Metabolic versatility of small archaea Micrarchaeota and Parvarchaeota

‘ARMAN’ archaea depend on association with euryarchaeal host in culture and in situ

(2017) Olga V. Golyshina et al.   Nature Communications

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms

(2017) Susanne Krause et al.   Scientific Reports

Microbial communities, processes and functions in acid mine drainage ecosystems

(2016) Lin-xing Chen et al.   CURRENT OPINION IN BIOTECHNOLOGY

The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales

(2016) Olga V. Golyshina et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

New CRISPR–Cas systems from uncultivated microbes

(2016) David Burstein et al.   NATURE

Genomics-informed isolation and characterization of a symbiotic Nanoarchaeota system from a terrestrial geothermal environment

(2016) Louie Wurch et al.   Nature Communications

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

(2016) Emiley A. Eloe-Fadrosh et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

(2015) Cindy J. Castelle et al.   CURRENT BIOLOGY

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

(2015) Christopher T. Brown et al.   NATURE

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Dongwan D. Kang et al.   PeerJ

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Biogeochemical Processes Governing Natural Pyrite Oxidation and Release of Acid Metalliferous Drainage

(2014) Ya-ting Chen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage

(2014) Lin-xing Chen et al.   ISME Journal

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’

(2014) Noha H Youssef et al.   ISME Journal

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

(2014) Zheng-Shuang Hua et al.   ISME Journal

Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

(2014) Celia Méndez-García et al.   ISME Journal

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

(2014) C. Brasen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

Archaea in Biogeochemical Cycles

(2013) Pierre Offre et al.   Annual Review of Microbiology

Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park

(2013) Mircea Podar et al.   Biology Direct

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

(2013) Alexis P Yelton et al.   BMC GENOMICS

Shifts in microbial community composition and function in the acidification of a lead/zinc mine tailings

(2013) Lin-xing Chen et al.   ENVIRONMENTAL MICROBIOLOGY

Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria

(2013) Sibylle Ziegler et al.   ISME Journal

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing

(2013) Weiguo Hou et al.   PLoS One

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment

(2013) Cindy J. Castelle et al.   Nature Communications

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

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

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

Spatial and Temporal Analysis of the Microbial Community in the Tailings of a Pb-Zn Mine Generating Acidic Drainage

(2011) Li-Nan Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The cytochrome bd respiratory oxygen reductases

(2011) Vitaliy B. Borisov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

(2011) Priya Narasingarao et al.   ISME Journal

Cyanobacterial NDH-1 complexes: Novel insights and remaining puzzles

(2010) Natalia Battchikova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature

(2010) Vincent J Denef et al.   ISME Journal

Multiple displacement amplification compromises quantitative analysis of metagenomes

(2010) Suzan Yilmaz et al.   NATURE METHODS

Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community

(2010) Martin Allgaier et al.   PLoS One

Enigmatic, ultrasmall, uncultivated Archaea

(2010) B. J. Baker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isoprenoid biosynthesis in Archaea – Biochemical and evolutionary implications

(2010) Rie Matsumi et al.   RESEARCH IN MICROBIOLOGY

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

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

An Anaerobic-Type α-Ketoglutarate Ferredoxin Oxidoreductase Completes the Oxidative Tricarboxylic Acid Cycle of Mycobacterium tuberculosis

(2009) Anthony D. Baughn et al.   PLoS Pathogens

Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon

(2008) Luis R Comolli et al.   ISME Journal

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Prediction of signal peptides in archaea

(2008) P.G. Bagos et al.   PROTEIN ENGINEERING DESIGN & SELECTION