Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism

Decline in global oceanic oxygen content during the past five decades

(2017) Sunke Schmidtko et al.   NATURE

Geochemical evidence for cryptic sulfur cycling in salt marsh sediments

(2016) Jennifer V. Mills et al.   EARTH AND PLANETARY SCIENCE LETTERS

Microbial Community Composition in the Marine Sediments of Jeju Island: Next-Generation Sequencing Surveys

(2016) Heebok Choi et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea

(2016) Qi Ye et al.   MicrobiologyOpen

Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling

(2015) Markus V. Lindh et al.   ENVIRONMENTAL MICROBIOLOGY

Oxygenation of anoxic sediments triggers hatching of zooplankton eggs

(2015) Elias Broman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities

(2015) Markus V. Lindh et al.   Frontiers in Microbiology

An Experiment with Forced Oxygenation of the Deepwater of the Anoxic By Fjord, Western Sweden

(2014) Anders Stigebrandt et al.   AMBIO

DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies

(2014) Luisa W. Hugerth et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Microbial consumption of zero-valence sulfur in marine benthic habitats

(2014) Petra Pjevac et al.   ENVIRONMENTAL MICROBIOLOGY

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

(2014) Jennifer D Rocca et al.   ISME Journal

Deoxygenation of the Baltic Sea during the last century

(2014) J. Carstensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data

(2013) C. E. Robertson et al.   BIOINFORMATICS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Bacteria Contribute to Sediment Nutrient Release and Reflect Progressed Eutrophication-Driven Hypoxia in an Organic-Rich Continental Sea

(2013) Hanna Sinkko et al.   PLoS One

Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags

(2012) Yu Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Biodiversity, metabolism and applications of acidophilic sulfur-metabolizing microorganisms

(2012) Mark Dopson et al.   ENVIRONMENTAL MICROBIOLOGY

Draft Genome Sequence of the Sulfur-Oxidizing Bacterium "Candidatus Sulfurovum sediminum" AR, Which Belongs to the Epsilonproteobacteria

(2012) S.-J. Park et al.   JOURNAL OF BACTERIOLOGY

Save the Baltic Sea

(2012) Daniel J. Conley   NATURE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Impact of climate change on the Baltic Sea ecosystem over the past 1,000 years

(2012) Karoline Kabel et al.   Nature Climate Change

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

(2011) Othilde Håvelsrud et al.   BMC MICROBIOLOGY

Hypoxia Is Increasing in the Coastal Zone of the Baltic Sea

(2011) Daniel J. Conley et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2011) Daniel PR Herlemann et al.   ISME Journal

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing

(2011) Henk Bolhuis et al.   ISME Journal

Measuring unbiased metatranscriptomics in suboxic waters of the central Baltic Sea using a new in situ fixation system

(2011) Janie Feike et al.   ISME Journal

16S rRNA-based bacterial diversity in the organic-rich sediments underlying oxygen-deficient waters of the eastern Arabian Sea

(2011) Baby Divya et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

(2010) D. E. Canfield et al.   SCIENCE

Archaeal and Bacterial Communities Respond Differently to Environmental Gradients in Anoxic Sediments of a California Hypersaline Lake, the Salton Sea

(2009) B. K. Swan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

(2009) Raquel Quatrini et al.   BMC GENOMICS

Contrasts between habitat generalists and specialists: an empirical extension to the basic metacommunity framework

(2009) Shubha N. Pandit et al.   ECOLOGY

Expression of genes for sulfur oxidation in the intracellular chemoautotrophic symbiont of the deep-sea bivalve Calyptogena okutanii

(2009) Maiko Harada et al.   EXTREMOPHILES

Microbial sulfide oxidation in the oxic–anoxic transition zone of freshwater sediment: involvement of lithoautotrophic Magnetospirillum strain J10

(2009) Jeanine S. Geelhoed et al.   FEMS MICROBIOLOGY ECOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Active bacterial community structure along vertical redox gradients in Baltic Sea sediment

(2008) Anna Edlund et al.   ENVIRONMENTAL MICROBIOLOGY

Spreading Dead Zones and Consequences for Marine Ecosystems

(2008) R. J. Diaz et al.   SCIENCE