Complete Genome Sequence of the Aerobic Marine Methanotroph Methylomonas methanica MC09

Abstract

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seawater obtained from the coast of Penarth, United Kingdom (lat 51.43, long Ϫ3.17) (M. Cunliffe and J. C. Murrell, unpublished data).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 (...

Microbial minorities modulate methane consumption through niche partitioning

“…(Supplementary Tables S2-S6). Although several genome sequences of MOB (Methylomonas methanica MC09 (Boden et al, 2011), Methylomicrobium album strain BG8, Methylococcus capsulatus strain Bath and Texas (Ward et al, 2004;Kleiveland et al, 2012), Methylocystis strain Rockwell (Stein et al, 2011), Methylocystis strain SC2 (Dam et al, 2012), Methylocystis parvus OBBP (del Cerro et al, 2012), Methylosinus trichosporium OB3b (Stein et al, 2010)) were deposited in the consulted NCBI nr database, almost no other labeled peptide sequences affiliated to MOB were identified besides peptides of Methylobacter tundripaludum SV96. In addition, most of the identified peptide sequences had to be excluded according to the stringent Mascot scoring parameters, which may be related to the soil matrix.…”

Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

“…Some methanotrophs have been identified with the ability of urea hydrolysis (Boden et al, 2011;Khmelenina et al, 2013); however, the 13 C-labeled active methanotrophs on the basis of the 16S rRNA gene (Fig. 4a) and the pmoA gene (Fig.…”

Trimethylamine and trimethylamine N-oxide are supplementary energy sources for a marine heterotrophic bacterium: implications for marine carbon and nitrogen cycling

“…Both strains were incubated at 30 1C on a rotary shaker (150 r.p.m). Methylomonas methanica MC09 (Boden et al, 2011a) was maintained on MAMS plates using methane (5%) as the sole carbon source. For growth experiments, M. methanica was grown in MAMS medium using methanol (2 mM) as the sole carbon source and incubated at 25 1C.…”

“…To test this hypothesis, we designed a co-culture experiment with R. pomeroyi and the methylotrophic bacterium, Methylomonas methanica MC09 (Boden et al, 2011a). We inoculated a C-starved and N-starved R. pomeroyi culture (B10 8 ml per cells) with M. methanica (B10 7 ml per cells) and supplied methanol (1 mM) as the only C source in the system, as methanol is only utilised by M. methanica.…”