AUTHOR=Orata Fabini D. , Meier-Kolthoff Jan P. , Sauvageau Dominic , Stein Lisa Y. 

TITLE=Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels

JOURNAL=Frontiers in Microbiology

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.03162

DOI=10.3389/fmicb.2018.03162

ISSN=1664-302X

ABSTRACT=<p>The order <italic>Methylococcales</italic> constitutes the methanotrophs – bacteria that can metabolize methane, a potent greenhouse gas, as their sole source of energy. These bacteria are significant players in the global carbon cycle and can produce value-added products from methane, such as biopolymers, biofuels, and single-cell proteins for animal feed, among others. Previous studies using single-gene phylogenies have shown inconsistencies in the currently established taxonomic structure of this group. This study aimed to determine and resolve these issues by using whole-genome sequence analyses. Phylogenomic analysis and the use of similarity indexes for genomic comparisons – average amino acid identity, digital DNA–DNA hybridization (dDDH), and average nucleotide identity (ANI) – were performed on 91 <italic>Methylococcales</italic> genomes. Results suggest the reclassification of members at the genus and species levels. Firstly, to resolve polyphyly of the genus <italic>Methylomicrobium</italic>, <italic>Methylomicrobium alcaliphilum</italic>, “<italic>Methylomicrobium buryatense</italic>,” <italic>Methylomicrobium japanense</italic>, <italic>Methylomicrobium kenyense</italic>, and <italic>Methylomicrobium pelagicum</italic> are reclassified to a newly proposed genus, <italic>Methylotuvimicrobium</italic> gen. nov.; they are therefore renamed to <italic>Methylotuvimicrobium alcaliphilum</italic> comb. nov., “<italic>Methylotuvimicrobium buryatense</italic>” comb. nov., <italic>Methylotuvimicrobium japanense</italic> comb. nov., <italic>Methylotuvimicrobium kenyense</italic> comb. nov., and <italic>Methylotuvimicrobium pelagicum</italic> comb. nov., respectively. Secondly, due to the phylogenetic affinity and phenotypic similarities of <italic>Methylosarcina lacus</italic> with <italic>Methylomicrobium agile</italic> and <italic>Methylomicrobium album</italic>, the reclassification of the former species to <italic>Methylomicrobium lacus</italic> comb. nov. is proposed. Thirdly, using established same-species delineation thresholds (70% dDDH and 95% ANI), <italic>Methylobacter whittenburyi</italic> is proposed to be a later heterotypic synonym of <italic>Methylobacter marinus</italic> (89% dDDH and 99% ANI). Also, the effectively but not validly published “<italic>Methylomonas denitrificans</italic>” was identified as <italic>Methylomonas methanica</italic> (92% dDDH and 100% ANI), indicating that the former is a later heterotypic synonym of the latter. Lastly, strains MC09, R-45363, and R-45371, currently identified as <italic>M. methanica</italic>, each represent a putative novel species of the genus <italic>Methylomonas</italic> (21–35% dDDH and 74–88% ANI against <italic>M. methanica</italic>) and were reclassified as <italic>Methylomonas</italic> sp. strains. It is imperative to resolve taxonomic inconsistencies within this group, first and foremost, to avoid confusion with ecological and evolutionary interpretations in subsequent studies.</p>