Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments

Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship

(2020) Jiwen Liu et al.   ISME Journal

Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary

(2020) Wenxiu Wang et al.   AMB Express

Understanding the evolution of interspecies interactions in microbial communities

(2020) Florien A. Gorter et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution

(2020) Sean K. Bay et al.   mSystems

Global diversity of microbial communities in marine sediment

(2020) Tatsuhiko Hoshino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor

(2020) Aurèle Vuillemin et al.   mBio

Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea

(2019) Hongpeng Cui et al.   MARINE ENVIRONMENTAL RESEARCH

Complex microbial communities drive iron and sulfur cycling in Arctic fjord sediments

(2019) J. Buongiorno et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Decoupling species richness variation and spatial turnover in beta diversity across a fragmented landscape

(2019) Guang Hu et al.   PeerJ

Strengthening Insights in Microbial Ecological Networks from Theory to Applications

(2019) Xiaofei Lv et al.   mSystems

Archaea dominate oxic subseafloor communities over multimillion-year time scales

(2019) Aurèle Vuillemin et al.   Science Advances

Soil pH and temperature regulate assembly processes of abundant and rare bacterial communities in agricultural ecosystems

(2019) Shuo Jiao et al.   ENVIRONMENTAL MICROBIOLOGY

Subseafloor life and its biogeochemical impacts

(2019) Steven D’Hondt et al.   Nature Communications

Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments

(2019) Hanna Sinkko et al.   Scientific Reports

Interaction and assembly processes of abundant and rare microbial communities during a diatom bloom process

(2019) Huajun Zhang et al.   ENVIRONMENTAL MICROBIOLOGY

Soil Microbial Networks Shift Across a High-Elevation Successional Gradient

(2019) Emily C. Farrer et al.   Frontiers in Microbiology

Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments

(2019) William D. Orsi et al.   Nature Microbiology

Biogeographic patterns of abundant and rare bacterioplankton in three subtropical bays resulting from selective and neutral processes

(2018) Yuanyuan Mo et al.   ISME Journal

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom

(2018) Yuanyuan Xue et al.   ISME Journal

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

(2018) Takuro Nunoura et al.   MICROBES AND ENVIRONMENTS

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

β-Diversity, Community Assembly, and Ecosystem Functioning

(2018) Akira S. Mori et al.   TRENDS IN ECOLOGY & EVOLUTION

Sediment Depth-Dependent Spatial Variations of Bacterial Communities in Mud Deposits of the Eastern China Marginal Seas

(2018) Yanlu Qiao et al.   Frontiers in Microbiology

Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

(2018) Michael F. Graw et al.   Frontiers in Microbiology

Clustering Coefficients for Correlation Networks

(2018) Naoki Masuda et al.   Frontiers in Neuroinformatics

Abundance and distribution of Archaea in the subseafloor sedimentary biosphere

(2018) Tatsuhiko Hoshino et al.   ISME Journal

Abundant and rare picoeukaryotic sub-communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern Pacific Ocean

(2017) Wenxue Wu et al.   ENVIRONMENTAL MICROBIOLOGY

A meta-analysis of nestedness and turnover components of beta diversity across organisms and ecosystems

(2017) Janne Soininen et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Where less may be more: how the rare biosphere pulls ecosystems strings

(2017) Alexandre Jousset et al.   ISME Journal

Early diagenesis and authigenic mineral formation in mobile muds of the Changjiang Estuary and adjacent shelf

(2017) Bin Zhao et al.   JOURNAL OF MARINE SYSTEMS

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

Spatiotemporal variations of deep-sea sediment components and their fluxes since the last glaciation in the northern South China Sea

(2017) ShaoHua Zhao et al.   Science China-Earth Sciences

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

(2017) Aurèle Vuillemin et al.   Frontiers in Microbiology

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment

(2017) Christian Wurzbacher et al.   Microbiome

Determination of phosphorus in natural waters: A historical review

(2016) Paul Worsfold et al.   ANALYTICA CHIMICA ACTA

Slow Microbial Life in the Seabed

(2016) Bo Barker Jørgensen et al.   Annual Review of Marine Science

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

(2016) Bin Ma et al.   ISME Journal

Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

(2016) Yong Wang et al.   Science Bulletin

Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments

(2016) Y. He et al.   Nature Microbiology

Denitrification, Anammox, and N2 Production in Marine Sediments

(2015) Allan H. Devol   Annual Review of Marine Science

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Variance and potential niche separation of microbial communities in subseafloor sediments off Shimokita Peninsula, Japan

(2015) Takuro Nunoura et al.   ENVIRONMENTAL MICROBIOLOGY

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

Bacterial diversity and community composition from seasurface to subseafloor

(2015) Emily A Walsh et al.   ISME Journal

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

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

(2015) F. Inagaki et al.   SCIENCE

Temporal patterns of rarity provide a more complete view of microbial diversity

(2015) Ashley Shade et al.   TRENDS IN MICROBIOLOGY

Microbial diversity in the hydrate-containing and -free surface sediments in the Shenhu area, South China Sea

(2015) Lu Jiao et al.   Geoscience Frontiers

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Revealing Beta-Diversity Patterns of Breeding Bird and Lizard Communities on Inundated Land-Bridge Islands by Separating the Turnover and Nestedness Components

(2015) Xingfeng Si et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Remineralization of sedimentary organic carbon in mud deposits of the Changjiang Estuary and adjacent shelf: Implications for carbon preservation and authigenic mineral formation

(2014) Peng Yao et al.   CONTINENTAL SHELF RESEARCH

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Interpreting the replacement and richness difference components of beta diversity

(2014) Pierre Legendre   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Spatial distribution patterns of benthic microbial communities along the Pearl Estuary, China

(2014) Jiwen Liu et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

BAT - Biodiversity Assessment Tools, an R package for the measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity

(2014) Pedro Cardoso et al.   Methods in Ecology and Evolution

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Loss in microbial diversity affects nitrogen cycling in soil

(2013) Laurent Philippot et al.   ISME Journal

Microbial minorities modulate methane consumption through niche partitioning

(2013) Paul LE Bodelier et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Energy, ecology and the distribution of microbial life

(2013) J. L. Macalady et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Spatial Variations in Microbial Community Composition in Surface Seawater from the Ultra-Oligotrophic Center to Rim of the South Pacific Gyre

(2013) Qi Yin et al.   PLoS One

Patterns and drivers of bacterial α- and β-diversity across vertical profiles from surface to subsurface sediments

(2013) Gian Marco Luna et al.   Environmental Microbiology Reports

Environment-Dependent Distribution of the Sediment nifH -Harboring Microbiota in the Northern South China Sea

(2012) Hongyue Dang et al.   APPLIED AND 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

The Rare Bacterial Biosphere

(2011) Carlos Pedrós-Alió   Annual Review of Marine Science

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

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

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

(2011) Lucie Zinger et al.   PLoS One

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Degradation of dissolved organic monomers and short-chain fatty acids in sandy marine sediment by fermentation and sulfate reduction

(2009) Thomas Valdemarsen et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Partitioning the turnover and nestedness components of beta diversity

(2009) Andrés Baselga   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

(2009) Simone I Böer et al.   ISME Journal

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

(2009) Regina Schauer et al.   ISME Journal

Dehalorespiration with Polychlorinated Biphenyls by an Anaerobic Ultramicrobacterium

(2008) H. D. May et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton

(2008) Achim Quaiser et al.   ENVIRONMENTAL MICROBIOLOGY

Prokaryotic diversity, distribution and insights into their role in biogeochemical cycling in marine basalts

(2008) Olivia U Mason et al.   ISME Journal

Detrital fine-grained sediment contribution from Taiwan to the northern South China Sea and its relation to regional ocean circulation

(2008) Zhifei Liu et al.   MARINE GEOLOGY