The deep-sea glass sponge L ophophysema eversa harbours potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Sponge symbionts and the marine P cycle

(2015) Albert S. Colman   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges

(2015) Fan Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lifestyle Evolution in Cyanobacterial Symbionts of Sponges

(2015) Ilia Burgsdorf et al.   mBio

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange

(2015) Cara L. Fiore et al.   Frontiers in Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge

(2014) Ren-Mao Tian et al.   ENVIRONMENTAL MICROBIOLOGY

Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality

(2014) Fan Zhang et al.   FEMS MICROBIOLOGY ECOLOGY

Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

(2014) Ren-Mao Tian et al.   mBio

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

Allying with armored snails: the complete genome of gammaproteobacterial endosymbiont

(2013) Satoshi Nakagawa et al.   ISME Journal

‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity

(2013) Simon J McIlroy et al.   ISME Journal

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

The Genome of Nitrospina gracilis Illuminates the Metabolism and Evolution of the Major Marine Nitrite Oxidizer

(2013) Sebastian Lücker et al.   Frontiers in Microbiology

Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, "Candidatus Nitrosopumilus sediminis" AR2, from Svalbard in the Arctic Circle

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

Genome Sequence of "Candidatus Nitrosopumilus salaria" BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary

(2012) A. C. Mosier et al.   JOURNAL OF BACTERIOLOGY

Draft Genome Sequence of an Ammonia-Oxidizing Archaeon, "Candidatus Nitrosopumilus koreensis" AR1, from Marine Sediment

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Bacterial and Archaeal Symbionts in the South China Sea Sponge Phakellia fusca: Community Structure, Relative Abundance, and Ammonia-Oxidizing Populations

(2012) Minqi Han et al.   MARINE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genomic insights into the marine sponge microbiome

(2012) Ute Hentschel et al.   NATURE REVIEWS MICROBIOLOGY

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Pyrosequencing of Bacterial Symbionts within Axinella corrugata Sponges: Diversity and Seasonal Variability

(2012) James R. White et al.   PLoS One

Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

(2012) L. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial distribution of prokaryotic symbionts and ammoxidation, denitrifier bacteria in marine sponge Astrosclera willeyana

(2012) Zhenya Yang et al.   Scientific Reports

Complete genome sequence of Thioalkalivibrio sp. K90mix

(2012) Gerard Muyzer et al.   Standards in Genomic Sciences

Sponge-specific clusters revisited: a comprehensive phylogeny of sponge-associated microorganisms

(2011) Rachel L. Simister et al.   ENVIRONMENTAL MICROBIOLOGY

Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges

(2011) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Complete genome sequence of Thioalkalivibrio “sulfidophilus” HL-EbGr7

(2011) Gerard Muyzer et al.   Standards in Genomic Sciences

Enrichment and Physiological Characterization of a Novel Nitrospira-Like Bacterium Obtained from a Marine Sponge

(2010) S. Off et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

(2010) On On Lee et al.   ISME Journal

Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis

(2010) Torsten Thomas et al.   ISME Journal

Association of Thioautotrophic Bacteria with Deep-Sea Sponges

(2010) Miyuki Nishijima et al.   MARINE BIOTECHNOLOGY

Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea

(2010) C. B. Walker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

In vitro cell-toxicity screening as an alternative animal model for coral toxicology: effects of heat stress, sulfide, rotenone, cyanide, and cuprous oxide on cell viability and mitochondrial function

(2009) Craig A. Downs et al.   ECOTOXICOLOGY

Complex nitrogen cycling in the spongeGeodia barretti

(2009) Friederike Hoffmann et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity of aerobic and anaerobic ammonia-oxidizing bacteria in marine sponges

(2009) Naglaa M Mohamed et al.   ISME Journal

Mimivirus and Mimiviridae: Giant viruses with an increasing number of potential hosts, including corals and sponges

(2009) Jean-Michel Claverie et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-based adaptive and heritable immunity in prokaryotes

(2009) John van der Oost et al.   TRENDS IN BIOCHEMICAL SCIENCES

Diversity and mode of transmission of ammonia-oxidizing archaea in marine sponges

(2008) Doris Steger et al.   ENVIRONMENTAL MICROBIOLOGY

Oxygen consumption by a coral reef sponge

(2008) E. Hadas et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Phylogenetic Diversity and Spatial Distribution of the Microbial Community Associated with the Caribbean Deep-water Sponge Polymastia cf. corticata by 16S rRNA, aprA, and amoA Gene Analysis

(2008) Birte Meyer et al.   MICROBIAL ECOLOGY

CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea

(2007) Rotem Sorek et al.   NATURE REVIEWS MICROBIOLOGY