Rhizosphere heterogeneity shapes abundance and activity of sulfur-oxidizing bacteria in vegetated salt marsh sediments

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

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

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

Methane-Carbon Flow into the Benthic Food Web at Cold Seeps – A Case Study from the Costa Rica Subduction Zone

(2013) Helge Niemann et al.   PLoS One

Phylogenetic diversity and functional gene patterns of sulfur-oxidizing subseafloor Epsilonproteobacteria in diffuse hydrothermal vent fluids

(2013) Nancy H. Akerman et al.   Frontiers in Microbiology

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Chemolithoautotrophic denitrification of epsilonproteobacteria in marine pelagic redox gradients

(2012) Christian G. Bruckner et al.   ENVIRONMENTAL MICROBIOLOGY

Analysis of community composition of sulfur-oxidizing bacteria in hypersaline and soda lakes usingsoxB as a functional molecular marker

(2012) Tatjana P. Tourova et al.   FEMS MICROBIOLOGY ECOLOGY

Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes

(2012) Sabine Lenk et al.   ISME Journal

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Use of computed tomography imaging for quantifying coarse roots, rhizomes, peat, and particle densities in marsh soils

(2011) Earl Davey et al.   ECOLOGICAL APPLICATIONS

Comparative survey of potential nitrate and sulfate reduction rates in aquatic sediments

(2011) Anniet M. Laverman et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

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

(2011) Daniel McDonald et al.   ISME Journal

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean

(2010) Michael Hügler et al.   Annual Review of Marine Science

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Novel groups of Gammaproteobacteria catalyse sulfur oxidation and carbon fixation in a coastal, intertidal sediment

(2010) Sabine Lenk et al.   ENVIRONMENTAL MICROBIOLOGY

Functional genes as markers for sulfur cycling and CO2 fixation in microbial communities of hydrothermal vents of the Logatchev field

(2010) Michael Hügler et al.   FEMS MICROBIOLOGY ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Epsilonproteobacteria Represent the Major Portion of Chemoautotrophic Bacteria in Sulfidic Waters of Pelagic Redoxclines of the Baltic and Black Seas

(2008) J. Grote et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

(2008) Alexander Loy et al.   ENVIRONMENTAL MICROBIOLOGY

Thiohalorhabdus denitrificans gen. nov., sp. nov., an extremely halophilic, sulfur-oxidizing, deep-lineage gammaproteobacterium from hypersaline habitats

(2008) D. Yu. Sorokin et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics