Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Global diversity and biogeography of deep-sea pelagic prokaryotes

(2015) Guillem Salazar et al.   ISME Journal

Conservation of dissolved organic matter molecular composition during mixing of the deep water masses of the northeast Atlantic Ocean

(2015) Roberta L. Hansman et al.   MARINE CHEMISTRY

Dilution limits dissolved organic carbon utilization in the deep ocean

(2015) J. M. Arrieta et al.   SCIENCE

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Oceanographic structure drives the assembly processes of microbial eukaryotic communities

(2014) Adam Monier et al.   ISME Journal

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea

(2014) John Larsson et al.   ISME Journal

Placing Environmental Next-Generation Sequencing Amplicons from Microbial Eukaryotes into a Phylogenetic Context

(2014) Micah Dunthorn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic and Metabolic Diversity of Marine Group I Thaumarchaeota in the Mesopelagic of Two Subtropical Gyres

(2014) Brandon K. Swan et al.   PLoS One

Bacterial Communities Associated with Subsurface Geochemical Processes in Continental Serpentinite Springs

(2013) William J. Brazelton et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Ecology of marine Bacteroidetes: a comparative genomics approach

(2013) Beatriz Fernández-Gómez et al.   ISME Journal

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

(2013) Jianjun Wang et al.   ISME Journal

Microbial control of the dark end of the biological pump

(2013) Gerhard J. Herndl et al.   Nature Geoscience

Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

(2013) Maria W. Smith et al.   Frontiers in Microbiology

Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA

(2013) Bibiana G. Crespo et al.   MicrobiologyOpen

Lineage-dependent ecological coherence in bacteria

(2012) Alexander F. Koeppel et al.   FEMS MICROBIOLOGY ECOLOGY

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

(2012) Lisa Zeigler Allen et al.   ISME Journal

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

Phylogenetic conservatism of functional traits in microorganisms

(2012) Adam C Martiny et al.   ISME Journal

Novel animal papillomavirus sequences and accurate phylogenetic placement

(2012) Beatriz Mengual-Chuliá et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Role for urea in nitrification by polar marine Archaea

(2012) L. Alonso-Saez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How to measure and test phylogenetic signal

(2012) Tamara Münkemüller et al.   Methods in Ecology and Evolution

Microbial oceanography of the dark ocean's pelagic realm

(2011) Javier Arístegui et al.   LIMNOLOGY AND OCEANOGRAPHY

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   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

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

(2010) HÉLÈNE AGOGUÉ et al.   MOLECULAR ECOLOGY

The ecological coherence of high bacterial taxonomic ranks

(2010) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

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

Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment

(2010) Emiley A. Eloe et al.   Environmental Microbiology Reports

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

Comparison of free-living, suspended particle, and aggregate-associated Bacterial and Archaeal communities in the Laptev Sea

(2009) CTE Kellogg et al.   AQUATIC MICROBIAL ECOLOGY

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea

(2009) Jean-François Ghiglione et al.   FEMS MICROBIOLOGY LETTERS

Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities

(2009) Anders F Andersson et al.   ISME Journal

The genomic basis of trophic strategy in marine bacteria

(2009) F. M. Lauro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

Phylocom: software for the analysis of phylogenetic community structure and trait evolution

(2008) Campbell O. Webb et al.   BIOINFORMATICS

Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter

(2008) Elena Ivars-Martinez et al.   ISME Journal

Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)

(2008) J. M. Gonzalez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA