Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria

Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia

(2018) Ruben Garrido-Oter et al.   Cell Host & Microbe

Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa

(2018) Mallory J. Choudoir et al.   ISME Journal

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

(2018) Eric J.B. von Wettberg et al.   Nature Communications

Specificity in Legume-Rhizobia Symbioses

(2017) Mitchell Andrews et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Evolutionary persistence of tripartite integrative and conjugative elements

(2017) Timothy L. Haskett et al.   PLASMID

Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits

(2017) Elena Plekhanova et al.   Scientific Reports

Why prokaryotes have pangenomes

(2017) James O. McInerney et al.   Nature Microbiology

Latitude delineates patterns of biogeography in terrestrial Streptomyces

(2016) Mallory J. Choudoir et al.   ENVIRONMENTAL MICROBIOLOGY

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Global biogeography of Prochlorococcus genome diversity in the surface ocean

(2016) Alyssa G Kent et al.   ISME Journal

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple post-domestication origins ofkabulichickpea through allelic variation in a diversification-associated transcription factor

(2016) R. Varma Penmetsa et al.   NEW PHYTOLOGIST

Assembly and transfer of tripartite integrative and conjugative genetic elements

(2016) Timothy L. Haskett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts

(2016) Philippe Remigi et al.   TRENDS IN MICROBIOLOGY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Continental-scale distributions of dust-associated bacteria and fungi

(2015) Albert Barberán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial Speciation

(2015) B. Jesse Shapiro et al.   Cold Spring Harbor Perspectives in Biology

Genetic and Genomic Diversity Studies of Acacia Symbionts in Senegal Reveal New Species of Mesorhizobium with a Putative Geographical Pattern

(2015) Fatou Diouf et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Prochlorococcus: the structure and function of collective diversity

(2014) Steven J. Biller et al.   NATURE REVIEWS MICROBIOLOGY

Naturalised populations of mesorhizobia in chickpea (Cicer arietinum L.) cropping soils: effects on nodule occupancy and productivity of commercial chickpea

(2014) Natalie V Elias et al.   PLANT AND SOIL

Transfer of noncoding DNA drives regulatory rewiring in bacteria

(2014) Yaara Oren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

Choosing and using diversity indices: insights for ecological applications from the German Biodiversity Exploratories

(2014) E. Kathryn Morris et al.   Ecology and Evolution

Global marine bacterial diversity peaks at high latitudes in winter

(2013) Joshua Ladau et al.   ISME Journal

Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications

(2013) N. DeLeon-Rodriguez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

Mesorhizobium muleiense sp. nov., nodulating with Cicer arietinum L.

(2012) J. J. Zhang et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

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

Widespread fitness alignment in the legume-rhizobium symbiosis

(2012) Maren L. Friesen   NEW PHYTOLOGIST

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Quantifying Phylogenetic Beta Diversity: Distinguishing between ‘True’ Turnover of Lineages and Phylogenetic Diversity Gradients

(2012) Fabien Leprieur et al.   PLoS One

Pole-to-pole biogeography of surface and deep marine bacterial communities

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

In Situ Evolutionary Rate Measurements Show Ecological Success of Recently Emerged Bacterial Hybrids

(2012) V. J. Denef et al.   SCIENCE

Patterns of Gene Flow Define Species of Thermophilic Archaea

(2012) Hinsby Cadillo-Quiroz et al.   PLOS BIOLOGY

Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations

(2011) Y. Boucher et al.   mBio

Biodiverse, a tool for the spatial analysis of biological and related diversity

(2010) Shawn W. Laffan et al.   ECOGRAPHY

Ecosystem-specific selection pressures revealed through comparative population genomics

(2010) M. L. Coleman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A high-resolution assessment on global nitrogen flows in cropland

(2010) Junguo Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bar-Coded Pyrosequencing Reveals Shared Bacterial Community Properties along the Temperature Gradients of Two Alkaline Hot Springs in Yellowstone National Park

(2009) S. R. Miller et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

The Biogeography of Ammonia-Oxidizing Bacterial Communities in Soil

(2009) Noah Fierer et al.   MICROBIAL ECOLOGY

Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes?

(2009) Catherine Masson-Boivin et al.   TRENDS IN MICROBIOLOGY

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

Global inputs of biological nitrogen fixation in agricultural systems

(2008) David F. Herridge et al.   PLANT AND SOIL