Sediments and Soils Act as Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River

Evaluation of water sampling methodologies for amplicon-based characterization of bacterial community structure

(2015) Christopher Staley et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Geographic isolation of Escherichia coli genotypes in sediments and water of the Seven Mile Creek — A constructed riverine watershed

(2015) Ramyavardhanee Chandrasekaran et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River

(2015) Christopher Staley et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds

(2014) Gavin Lear et al.   ISME Journal

Characteristics of bacterial community in the water and surface sediment of the Yellow River, China, the largest turbid river in the world

(2014) Na Xia et al.   JOURNAL OF SOILS AND SEDIMENTS

Spatial Ecology of Bacteria at the Microscale in Soil

(2014) Xavier Raynaud et al.   PLoS One

Wastewater Treatment Effluent Reduces the Abundance and Diversity of Benthic Bacterial Communities in Urban and Suburban Rivers

(2013) Bradley Drury et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of bacterial communities in soil and sediment of a created riverine wetland complex using high-throughput 16S rRNA amplicon sequencing

(2013) Teele Ligi et al.   ECOLOGICAL ENGINEERING

Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients

(2013) Melanie Y. Sun et al.   ENVIRONMENTAL MICROBIOLOGY

Effects of environmental variation and spatial distance on Bacteria, Archaea and viruses in sub-polar and arctic waters

(2013) Christian Winter et al.   ISME Journal

Application of Illumina next-generation sequencing to characterize the bacterial community of the Upper Mississippi River

(2013) C. Staley et al.   JOURNAL OF APPLIED MICROBIOLOGY

A Microbial Signature Approach to Identify Fecal Pollution in the Waters Off an Urbanized Coast of Lake Michigan

(2013) Ryan J. Newton et al.   MICROBIAL ECOLOGY

Terrestrial Runoff Controls the Bacterial Community Composition of Biofilms along a Water Quality Gradient in the Great Barrier Reef

(2012) Verena Witt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Airborne hyperspectral remote sensing to assess spatial distribution of water quality characteristics in large rivers: The Mississippi River and its tributaries in Minnesota

(2012) Leif G. Olmanson et al.   REMOTE SENSING OF ENVIRONMENT

Assessment of sources of human pathogens and fecal contamination in a Florida freshwater lake

(2012) Christopher Staley et al.   WATER RESEARCH

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

(2011) Thomas M. Gihring et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2011) Caroline S Fortunato et al.   ISME Journal

The Western English Channel contains a persistent microbial seed bank

(2011) J Gregory Caporaso et al.   ISME Journal

Defining seasonal marine microbial community dynamics

(2011) Jack A Gilbert et al.   ISME Journal

Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors

(2011) Aline Frossard et al.   ISME Journal

Bacterioplankton Community Variation Across River to Ocean Environmental Gradients

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

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Local and regional factors influencing bacterial community assembly

(2011) Eva S. Lindström et al.   Environmental Microbiology Reports

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Contaminants in the Upper Mississippi River: historic trends, responses to regulatory controls, and emerging concerns

(2010) James G. Wiener et al.   HYDROBIOLOGIA

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

Testing the functional significance of microbial community composition

(2009) Michael S. Strickland et al.   ECOLOGY

The seasonal structure of microbial communities in the Western English Channel

(2009) Jack A. Gilbert et al.   ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

A sediment record of trace metal loadings in the Upper Mississippi River

(2009) Steven J. Balogh et al.   JOURNAL OF PALEOLIMNOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH