Phylogeny and Metabolic Potential of the Candidate Phylum SAR324

Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf

(2022) Clara Martínez-Pérez et al.   Nature Communications

Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage

(2021) Dominique Boeuf et al.   Microbiome

Tara Oceans: towards global ocean ecosystems biology

(2020) Shinichi Sunagawa et al.   NATURE REVIEWS MICROBIOLOGY

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics

(2020) Shunan Cao et al.   Microbiome

Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes

(2020) Zihao Zhao et al.   Science Advances

Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns

(2019) Benjamin J. Tully   Nature Communications

Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria

(2019) Tom Berben et al.   Frontiers in Microbiology

Global change microbiology — big questions about small life for our future

(2019) Antje Boetius   NATURE REVIEWS MICROBIOLOGY

Climate change microbiology — problems and perspectives

(2019) David A. Hutchins et al.   NATURE REVIEWS MICROBIOLOGY

Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival

(2019) Paul R. F. Cordero et al.   ISME Journal

Towards Integrating Evolution, Metabolism, and Climate Change Studies of Marine Ecosystems

(2019) Federico Baltar et al.   TRENDS IN ECOLOGY & EVOLUTION

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

(2019) Guillem Salazar et al.   CELL

Inorganic and Organic Carbon Uptake Processes and Their Connection to Microbial Diversity in Meso- and Bathypelagic Arctic Waters (Eastern Fram Strait)

(2019) Grazia Marina Quero et al.   MICROBIAL ECOLOGY

Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre

(2018) Daniel K. Olson et al.   ISME Journal

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

(2018) Tom O. Delmont et al.   PeerJ

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

The enigmatic SAR202 cluster up close: shedding light on a globally distributed dark ocean lineage involved in sulfur cycling

(2017) Maliheh Mehrshad et al.   ISME Journal

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate

(2017) Casper Thorup et al.   mBio

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge

(2016) Huiluo Cao et al.   Scientific Reports

HydDB: A web tool for hydrogenase classification and analysis

(2016) Dan Søndergaard et al.   Scientific Reports

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Global diversity and biogeography of deep-sea pelagic prokaryotes

(2015) Guillem Salazar et al.   ISME Journal

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

(2014) J Cameron Thrash et al.   ISME Journal

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria

(2014) J. Palovaara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Challenging the paradigms of deep-sea ecology

(2014) Roberto Danovaro et al.   TRENDS IN ECOLOGY & EVOLUTION

Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics

(2013) Cody S. Sheik et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial control of the dark end of the biological pump

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

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Microbial ecology of expanding oxygen minimum zones

(2012) Jody J. Wright et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures

(2012) Marc Strous et al.   Frontiers in Microbiology

Metabolic strategies of free-living and aggregate-associated bacterial communities inferred from biologic and chemical profiles in the Black Sea suboxic zone

(2011) Clara A. Fuchsman et al.   FEMS MICROBIOLOGY ECOLOGY

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Genome characteristics of a generalist marine bacterial lineage

(2010) Ryan J Newton et al.   ISME Journal

Proteorhodopsin Phototrophy Promotes Survival of Marine Bacteria during Starvation

(2010) Laura Gómez-Consarnau et al.   PLOS BIOLOGY

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

Identification of ribosomal RNA genes in metagenomic fragments

(2009) Ying Huang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Regulation of aquatic microbial processes: the ‘microbial loop’ of the sunlit surface waters and the dark ocean dissected

(2008) GJ Herndl et al.   AQUATIC MICROBIAL ECOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS