic perspective

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

Interpreting the replacement and richness difference components of beta diversity

(2014) Pierre Legendre   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Bacterial community responses to a gradient of alkaline mountaintop mine drainage in Central Appalachian streams

(2014) Raven L Bier et al.   ISME Journal

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

betapart: an R package for the study of beta diversity

(2012) Andrés Baselga et al.   Methods in Ecology and Evolution

Determining the relative roles of species replacement and species richness differences in generating beta-diversity patterns

(2011) José C. Carvalho et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

ggplot2: Elegant Graphics for Data Analysis

(2011) Cedric Ginestet   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY

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

Contrasts between habitat generalists and specialists: an empirical extension to the basic metacommunity framework

(2009) Shubha N. Pandit et al.   ECOLOGY

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

(2009) Alex J Dumbrell et al.   ISME Journal