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

Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium

(2015) M. Tank et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Refining the phylum Chlorobi by resolving the phylogeny and metabolic potential of the representative of a deeply branching, uncultivated lineage

(2015) Jennifer Hiras et al.   ISME Journal

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

(2015) Masaru K Nobu et al.   ISME Journal

Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

(2015) Young-Mo Kim et al.   Frontiers in Microbiology

The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light

(2015) Shane Nowack et al.   Frontiers in Microbiology

The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

(2015) Eric D. Becraft et al.   Frontiers in Microbiology

Nutrient requirements and growth physiology of the photoheterotrophic Acidobacterium, Chloracidobacterium thermophilum

(2015) Marcus Tank et al.   Frontiers in Microbiology

The molecular dimension of microbial species: 3. Comparative genomics of Synechococcus strains with different light responses and in situ diel transcription patterns of associated putative ecotypes in the Mushroom Spring microbial mat

(2015) Millie T. Olsen et al.   Frontiers in Microbiology

Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov., thermophilic anaerobic representatives of the phylum Planctomycetes

(2014) G. B. Slobodkina et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Global Patterns of Abundance, Diversity and Community Structure of the Aminicenantes (Candidate Phylum OP8)

(2014) Ibrahim F. Farag et al.   PLoS One

Cyanobacterial Light-Driven Proton Pump, Gloeobacter Rhodopsin: Complementarity between Rhodopsin-Based Energy Production and Photosynthesis

(2014) Ah Reum Choi et al.   PLoS One

Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations

(2013) Vaibhav Bhandari et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Phylogenetic Delineation of the Novel Phylum Armatimonadetes (Former Candidate Division OP10) and Definition of Two Novel Candidate Divisions

(2013) K. C. Y. Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

AmphoraNet: The webserver implementation of the AMPHORA2 metagenomic workflow suite

(2013) Csaba Kerepesi et al.   GENE

Temporal metatranscriptomic patterning in phototrophic Chloroflexi inhabiting a microbial mat in a geothermal spring

(2013) Christian G Klatt et al.   ISME Journal

Isolation and Characterization of a Thermophilic, Obligately Anaerobic and Heterotrophic Marine Chloroflexi Bacterium from a Chloroflexi-dominated Microbial Community Associated with a Japanese Shallow Hydrothermal System, and Proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov.

(2013) Takuro Nunoura et al.   MICROBES AND ENVIRONMENTS

Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units

(2013) Alexander F. Koeppel et al.   NUCLEIC ACIDS RESEARCH

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

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

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

(2013) Jeremy A. Dodsworth et al.   Nature Communications

Community Structure and Function of High-Temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments

(2013) Christian G. Klatt et al.   Frontiers in Microbiology

Description of Fimbriimonas ginsengisoli gen. nov., sp. nov. within the Fimbriimonadia class nov., of the phylum Armatimonadetes

(2012) Wan-Taek Im et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov.

(2012) Radhey S. Gupta et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

‘Candidatus Thermochlorobacter aerophilum:’ an aerobic chlorophotoheterotrophic member of the phylum Chlorobi defined by metagenomics and metatranscriptomics

(2012) Zhenfeng Liu et al.   ISME Journal

Fine-Scale Distribution Patterns of Synechococcus Ecological Diversity in Microbial Mats of Mushroom Spring, Yellowstone National Park

(2011) Eric D. Becraft et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria

(2011) Amaya M. Garcia Costas et al.   ENVIRONMENTAL MICROBIOLOGY

Hydrothermal ecotones and streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park

(2011) D'Arcy R Meyer-Dombard et al.   ENVIRONMENTAL MICROBIOLOGY

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

(2011) Christian G Klatt et al.   ISME Journal

Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat

(2011) Zhenfeng Liu et al.   ISME Journal

Identification of the Bacteriochlorophylls, Carotenoids, Quinones, Lipids, and Hopanoids of "Candidatus Chloracidobacterium thermophilum"

(2011) A. M. Garcia Costas et al.   JOURNAL OF BACTERIOLOGY

Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076

(2011) Jean F. Challacombe et al.   PLoS One

Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum “Chloroflexi”, isolated from a deep hot aquifer in the Aquitaine Basin

(2011) Patrick Grégoire et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Influence of Molecular Resolution on Sequence-Based Discovery of Ecological Diversity amongSynechococcusPopulations in an Alkaline Siliceous Hot Spring Microbial Mat

(2010) Melanie C. Melendrez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Chthonomonas calidirosea gen. nov., sp. nov., an aerobic, pigmented, thermophilic micro-organism of a novel bacterial class, Chthonomonadetes classis nov., of the newly described phylum Armatimonadetes originally designated candidate division OP10

(2010) K. C.- Y. Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10

(2010) H. Tamaki et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

In situ dynamics of O2, pH and cyanobacterial transcripts associated with CCM, photosynthesis and detoxification of ROS

(2010) Sheila I Jensen et al.   ISME Journal

Cultivation and Genomic, Nutritional, and Lipid Biomarker Characterization of Roseiflexus Strains Closely Related to Predominant In Situ Populations Inhabiting Yellowstone Hot Spring Microbial Mats

(2010) M. T. J. van der Meer et al.   JOURNAL OF BACTERIOLOGY

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

(2010) Takuro Nunoura et al.   NUCLEIC ACIDS RESEARCH

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria

(2009) T. Iino et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Microbial methane production in deep aquifer associated with the accretionary prism in Southwest Japan

(2009) Hiroyuki Kimura et al.   ISME Journal

Mapping the Tree of Life: Progress and Prospects

(2009) N. R. Pace   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum

(2009) Dongying Wu et al.   PLoS One

Roseomonas aestuarii sp. nov., a bacteriochlorophyll-a containing alphaproteobacterium isolated from an estuarine habitat of India

(2009) V. Venkata Ramana et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol

(2008) José R. de la Torre et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial community composition in thermophilic microbial mats from five hot springs in central Tibet

(2008) Maggie C. Y. Lau et al.   EXTREMOPHILES

Elioraea tepidiphila gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria

(2008) L. Albuquerque et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Regulation of nif gene expression and the energetics of N2 fixation over the diel cycle in a hot spring microbial mat

(2008) Anne-Soisig Steunou et al.   ISME Journal

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH