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Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

https://doi.org/10.1101/2020.09.14.296780

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Physiology and Biochemistry of the Aerobic Methanotrophs

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Aerobic Methylotrophic Prokaryotes

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Microbial Ecology of Lake Kivu

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Deep Sequencing of Myxilla (Ectyomyxilla) methanophila, an Epibiotic Sponge on Cold-Seep Tubeworms, Reveals Methylotrophic, Thiotrophic, and Putative Hydrocarbon-Degrading Microbial Associations

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Alkane hydroxylases involved in microbial alkane degradation

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Methylotrophs in natural habitats: current insights through metagenomics

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Differential expression of particulate methane monooxygenase genes in the verrucomicrobial methanotroph ‘Methylacidiphilum kamchatkense’ Kam1

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Production, characterization and antimicrobial activities of bio-pigments by Aquisalibacillus elongatus MB592, Salinicoccus sesuvii MB597, and Halomonas aquamarina MB598 isolated from Khewra Salt Range, Pakistan

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Evolution of photosynthetic reaction centers: insights from the structure of the heliobacterial reaction center

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The Model [NiFe]-Hydrogenases of Escherichia coli

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Crystal Structure of Long-Chain Alkane Monooxygenase (LadA) in Complex with Coenzyme FMN: Unveiling the Long-Chain Alkane Hydroxylase

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

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Mitigation of methane gas emissions in flooded paddy soil through the utilization of methanotrophs

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Crystal Structure of the O 2 -Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b

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Deinococcus misasensis and Deinococcus roseus, novel members of the genus Deinococcus, isolated from a radioactive site in Japan

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Roseimaritima ulvae gen. nov., sp. nov. and Rubripirellula obstinata gen. nov., sp. nov. two novel planctomycetes isolated from the epiphytic community of macroalgae

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The importance of designating type material for uncultured taxa

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Production, oxidation, emission and consumption of methane by soils: A review

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Nicotinoprotein methanol dehydrogenase enzymes in Gram-positive methylotrophic bacteria

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Structural Analysis of Alternative Complex III in the Photosynthetic Electron Transfer Chain of Chloroflexus aurantiacus

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Ambient light emission from hydrothermal vents on the Mid‐Atlantic Ridge

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Diffusive methane emissions to the atmosphere from Lake Kivu (Eastern Africa)

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Methane sources and sinks in Lake Kivu

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Synthesis of Cell Constituents from C2-Units by a Modified Tricarboxylic Acid Cycle

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An uncultivated crenarchaeota contains functional bacteriochlorophyll a synthase

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Mixotrophy drives niche expansion of verrucomicrobial methanotrophs

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Algae acquire vitamin B12 through a symbiotic relationship with bacteria

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Methanotrophy below pH 1 by a new Verrucomicrobia species

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Nitrite-driven anaerobic methane oxidation by oxygenic bacteria

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Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria

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Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions

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Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria

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

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

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Structure of the alternative complex III in a supercomplex with cytochrome oxidase

inferredcites →https://doi.org/10.1038/s41587-020-0501-8openalex-snapshot

A complete domain-to-species taxonomy for Bacteria and Archaea

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A genomic catalog of Earth’s microbiomes

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HydDB: A web tool for hydrogenase classification and analysis

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Analysis of sMMO‐containing Type I methanotrophs in Lake Washington sediment

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Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders

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The Particulate Methane Monooxygenase from Methylococcus capsulatus (Bath) Is a Novel Copper-containing Three-subunit Enzyme

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

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

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PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

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Conservation of Distantly Related Membrane Proteins: Photosynthetic Reaction Centers Share a Common Structural Core

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RNAmmer: consistent and rapid annotation of ribosomal RNA genes

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

inferredcites →https://doi.org/10.1093/nar/gky427openalex-snapshot

SWISS-MODEL: homology modelling of protein structures and complexes

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IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes

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Genomes OnLine database (GOLD) v.7: updates and new features

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AnnoTree: visualization and exploration of a functionally annotated microbial tree of life

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Revised Taxonomy of the Methanotrophs: Description of Methylobacter gen. nov., Emendation of Methylococcus, Validation of Methylosinus and Methylocystis Species, and a Proposal that the Family Methylococcaceae Includes Only the Group I Methanotrophs

inferredcites →https://doi.org/10.1099/ijsem.0.002761openalex-snapshot

Carboxylicivirga sediminis sp. nov., isolated from coastal sediment

inferredcites →https://doi.org/10.1099/ijsem.0.003051openalex-snapshot

Halococcus salsus sp. nov., a novel halophilic archaeon isolated from rock salt

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Methylicorpusculum oleiharenae gen. nov., sp. nov., an aerobic methanotroph isolated from an oil sands tailings pond

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Formaldehyde degradation in Corynebacterium glutamicum involves acetaldehyde dehydrogenase and mycothiol-dependent formaldehyde dehydrogenase

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Heimdallarchaeota harness light energy through photosynthesis

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Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center

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Biology of Extreme Radiation Resistance: The Way of Deinococcus radiodurans

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

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Metabolic flexibility of enigmatic SAR 324 revealed through metagenomics and metatranscriptomics

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Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep‐sea hydrocarbon plume

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Methane oxidation coupled to nitrate reduction under hypoxia by the G ammaproteobacterium M ethylomonas denitrificans , sp. nov. type strain FJG1

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Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

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Study of an alternate glyoxylate cycle for acetate assimilation by Rhodobacter sphaeroides

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Novel methylotrophic bacteria isolated from the River Thames (London, UK)

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Modularity of methylotrophy, revisited

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Aerobic methanol-oxidizingBacteria in soil

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Soluble and particulate methane monooxygenase gene clusters of the type I methanotroph Methylovulum miyakonense HT12

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The global methane cycle: recent advances in understanding the microbial processes involved

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A novel family of functional operons encoding methane/ammonia monooxygenase‐related proteins in gammaproteobacterial methanotrophs

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Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community

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Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum

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Fluorescence In Situ Hybridization-Flow Cytometry-Cell Sorting-Based Method for Separation and Enrichment of Type I and Type II Methanotroph Populations

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Genomic and Transcriptomic Analyses of the Facultative Methanotroph Methylocystis sp. Strain SB2 Grown on Methane or Ethanol

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Methylotrophy in a Lake: from Metagenomics to Single-Organism Physiology

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Partial Genome Assembly for a Candidate Division OP11 Single Cell from an Anoxic Spring (Zodletone Spring, Oklahoma)

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Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26

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Molecular Characterization of Methanotrophic Isolates from Freshwater Lake Sediment

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Two Distinct Monooxygenases for Alkane Oxidation in Nocardioides sp. Strain CF8

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Characterization and Description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an Aryl-Halorespiring Facultative Anaerobic Myxobacterium

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Comparative Analysis of the Conventional and Novel pmo (Particulate Methane Monooxygenase) Operons from Methylocystis Strain SC2

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Characterization of a Novel Methanol Dehydrogenase in Representatives of Burkholderiales : Implications for Environmental Detection of Methylotrophy and Evidence for Convergent Evolution

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Methylotrophy in Mycobacteria: Dissection of the Methanol Metabolism Pathway in Mycobacterium smegmatis

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Phenotypic characterization of the archaebacterial genus Sulfolobus: comparison of five wild-type strains

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Growth on octane alters the membrane lipid fatty acids of Pseudomonas oleovorans due to the induction of alkB and synthesis of octanol

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The Membrane-Associated Methane Monooxygenase (pMMO) and pMMO-NADH:Quinone Oxidoreductase Complex from Methylococcus capsulatus Bath

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Isolation and Characterization of Carotenoid Pigments of Micrococcus roseus

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Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Methane Emissions

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It Takes a Village: Microbial Communities Thrive through Interactions and Metabolic Handoffs

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Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge

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Evolution of Photosynthesis

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The Expanding World of Methylotrophic Metabolism

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Prodigal: prokaryotic gene recognition and translation initiation site identification

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Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

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FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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The Abundance of Pink-Pigmented Facultative Methylotrophs in the Root Zone of Plant Species in Invaded Coastal Sage Scrub Habitat

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

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Antioxidant effects of carotenoids in a model pigment-protein complex.

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Laboratory Simulations of Abiotic Hydrocarbon Formation in Earth's Deep Subsurface

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Diversity and Habitat Preferences of Cultivated and Uncultivated Aerobic Methanotrophic Bacteria Evaluated Based on pmoA as Molecular Marker

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Ammonia Oxidation and Nitrite Reduction in the Verrucomicrobial Methanotroph Methylacidiphilum fumariolicum SolV

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Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla

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Characterization of the Desiccation Tolerance of Cronobacter sakazakii Strains

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Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN

inferredcites →https://doi.org/10.3390/microorganisms3010094openalex-snapshot

Genomics of Methylotrophy in Gram-Positive Methylamine-Utilizing Bacteria

inferredcites →https://doi.org/10.4319/lo.1988.33.4.0571openalex-snapshot

Methane cycling in the sediments of Lake Washington

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Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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