Spatiotemporal Characterization of San Francisco Bay Denitrifying Communities: a Comparison of nirK and nirS Diversity and Abundance

Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers

(2016) Decleyre Helen et al.   BMC GENOMICS

Higher diversity and abundance of denitrifying microorganisms in environments than considered previously

(2015) Wei Wei et al.   ISME Journal

Seasonal variation in denitrification and dissimilatory nitrate reduction to ammonia process rates and corresponding key functional genes along an estuarine nitrate gradient

(2015) Cindy J. Smith et al.   Frontiers in Microbiology

Nutrient Fluxes from Sediments in the San Francisco Bay Delta

(2014) Jeffrey C. Cornwell et al.   Estuaries and Coasts

Diversity and Distribution of nirK-Harboring Denitrifying Bacteria in the Water Column in the Yellow River Estuary

(2014) Jing Li et al.   MICROBES AND ENVIRONMENTS

Spatiotemporal Relationships Between the Abundance, Distribution, and Potential Activities of Ammonia-Oxidizing and Denitrifying Microorganisms in Intertidal Sediments

(2014) Jason M. Smith et al.   MICROBIAL ECOLOGY

Intergenomic Comparisons Highlight Modularity of the Denitrification Pathway and Underpin the Importance of Community Structure for N2O Emissions

(2014) Daniel R. H. Graf et al.   PLoS One

Nitrifying and denitrifying microbial communities and their relationship to nutrient fluxes and sediment geochemistry in the Derwent Estuary, Tasmania

(2013) GCJ Abell et al.   AQUATIC MICROBIAL ECOLOGY

Diversity, abundance, and distribution of NO-forming nitrite reductase-encoding genes in deep-sea subsurface sediments of the South China Sea

(2013) M. Li et al.   Geobiology

Quantity and quality of organic matter (detritus) drives N2effluxes (net denitrification) across seasons, benthic habitats, and estuaries

(2013) Bradley D. Eyre et al.   GLOBAL BIOGEOCHEMICAL CYCLES

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

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

FunGene: the functional gene pipeline and repository

(2013) Jordan A. Fish et al.   Frontiers in Microbiology

Functional gene pyrosequencing and network analysis: an approach to examine the response of denitrifying bacteria to increased nitrogen supply in salt marsh sediments

(2013) Jennifer L. Bowen et al.   Frontiers in Microbiology

Transitions in nirS-type denitrifier diversity, community composition, and biogeochemical activity along the Chesapeake Bay estuary

(2013) Christopher A. Francis et al.   Frontiers in Microbiology

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Distribution of denitrifying bacterial communities in the stratified water column and sediment–water interface in two freshwater lakes and the Baltic Sea

(2010) Ok-Sun Kim et al.   AQUATIC ECOLOGY

Picante: R tools for integrating phylogenies and ecology

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

The Effects of Salinity on Nitrogen Losses from an Oligohaline Estuarine Sediment

(2010) Anne E. Giblin et al.   Estuaries and Coasts

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Ecological and evolutionary factors underlying global and local assembly of denitrifier communities

(2010) Christopher M Jones et al.   ISME Journal

Denitrifier abundance and activity across the San Francisco Bay estuary

(2010) Annika C. Mosier et al.   Environmental Microbiology Reports

Changes in Benthic Denitrification, Nitrate Ammonification, and Anammox Process Rates and Nitrate and Nitrite Reductase Gene Abundances along an Estuarine Nutrient Gradient (the Colne Estuary, United Kingdom)

(2009) L. F. Dong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Nitrifier and denitrifier molecular operational taxonomic unit compositions from sites of a freshwater estuary of Chesapeake Bay

(2009) Caroline S. Fortunato et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary

(2009) Guy C J Abell et al.   ISME Journal

Denitrifying Bacterial Community Composition Changes Associated with Stages of Denitrification in Oxygen Minimum Zones

(2009) A. Jayakumar et al.   MICROBIAL ECOLOGY

Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil

(2009) Megumi Yoshida et al.   SOIL BIOLOGY & BIOCHEMISTRY

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary

(2008) Annika C. Mosier et al.   ENVIRONMENTAL MICROBIOLOGY

Sediment denitrifier community composition andnirSgene expression investigated with functional gene microarrays

(2008) Silvia E. Bulow et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and Distribution of Sediment NirS-Encoding Bacterial Assemblages in Response to Environmental Gradients in the Eutrophied Jiaozhou Bay, China

(2008) Hongyue Dang et al.   MICROBIAL ECOLOGY

Phylogenetic Analysis of Nitrite, Nitric Oxide, and Nitrous Oxide Respiratory Enzymes Reveal a Complex Evolutionary History for Denitrification

(2008) Christopher M. Jones et al.   MOLECULAR BIOLOGY AND EVOLUTION