Ecology and evolution of seafloor and subseafloor microbial communities

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition

(2018) Ian P.G. Marshall et al.   Marine Genomics

Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea

(2018) Verona Vandieken et al.   Frontiers in Microbiology

Necromass as a Limited Source of Energy for Microorganisms in Marine Sediments

(2018) James A. Bradley et al.   Journal of Geophysical Research-Biogeosciences

Exploration of cultivable fungal communities in deep coal-bearing sediments from ∼1.3 to 2.5 km below the ocean floor

(2017) Chang-Hong Liu et al.   ENVIRONMENTAL MICROBIOLOGY

An alternative polysaccharide uptake mechanism of marine bacteria

(2017) Greta Reintjes et al.   ISME Journal

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

(2017) Benjamin J Tully et al.   ISME Journal

A simple and inexpensive technique for assessing contamination during drilling operations

(2017) André Friese et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Control on rate and pathway of anaerobic organic carbon degradation in the seabed

(2017) F. Beulig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial community assembly and evolution in subseafloor sediment

(2017) Piotr Starnawski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

(2017) Elizabeth Trembath-Reichert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thriving or surviving? Evaluating active microbial guilds in Baltic Sea sediment

(2017) Laura A. Zinke et al.   Environmental Microbiology Reports

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

(2017) Kenneth Wasmund et al.   Environmental Microbiology Reports

Homoacetogenesis in Deep-Sea Chloroflexi , as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes

(2017) Holly L. Sewell et al.   mBio

Reverse Methanogenesis and Respiration in Methanotrophic Archaea

(2017) Peer H. A. Timmers et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Atribacteria from the Subseafloor Sedimentary Biosphere Disperse to the Hydrosphere through Submarine Mud Volcanoes

(2017) Tatsuhiko Hoshino et al.   Frontiers in Microbiology

Predicted microbial secretomes and their target substrates in marine sediment

(2017) William D. Orsi et al.   Nature Microbiology

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

(2016) Benjamin J. Tully et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments

(2016) Cassandre Sara Lazar et al.   ENVIRONMENTAL MICROBIOLOGY

Cellulosomes: bacterial nanomachines for dismantling plant polysaccharides

(2016) Lior Artzi et al.   NATURE REVIEWS MICROBIOLOGY

Extracellular electron transfer systems fuel cellulose oxidative degradation

(2016) D. Kracher et al.   SCIENCE

Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction

(2016) S. Scheller et al.   SCIENCE

Lytic Polysaccharide Monooxygenases: The Microbial Power Tool for Lignocellulose Degradation

(2016) Katja Salomon Johansen   TRENDS IN PLANT SCIENCE

Transcriptional analysis of sulfate reducing and chemolithoautotrophic sulfur oxidizing bacteria in the deep subseafloor

(2016) William D. Orsi et al.   Environmental Microbiology Reports

Soil Fungal:Bacterial Ratios Are Linked to Altered Carbon Cycling

(2016) Ashish A. Malik et al.   Frontiers in Microbiology

Deep Subsurface Life from North Pond: Enrichment, Isolation, Characterization and Genomes of Heterotrophic Bacteria

(2016) Joseph A. Russell et al.   Frontiers in Microbiology

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea

(2016) Brett J. Baker et al.   Nature Microbiology

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria

(2016) Christina Bienhold et al.   PLoS One

Towards a better quantitative assessment of the relevance of deep-sea viruses, Bacteria and Archaea in the functioning of the ocean seafloor

(2015) R Danovaro et al.   AQUATIC MICROBIAL ECOLOGY

Cellular maintenance processes that potentially underpin the survival of subseafloor fungi over geological timescales

(2015) William D. Orsi et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses

(2015) Anne E Dekas et al.   ISME Journal

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

(2015) Masaru K Nobu et al.   ISME Journal

Bacterial diversity and community composition from seasurface to subseafloor

(2015) Emily A Walsh et al.   ISME Journal

Fungal Traits That Drive Ecosystem Dynamics on Land

(2015) Kathleen K. Treseder et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria

(2015) Gunter Wegener et al.   NATURE

Single cell activity reveals direct electron transfer in methanotrophic consortia

(2015) Shawn E. McGlynn et al.   NATURE

Presence of oxygen and aerobic communities from sea floor to basement in deep-sea sediments

(2015) Steven D’Hondt et al.   Nature Geoscience

Virus decomposition provides an important contribution to benthic deep-sea ecosystem functioning

(2015) Antonio Dell’Anno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global dispersion and local diversification of the methane seep microbiome

(2015) S. Emil Ruff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring deep microbial life in coal-bearing sediment down to  2.5 km below the ocean floor

(2015) F. Inagaki et al.   SCIENCE

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

Viral activities and life cycles in deep subseafloor sediments

(2015) Tim Engelhardt et al.   Environmental Microbiology Reports

Dark fermentative hydrogen production from lignocellulosic hydrolyzates – A review

(2014) Marika E. Nissilä et al.   BIOMASS & BIOENERGY

Physiological and cell morphology adaptation ofBacillus subtilisat near-zero specific growth rates: a transcriptome analysis

(2014) Wout Overkamp et al.   ENVIRONMENTAL MICROBIOLOGY

High virus-to-cell ratios indicate ongoing production of viruses in deep subsurface sediments

(2014) Tim Engelhardt et al.   ISME Journal

Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin

(2014) Anne-Kristin Kaster et al.   ISME Journal

High Fungal Diversity and Abundance Recovered in the Deep-Sea Sediments of the Pacific Ocean

(2014) Wei Xu et al.   MICROBIAL ECOLOGY

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

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

Global rates of marine sulfate reduction and implications for sub-sea-floor metabolic activities

(2014) M. W. Bowles et al.   SCIENCE

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

(2014) Mikihiko Kawai et al.   Frontiers in Microbiology

Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

(2013) Karen G. Lloyd et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Deciphering the presence and activity of fungal communities in marine sediments using a model estuarine system

(2013) G Burgaud et al.   AQUATIC MICROBIAL ECOLOGY

Spatial distribution of nitrogen fixation in methane seep sediment and the role of the ANME archaea

(2013) Anne E. Dekas et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial community analysis of deeply buried marine sediments of the New Jersey shallow shelf (IODP Expedition 313)

(2013) Anja Breuker et al.   FEMS MICROBIOLOGY ECOLOGY

Dark inorganic carbon fixation sustains the functioning of benthic deep-sea ecosystems

(2013) Massimiliano Molari et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Intraterrestrial lifestyles

(2013) David L. Valentine   NATURE

Gene expression in the deep biosphere

(2013) William D. Orsi et al.   NATURE

Predominant archaea in marine sediments degrade detrital proteins

(2013) Karen G. Lloyd et al.   NATURE

Microbial life under extreme energy limitation

(2013) Tori M. Hoehler et al.   NATURE REVIEWS MICROBIOLOGY

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

(2013) William Orsi et al.   PLoS One

Cyclic 100-ka (glacial-interglacial) migration of subseafloor redox zonation on the Peruvian shelf

(2013) S. Contreras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

(2013) B. K. Swan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Turnover of microbial lipids in the deep biosphere and growth of benthic archaeal populations

(2013) S. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interstitial fluid chemistry of sediments underlying the North Atlantic gyre and the influence of subsurface fluid flow

(2012) Wiebke Ziebis et al.   EARTH AND PLANETARY SCIENCE LETTERS

Biogeography of Rhizobium radiobacter and distribution of associated temperate phages in deep subseafloor sediments

(2012) Tim Engelhardt et al.   ISME Journal

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

(2012) Bente Aa. Lomstein et al.   NATURE

Nitrogen loss from soil through anaerobic ammonium oxidation coupled to iron reduction

(2012) Wendy H. Yang et al.   Nature Geoscience

Global distribution of microbial abundance and biomass in subseafloor sediment

(2012) J. Kallmeyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge

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

Aerobic Microbial Respiration in 86-Million-Year-Old Deep-Sea Red Clay

(2012) H. Roy et al.   SCIENCE

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Prospects for the study of evolution in the deep biosphere

(2012) Jennifer F. Biddle   Frontiers in Microbiology

Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages

(2012) Alan M. Durbin et al.   Frontiers in Microbiology

Marine Fungi: Their Ecology and Molecular Diversity

(2011) Thomas A. Richards et al.   Annual Review of Marine Science

Dissimilatory Reduction of Extracellular Electron Acceptors in Anaerobic Respiration

(2011) Katrin Richter et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea

(2011) Karen G. Lloyd et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial diversity and stratification of South Pacific abyssal marine sediments

(2011) Alan M. Durbin et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

(2011) B. N. Orcutt et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Untapped potential: exploiting fungi in bioremediation of hazardous chemicals

(2011) Hauke Harms et al.   NATURE REVIEWS MICROBIOLOGY

Carbon and nitrogen assimilation in deep subseafloor microbial cells

(2011) Y. Morono et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers

(2011) M. Mussmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induction of prophages from deep-subseafloor bacteria

(2011) Tim Engelhardt et al.   Environmental Microbiology Reports

Microbial Extracellular Enzymes and the Marine Carbon Cycle

(2010) Carol Arnosti   Annual Review of Marine Science

Sediment-associated microdiversity within the Marine Group I Crenarchaeota

(2010) Alan M. Durbin et al.   Environmental Microbiology Reports

Subseafloor sedimentary life in the South Pacific Gyre

(2009) Steven D'Hondt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Constant Flux of Diverse Thermophilic Bacteria into the Cold Arctic Seabed

(2009) C. Hubert et al.   SCIENCE

Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia

(2009) A. E. Dekas et al.   SCIENCE