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

Bowman, JP; Sly, Lindsay I.; Nichols, Peter D.; Hayward, A. C.

doi:10.1099/00207713-43-4-735

Cited by 426 publications

(265 citation statements)

References 39 publications

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“…The 13 C-isotopic depletion within C 16 (particularly C 16:1v7 ), rather than C 18 FAs compared to other lipids (Fig. 1g), indicates a dominance of type I methanotrophs (Bowman et al 1993;Hanson and Hanson 1996). Moreover, the fractional abundances of the C 16:1v5-8 FAs correspond to those reported for Methylobacter sp.…”

Section: Discussionmentioning

confidence: 95%

Micro‐aerobic bacterial methane oxidation in the chemocline and anoxic water column of deep south‐Alpine Lake Lugano (Switzerland)

Blees

Niemann

Wenk

et al. 2014

Limnology & Oceanography

133

207

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We measured seasonal variations in the vertical distribution of methane concentration, methane oxidation rates, and lipid biomarkers in the northern basin of Lake Lugano. Methane consumption below the oxic-anoxic interface co-occurred with concentration maxima of 13 C-depleted C 16 fatty acid biomarkers (with d 13 C values as low as 270%) in the anoxic water column, as well as characteristic d 13 C CH 4 profiles. We argue that the conspicuous methane concentration gradients are primarily driven by (micro-)aerobic methane oxidation (MOx) below the chemocline. We measured a strong MOx potential throughout the anoxic water column, while MOx rates at in situ O 2 concentration . 10 nmol L 21 were undetectable. Similarly, we found MOx-related biomarkers and gene sequences encoding the particulate methane monooxygenase in the anoxic, but not the oxic, water. The mechanism of (episodic) oxygen supply sustaining the MOx community in anoxic waters is still uncertain. Our results indicate that a bacterial methanotrophic community is responsible for the methane consumption in Lake Lugano, without detectable contribution from archaeal methanotrophs. Bacterial populations that accumulated both at the suboxic-anoxic interface and in the deeper anoxic hypolimnion, where maximum potential MOx rates were observed throughout the year (1.5-2.5 mmol L 21 d 21 ) were mainly related to Methylobacter sp. Close relatives are found in lacustrine environments throughout the world, and their potential to thrive under micro-and anoxic conditions in Lake Lugano may imply that micro-aerobic methane oxidation is important in methane cycling and competition for methane and oxygen in stratified lakes worldwide.

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Section: Discussionmentioning

confidence: 95%

Micro‐aerobic bacterial methane oxidation in the chemocline and anoxic water column of deep south‐Alpine Lake Lugano (Switzerland)

Blees

Niemann

Wenk

et al. 2014

Limnology & Oceanography

133

207

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“…BFH1 and BFH2 with optimal pH 5.5–6.0, respectively (Islam et al, 2016). Although members of Methylobacter have been detected in acidic forest soils, Sphagnum peatlands, and acidic enrichment cultures (Kolb et al, 2005; Kip et al, 2011; Baesman et al, 2015), no taxonomically characterized isolate belonging to the Methylobacter has shown capacity to grow at a pH below 5.0, including the recently descried taxa Methylobacter tundripaludum (Bowman et al, 1993; Wartiainen et al, 2006). …”

Section: Introductionmentioning

confidence: 99%

Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils

Nguyen

Gwak

et al. 2018

Front. Microbiol.

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Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.

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“…Type Ia and Ib), the Alphaproteobacteria (Type II methanotrophs) [3,4], and the Verrucomicrobia [5]. These methanotrophs appear physiologically diverse, especially in regard to their nitrogen metabolism [6], with strains demonstrating co-metabolic oxidization of ammonia [4], nitrate reduction to nitrite [7], detoxification of hydroxylamine and nitrite to the greenhouse gas nitrous oxide via a multitude of pathways [8-10], and fixation of atmospheric nitrogen [11-14]. …”

Section: Introductionmentioning

confidence: 99%

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

Hoefman

Boon

et al. 2014

BMC Microbiol

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BackgroundThe currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments.ResultsWe demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features.ConclusionsDifferential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.

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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

Abstract: Numerical taxonomic, DNA-DNA hybridization, and phospholipid fatty acid composition analyses were performed on an extensive range of methanotrophic strains, including reference strains and environmental

Cited by 426 publications

References 39 publications

Micro‐aerobic bacterial methane oxidation in the chemocline and anoxic water column of deep south‐Alpine Lake Lugano (Switzerland)

Micro‐aerobic bacterial methane oxidation in the chemocline and anoxic water column of deep south‐Alpine Lake Lugano (Switzerland)

Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit

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