Genome-Resolved Metagenomics Informs the Functional Ecology of Uncultured Acidobacteria in Redox Oscillated Sphagnum Peat

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Decrypting bacterial polyphenol metabolism in an anoxic wetland soil

(2021) Bridget B. McGivern et al.   Nature Communications

Genomic Analysis of Family UBA6911 (Group 18 Acidobacteria ) Expands the Metabolic Capacities of the Phylum and Highlights Adaptations to Terrestrial Habitats

(2021) Archana Yadav et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The role of oxygen in stimulating methane production in wetlands

(2021) Jared L. Wilmoth et al.   GLOBAL CHANGE BIOLOGY

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy

(2021) Donovan H Parks et al.   NUCLEIC ACIDS RESEARCH

Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum‐cofactor utilization

(2020) Amanda K. Garcia et al.   Geobiology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biological nitrogen fixation by alternative nitrogenases in terrestrial ecosystems: a review

(2020) J. P. Bellenger et al.   BIOGEOCHEMISTRY

Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

(2020) Alexander Crits-Christoph et al.   ISME Journal

Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils

(2020) Anastasia A. Ivanova et al.   PLoS One

Woody litter protects peat carbon stocks during drought

(2020) Nathalie Fenner et al.   Nature Climate Change

Iron-Only and Vanadium Nitrogenases: Fail-Safe Enzymes or Something More?

(2020) Caroline S. Harwood   Annual Review of Microbiology

Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study

(2020) Andrew R. St. James et al.   ISME Journal

Community-led, integrated, reproducible multi-omics with anvi’o

(2020) A. Murat Eren et al.   Nature Microbiology

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

Mediterranean grassland soil C–N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

(2019) Spencer Diamond et al.   Nature Microbiology

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

KEGG Mapper for inferring cellular functions from protein sequences

(2019) Minoru Kanehisa et al.   PROTEIN SCIENCE

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

(2018) Stephanie A. Eichorst et al.   ENVIRONMENTAL MICROBIOLOGY

Peatland Acidobacteria with a dissimilatory sulfur metabolism

(2018) Bela Hausmann et al.   ISME Journal

The underappreciated potential of peatlands in global climate change mitigation strategies

(2018) J. Leifeld et al.   Nature Communications

Genome-centric view of carbon processing in thawing permafrost

(2018) Ben J. Woodcroft et al.   NATURE

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Refining the taxonomic structure of the phylum Acidobacteria

(2018) Svetlana N. Dedysh et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Are oxygen limitations under recognized regulators of organic carbon turnover in upland soils?

(2016) Marco Keiluweit et al.   BIOGEOCHEMISTRY

Elemental composition and optical properties reveal changes in dissolved organic matter along a permafrost thaw chronosequence in a subarctic peatland

(2016) Suzanne B. Hodgkins et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2016) Dinghua Li et al.   METHODS

Identification of microbial populations driving biopolymer degradation in acidic peatlands by metatranscriptomic analysis

(2016) Anastasia A. Ivanova et al.   MOLECULAR ECOLOGY

TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

(2016) Liam D. H. Elbourne et al.   NUCLEIC ACIDS RESEARCH

The Ecology of Acidobacteria: Moving beyond Genes and Genomes

(2016) Anna M. Kielak et al.   Frontiers in Microbiology

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

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li 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

Significant nonsymbiotic nitrogen fixation in Patagonian ombrotrophic bogs

(2015) Klaus-Holger Knorr et al.   GLOBAL CHANGE BIOLOGY

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival

(2015) Chris Greening et al.   ISME Journal

The contentious nature of soil organic matter

(2015) Johannes Lehmann et al.   NATURE

Diazotrophic methanotrophs in peatlands: the missing link?

(2015) Adrian Ho et al.   PLANT AND SOIL

N2-fixation by methanotrophs sustains carbon and nitrogen accumulation in pristine peatlands

(2014) Melanie A. Vile et al.   BIOGEOCHEMISTRY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Pyrosequencing-Based Assessment of the Bacteria Diversity in Surface and Subsurface Peat Layers of a Northern Wetland, with Focus on Poorly Studied Phyla and Candidate Divisions

(2013) Yulia M. Serkebaeva et al.   PLoS One

Methanotrophy induces nitrogen fixation during peatland development

(2013) T. Larmola et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into functional bacterial diversity and its effects on Alpine bog ecosystem functioning

(2013) Anastasia Bragina et al.   Scientific Reports

Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms

(2012) Alexander Tveit et al.   ISME Journal

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Degradation of natural organic matter: A thermodynamic analysis

(2011) Douglas E. LaRowe et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Telmatobacter bradus gen. nov., sp. nov., a cellulolytic facultative anaerobe from subdivision 1 of the Acidobacteria, and emended description of Acidobacterium capsulatum Kishimoto et al. 1991

(2011) T. A. Pankratov et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Persistence of soil organic matter as an ecosystem property

(2011) Michael W. I. Schmidt et al.   NATURE

Cultivating Uncultured Bacteria from Northern Wetlands: Knowledge Gained and Remaining Gaps

(2011) Svetlana N. Dedysh   Frontiers in Microbiology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Trophic links between fermenters and methanogens in a moderately acidic fen soil

(2009) Pia K. Wüst et al.   ENVIRONMENTAL MICROBIOLOGY

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

(2009) Ryan T Jones et al.   ISME Journal

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS