Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO2concentrations

(2016) Alexander J. Probst et al.   ENVIRONMENTAL MICROBIOLOGY

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

(2016) Richard Allen White et al.   mSystems

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

XoxFencoding an alternative methanol dehydrogenase is widespread in coastal marine environments

(2015) Martin Taubert et al.   ENVIRONMENTAL MICROBIOLOGY

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

(2015) Laura A. Hug et al.   ENVIRONMENTAL MICROBIOLOGY

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment

(2015) Özge Eyice et al.   ISME Journal

Aquifer environment selects for microbial species cohorts in sediment and groundwater

(2015) Laura A Hug et al.   ISME Journal

Smooth brome invasion increases rare soil bacterial species prevalence, bacterial species richness and evenness

(2015) Candace L. Piper et al.   JOURNAL OF ECOLOGY

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

(2015) Jenni Hultman et al.   NATURE

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

Just add lanthanides

(2015) E. Skovran et al.   SCIENCE

Untargeted soil metabolomics methods for analysis of extractable organic matter

(2015) Tami L. Swenson et al.   SOIL BIOLOGY & BIOCHEMISTRY

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant

(2015) Brandon Brooks et al.   Frontiers in Microbiology

Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics

(2015) Tom O. Delmont et al.   Frontiers in Microbiology

Bouncing Back: Plant-Associated Soil Microbes Respond Rapidly to Prairie Establishment

(2015) Anna J. Herzberger et al.   PLoS One

PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference

(2014) Jan T. Keltjens et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

DFT Study of the Active Site of the XoxF-Type Natural, Cerium-Dependent Methanol Dehydrogenase Enzyme

(2014) Justin A. Bogart et al.   CHEMISTRY-A EUROPEAN JOURNAL

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

(2014) Suzanne M. Prober et al.   ECOLOGY LETTERS

Linking soil bacterial biodiversity and soil carbon stability

(2014) Rebecca L Mau et al.   ISME Journal

Elevated temperature alters proteomic responses of individual organisms within a biofilm community

(2014) Annika C Mosier et al.   ISME Journal

The Expanded Diversity of Methylophilaceae from Lake Washington through Cultivation and Genomic Sequencing of Novel Ecotypes

(2014) David A. C. Beck et al.   PLoS One

Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

(2014) Y. Verastegui et al.   mBio

Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

(2014) Zhou Li et al.   Nature Communications

Novel Cultivation-Based Approach To Understanding the Miscellaneous Crenarchaeotic Group (MCG) Archaea from Sedimentary Ecosystems

(2013) Emma J. Gagen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics

(2013) Chengwei Luo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sipros/ProRata: a versatile informatics system for quantitative community proteomics

(2013) Yingfeng Wang et al.   BIOINFORMATICS

Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil

(2013) Steven J. Blazewicz et al.   ECOLOGY

Rare earth metals are essential for methanotrophic life in volcanic mudpots

(2013) Arjan Pol et al.   ENVIRONMENTAL MICROBIOLOGY

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

Short-term utilization of carbon by the soil microbial community under future climatic conditions in a temperate heathland

(2013) Sabine Reinsch et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil phosphorus depletion and shifts in plant communities change bacterial community structure in a long-term grassland management trial

(2013) Karen L. Adair et al.   Environmental Microbiology Reports

Exhaustive database searching for amino acid mutations in proteomes

(2012) Doug Hyatt et al.   BIOINFORMATICS

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs

(2012) Astrid Stacheter et al.   ISME Journal

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments

(2012) Kyoko Kubo et al.   ISME Journal

Soil Fertilization Leads to a Decline in Between-Samples Variability of Microbial Community δ13C Profiles in a Grassland Fertilization Experiment

(2012) Stavros D. Veresoglou et al.   PLoS One

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Synthesis of Methylphosphonic Acid by Marine Microbes: A Source for Methane in the Aerobic Ocean

(2012) W. W. Metcalf et al.   SCIENCE

Sensitivity of soil respiration and microbial communities to altered snowfall

(2012) Zachary T. Aanderud et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial control over carbon cycling in soil

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

Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration

(2011) Natasha C. Banning et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Soil microbial community response to drying and rewetting stress: does historical precipitation regime matter?

(2011) Sarah E. Evans et al.   BIOGEOCHEMISTRY

amoA-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoA genes from soils of four different geographic regions

(2011) Michael Pester et al.   ENVIRONMENTAL MICROBIOLOGY

Modularity of methylotrophy, revisited

(2011) Ludmila Chistoserdova   ENVIRONMENTAL MICROBIOLOGY

Soil characteristics more strongly influence soil bacterial communities than land-use type

(2011) Eiko E. Kuramae et al.   FEMS MICROBIOLOGY ECOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

(2011) Katherine C. Goldfarb et al.   Frontiers in Microbiology

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

Microbial uptake of low-molecular-weight organic substances out-competes sorption in soil

(2010) H. Fischer et al.   EUROPEAN JOURNAL OF SOIL SCIENCE

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Aerobic methanol-oxidizingBacteria in soil

(2009) Steffen Kolb   FEMS MICROBIOLOGY LETTERS

Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland

(2009) Karelyn Cruz-Martínez et al.   ISME Journal

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

(2009) N. Delmotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environmental, genomic and taxonomic perspectives on methanotrophicVerrucomicrobia

(2009) Huub J. M. Op den Camp et al.   Environmental Microbiology Reports

Aerobic production of methane in the sea

(2008) David M. Karl et al.   Nature Geoscience