The biogeography of Streptomyces in New Zealand enabled by high‐throughput sequencing of genus‐specific rpoB amplicons

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

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

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Do latitudinal gradients exist in New Zealand stream invertebrate metacommunities?

(2018) Jonathan D. Tonkin et al.   PeerJ

Ecological implications of hypoxia-triggered shifts in secondary metabolism

(2017) Kelley A. Gallagher et al.   ENVIRONMENTAL MICROBIOLOGY

Plant Community Richness Mediates Inhibitory Interactions and Resource Competition between Streptomyces and Fusarium Populations in the Rhizosphere

(2017) Adil Essarioui et al.   MICROBIAL ECOLOGY

The preservation of microbial DNA in archived soils of various genetic types

(2017) Ekaterina A. Ivanova et al.   PLoS One

Genome Surfing As Driver of Microbial Genomic Diversity

(2017) Mallory J. Choudoir et al.   TRENDS IN MICROBIOLOGY

Plenty Is No Plague: Streptomyces Symbiosis with Crops

(2017) Thomas Rey et al.   TRENDS IN PLANT SCIENCE

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

(2017) Bradon R. McDonald et al.   mBio

Palaeoclimate explains a unique proportion of the global variation in soil bacterial communities

(2017) Manuel Delgado-Baquerizo et al.   Nature Ecology & Evolution

Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences

(2017) Sanjay Antony-Babu et al.   Scientific Reports

Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis

(2016) David P. Labeda et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Latitude delineates patterns of biogeography in terrestrial Streptomyces

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

Widespread interspecies homologous recombination reveals reticulate evolution within the genus Streptomyces

(2016) Kun Cheng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Promiscuous Pathogenicity Islands and Phylogeny of Pathogenic Streptomyces spp.

(2016) Yucheng Zhang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

(2016) Cheryl P. Andam et al.   mBio

How to make a sex chromosome

(2016) Alison E. Wright et al.   Nature Communications

codyn: Anrpackage of community dynamics metrics

(2016) Lauren M. Hallett et al.   Methods in Ecology and Evolution

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Expanding the UniFrac Toolbox

(2016) Ruth G. Wong et al.   PLoS One

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

From regional to global patterns in vertebrate scavenger communities subsidized by big game hunting

(2015) Patricia Mateo-Tomás et al.   DIVERSITY AND DISTRIBUTIONS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Atmospheric Dispersal of Bioactive Streptomyces albidoflavus Strains Among Terrestrial and Marine Environments

(2015) Aida Sarmiento-Vizcaíno et al.   MICROBIAL ECOLOGY

Natural products in soil microbe interactions and evolution

(2015) Matthew F. Traxler et al.   NATURAL PRODUCT REPORTS

The importance of soil archives for microbial ecology

(2015) Jan Dolfing et al.   NATURE REVIEWS MICROBIOLOGY

Estimating and mapping ecological processes influencing microbial community assembly

(2015) James C. Stegen et al.   Frontiers in Microbiology

mice: Multivariate Imputation by Chained Equations inR

(2015) Stef van Buuren et al.   Journal of Statistical Software

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach

(2014) Gabriel Renaud et al.   BIOINFORMATICS

The importance of sample archiving in microbial ecology

(2014) S. Craig Cary et al.   NATURE REVIEWS MICROBIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2013) J. Zhang et al.   BIOINFORMATICS

Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies

(2013) Anne Chao et al.   ECOLOGICAL MONOGRAPHS

Taxonomic and functional diversity ofStreptomycesin a forest soil

(2013) Cyril Bontemps et al.   FEMS MICROBIOLOGY LETTERS

Species matter: the role of competition in the assembly of congeneric bacteria

(2013) Alexander F Koeppel et al.   ISME Journal

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Resource Use of Soilborne Streptomyces Varies with Location, Phylogeny, and Nitrogen Amendment

(2013) Daniel C. Schlatter et al.   MICROBIAL ECOLOGY

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

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

Classification of Streptomyces phylogroup pratensis (Doroghazi and Buckley, 2010) based on genetic and phenotypic evidence, and proposal of Streptomyces pratensis sp. nov.

(2013) Xiaoying Rong et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Effects of plant host species and plant community richness on streptomycete community structure

(2012) Matthew G. Bakker et al.   FEMS MICROBIOLOGY ECOLOGY

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

The vegetation cover of New Zealand at the Last Glacial Maximum

(2012) Rewi Newnham et al.   QUATERNARY SCIENCE REVIEWS

Ecological Populations of Bacteria Act as Socially Cohesive Units of Antibiotic Production and Resistance

(2012) O. X. Cordero et al.   SCIENCE

Dispersal limitation and the assembly of soilActinobacteriacommunities in a long-term chronosequence

(2012) Sarah D. Eisenlord et al.   Ecology and Evolution

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Refugia: identifying and understanding safe havens for biodiversity under climate change

(2011) Gunnar Keppel et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils

(2011) Heiko Nacke et al.   PLoS One

Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA–DNA hybridization, validating the MLSA scheme for systematics of the whole genus

(2011) Xiaoying Rong et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Structure and Evolution of Streptomyces Interaction Networks in Soil and In Silico

(2011) Kalin Vetsigian et al.   PLOS BIOLOGY

Using null models to disentangle variation in community dissimilarity from variation in α-diversity

(2011) Jonathan M. Chase et al.   Ecosphere

Picante: R tools for integrating phylogenies and ecology

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

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Global patterns in the biogeography of bacterial taxa

(2010) Diana R. Nemergut et al.   ENVIRONMENTAL MICROBIOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

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

New Zealand phylogeography: evolution on a small continent

(2009) GRAHAM P. WALLIS et al.   MOLECULAR ECOLOGY

Phylogenetic Resolution and Quantifying the Phylogenetic Diversity and Dispersion of Communities

(2009) Nathan G. Swenson   PLoS One

Hidden levels of phylodiversity in Antarctic green algae: further evidence for the existence of glacial refugia

(2009) A. De Wever et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genetic and phenotypic evidence for Streptomyces griseus ecovars isolated from a beach and dune sand system

(2008) Sanjay Antony-Babu et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Resource Amendments Influence Density and Competitive Phenotypes of Streptomyces in Soil

(2008) Daniel Schlatter et al.   MICROBIAL ECOLOGY

Using theTxtABOperon to Quantify PathogenicStreptomycesin Potato Tubers and Soil

(2008) Xinshun Qu et al.   PHYTOPATHOLOGY

Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity

(2008) Vesela A. Tzeneva et al.   RESEARCH IN MICROBIOLOGY

Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment

(2008) Ian M. Clark et al.   SOIL BIOLOGY & BIOCHEMISTRY

Phylogeographic insights into cryptic glacial refugia

(2008) J PROVAN et al.   TRENDS IN ECOLOGY & EVOLUTION

The rpoB gene as a tool for clinical microbiologists

(2008) Toïdi Adékambi et al.   TRENDS IN MICROBIOLOGY