Methanotrophic Bacteria

Graham, David W.; Kim, Hyung J.; Lindner, Angela S.

doi:10.1002/0471263397.env316

Cited by 9 publications

(12 citation statements)

References 135 publications

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“…However, the ratios of 13 C-labeled type II to type I methanotrophs were 20.0 to 101 in the low-pH soils of YX, YT and TY (Table S4). Assuming that one cell contained two copies of pmoA genes (Kolb et al, 2003), type II methanotrophs could reach a cell-specific methane oxidation rate of 0.2-9.6 fmol CH 4 h −1 cell −1 in these three soils (calculated in Table S4), being consistent with previous report of 0.2-15 fmol CH 4 h −1 cell −1 obtained from both pure cultures and complex soils (Hanson and Hanson, 1996). These results thus suggest that aerobic methanotrophy was mostly sustained by the growth of type II methanotrophs in these low-pH paddy soils.…”

Section: Discussionsupporting

confidence: 91%

“…Despite different compositions of active methanotrophs, there was no fundamental difference of methane oxidation rate between low-pH and high-pH paddy soils, indicating similar methane oxidation rate of type II and I methanotrophs in rice paddy fields. The culture-dependent studies have showed similar kinetic traits between these two groups of methanotrophs, including substrate affinity and specific cell activity (Bedard and Knowles, 1989;Calhoun and King, 1998;Hanson and Hanson, 1996), which might explain the similar methane oxidation rates in different soils in the present study. The significant 13 C enrichment of soil organic C indicated that 13 CH 4 -derived microbial biomass contributed significantly to the turnover of soil C. Metaanalysis indicated microbial biomass represents 0.6 %-1.1 % of total soil organic C (Fierer et al, 2009), but the contri-bution of methane-driven microbial food web to soil fertility and quality remained largely unknown (Murase and Frenzel, 2007).…”

Section: Discussionsupporting

confidence: 67%

“…Accumulating evidence has indicated that the specialized MOB clades designated as upland soil clusters α and γ (USCα and USCγ , respectively) have high CH 4 affinity and catalyze atmospheric methane oxidation in unsaturated soils (Holmes et al, 1999;Knief et al, 2003;Roslev and Iversen, 1999;Tveit et al, 2019), while the canonical α and γ Proteobacteria MOB (known as type II and type I methan-otrophs) are considered to adapt better to high-concentration methane and thus regulate the methane oxidation in ecosystems with constant methane production, such as wetlands. Despite coexistence of type I and II methanotrophs in these ecosystems, their activity and contribution to methane oxidation has often been observed to vary largely depending on different environmental conditions and the predominant activity of either type I or type II methanotrophs (Chen et al, 2008a;Daebeler et al, 2014;He et al, 2012;Liebner and Wagner, 2007;Lin et al, 2004). This might be due to some major physiological differences that exist between these two groups.…”

Section: Introductionmentioning

confidence: 99%

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The pH-based ecological coherence of active canonical methanotrophs in paddy soils

2020

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Abstract. Soil pH is considered one of the main determinants of the assembly of globally distributed microorganisms that catalyze the biogeochemical cycles of carbon (C) and nitrogen (N). However, direct evidence for niche specialization of microorganisms in association with soil pH is still lacking. Using methane-oxidizing bacteria (methanotrophs) as a model system of C cycling, we show that pH is potentially the key driving force selecting for canonical γ (type I) and α (type II) methanotrophs in rice paddy soils. DNA-based stable isotope probing (DNA-SIP) was combined with high-throughput sequencing to reveal the taxonomic identities of active methanotrophs in physiochemically contrasting soils from six different paddy fields across China. Following microcosm incubation amended with 13CH4, methane was primarily consumed by Methylocystis-affiliated type II methanotrophs in soils with a relatively low pH (5.44–6.10), whereas Methylobacter- or Methylosarcina-affiliated type I methanotrophs dominated methane consumption in soils with a high pH (7.02–8.02). Consumption of 13CH4 contributed 0.203 % to 1.25 % of soil organic C, but no significant difference was observed between high-pH and low-pH soils. The fertilization of ammonium nitrate resulted in no significant changes in the compositions of 13C-labeled methanotrophs in the soils, although significant inhibition of methane oxidation activity was consistently observed in low-pH soils. Mantel analysis further validated that soil pH, rather than other parameters tested, had significant correlation to the variation in active methanotrophic compositions across different rice paddy soils. These results suggest that soil pH might have played a pivotal role in mediating the niche differentiation of ecologically important aerobic methanotrophs in terrestrial ecosystems and imply the importance of such niche specialization in regulating methane emissions in paddy fields following increasingly intensified input of anthropogenic N fertilizers.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionsupporting

confidence: 67%

Section: Introductionmentioning

confidence: 99%

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The pH-based ecological coherence of active canonical methanotrophs in paddy soils

2020

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“…Through the oxidation of methane, a significant greenhouse gas, they play an important role in the global cycling of carbon. Furthermore, they play a significant role in contaminant co-metabolism [2]. Their ability to co-metabolize chlorinated ethenes is important because these compounds are persistent in soils and aquifers that have been exposed to them, for example, as a result of container leaks or inappropriate disposal practices.…”

Section: Introductionmentioning

confidence: 99%

Diversity of methanotroph communities in a basalt aquifer

Newby

Reed

Petzke

et al. 2004

FEMS Microbiology Ecology

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Methanotrophic bacteria play an important role in global cycling of carbon and co-metabolism of contaminants. Methanotrophs from pristine regions of the Snake River Plain Aquifer (SRPA; Idaho, USA) were studied in order to gain insight into the native groundwater communities' genetic potential to carry out TCE co-metabolism. Wells were selected that were proximal to a TCE plume believed to be undergoing natural attenuation. Methane concentrations ranged from 1 to >1000 nM. Carbon isotope ratios and diversity data together suggest that the SRPA contains active communities of methanotrophs that oxidize microbially produced methane. Microorganisms removed from groundwater by filtration were used as inocula for enrichments or frozen immediately and DNA was subsequently extracted for molecular characterization. Primers that specifically target methanotroph 16S rRNA genes or genes that code for subunits of soluble or particulate methane monooxygenase, mmoX and pmoA, respectively, were used to characterize the indigenous methanotrophs via PCR, cloning, RFLP analysis, and sequencing. Type I methanotroph clones aligned with Methylomonas, Methylocaldum, and Methylobacter sequences and a distinct 16S rRNA phylogenetic lineage grouped near Methylobacter. The majority of clone sequences in type II methanotroph 16S rRNA, pmoA, and mmoX gene libraries grouped closely with sequences in the Methylocystis genus. A subset of the type II methanotroph clones from the aquifer had sequences that aligned most closely to Methylosinus trichosporium OB3b and Methylocystis spp., known TCE-co-metabolizing methanotrophs.

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“…Species of the genus Methylocystis are type II methanotrophs, classified, in part, by their possession of paired membranes aligned with the cell periphery, the serine pathway and predominant fatty acids with 18 carbons (Hanson & Hanson, 1996;Graham et al, 2002). Until recently, it was believed that all type II methanotrophs, including Methylocystis species, express the particulate form of methane monooxygenase (pMMO), and, with the exception of Methylocystis parvus OBBP T and the recently reported Methylocystis rosea SV97 T , all express the soluble form of methane monooxygenase (sMMO) at low copper concentrations (Stanley et al, 1983;Prior & Dalton, 1985;Choi et al, 2003;Wartiainen et al, 2006).…”

mentioning

confidence: 99%

Methylocystis hirsuta sp. nov., a novel methanotroph isolated from a groundwater aquifer

Lindner

Pacheco

Aldrich

et al. 2007

International Journal of Systematic and Evolutionary Microbiology

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Strain CSC1T , a Gram-negative, aerobic, methane-oxidizing bacterium, was isolated from an uncontaminated aquifer nearly 20 years ago. Based on 16S rRNA gene sequence similarity, this strain was identified as a member of the Alphaproteobacteria, most closely related to an uncultured member of the Methylocystaceae as well as two cultured organisms, Species of the genus Methylocystis are strictly aerobic, Gram-negative bacteria that are able to grow on onecarbon compounds (e.g. methane or methanol) (Bowman et al., 1993). The genus Methylocystis belongs to the class Alphaproteobacteria and currently consists of three species with standing in nomenclature, Methylocystis parvus, Methylocystis echinoides and Methylocystis rosea (Whittenbury et al., 1970;Gal'chenko et al., 1977;Bowman et al., 1993; Wartainen et al., 2006). Numerous Methylocystis strains have been identified in a variety of environments, including lake, ocean, marsh and creek sediments and water, coal mine drainage water and the roots of plants (Whittenbury et al., 1970;Gal'chenko et al., 1977;Bowman et al., 1993;Hanson & Hanson, 1996;Calhoun & King, 1998;Heyer et al., 2002 (Stanley et al., 1983;Prior & Dalton, 1985;Choi et al., 2003;Wartiainen et al., 2006). Methylocystis parvus OBBP T and Methylocystis rosea SV97 T do not possess genes encoding sMMO (Tsien & Hanson, 1992;Lloyd et al., 1999;Wartiainen et al., 2006). The genera Methylocella and Methylocapsa are classified as type II methanotrophs; however, they possess morphological and Abbreviations: PHB, poly-b-hydroxybutyrate; pMMO, particulate methane mononoxygenase; sMMO, soluble methane monooxygenase; TEM, transmission electron microscopy. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and partial mxaF, mmoX and pmoA gene sequences of strain CSC1T are respectively DQ364433, DQ664499, DQ664498 and DQ364434.Neighbour-joining trees based on partial mmoX and mxaF gene sequences and results of electron microscope cytochemistry of the S-layer of strain CSC1T are available as supplementary material with the online version of this paper.

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Methanotrophic Bacteria

Abstract: Classification of Methanotrophs Biochemistry and Molecular Biology of Methanotrophic Bacteria Ecology of Methanotrophic Bacteria Methanotrophs and Biotechnology

Cited by 9 publications

References 135 publications

The pH-based ecological coherence of active canonical methanotrophs in paddy soils

The pH-based ecological coherence of active canonical methanotrophs in paddy soils

Diversity of methanotroph communities in a basalt aquifer

Methylocystis hirsuta sp. nov., a novel methanotroph isolated from a groundwater aquifer

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