Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes

Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota

(2018) Yang Liu et al.   ISME Journal

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

(2018) Karthik Anantharaman et al.   ISME Journal

Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond

(2017) Aurélien Saghaï et al.   ENVIRONMENTAL MICROBIOLOGY

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

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

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis

(2017) Daniel Kurth et al.   Scientific Reports

Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient

(2016) Aurélien Saghaï et al.   ENVIRONMENTAL MICROBIOLOGY

Patterns of metal distribution in hypersaline microbialites during early diagenesis: Implications for the fossil record

(2016) M. C. Sforna et al.   Geobiology

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi ) in Sulfur Cycling

(2016) Kenneth Wasmund et al.   mBio

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. I. Microbial Diversity Based on 16S rRNA Gene Amplicons and Metagenomic Sequencing

(2016) Vera Thiel et al.   Frontiers in Microbiology

Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines

(2016) Charlotte D. Vavourakis et al.   Frontiers in Microbiology

Lokiarchaeon is hydrogen dependent

(2016) Filipa L. Sousa et al.   Nature Microbiology

The physiology and habitat of the last universal common ancestor

(2016) Madeline C. Weiss et al.   Nature Microbiology

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

(2015) Dinghua Li et al.   BIOINFORMATICS

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

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

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

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

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

(2015) Rendy Ruvindy et al.   ISME Journal

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

Cyanobacterial reuse of extracellular organic carbon in microbial mats

(2015) Rhona K Stuart et al.   ISME Journal

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Carbon monoxide as a metabolic energy source for extremely halophilic microbes: Implications for microbial activity in Mars regolith

(2015) Gary M. King   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria

(2015) Brett J Baker et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

BREX is a novel phage resistance system widespread in microbial genomes

(2014) T. Goldfarb et al.   EMBO JOURNAL

Diel fluctuations in solute distributions and biogeochemical cycling in a hypersaline microbial mat from Shark Bay, WA

(2014) Anais Pages et al.   MARINE CHEMISTRY

Evidence for arsenic metabolism and cycling by microorganisms 2.7 billion years ago

(2014) Marie Catherine Sforna et al.   Nature Geoscience

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Cyanophycin Mediates the Accumulation and Storage of Fixed Carbon in Non-Heterocystous Filamentous Cyanobacteria from Coniform Mats

(2014) Biqing Liang et al.   PLoS One

DNA as genetic material and as a nutrient in halophilic Archaea

(2014) Aharon Oren   Frontiers in Microbiology

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Microbial biodiversity in saline shallow lakes of the Monegros Desert, Spain

(2013) Emilio O. Casamayor et al.   FEMS MICROBIOLOGY ECOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genomic Analysis of Melioribacter roseus, Facultatively Anaerobic Organotrophic Bacterium Representing a Novel Deep Lineage within Bacteriodetes/Chlorobi Group

(2013) Vitaly V. Kadnikov et al.   PLoS One

Arsenics as bioenergetic substrates

(2012) Robert van Lis et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Inside the alkalinity engine: the role of electron donors in the organomineralization potential of sulfate-reducing bacteria

(2012) K. L. Gallagher et al.   Geobiology

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

(2012) J Kirk Harris et al.   ISME Journal

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

(2012) Mark A Kozubal et al.   ISME Journal

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Ecological Aspects of the Distribution of Different Autotrophic CO2Fixation Pathways

(2011) Ivan A. Berg   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Osmoadaptive Strategies of the Archaeon Halococcus hamelinensis Isolated from a Hypersaline Stromatolite Environment

(2011) Falicia Goh et al.   ASTROBIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Niche differentiation among mat-forming, sulfide-oxidizing bacteria at cold seeps of the Nile Deep Sea Fan (Eastern Mediterranean Sea)

(2011) S. GRÜNKE et al.   Geobiology

Hydrogen production in photosynthetic microbial mats in the Elkhorn Slough estuary, Monterey Bay

(2011) Luke C Burow et al.   ISME Journal

Significance of subtidal microbial deposits in Shark Bay, Australia

(2011) Ricardo J. Jahnert et al.   MARINE GEOLOGY

Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?

(2010) Georg Fuchs   Annual Review of Microbiology

Identification and regulation of novel compatible solutes from hypersaline stromatolite-associated cyanobacteria

(2010) Falicia Goh et al.   ARCHIVES OF MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Chemical Challenges to Bacterial AHL Signaling in the Environment

(2010) Alan W. Decho et al.   CHEMICAL REVIEWS

Diversity and physiology of polyhydroxyalkanoate-producing and -degrading strains in microbial mats

(2010) Laura Villanueva et al.   FEMS MICROBIOLOGY ECOLOGY

Exopolymeric substances (EPS) from Bacillus subtilis : polymers and genes encoding their synthesis

(2010) Massimiliano Marvasi et al.   FEMS MICROBIOLOGY LETTERS

Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme

(2010) Rafael F. Say et al.   NATURE

CRISPR/Cas, the Immune System of Bacteria and Archaea

(2010) P. Horvath et al.   SCIENCE

Quorum sensing in natural environments: emerging views from microbial mats

(2010) Alan W. Decho et al.   TRENDS IN MICROBIOLOGY

Bacterial, archaeal and eukaryotic diversity of smooth and pustular microbial mat communities in the hypersaline lagoon of Shark Bay

(2009) M. A. ALLEN et al.   Geobiology

Arsenic in the Evolution of Earth and Extraterrestrial Ecosystems

(2009) Ronald S. Oremland et al.   GEOMICROBIOLOGY JOURNAL

Modern analogues and the early history of microbial life

(2009) Brendan P. Burns et al.   PRECAMBRIAN RESEARCH

Autoinducers extracted from microbial mats reveal a surprising diversity ofN-acylhomoserine lactones (AHLs) and abundance changes that may relate to diel pH

(2008) Alan W. Decho et al.   ENVIRONMENTAL MICROBIOLOGY

Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico

(2008) Mya Breitbart et al.   ENVIRONMENTAL MICROBIOLOGY

Characteristics and turnover of exopolymeric substances in a hypersaline microbial mat

(2008) Olivier Braissant et al.   FEMS MICROBIOLOGY ECOLOGY

Quorum quenching activity inAnabaenasp. PCC 7120: identification of AiiC, a novel AHL-acylase

(2008) Manuel Romero et al.   FEMS MICROBIOLOGY LETTERS

Niche differentiation among sulfur-oxidizing bacterial populations in cave waters

(2008) Jennifer L Macalady et al.   ISME Journal

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

(2008) Victor Kunin et al.   Molecular Systems Biology

Geological setting of Earth's oldest fossils in the ca. 3.5Ga Dresser Formation, Pilbara Craton, Western Australia

(2008) M VANKRANENDONK et al.   PRECAMBRIAN RESEARCH