Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

Biotic interactions mediate soil microbial feedbacks to climate change

(2015) Thomas W. Crowther et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultra-high-sensitivity stable-isotope probing of rRNA by high-throughput sequencing of isopycnic centrifugation gradients

(2015) Tomo Aoyagi et al.   Environmental Microbiology Reports

Microbial community dynamics alleviate stoichiometric constraints during litter decay

(2014) Christina Kaiser et al.   ECOLOGY LETTERS

Effect of soil sieving on respiration induced by low-molecular-weight substrates

(2014) Rahul Datta et al.   International Agrophysics

Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

(2014) Y. Verastegui et al.   mBio

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Climate change alters ecological strategies of soil bacteria

(2013) Sarah E. Evans et al.   ECOLOGY LETTERS

Kallotenue papyrolyticum gen. nov., sp. nov., a cellulolytic and filamentous thermophile that represents a novel lineage (Kallotenuales ord. nov., Kallotenuaceae fam. nov.) within the class Chloroflexia

(2013) J. K. Cole et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Agricultural Management and Labile Carbon Additions Affect Soil Microbial Community Structure and Interact with Carbon and Nitrogen Cycling

(2013) Sean T. Berthrong et al.   MICROBIAL ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States

(2013) N. Fierer et al.   SCIENCE

Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

(2013) D. P. R. Herlemann et al.   mBio

Global soil carbon projections are improved by modelling microbial processes

(2013) William R. Wieder et al.   Nature Climate Change

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

(2013) Sara C Di Rienzi et al.   eLife

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

(2013) Laura A Hug et al.   Microbiome

Phylogenetic Distribution of Potential Cellulases in Bacteria

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

Roseimicrobium gellanilyticum gen. nov., sp. nov., a new member of the class Verrucomicrobiae

(2012) S. Otsuka et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

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

Integrating microbial ecology into ecosystem models: challenges and priorities

(2011) Kathleen K. Treseder et al.   BIOGEOCHEMISTRY

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

(2011) Gaddy T. Bergmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

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

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

adephylo: new tools for investigating the phylogenetic signal in biological traits

(2010) Thibaut Jombart et al.   BIOINFORMATICS

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

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Switchgrass as an energy crop for biofuel production: A review of its ligno-cellulosic chemical properties

(2010) Kasi David et al.   Energy & Environmental Science

Soil-carbon response to warming dependent on microbial physiology

(2010) Steven D. Allison et al.   Nature Geoscience

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

When metagenomics meets stable-isotope probing: progress and perspectives

(2010) Yin Chen et al.   TRENDS IN MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Infernal 1.0: inference of RNA alignments

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

Chemical compositions of four switchgrass populations

(2009) Jinhua Yan et al.   BIOMASS & BIOENERGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Testing the functional significance of microbial community composition

(2009) Michael S. Strickland et al.   ECOLOGY

Metabolic responses of novel cellulolytic and saccharolytic agricultural soil Bacteria to oxygen

(2009) Stefanie Schellenberger et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial communities and their relevance for ecosystem models: Decomposition as a case study

(2009) Krista L. McGuire et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil carbon stocks in experimental mesocosms are dependent on the rate of labile carbon, nitrogen and phosphorus inputs to soils

(2008) M. A. Bradford et al.   FUNCTIONAL ECOLOGY

Evidence for the functional significance of diazotroph community structure in soil

(2008) Shi-Fang Hsu et al.   ISME Journal

Microbial utilization and mineralization of [14C]glucose added in six orders of concentration to soil

(2008) Katja Schneckenberger et al.   SOIL BIOLOGY & BIOCHEMISTRY

The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains

(2008) Pablo Yarza et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY