Emended description of Methylomonas rubra sp. nov.

Romanovskaya, V. A.; Rokitko, P. V.; Shi-lin, SU; Malashenko, Yu. R.

doi:10.1134/s0026261706060117

Cited by 9 publications

(5 citation statements)

References 15 publications

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“… c Listed publications describe the initial isolation, current classification and genome sequence of the strain as far as already available . d The type strain of Methylomonas rubra was reported to belong to the species “Methylomonas methanica” (Bowman et al, 1993 ), but later it was proposed to represent a separate species (Romanovskaya et al, 2006 ); this has not been validated yet . e According to Bergey's manual of systematic bacteriology, strains of these species do not exist anymore and the species are not considered as valid (Bowman, 2005a ), but at least for Methylococcus mobilis, this appears not to be correct, as the type strain is listed in the NCCB catalog .…”

Section: Diversity and Ecophysiology Of Cultivated Methanotrophic Bacmentioning

confidence: 99%

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

2015

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Methane-oxidizing bacteria are characterized by their capability to grow on methane as sole source of carbon and energy. Cultivation-dependent and -independent methods have revealed that this functional guild of bacteria comprises a substantial diversity of organisms. In particular the use of cultivation-independent methods targeting a subunit of the particulate methane monooxygenase (pmoA) as functional marker for the detection of aerobic methanotrophs has resulted in thousands of sequences representing “unknown methanotrophic bacteria.” This limits data interpretation due to restricted information about these uncultured methanotrophs. A few groups of uncultivated methanotrophs are assumed to play important roles in methane oxidation in specific habitats, while the biology behind other sequence clusters remains still largely unknown. The discovery of evolutionary related monooxygenases in non-methanotrophic bacteria and of pmoA paralogs in methanotrophs requires that sequence clusters of uncultivated organisms have to be interpreted with care. This review article describes the present diversity of cultivated and uncultivated aerobic methanotrophic bacteria based on pmoA gene sequence diversity. It summarizes current knowledge about cultivated and major clusters of uncultivated methanotrophic bacteria and evaluates habitat specificity of these bacteria at different levels of taxonomic resolution. Habitat specificity exists for diverse lineages and at different taxonomic levels. Methanotrophic genera such as Methylocystis and Methylocaldum are identified as generalists, but they harbor habitat specific methanotrophs at species level. This finding implies that future studies should consider these diverging preferences at different taxonomic levels when analyzing methanotrophic communities.

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Section: Diversity and Ecophysiology Of Cultivated Methanotrophic Bacmentioning

confidence: 99%

“… d The type strain of Methylomonas rubra was reported to belong to the species “Methylomonas methanica” (Bowman et al, 1993 ), but later it was proposed to represent a separate species (Romanovskaya et al, 2006 ); this has not been validated yet . …”

Section: Diversity and Ecophysiology Of Cultivated Methanotrophic Bacmentioning

confidence: 99%

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

2015

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“…Several other Methylomonas species without validly published names have also been described, including "M. clara" (8) and "M. rubra" (18). All members of the genus use methane as the sole carbon and energy source.…”

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confidence: 99%

Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09

et al. 2011

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Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria, isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph.Methylomonas methanica (11,21) is one of four recognized species within the genus Methylomonas in the Gammaproteobacteria, which includes M. aurantiaca (3, 12), M. fodinarum (3,12), and M. scandinavica (13,14). Several other Methylomonas species without validly published names have also been described, including "M. clara" (8) and "M. rubra" (18). All members of the genus use methane as the sole carbon and energy source. The majority of known strains were obtained from terrestrial environments; however, M. methanica MC09 was isolated from a methane enrichment culture inoculated with seawater obtained from the coast of Penarth, United Kingdom (lat 51.43, long Ϫ3.17) (M. Cunliffe and J. C. Murrell, unpublished data). Methylomonas spp. are prevalent in various marine and estuarine environments (5,9,16,19,20). The complete genome sequence of M. methanica MC09 is the first available for a marine methanotroph, providing insights into methane cycling in marine environments.The genome (5.05 Mbp) of M. methanica MC09 was assembled using VELVET (22) and Newbler from an Illumina GAii (2) shotgun library (74,177,086 reads; 2.67 Gbp) and 454 Titanium (15) standard (215,708 reads) and paired-end (154 Mbp) libraries representing 24.3ϫ coverage. Gaps were closed by PCR and Bubble PCR primer walks (350 reactions and 1 shatter library) using Consed (7). The genome is a single circular replicon with 4,494 candidate protein-encoding genes, as predicted by Prodigal (10) and GenePrimp (17). The mean GC content of the sequence was 51.3 mol%.Synthetic pathways for tRNAs of all 20 structural amino acids were accounted for, along with a single rRNA operon. Three terminal oxidases were predicted: aa 3 , o-quinol, and bd-quinol.All genes for the 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase variant of the ribulose monophosphate (RuMP) pathway of formaldehyde fixation were predicted, consistent with experimental data for Methylomonas spp. (1). All genes of the pentose phosphate and Embden-Meyerhof-Parnas pathways were predicted. Genes for all enzymes of Krebs' cycle, with the exception of fumarase, were predicted. Genes for RubisCO were not found. The mxaFJGIRSACKLDEK cluster encoding methanol dehydrogenase was predicted, along with the cluster pqqBCDE for biosynthesis of the cofactor pyrroloquinoline quinone. Both particulate (pmoCAB) and soluble (mmoXYBZDCGR) methane monooxygenases were predicted. Acetate kinase and acetyl coenzyme A synthase were predicted, potentially allowing C 2 -compound assimilation.All genes required for dinitrogen fixation were predicted, as were those for nitrate/nitrite transport (nasFED), ammonification (nasCA, nasB, and nirBD), direct ammonium uptake (amtB), and nitrogen assimilation (glnA, gltB, and ald). Urea metabolism genes were predicted (...

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“…Genome sizes of members of the genus Methylomonas range between 3.67 and 5.48 Mb, although most available complete genomes exceed 5 Mb [13]. The DNA G+C content of OY6 T , calculated from the whole-genome sequence, was 51.7 mol%, closely resembling values in ' M. rubra ', M. albis and M. fluvii (51.0–52.0, 51.1 and 51.5 mol%, respectively) [12, 58] and within the range of known DNA G+C contents of species of the genus Methylomonas (47.0–58.4 mol%). As complementary methods, DDH and ANI values are commonly employed as gold standards for prokaryotic species definition.…”

Section: Resultsmentioning

confidence: 90%

“…Strains: 1, OY6 T ; 2, M. methanica ATCC 35067 T , JB5, JB9, JB17, JB227, JB40, JB182, JB193, JB194, JB195 and JB228 [8]; 3, M. aurantiaca JB25, JB27, JB96, JB97, JB98, JB99, JB100, JB102, JB103 T , JB104, JB101, JB105, JB106, JB114, JB121, JB122, JB126, JB129, JB142, JB176, JB177A, JB177B, JB179A, JB178A, JB178B and JB179B [18]; 4, M. fodinarum JB2, JB3, JB4, JB6, JB7, JB10, UQM3268 T , JB15, JB34, JB37 and JB70 [18]; 5, M. scandinavica SR5 T [6]; 6, 'M. rubra' 15sh [58]; 7, M. koyamae Fw12E-Y T [15]; 8, M. paludis MG30 T [16]; 9, M. lenta R-45377 T [14]; 10, 'M. rhizoryzae' GJ1 [56]; 11, M. albis EbA T [12]; 12, M. fluvii EbB T [12]; 13, M. rapida MP1 T [13].…”

Section: Table 1 Major Characteristics Of Oy6 T In Comparison With Ot...mentioning

confidence: 99%

Methylomonas defluvii sp. nov., a type I methane-oxidizing bacterium from a secondary sedimentation tank of a wastewater treatment plant

Ouyang,

Wang,

Nie

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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An aerobic methanotroph was isolated from a secondary sedimentation tank of a wastewater treatment plant and designated strain OY6T. Cells of OY6T were Gram-stain-negative, pink-pigmented, motile rods and contained an intracytoplasmic membrane structure typical of type I methanotrophs. OY6T could grow at a pH range of 4.5–7.5 (optimum pH 6.5) and at temperatures ranging from 20 °C to 37 °C (optimum 30 °C). The major cellular fatty acids were C14 : 0, C16 : 1ω7c/C16 : 1ω6c and C16 : 1ω5c; the predominant respiratory quinone was MQ-8. The genome size was 5.41 Mbp with a DNA G+C content of 51.7 mol%. OY6T represents a member of the family Methylococcaceae of the class Gammaproteobacteria and displayed 95.74–99.64 % 16S rRNA gene sequence similarity to the type strains of species of the genus Methylomonas. Whole-genome comparisons based on average nucleotide identity (ANI) and digital DNA–DNA hybridisation (dDDH) confirmed that OY6T should be classified as representing a novel species. The most closely related type strain was Methylomonas fluvii EbBT, with 16S rRNA gene sequence similarity, ANI by blast (ANIb), ANI by MUMmer (ANIm) and dDDH values of 99.64, 90.46, 91.92 and 44.5 %, respectively. OY6T possessed genes encoding both the particulate methane monooxygenase enzyme and the soluble methane monooxygenase enzyme. It grew only on methane or methanol as carbon sources. On the basis of phenotypic, genetic and phylogenetic data, strain OY6T represents a novel species within the genus Methylomonas for which the name Methylomonas defluvii sp. nov. is proposed, with strain OY6T (=GDMCC 1.4114T=KCTC 8159T=LMG 33371T) as the type strain.

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Emended description of Methylomonas rubra sp. nov.

Cited by 9 publications

References 15 publications

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

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

Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09

Methylomonas defluvii sp. nov., a type I methane-oxidizing bacterium from a secondary sedimentation tank of a wastewater treatment plant

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