Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics

Hologenome analysis of two marine sponges with different microbiomes

(2016) Taewoo Ryu et al.   BMC GENOMICS

Pathways and key intermediates required for obligate aerobic ammonia-dependent chemolithotrophy in bacteria and Thaumarchaeota

(2016) Jessica A Kozlowski et al.   ISME Journal

The Sponge Hologenome

(2016) Nicole S. Webster et al.   mBio

Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts

(2016) Angela E. Douglas et al.   mBio

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

Sample Processing Impacts the Viability and Cultivability of the Sponge Microbiome

(2016) Ana I. S. Esteves et al.   Frontiers in Microbiology

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

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

Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation

(2015) Barbara Bayer et al.   ISME Journal

Cyanate as an energy source for nitrifiers

(2015) Marton Palatinszky et al.   NATURE

Complete nitrification by a single microorganism

(2015) Maartje A. H. J. van Kessel et al.   NATURE

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

(2015) Harriet Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genusNitrospira

(2015) Hanna Koch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Revealing microbial functional activities in the Red Sea spongeStylissa carteriby metatranscriptomics

(2014) Lucas Moitinho-Silva et al.   ENVIRONMENTAL MICROBIOLOGY

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

(2014) Kristina Bayer et al.   FEMS MICROBIOLOGY ECOLOGY

Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota

(2014) M. Stieglmeier et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Seasonal Variation of Fatty Acids and Stable Carbon Isotopes in Sponges as Indicators for Nutrition: Biomarkers in Sponges Identified

(2014) Marieke Koopmans et al.   MARINE BIOTECHNOLOGY

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel Genomic Features of the Ammonia-Oxidizing Archaea

(2014) Kateryna V. Zhalnina et al.   PLoS One

Ammonia-oxidizing archaea use the most energy-efficient aerobic pathway for CO2 fixation

(2014) M. Konneke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Marine ammonia-oxidizing archaeal isolates display obligate mixotrophy and wide ecotypic variation

(2014) W. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

The formate/nitrite transporter family of anion channels

(2013) Wei Lü et al.   BIOLOGICAL CHEMISTRY

Quality or quantity: is nutrient transfer driven more by symbiont identity and productivity than by symbiont abundance?

(2013) Christopher J Freeman et al.   ISME Journal

Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

(2013) Janine Kamke et al.   ISME Journal

Crystal structure of a nitrate/nitrite exchanger

(2013) Hongjin Zheng et al.   NATURE

Shallow breathing: bacterial life at low O2

(2013) Rachel L. Morris et al.   NATURE REVIEWS MICROBIOLOGY

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Phylogenetically Diverse ureC Genes and Their Expression Suggest the Urea Utilization by Bacterial Symbionts in Marine Sponge Xestospongia testudinaria

(2013) Jing Su et al.   PLoS One

Surviving in a Marine Desert: The Sponge Loop Retains Resources Within Coral Reefs

(2013) Jasper M. de Goeij et al.   SCIENCE

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

(2013) Sebastian Lücker et al.   Frontiers in Microbiology

Functional convergence of microbes associated with temperate marine sponges

(2012) M. Ribes et al.   ENVIRONMENTAL MICROBIOLOGY

Metatranscriptomics of the marine sponge Geodia barretti: tackling phylogeny and function of its microbial community

(2012) Regina Radax et al.   ENVIRONMENTAL MICROBIOLOGY

The genome of the ammonia-oxidizingCandidatusNitrososphaera gargensis: insights into metabolic versatility and environmental adaptations

(2012) Anja Spang et al.   ENVIRONMENTAL MICROBIOLOGY

Metaproteogenomic analysis of a community of sponge symbionts

(2012) Michael Liu et al.   ISME Journal

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

Role for urea in nitrification by polar marine Archaea

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

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

Metagenomic Analysis of Ammonia-Oxidizing Archaea Affiliated with the Soil Group

(2012) Rita Bartossek et al.   Frontiers in Microbiology

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM

(2011) Jiandong Ding et al.   BMC BIOINFORMATICS

Urea is a dynamic pool of bioavailable nitrogen in coral reefs

(2011) J. B. Crandall et al.   CORAL REEFS

Integrative analysis of environmental sequences using MEGAN4

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

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

Microbial nitrate respiration – Genes, enzymes and environmental distribution

(2011) Beate Kraft et al.   JOURNAL OF BIOTECHNOLOGY

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

(2011) Andrew E. Allen et al.   NATURE

Genome of a Low-Salinity Ammonia-Oxidizing Archaeon Determined by Single-Cell and Metagenomic Analysis

(2011) Paul C. Blainey et al.   PLoS One

Prolyl 4-hydroxylase

(2010) Kelly L. Gorres et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Functional genomic analysis of an uncultured δ-proteobacterium in the sponge Cymbastela concentrica

(2010) Michael Yizhe Liu et al.   ISME Journal

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

(2010) Torsten Thomas et al.   ISME Journal

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

(2010) Alexander Siegl et al.   ISME Journal

Labeling and Enzyme Studies of the Central Carbon Metabolism in Metallosphaera sedula

(2010) S. Estelmann et al.   JOURNAL OF BACTERIOLOGY

Heterogeneous oxygenation resulting from active and passive flow in two Mediterranean sponges, Dysida avara and Chondrosia reniformis

(2010) M.-L. Schläppy et al.   LIMNOLOGY AND OCEANOGRAPHY

A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

(2010) S. Lucker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Role of urea in microbial metabolism in aquatic systems: a biochemical and molecular review

(2009) CM Solomon et al.   AQUATIC MICROBIAL ECOLOGY

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

Complex nitrogen cycling in the spongeGeodia barretti

(2009) Friederike Hoffmann et al.   ENVIRONMENTAL MICROBIOLOGY

Particulate organic matter as a food source for a coral reef sponge

(2009) E. Hadas et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Molecular Microbial Diversity Survey of Sponge Reproductive Stages and Mechanistic Insights into Vertical Transmission of Microbial Symbionts

(2008) S. Schmitt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The functional roles of marine sponges

(2008) James J. Bell   ESTUARINE COASTAL AND SHELF SCIENCE

Major bulk dissolved organic carbon (DOC) removal by encrusting coral reef cavity sponges

(2008) JM de Goeij et al.   MARINE ECOLOGY PROGRESS SERIES