Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing ‘signature’ fatty acids of type I methanotrophs

Dedysh, Svetlana N.; Belova, Svetlana E.; Bodelier, Paul L. E.; Smirnova, K. V.; Khmelenina, V. N.; Chidthaisong, Amnat; Trotsenko, Yu. A.; Liesack, Werner; Dunfield, Peter F.

doi:10.1099/ijs.0.64623-0

Cited by 129 publications

(102 citation statements)

References 26 publications

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“…The labeling of the MOBspecific PLFA (i.e., not present in other microbes; C16:1o5t and C16:1o8c) is direct evidence for the methane consumption by representatives of the genera Methylomonas/Methylomicrobium/Methylobacter/Methylosarcina (type Ia) (Bodelier et al, 2009), which were also linked to methane consumption in vitro by microarray analyses (Supplementary Figures S5 and S6 and Supplementary Table S1). The PLFA C16:1o8c is also present in two type II strains, isolated from acidic habitats (Dedysh et al, 2007); however, significant incorporation by these species would be mirrored by an increase of labeling of the PLFA C18:1o8c, which they also posses in large amount. In our samples, this did not occur, strengthening the conclusion that type Ia MOB are responsible for incorporation of label in C16:1o8c.…”

Section: Resultsmentioning

confidence: 98%

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: 98%

Microbial minorities modulate methane consumption through niche partitioning

et al. 2013

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“…The fatty acid 16:1o7 received most of the 13 Clabel in our experiment (Figure 3). This fatty acid is common not only in type I methanotrophs but also in ammonia oxidizers, even in one type II methanotroph (Dedysh et al, 2007). Although ammonia oxidizers can oxidize CH 4 and contain the PLFAs 16:0 and 16:1o7 (Roslev and Iversen, 1999), they seem to play no role for CH 4 oxidation in rice field soil (Bodelier and Frenzel, 1999).…”

Section: Discussionmentioning

confidence: 99%

Applying stable isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field to study activity and composition of the methanotrophic bacterial communities in situ

et al. 2008

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Methanotrophs in the rhizosphere play an important role in global climate change since they attenuate methane emission from rice field ecosystems into the atmosphere. Most of the CH 4 is emitted via transport through the plant gas vascular system. We used this transport for stable isotope probing (SIP) of the methanotrophs in the rhizosphere under field conditions and pulselabelled rice plants in a Chinese rice field with CH 4 (99% 13 C) for 7 days. The rate of 13 CH 4 loss rate during 13 C application was comparable to the CH 4 oxidation rate measured by the difluoromethane inhibition technique. The methanotrophic communities on the roots and in the rhizospheric soil were analyzed by terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing of the particulate methane monooxygenase (pmoA) gene. Populations of type I methanotrophs were larger than those of type II. Both methane oxidation rates and composition of methanotrophic communities suggested that there was little difference between urea-fertilized and unfertilized fields. SIP of phospholipid fatty acids (PLFA-SIP) and rRNA (RNA-SIP) were used to analyze the metabolically active methanotrophic community in rhizospheric soil. PLFA of type I compared with type II methanotrophs was labelled more strongly with 13 C, reaching a maximum of 6.8 atom-%. T-RFLP analysis and cloning/sequencing of 16S rRNA genes showed that methanotrophs, especially of type I, were slightly enriched in the 'heavy' fractions. Our results indicate that CH 4 oxidation in the rice rhizosphere under in situ conditions is mainly due to type I methanotrophs.

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“…However, great care should be taken in interpreting PLFA data since the PLFA database for methanotrophs is much less extensive than the 16S rRNA and functional gene databases. For example, a recent study showed that Methylocystis heyeri strains (type II methanotrophs) contained large amounts of 16:18c, a PLFA that was previously thought to be associated with type I methanotrophs only (31). In another study, Chen et al suggested that acid tolerant, acidophilic type II methanotrophs may contain PLFAs that are different from their neutral pH counterparts (22).…”

Section: Other Molecular Markers: Lipidsmentioning

confidence: 99%

Molecular Ecology Techniques for the Study of Aerobic Methanotrophs

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et al. 2008

Appl Environ Microbiol

349

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3Methane oxidation can occur in both aerobic and anaerobic environments; however, these are completely different processes involving different groups of prokaryotes. Aerobic methane oxidation is carried out by aerobic methanotrophs, and anaerobic methane oxidizers, discovered recently, thrive under anaerobic conditions and use sulfate or nitrate as electron donors for methane oxidation (11,104). This review will focus on the aerobic oxidation of methane.Aerobic methanotrophs are a unique group of methylotrophic bacteria that utilize methane as a sole carbon and energy source (52). Based on their cell morphology, ultrastructure, phylogeny, and metabolic pathways, methanotrophs can be divided into two taxonomic groups: type I and type II. Type I methanotrophs include the genera Methylobacter, Methylomicrobium, Methylomonas, Methylocaldum, Methylosphaera, Methylothermus, Methylosarcina, Methylohalobius, Methylosoma, and Methylococcus, which belong to the gamma subdivision of the Proteobacteria (Fig. 1). The type II methanotrophs Methylocystis, Methylosinus, Methylocella, and Methylocapsa are in the alpha subdivision of the Proteobacteria (52) (Fig. 1). Recently, two filamentous methane oxidizers have been described, Crenothrix polyspora (113), which has a novel pmoA, and Clonothrix fusca (125), which has a conventional pmoA. Both are gammaproteobacteria and are closely related to the type I methanotrophs. Most extant methanotrophs are cultured at 20 to 45°C and neutral pH but have also recently been isolated from extreme environments (reviewed in reference 122).The first step in the oxidation of methane to CO 2 is the conversion of methane to methanol by the enzyme methane monooxygenase. There are two forms of this enzyme: a particulate membrane bound form (pMMO) and a soluble cytoplasmic form (sMMO). The pMMO has been reported in all methanotrophs except for the genus Methylocella (121), whereas the sMMO is present only in certain methanotroph strains (94). The pMMO is a membrane bound copper and iron containing enzyme (reviewed in reference 49). The structural genes for this enzyme have been cloned and sequenced from Methylococcus capsulatus Bath (107, 114), Methylocystis sp. strain M, and Methylosinus trichosporium OB3b (45). They lie in a three-gene operon, pmoCAB, which code for three integral membrane polypeptides of approximately 23, 27, and 45 kDa, respectively. These operons are present in duplicate copies in all three organisms. These duplicate copies of pmoCAB are virtually identical and are transcribed from 70 -type promoters found upstream of the pmoC gene (45, 110).The sMMO is a cytoplasmic enzyme containing a unique di-iron site at its catalytic center. It has a broad substrate range, including trichloroethylene, alkanes, alkenes, and aromatic compounds. The biochemistry of the sMMO has been studied in detail (reviewed in reference 75). It consists of three components: a hydroxylase, which is a dimer of three subunits, (␣␤␥) 2 ; a regulatory protein (protein B); and a reductase (protein C). It is e...

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Methylocystis heyeri sp. nov., a novel type II methanotrophic bacterium possessing ‘signature’ fatty acids of type I methanotrophs

Cited by 129 publications

References 26 publications

Microbial minorities modulate methane consumption through niche partitioning

Microbial minorities modulate methane consumption through niche partitioning

Applying stable isotope probing of phospholipid fatty acids and rRNA in a Chinese rice field to study activity and composition of the methanotrophic bacterial communities in situ

Molecular Ecology Techniques for the Study of Aerobic Methanotrophs

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