Complete Genome Sequence of Methylocystis sp. Strain SC2, an Aerobic Methanotroph with High-Affinity Methane Oxidation Potential

Dam, Bomba; Dam, Somasri; Kube, Michael; Reinhardt, Richard; Liesack, Werner

doi:10.1128/jb.01446-12

Cited by 47 publications

(46 citation statements)

References 18 publications

(16 reference statements)

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“…(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.…”

Section: Resultsmentioning

confidence: 99%

Microbial minorities modulate methane consumption through niche partitioning

et al. 2013

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Microbes catalyze all major geochemical cycles on earth. However, the role of microbial traits and community composition in biogeochemical cycles is still poorly understood mainly due to the inability to assess the community members that are actually performing biogeochemical conversions in complex environmental samples. Here we applied a polyphasic approach to assess the role of microbial community composition in modulating methane emission from a riparian floodplain. We show that the dynamics and intensity of methane consumption in riparian wetlands coincide with relative abundance and activity of specific subgroups of methane-oxidizing bacteria (MOB), which can be considered as a minor component of the microbial community in this ecosystem. Microarray-based community composition analyses demonstrated linear relationships of MOB diversity parameters and in vitro methane consumption. Incubations using intact cores in combination with stable isotope labeling of lipids and proteins corroborated the correlative evidence from in vitro incubations demonstrating c-proteobacterial MOB subgroups to be responsible for methane oxidation. The results obtained within the riparian flooding gradient collectively demonstrate that niche partitioning of MOB within a community comprised of a very limited amount of active species modulates methane consumption and emission from this wetland. The implications of the results obtained for biodiversity-ecosystem functioning are discussed with special reference to the role of spatial and temporal heterogeneity and functional redundancy.

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Section: Resultsmentioning

confidence: 99%

Microbial minorities modulate methane consumption through niche partitioning

et al. 2013

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“…Alternatively, Smo/Hmo may be a high-affinity/low-affinity pair. There is precedent for this also in methanotrophs (46), but this still does not explain why copper-free medium or allylthourea would so strongly inhibit growth of NBB4 on C 2 to C 4 alkanes: should not Smo enable growth under these conditions? The relationship between Smo and Hmo remains unclear at this stage.…”

Section: Discussionmentioning

confidence: 99%

SmoXYB1C1Z of Mycobacterium sp. Strain NBB4: a Soluble Methane Monooxygenase (sMMO)-Like Enzyme, Active on C ₂ to C ₄ Alkanes and Alkenes

Martin

Ozsvar

Coleman

2014

Appl Environ Microbiol

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“…Some comparisons used related genomes, particularly Methylosinus trichosporium OB3b (Stein et al, 2010), Methylocystis strain SC2 (Dam et al, 2012), Methylocystis strain ATCC 49242 and several strains of the genius Methylobacterium (Marx et al, 2012). A database of 115 genes involved in methane and methanol oxidation (Supplementary Table 3) including formaldehyde oxidation, formaldehyde fixation and alleviation of stress caused by ammonia cooxidation was assembled and the genomes were searched for these genes via BLAST.…”

Section: Comparative Genomicsmentioning

confidence: 99%

The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis

Tamaš

Smirnova

et al. 2013

The ISME Journal

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The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) viaLGT. This was supported by a compositional analysis suggesting that all MMOs in Alphaproteobacteria methanotrophs are foreign in origin. Some members of the Beijerinckiaceae subsequently lost methanotrophic functions and regained the ability to grow on multicarbon energy substrates. We conclude that B. indica is a recidivist multitroph, the only known example of a bacterium having completely abandoned an evolved lifestyle of specialized methanotrophy.

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Complete Genome Sequence of Methylocystis sp. Strain SC2, an Aerobic Methanotroph with High-Affinity Methane Oxidation Potential

Cited by 47 publications

References 18 publications

Microbial minorities modulate methane consumption through niche partitioning

Microbial minorities modulate methane consumption through niche partitioning

SmoXYB1C1Z of Mycobacterium sp. Strain NBB4: a Soluble Methane Monooxygenase (sMMO)-Like Enzyme, Active on C ₂ to C ₄ Alkanes and Alkenes

The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis

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Complete Genome Sequence of Methylocystis sp. Strain SC2, an Aerobic Methanotroph with High-Affinity Methane Oxidation Potential

Cited by 47 publications

References 18 publications

Microbial minorities modulate methane consumption through niche partitioning

Microbial minorities modulate methane consumption through niche partitioning

SmoXYB1C1Z of Mycobacterium sp. Strain NBB4: a Soluble Methane Monooxygenase (sMMO)-Like Enzyme, Active on C 2 to C 4 Alkanes and Alkenes

The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis

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SmoXYB1C1Z of Mycobacterium sp. Strain NBB4: a Soluble Methane Monooxygenase (sMMO)-Like Enzyme, Active on C ₂ to C ₄ Alkanes and Alkenes