Niche differentiation is spatially and temporally regulated in the rhizosphere

Disentangling carbon flow across microbial kingdoms in the rhizosphere of maize

(2019) Maike Hünninghaus et al.   SOIL BIOLOGY & BIOCHEMISTRY

Predictive genomic traits for bacterial growth in culture versus actual growth in soil

(2019) Junhui Li et al.   ISME Journal

Litter chemistry influences decomposition through activity of specific microbial functional guilds

(2018) Jennifer M. Bhatnagar et al.   ECOLOGICAL MONOGRAPHS

Decomposer food web in a deciduous forest shows high share of generalist microorganisms and importance of microbial biomass recycling

(2018) Ruben López-Mondéjar et al.   ISME Journal

Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon

(2018) Evan P. Starr et al.   Microbiome

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

(2018) Alexander J. Probst et al.   Nature Microbiology

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

(2018) Kateryna Zhalnina et al.   Nature Microbiology

Function and functional redundancy in microbial systems

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

Microbial community assembly differs across minerals in a rhizosphere microcosm

(2018) Thea Whitman et al.   ENVIRONMENTAL MICROBIOLOGY

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Combining multiple functional annotation tools increases coverage of metabolic annotation

(2018) Marc Griesemer et al.   BMC GENOMICS

Microbial formation of stable soil carbon is more efficient from belowground than aboveground input

(2018) Noah W. Sokol et al.   Nature Geoscience

Cover crop root contributions to soil carbon in a no-till corn bioenergy cropping system

(2017) Emily E. Austin et al.   Global Change Biology Bioenergy

Carbon input by roots into the soil: Quantification of rhizodeposition from root to ecosystem scale

(2017) Johanna Pausch et al.   GLOBAL CHANGE BIOLOGY

Genomic features of bacterial adaptation to plants

(2017) Asaf Levy et al.   NATURE GENETICS

Modeling Global Soil Carbon and Soil Microbial Carbon by Integrating Microbial Processes into the Ecosystem Process Model TRIPLEX-GHG

(2017) Kefeng Wang et al.   Journal of Advances in Modeling Earth Systems

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass

(2016) Erin E. Nuccio et al.   ECOLOGY

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Cephaloticoccus gen. nov., a new genus of ‘Verrucomicrobia’ containing two novel species isolated from Cephalotes ant guts

(2016) Jonathan Y. Lin et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere

(2016) Yan Yan et al.   ISME Journal

Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis

(2016) Anastasia A. Ivanova et al.   MOLECULAR ECOLOGY

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

(2016) Cynthia M. Kallenbach et al.   Nature Communications

Commentary: Oil degradation and biosurfactant production by the deep sea bacterium Dietzia maris As-13-3

(2016) Pattanathu K. S. M. Rahman et al.   Frontiers in Microbiology

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

(2016) Damian Rafal Plichta et al.   Nature Microbiology

A new view of the tree of life

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

Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis

(2015) Danilo J. P. Rocha et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

ProDeGe: a computational protocol for fully automated decontamination of genomes

(2015) Kristin Tennessen 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

Structure, variation, and assembly of the root-associated microbiomes of rice

(2015) Joseph Edwards 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

Microbial hotspots and hot moments in soil: Concept & review

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

Mineral protection of soil carbon counteracted by root exudates

(2015) Marco Keiluweit et al.   Nature Climate Change

Genomic Potential for Polysaccharide Deconstruction in Bacteria

(2014) Renaud Berlemont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics

(2014) Christian Rinke et al.   Nature Protocols

Spatial and temporal dynamics of hotspots of enzyme activity in soil as affected by living and dead roots—a soil zymography analysis

(2014) Marie Spohn et al.   PLANT AND SOIL

Niche and host-associated functional signatures of the root surface microbiome

(2014) Maya Ofek-Lalzar et al.   Nature Communications

Stimulation of Different Functional Groups of Bacteria by Various Plant Residues as a Driver of Soil Priming Effect

(2013) Noémie Pascault et al.   ECOSYSTEMS

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

(2013) Etienne Yergeau et al.   ISME Journal

Rhizosphere microbiome assemblage is affected by plant development

(2013) Jacqueline M Chaparro et al.   ISME Journal

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

(2013) Romain L Barnard et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

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

Synthesis and modeling perspectives of rhizosphere priming

(2013) Weixin Cheng et al.   NEW PHYTOLOGIST

Phylogenetic Distribution of Potential Cellulases in Bacteria

(2012) Renaud Berlemont et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing

(2012) Stephanie A. Eichorst et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Manipulating the soil microbiome to increase soil health and plant fertility

(2012) Jacqueline M. Chaparro et al.   BIOLOGY AND FERTILITY OF SOILS

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Sizing up metatranscriptomics

(2012) Mary Ann Moran 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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groups

(2012) S. A. Placella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial control over carbon cycling in soil

(2012) Joshua P. Schimel et al.   Frontiers in Microbiology

Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes

(2011) John T. Wertz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Resource partitioning in relation to cohabitation of Lactobacillus species in the mouse forestomach

(2011) Gerald W Tannock 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

Genome Sequence of the Verrucomicrobium Opitutus terrae PB90-1, an Abundant Inhabitant of Rice Paddy Soil Ecosystems

(2011) M. W. J. van Passel et al.   JOURNAL OF BACTERIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

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

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

tRNADB-CE 2011: tRNA gene database curated manually by experts

(2010) T. Abe et al.   NUCLEIC ACIDS RESEARCH

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

Rhizosphere priming of soil organic matter by bacterial groups in a grassland soil

(2010) Jeffrey A. Bird et al.   SOIL BIOLOGY & BIOCHEMISTRY

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

(2008) Marcel G. A. van der Heijden et al.   ECOLOGY LETTERS

Bacterial quorum sensing and nitrogen cycling in rhizosphere soil

(2008) Kristen M. DeAngelis et al.   FEMS MICROBIOLOGY ECOLOGY

Selective progressive response of soil microbial community to wild oat roots

(2008) Kristen M DeAngelis et al.   ISME Journal

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

(2008) P. P. Chan et al.   NUCLEIC ACIDS RESEARCH