Unraveling negative biotic interactions determining soil microbial community assembly and functioning

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

(2020) Lucas P. P. Braga et al.   Microbiome

DIABLO: an integrative approach for identifying key molecular drivers from multi-omic assays

(2019) Amrit Singh et al.   BIOINFORMATICS

A general framework for quantitatively assessing ecological stochasticity

(2019) Daliang Ning et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial predator-prey coevolution accelerates genome evolution and selects on virulence-associated prey defences

(2019) Ramith R. Nair et al.   Nature Communications

Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system

(2018) Ilonka C. Engelhardt et al.   ISME Journal

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data

(2018) Li Chen et al.   PeerJ

Biogeography of soil bacteria and archaea across France

(2018) Battle Karimi et al.   Science Advances

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Bacterial antagonism in host-associated microbial communities

(2018) Leonor García-Bayona et al.   SCIENCE

A low proportion of rare bacterial taxa responds to abiotic changes compared with dominant taxa

(2018) Viola Kurm et al.   ENVIRONMENTAL MICROBIOLOGY

Next-generation experiments linking community structure and ecosystem functioning

(2018) Thomas Bell   Environmental Microbiology Reports

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

Antagonism correlates with metabolic similarity in diverse bacteria

(2017) Jakob Russel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

Community structure follows simple assembly rules in microbial microcosms

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

Evolution and Ecology ofActinobacteriaand Their Bioenergy Applications

(2016) Gina R. Lewin et al.   Annual Review of Microbiology

Bacterial predation: 75 years and counting!

(2016) Juana Pérez et al.   ENVIRONMENTAL MICROBIOLOGY

Effectiveness of ecological rescue for altered soil microbial communities and functions

(2016) Kadiya Calderón et al.   ISME Journal

Division of labour in microorganisms: an evolutionary perspective

(2016) Stuart A. West et al.   NATURE REVIEWS MICROBIOLOGY

The Ecology and Evolution of Microbial Competition

(2016) Melanie Ghoul et al.   TRENDS IN MICROBIOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Complete nitrification by Nitrospira bacteria

(2015) Holger Daims et al.   NATURE

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Context dependency and saturating effects of loss of rare soil microbes on plant productivity

(2015) W. H. Gera Hol et al.   Frontiers in Plant Science

A role for biotic filtering in driving phylogenetic clustering in soil bacterial communities

(2014) Marta Goberna et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Chemical warfare and survival strategies in bacterial range expansions

(2014) M. F. Weber et al.   Journal of the Royal Society Interface

Volatile-mediated interactions between phylogenetically different soil bacteria

(2014) Paolina Garbeva et al.   Frontiers in Microbiology

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

(2013) J. Zhang et al.   BIOINFORMATICS

Diversity of protists and bacteria determines predation performance and stability

(2013) Muhammad Saleem et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

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

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

Competition, Not Cooperation, Dominates Interactions among Culturable Microbial Species

(2012) Kevin R. Foster et al.   CURRENT BIOLOGY

Nitrification expanded: discovery, physiology and genomics of a nitrite-oxidizing bacterium from the phylum Chloroflexi

(2012) Dimitry Y Sorokin et al.   ISME Journal

Microbial interactions: from networks to models

(2012) Karoline Faust 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

Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation

(2012) James I. Prosser et al.   TRENDS IN MICROBIOLOGY

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

(2011) Noah Fierer et al.   ISME Journal

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Picante: R tools for integrating phylogenies and ecology

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest

(2010) Frank Rasche et al.   ISME Journal

Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale

(2010) D Bru et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Dormancy contributes to the maintenance of microbial diversity

(2010) S. E. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

(2009) Ryan T Jones et al.   ISME Journal

Bacterial competition: surviving and thriving in the microbial jungle

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

Effect of gamma-sterilization and autoclaving on soil organic matter structure as studied by solid state NMR, UV and fluorescence spectroscopy

(2008) A. E. Berns et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

The Microbial Engines That Drive Earth's Biogeochemical Cycles

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