相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Cultivation of a vampire: 'Candidatus Absconditicoccus praedator'
Michail M. Yakimov et al.
ENVIRONMENTAL MICROBIOLOGY (2022)
Microbiomes in the Challenger Deep slope and bottom-axis sediments
Ying-Li Zhou et al.
NATURE COMMUNICATIONS (2022)
Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR
Maria-Cecilia Chiriac et al.
MICROBIOME (2022)
Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors
Kyohei Kuroda et al.
MBIO (2022)
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems
Christine He et al.
NATURE MICROBIOLOGY (2021)
The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers
Narendrakumar M. Chaudhari et al.
ENVIRONMENTAL MICROBIOME (2021)
A rooted phylogeny resolves early bacterial evolution
Gareth A. Coleman et al.
SCIENCE (2021)
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing
Caitlin M. Singleton et al.
NATURE COMMUNICATIONS (2021)
Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii
David Moreira et al.
NATURE COMMUNICATIONS (2021)
Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams
Steven Batinovic et al.
NATURE MICROBIOLOGY (2021)
Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients
Clemens Schauberger et al.
ISME JOURNAL (2021)
Ammonia-oxidizing archaea have similar power requirements in diverse marine oxic sediments
Rui Zhao et al.
ISME JOURNAL (2021)
Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities
Alexa M. Nicolas et al.
MSYSTEMS (2021)
Functional diversity of microbial communities in inactive seafloor sulfide deposits
Xiyang Dong et al.
FEMS MICROBIOLOGY ECOLOGY (2021)
Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin
Rui Zhao et al.
ISME COMMUNICATIONS (2021)
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Pierre-Alain Chaumeil et al.
BIOINFORMATICS (2020)
Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater
Patricia Geesink et al.
ENVIRONMENTAL MICROBIOLOGY (2020)
Microbial community and geochemical analyses of trans-trench sediments for understanding the roles of hadal environments
Satoshi Hiraoka et al.
ISME JOURNAL (2020)
Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System
Nancy Merino et al.
FRONTIERS IN MICROBIOLOGY (2020)
Global diversity of microbial communities in marine sediment
Tatsuhiko Hoshino et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN
Jacob P. Beam et al.
FRONTIERS IN MICROBIOLOGY (2020)
Geochemical transition zone powering microbial growth in subsurface sediments
Rui Zhao et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
Harald R. Gruber-Vodicka et al.
MSYSTEMS (2020)
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Alon Shaiber et al.
GENOME BIOLOGY (2020)
Ultra-small and abundant: Candidate phyla radiation bacteria are potential catalysts of carbon transformation in a thermokarst lake ecosystem
Adrien Vigneron et al.
LIMNOLOGY AND OCEANOGRAPHY LETTERS (2020)
Candidate Phyla Radiation Roizmanbacteria From Hot Springs Have Novel and Unexpectedly Abundant CRISPR-Cas Systems
Lin-Xing Chen et al.
FRONTIERS IN MICROBIOLOGY (2019)
Nitrifier abundance and diversity peak at deep redox transition zones
Rui Zhao et al.
SCIENTIFIC REPORTS (2019)
Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions
Martina Herrmann et al.
FRONTIERS IN MICROBIOLOGY (2019)
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
Dongwan D. Kang et al.
PEERJ (2019)
Interplay of Subduction Tectonics, Sedimentation, and Carbon Cycling Interplay of subduction tectonics, sedimentation, and carbon cycling
N. Riedinger et al.
GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS (2019)
Subseafloor life and its biogeochemical impacts
Steven D'Hondt et al.
NATURE COMMUNICATIONS (2019)
UFBoot2: Improving the Ultrafast Bootstrap Approximation
Diep Thi Hoang et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Predicted microbial secretomes and their target substrates in marine sediment
William D. Orsi et al.
NATURE MICROBIOLOGY (2018)
Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life
Cindy J. Castelle et al.
CELL (2018)
Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias
Soren M. Karst et al.
NATURE BIOTECHNOLOGY (2018)
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
Christian M. K. Sieber et al.
NATURE MICROBIOLOGY (2018)
Differential depth distribution of microbial function and putative symbionts through sediment- hosted aquifers in the deep terrestrial subsurface
Alexander J. Probst et al.
NATURE MICROBIOLOGY (2018)
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Donovan H. Parks et al.
NATURE BIOTECHNOLOGY (2018)
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations
Cindy J. Castelle et al.
NATURE REVIEWS MICROBIOLOGY (2018)
Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes
Karen G. Lloyd et al.
MSYSTEMS (2018)
Rapid evolution of decreased host susceptibility drives a stable relationship between ultrasmall parasite TM7x and its bacterial host
Batbileg Bor et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1)
Rosa Leon-Zayas et al.
ENVIRONMENTAL MICROBIOLOGY (2017)
Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars
Shino Suzuki et al.
ISME JOURNAL (2017)
ModelFinder: fast model selection for accurate phylogenetic estimates
Subha Kalyaanamoorthy et al.
NATURE METHODS (2017)
Towards a balanced view of the bacterial tree of life
Frederik Schulz et al.
MICROBIOME (2017)
Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities
R. E. Danczak et al.
MICROBIOME (2017)
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks et al.
NATURE MICROBIOLOGY (2017)
Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation
Cindy J. Castelle et al.
SCIENTIFIC REPORTS (2017)
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
Yu-Wei Wu et al.
BIOINFORMATICS (2016)
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
Jaime Huerta-Cepas et al.
NUCLEIC ACIDS RESEARCH (2016)
Slow Microbial Life in the Seabed
Bo Barker Jorgensen et al.
ANNUAL REVIEW OF MARINE SCIENCE, VOL 8 (2016)
The bright side of microbial dark matter: lessons learned from the uncultivated majority
Lindsey Solden et al.
CURRENT OPINION IN MICROBIOLOGY (2016)
Dense microbial community on a ferromanganese nodule from the ultra-oligotrophic South Pacific Gyre: Implications for biogeochemical cycles
Fumito Shiraishi et al.
EARTH AND PLANETARY SCIENCE LETTERS (2016)
BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences
Minoru Kanehisa et al.
JOURNAL OF MOLECULAR BIOLOGY (2016)
Measurement of bacterial replication rates in microbial communities
Christopher T. Brown et al.
NATURE BIOTECHNOLOGY (2016)
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system
Karthik Anantharaman et al.
NATURE COMMUNICATIONS (2016)
Distinct Bacterial Communities in Surficial Seafloor Sediments Following the 2010 Deepwater Horizon Blowout
Tingting Yang et al.
FRONTIERS IN MICROBIOLOGY (2016)
Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum
Karthik Anantharaman et al.
PEERJ (2016)
Metagenomics uncovers gaps in amplicon-based detection of microbial diversity
Emiley A. Eloe-Fadrosh et al.
NATURE MICROBIOLOGY (2016)
Catabolic rates, population sizes and doubling/replacement times of microorganisms in natural settings
Douglas E. Larowe et al.
AMERICAN JOURNAL OF SCIENCE (2015)
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Dinghua Li et al.
BIOINFORMATICS (2015)
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Donovan H. Parks et al.
GENOME RESEARCH (2015)
Unusual biology across a group comprising more than 15% of domain Bacteria
Christopher T. Brown et al.
NATURE (2015)
Exploring deep microbial life in coal-bearing sediment down to ∼2.5 km below the ocean floor
F. Inagaki et al.
SCIENCE (2015)
Viral activities and life cycles in deep subseafloor sediments
Tim Engelhardt et al.
ENVIRONMENTAL MICROBIOLOGY REPORTS (2015)
Diverse uncultivated ultra-small bacterial cells in groundwater
Birgit Luef et al.
NATURE COMMUNICATIONS (2015)
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
Zachary D. Kurtz et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle
William C. Nelson et al.
FRONTIERS IN MICROBIOLOGY (2015)
gbtools: Interactive Visualization of Metagenome Bins in R
Brandon K. B. Seah et al.
FRONTIERS IN MICROBIOLOGY (2015)
Anvi'o: an advanced analysis and visualization platformfor 'omics data
A. Murat Eren et al.
PEERJ (2015)
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Lam-Tung Nguyen et al.
MOLECULAR BIOLOGY AND EVOLUTION (2015)
Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle
Xuesong He et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Prokka: rapid prokaryotic genome annotation
Torsten Seemann
BIOINFORMATICS (2014)
A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere:geosphere interactions
R. John Parkes et al.
MARINE GEOLOGY (2014)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
Insights into the phylogeny and coding potential of microbial dark matter
Christian Rinke et al.
NATURE (2013)
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast et al.
NUCLEIC ACIDS RESEARCH (2013)
Unipro UGENE: a unified bioinformatics toolkit
Konstantin Okonechnikov et al.
BIOINFORMATICS (2012)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2012)
KEGG for integration and interpretation of large-scale molecular data sets
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2012)
CREST - Classification Resources for Environmental Sequence Tags
Anders Lanzen et al.
PLOS ONE (2012)
Global distribution of microbial abundance and biomass in subseafloor sediment
Jens Kallmeyer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field
Regina Schauer et al.
ENVIRONMENTAL MICROBIOLOGY (2011)
Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt et al.
BMC BIOINFORMATICS (2010)
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Salvador Capella-Gutierrez et al.
BIOINFORMATICS (2009)
Uncultured archaea in deep marine subsurface sediments: have we caught them all?
Andreas Teske et al.
ISME JOURNAL (2008)
Regulation of atmospheric CO2 by deep-sea sediments in an Earth system model
Andy Ridgwell et al.
GLOBAL BIOGEOCHEMICAL CYCLES (2007)
Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments, on the Pacific Ocean Margin
F Inagaki et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Rhizon sampling of porewaters near the sediment-water interface of aquatic systems
J Seeberg-Elverfeldt et al.
LIMNOLOGY AND OCEANOGRAPHY-METHODS (2005)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
RC Edgar
NUCLEIC ACIDS RESEARCH (2004)
DNA uptake during bacterial transformation
I Chen et al.
NATURE REVIEWS MICROBIOLOGY (2004)