Methylomicrobium

Abstract

Me.thy.lo.mi.cro' bi.um. N.L. pref. methylo ‐ pertaining to the methyl radical; Gr. adj. micros small; Gr. n. bios life; M.L. n. Methylomicrobium a small organism able to utilize methyl units. Proteobacteria / Gammaproteobacteria / Methylococcales / Methylococcaceae / Methylomicrobium Cells are short rods, 0.5–1.5 µm × 1.5–3.0 µm. Motile, monotrichous, or peritrichous. Reproduce by binary fission. Lack cysts or other differentiated resting stages. Cells form intracytoplasmic membranes as stacks of vesicular disks . Cells may possess a thin slime capsule and form regular glycoprotein S‐layers arranged in p2 , p4 , or p6 symmetries. Aerobic , can grow at low‐oxygen tension and display fermentation and denitrification capabilities . Some species can oxidize ammonium and inorganic and organic sulfur compounds as additional sources of energy. Obligate methanotrophs utilizing methane or methanol as the carbon and energy sources but not other C 1 and C n compounds. Assimilate formaldehyde via the ribulose monophosphate pathway , and all strains have a partial serine cycle . Utilize nitrate and ammonium salts as nitrogen sources. Some species can use urea, methylamine, and amino acids as nitrogen sources. Mostly mesophilic , with optimal growth at 25–35°C. Some strains are alkalitolerant or alkaliphilic, growing well in the pH range between 9 and 10.5, and require sodium ions for growth. Possess a particulate methane monooxygenase (MMO), and some strains may also contain a soluble MMO. The most abundant fatty acids are C 16:1 ω 7 c , C 16:1 , C 16:0 , C 14:0 , and C 16:1 ω 8 c . Ubiquinone‐8 (Q‐8) is the predominant quinone. Isolated from sediments of freshwater lakes and rivers, saline soda lakes, wetland muds, agricultural and swampy soils, upper mixing layers of oceans, and estuarine waters. Belongs to the Gammaproteobacteria, order Methylococcales , family Methylococcaceae . DNA G + C content (mol%) : 46–51. Type species : Methylomicrobium agile (Bowman, Sly, Nichols and Hayward 1993) Bowman, Sly and Stackebrandt 1995, 183 VP ( Methylobacter agilis Bowman, Sly, Nichols and Hayward 1993, 749.).

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

“…Comparisons between M. agile ATCC 35068 T and M. album BG8 T resulted in 90% dDDH and 99% ANI (Supplementary Table S4), and both strains should represent the same species (cluster 50) (Figure 2). This high ANI was also shown in a previous work (Kalyuzhnaya, 2016a). With M. agile , being the type species of the genus and described before M. album (Bowman et al, 1995), the former species should take name priority over M. album (Rule 23a, section 5 and Rule 38, section 7 of the Bacteriological Code; Lapage et al, 1992); thus, M. album is presumed to be a later heterotypic synonym.…”

“…nov. type species status of the novel genus. However, type strain AA-23 T has been lost from culture collections, and there are no other cultures available to replace/represent this species (Kalyuzhnaya et al, 2008; Kalyuzhnaya, 2016a). Thus, we also propose M. alcaliphilum comb.…”

“…nov. 20Z T and “ M. buryatense ” comb. nov. 5G, be considered a single species based on 95% ANI (Kalyuzhnaya, 2016a). While we obtained a similar borderline ANI value, dDDH is only 63%, providing a much stronger argument to maintain the two as different species (clusters 47 and 48, respectively) (Figure 2 and Supplementary Table S4).…”

“…In cases were phenotypic information was needed to clarify taxon affiliation, data on several phenotypic characteristics commonly tested between organisms were collected from the original isolation papers and the Bergey’s Manual of Systematics of Archaea and Bacteria (Table 1; Bowman, 2016a,b; Hirayama, 2016; Kalyuzhnaya, 2016a,b; Collins et al, 2017; Bowman, 2018). Data missing from isolation papers and information on isolates that are not type strains were retrieved from other references as stipulated.…”

“…Similarly, average nucleotide identity (ANI) also measures the nucleotide-level similarity between two genomes (Richter and Rosselló-Móra, 2009), which represent the same species if they have at least 95% ANI (Goris et al, 2007). The use of ANI had uncovered high levels of genomic similarity between methanotrophic species Methylomicrobium agile and Methylomicrobium album (Kalyuzhnaya, 2016a), as well as Methylobacter marinus and Methylobacter whittenburyi (Collins et al, 2017), therefore questioning their identities. Although not as widely used, average amino acid identity (AAI) (Konstantinidis and Tiedje, 2005) and the percentage of conserved proteins (POCP) (Qin et al, 2014), which both measure amino acid-level genomic similarity between protein-coding regions, have been proposed to delineate organisms at the genus level.…”