Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments

Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community

(2019) Satoshi Hiraoka et al.   Nature Communications

Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches

(2019) Logan M. Peoples et al.   Frontiers in Microbiology

Spatial variations of microbial communities in abyssal and hadal sediments across the Challenger Deep

(2019) Guojie Cui et al.   PeerJ

Viral Infections Boost Prokaryotic Biomass Production and Organic C Cycling in Hadal Trench Sediments

(2019) Elisabetta Manea et al.   Frontiers in Microbiology

A contemporary perspective on hadal science

(2018) Alan J. Jamieson   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Nitrate isotope distribution in the subarctic and subtropical North Pacific

(2018) Chisato Yoshikawa et al.   GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS

Causes of earthquake spatial distribution beneath the Izu-Bonin-Mariana Arc

(2018) Xiangchao Kong et al.   JOURNAL OF ASIAN EARTH SCIENCES

Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench

(2018) Takuro Nunoura et al.   MICROBES AND ENVIRONMENTS

Ecology and evolution of seafloor and subseafloor microbial communities

(2018) William D. Orsi   NATURE REVIEWS MICROBIOLOGY

Vertically distinct microbial communities in the Mariana and Kermadec trenches

(2018) Logan M. Peoples et al.   PLoS One

Chemical characteristics of hadal waters in the Izu-Ogasawara Trench of the western Pacific Ocean

(2018) Toshitaka GAMO et al.   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

Distribution of extracellular flavins in a coastal marine basin and their relationship to redox gradients and microbial community members

(2018) Danielle Monteverde et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

A full-ocean-depth rated modular lander and pressure-retaining sampler capable of collecting hadal-endemic microbes under in situ conditions

(2018) Logan M. Peoples et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Genomic Insight Into the Predominance of Candidate Phylum Atribacteria JS1 Lineage in Marine Sediments

(2018) Yung Mi Lee et al.   Frontiers in Microbiology

Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column

(2017) Anthony D. Bertagnolli et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial nutrient niches in the gut

(2017) Fátima C. Pereira et al.   ENVIRONMENTAL MICROBIOLOGY

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments

(2017) Marc Mußmann et al.   ISME Journal

Provenances, distribution, and accumulation of organic matter in the southern Mariana Trench rim and slope: Implication for carbon cycle and burial in hadal trenches

(2017) Min Luo et al.   MARINE GEOLOGY

Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments

(2017) Miho Hirai et al.   MICROBES AND ENVIRONMENTS

Analysis of large 16S rRNA Illumina data sets: Impact of singleton read filtering on microbial community description

(2017) Lucas Auer et al.   Molecular Ecology Resources

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

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients

(2017) Alyse K. Hawley et al.   Nature Communications

From the Surface to the Deep-Sea: Bacterial Distributions across Polymetallic Nodule Fields in the Clarion-Clipperton Zone of the Pacific Ocean

(2017) Markus V. Lindh et al.   Frontiers in Microbiology

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

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

Community structure and diversity of scavenging amphipods from bathyal to hadal depths in three South Pacific Trenches

(2016) Nichola C. Lacey et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Comparison between infaunal communities of the deep floor and edge of the Tonga Trench: Possible effects of differences in organic matter supply

(2016) Daniel Leduc et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Benthic carbon mineralization in hadal trenches: Assessment by in situ O 2 microprofile measurements

(2016) F. Wenzhöfer et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi ) in Sulfur Cycling

(2016) Kenneth Wasmund et al.   mBio

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well

(2016) Steven J. Robbins et al.   Frontiers in Microbiology

Identification of Free-Living and Particle-Associated Microbial Communities Present in Hadal Regions of the Mariana Trench

(2016) Jonathan Tarn et al.   Frontiers in Microbiology

Distribution and Niche Separation of Planktonic Microbial Communities in the Water Columns from the Surface to the Hadal Waters of the Japan Trench under the Eutrophic Ocean

(2016) Takuro Nunoura et al.   Frontiers in Microbiology

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

(2016) Elizabeth Trembath-Reichert et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Virus-mediated archaeal hecatomb in the deep seafloor

(2016) R. Danovaro et al.   Science Advances

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems

(2016) R. Danovaro et al.   Science Advances

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

The distribution of benthic biomass in hadal trenches: A modelling approach to investigate the effect of vertical and lateral organic matter transport to the seafloor

(2015) Matteo C. Ichino et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

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

Sedimentary organic matter contents and porewater chemistry at upper bathyal depths influenced by the 2011 off the Pacific coast of Tohoku Earthquake and tsunami

(2015) Hidetaka Nomaki et al.   JOURNAL OF OCEANOGRAPHY

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

Hadal biosphere: Insight into the microbial ecosystem in the deepest ocean on Earth

(2015) Takuro Nunoura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes

(2015) A. Z. Worden et al.   SCIENCE

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Bacterial networks and co-occurrence relationships in the lettuce root microbiota

(2014) Massimiliano Cardinale et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Decadal trends in global pelagic ocean chlorophyll: A new assessment integrating multiple satellites, in situ data, and models

(2014) Watson W. Gregg et al.   JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS

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

Assemblages gradually change from bathyal to hadal depth: A case study on harpacticoid copepods around the Kuril Trench (north-west Pacific Ocean)

(2013) Tomo Kitahashi et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle

(2013) Jody J Wright et al.   ISME Journal

Deep-sea amphipod community structure across abyssal to hadal depths in the Peru-Chile and Kermadec trenches

(2013) T Fujii et al.   MARINE ECOLOGY PROGRESS SERIES

High rates of microbial carbon turnover in sediments in the deepest oceanic trench on Earth

(2013) Ronnie N. Glud et al.   Nature Geoscience

Hadal disturbance in the Japan Trench induced by the 2011 Tohoku–Oki Earthquake

(2013) Kazumasa Oguri et al.   Scientific Reports

ArchaealamoA gene diversity points to distinct biogeography of ammonia-oxidizingCrenarchaeotain the ocean

(2012) Eva Sintes et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

(2012) Elke Allers et al.   ISME Journal

Microbial Diversity in Deep-sea Methane Seep Sediments Presented by SSU rRNA Gene Tag Sequencing

(2012) Takuro Nunoura et al.   MICROBES AND ENVIRONMENTS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

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

Disturbance of deep-sea environments induced by the M9.0 Tohoku Earthquake

(2012) Shinsuke Kawagucci et al.   Scientific Reports

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

(2011) Michael Pester et al.   CURRENT OPINION IN MICROBIOLOGY

Microbial diversity and stratification of South Pacific abyssal marine sediments

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

Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species–area relationships

(2011) Jürg Brendan Logue et al.   ISME Journal

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Bait-attending fauna of the Kermadec Trench, SW Pacific Ocean: Evidence for an ecotone across the abyssal–hadal transition zone

(2010) A.J. Jamieson et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean

(2010) Paola R Gómez-Pereira et al.   ISME Journal

The ABISMO Mud and Water Sampling ROV for Surveys at 11,000 m Depth

(2010) Hiroshi Yoshida et al.   MARINE TECHNOLOGY SOCIETY JOURNAL

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Sediment-associated microdiversity within the Marine Group I Crenarchaeota

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

Archaeal Diversity and Distribution along Thermal and Geochemical Gradients in Hydrothermal Sediments at the Yonaguni Knoll IV Hydrothermal Field in the Southern Okinawa Trough

(2009) T. Nunoura et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dehalogenation Activities and Distribution of Reductive Dehalogenase Homologous Genes in Marine Subsurface Sediments

(2009) T. Futagami et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean

(2009) Regina Schauer et al.   ISME Journal

Discriminative detection and enumeration of microbial life in marine subsurface sediments

(2009) Yuki Morono et al.   ISME Journal

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

Hadal trenches: the ecology of the deepest places on Earth

(2009) Alan J. Jamieson et al.   TRENDS IN ECOLOGY & EVOLUTION