Microbial Gene Abundance and Expression Patterns across a River to Ocean Salinity Gradient

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

(2014) Chris L. Dupont et al.   PLoS One

Metatranscriptomic Analyses of Plankton Communities Inhabiting Surface and Subpycnocline Waters of the Chesapeake Bay during Oxic-Anoxic-Oxic Transitions

(2013) Ian Hewson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

(2013) Alexander Eiler et al.   ENVIRONMENTAL MICROBIOLOGY

Dark Carbon Fixation in the Columbia River’s Estuarine Turbidity Maxima: Molecular Characterization of Red-Type cbbL Genes and Measurement of DIC Uptake Rates in Response to Added Electron Donors

(2013) S. L. Bräuer et al.   Estuaries and Coasts

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin

(2013) Caroline S Fortunato et al.   ISME Journal

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

(2013) Sangita Ganesh et al.   ISME Journal

Glycolytic strategy as a tradeoff between energy yield and protein cost

(2013) A. Flamholz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Manganese uptake in marine bacteria; the novel MntX transporter is widespread in Roseobacters, Vibrios, Alteromonadales and the SAR11 and SAR116 clades

(2012) Robert T Green et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Draft genome sequence of strain HIMB100, a cultured representative of the SAR116 clade of marine Alphaproteobacteria

(2012) Jana Grote et al.   Standards in Genomic Sciences

Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem

(2011) Seungdae Oh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

(2011) Frank J. Stewart et al.   ENVIRONMENTAL MICROBIOLOGY

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

Spatial variability overwhelms seasonal patterns in bacterioplankton communities across a river to ocean gradient

(2011) Caroline S Fortunato et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Bacterioplankton Community Variation Across River to Ocean Environmental Gradients

(2011) Caroline S. Fortunato et al.   MICROBIAL ECOLOGY

A Guide to the Natural History of Freshwater Lake Bacteria

(2011) R. J. Newton et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

IMG/M: the integrated metagenome data management and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River

(2011) Rohit Ghai et al.   PLoS One

Bacteriochlorophyll and community structure of aerobic anoxygenic phototrophic bacteria in a particle-rich estuary

(2010) Matthew T Cottrell et al.   ISME Journal

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

(2010) Frank J Stewart et al.   ISME Journal

Complete Genome Sequence of "Candidatus Puniceispirillum marinum" IMCC1322, a Representative of the SAR116 Clade in the Alphaproteobacteria

(2010) H.-M. Oh et al.   JOURNAL OF BACTERIOLOGY

River Influences on Shelf Ecosystems: Introduction and synthesis

(2010) B. M. Hickey et al.   JOURNAL OF GEOPHYSICAL RESEARCH

Seasonal Changes in Bacterial and Archaeal Gene Expression Patterns across Salinity Gradients in the Columbia River Coastal Margin

(2010) Maria W. Smith et al.   PLoS One

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

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY