Vertically distinct microbial communities in the Mariana and Kermadec trenches

Colwellia marinimaniae sp. nov., a hyperpiezophilic species isolated from an amphipod within the Challenger Deep, Mariana Trench

(2017) Masataka Kusube et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

In situ respiration measurements of megafauna in the Kermadec Trench

(2016) Clifton C. Nunnally et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS

Fishes of the hadal zone including new species, in situ observations and depth records of Liparidae

(2016) Thomas D. Linley 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

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia

(2016) Roland Hatzenpichler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geographic Distribution of Archaeal Ammonia Oxidizing Ecotypes in the Atlantic Ocean

(2016) Eva Sintes 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

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

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

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Global diversity and biogeography of deep-sea pelagic prokaryotes

(2015) Guillem Salazar et al.   ISME Journal

Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

(2015) Guillem Salazar et al.   MOLECULAR ECOLOGY

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

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

Diverse uncultivated ultra-small bacterial cells in groundwater

(2015) Birgit Luef et al.   Nature Communications

Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump

(2015) S. Agusti et al.   Nature Communications

Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre

(2015) Kristina M. Fontanez et al.   Frontiers in Microbiology

Ecophysiological diversity of a novel member of the genus Alteromonas, and description of Alteromonas mediterranea sp. nov.

(2014) Elena P. Ivanova et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Single bacterial strain capable of significant contribution to carbon cycling in the surface ocean

(2014) B. E. Pedler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Novel Psychropiezophilic Oceanospirillales Species Profundimonas piezophila gen. nov., sp. nov., Isolated from the Deep-Sea Environment of the Puerto Rico Trench

(2013) Yi Cao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokaryotic responses to hydrostatic pressure in the ocean - a review

(2013) Christian Tamburini et al.   ENVIRONMENTAL MICROBIOLOGY

So, How DeepIsthe Mariana Trench?

(2013) James V. Gardner et al.   MARINE GEODESY

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

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

Microbial control of the dark end of the biological pump

(2013) Gerhard J. Herndl et al.   Nature Geoscience

Metagenomic Analysis of Viral Communities in (Hado)Pelagic Sediments

(2013) Mitsuhiro Yoshida et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R

(2013) Eric Pante et al.   PLoS One

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

The supergiant amphipod Alicella gigantea (Crustacea: Alicellidae) from hadal depths in the Kermadec Trench, SW Pacific Ocean

(2012) A.J. Jamieson et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan-Vavilov Deep

(2012) Francesco Smedile et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2012) Eva Sintes et al.   ENVIRONMENTAL MICROBIOLOGY

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

Isolation and Characterization of a Psychropiezophilic Alphaproteobacterium

(2011) Emiley A. Eloe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2011) T. Magoc et al.   BIOINFORMATICS

Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics

(2010) Toshi Nagata et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Halomonas and Marinobacter ecotypes from hydrothermal vent, subseafloor and deep-sea environments

(2010) Jonathan Z. Kaye et al.   FEMS MICROBIOLOGY ECOLOGY

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Journey to the Challenger Deep: 50 Years Later With the Nereus Hybrid Remotely Operated Vehicle

(2010) Barbara Fletcher et al.   MARINE TECHNOLOGY SOCIETY JOURNAL

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment

(2010) Emiley A. Eloe et al.   Environmental Microbiology Reports

Effects of hydrostatic pressure on microbial alteration of sinking fecal pellets

(2009) Christian Tamburini et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Pseudomonas pelagia sp. nov., isolated from a culture of the Antarctic green alga Pyramimonas gelidicola

(2009) C. Y. Hwang et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Hydrography shapes bacterial biogeography of the deep Arctic Ocean

(2009) Pierre E Galand et al.   ISME Journal

Microbial community structure in the North Pacific ocean

(2009) Mark V Brown et al.   ISME Journal

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

Ecology of the rare microbial biosphere of the Arctic Ocean

(2009) Pierre E. Galand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter

(2008) Elena Ivars-Martinez et al.   ISME Journal