Methylomonas koyamae sp. nov., a type I methane-oxidizing bacterium from floodwater of a rice paddy field (original) (raw)
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International Journal of Systematic and Evolutionary Microbiology, 2015
An aerobic, methane-oxidizing bacterium (strain RS11D-PrT) was isolated from rice rhizosphere. Cells of strain RS11D-PrT were Gram-stain-negative, motile rods with a single polar flagellum and contained an intracytoplasmic membrane system typical of type I methanotrophs. The strain utilized methane and methanol as sole carbon and energy sources. It could grow at 20–37 °C (optimum 31–33 °C), at pH 6.8–7.4 (range 5.5–9.0) and with 0–0.2 % (w/v) NaCl (there was no growth at above 0.5 % NaCl). pmoA and mmoX genes were present. The ribulose monophosphate and/or ribulose bisphosphate pathways were used for carbon assimilation. Results of sequence analysis of 16S rRNA genes showed that strain RS11D-PrT is related closely to the genera Methylococcus, Methylocaldum, Methyloparacoccus and Methylogaea in the family Methylococcaceae. The similarity was low (94.6 %) between strain RS11D-PrT and the most closely related type strain (Methyloparacoccus murrellii R-49797T). The DNA G+C content was 6...
Journal of Bioscience and Bioengineering, 2020
Methane-oxidizing bacteria (MOB) possess the metabolic potential to assimilate the highly potent greenhouse gas, CH 4 , and can also synthesize valuable products. Depending on their distinct and fastidious metabolic pathways, MOB are mainly divided into Type I and Type II; the latter are known as producers of polyhydroxyalkanoate (PHA). Despite the metabolic potential of MOB to synthesize PHA, the ecophysiology of MOB, especially under high CH 4 flux conditions, is yet to be understood. Therefore, in this study, a rice paddy soil receiving a high CH 4 flux from underground was used as an inoculum to enrich MOB using fed-batch operation, then the enriched Type II MOB were characterized. The transitions in the microbial community composition and CH 4 oxidation rates were monitored by 16S rRNA gene amplicon sequencing and degree of CH 4 consumption. With increasing incubation time, the initially dominant Methylomonas sp., affiliated with Type I MOB, was gradually replaced with Methylocystis sp., Type II MOB, resulting in a maximum CH 4 oxidation rate of 1.40 g-CH 4 /g-biomass/day. The quantification of functional genes encoding methane monooxygenase, pmoA and PHA synthase, phaC, by quantitative PCR revealed concomitant increases in accordance with the Type II MOB enrichment. These increases in the functional genes underscore the significance of Type II MOB to mitigate greenhouse gas emission and produce PHA.
Microorganisms, 2020
Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate...
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2011
Methyloferula stellata gen. nov., sp. nov., an acidophilic, obligately methanotrophic bacterium that possesses only a soluble methane monooxygenase Two strains of aerobic methanotrophic bacteria, AR4 T and SOP9, were isolated from acidic (pH 3.8-4.0) Sphagnum peat bogs in Russia. Another phenotypically similar isolate, strain LAY, was obtained from an acidic (pH 4.0) forest soil in Germany. Cells of these strains were Gramnegative, non-pigmented, non-motile, thin rods that multiplied by irregular cell division and formed rosettes or amorphous cell conglomerates. Similar to Methylocella species, strains AR4 T , SOP9 and LAY possessed only a soluble form of methane monooxygenase (sMMO) and lacked intracytoplasmic membranes. Growth occurred only on methane and methanol; the latter was the preferred growth substrate. mRNA transcripts of sMMO were detectable in cells when either methane or both methane and methanol were available. Carbon was assimilated via the serine and ribulose-bisphosphate (RuBP) pathways; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strains AR4 T , SOP9 and LAY were moderately acidophilic, mesophilic organisms capable of growth between pH 3.5 and 7.2 (optimum pH 4.8-5.2) and at 4-33 6C (optimum 20-23 6C). The major cellular fatty acid was 18 : 1v7c and the quinone was Q-10. The DNA G+C content was 55.6-57.5 mol%. The isolates belonged to the family Beijerinckiaceae of the class Alphaproteobacteria and were most closely related to the sMMO-possessing methanotrophs of the genus Methylocella (96.4-97.0 % 16S rRNA gene sequence similarity), particulate MMO (pMMO)-possessing methanotrophs of the genus Methylocapsa (96.1-97.0 %), facultative methylotrophs of the genus Methylovirgula (96.1-96.3 %) and non-methanotrophic organotrophs of the genus Beijerinckia (96.5-97.0 %). Phenotypically, strains AR4 T , SOP9 and LAY were most similar to Methylocella species, but differed from members of this genus by cell morphology, greater tolerance of low pH, detectable activities of RuBP pathway enzymes and inability to grow on multicarbon compounds. Therefore, we propose a novel genus and species, Methyloferula stellata gen. nov., sp. nov., to accommodate strains AR4 T , SOP9 and LAY. Strain AR4 T (5DSM 22108 T 5LMG 25277 T 5VKM B-2543 T ) is the type strain of Methyloferula stellata.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2013
Methylomonas paludis sp. nov., the first acidtolerant member of the genus Methylomonas, from an acidic wetland An aerobic methanotrophic bacterium was isolated from an acidic (pH 3.9) Sphagnum peat bog in north-eastern Russia and designated strain MG30 T . Cells of this strain were Gram-negative, pale pink-pigmented, non-motile, thick rods that were covered by large polysaccharide capsules and contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme (pMMO) and utilized only methane and methanol. Carbon was assimilated via the ribulose-monophosphate pathway; nitrogen was fixed via an oxygen-sensitive nitrogenase. Strain MG30 T was able to grow at a pH range of 3.8-7.3 (optimum pH 5.8-6.4) and at temperatures between 8 and 30 6C (optimum 20-25 6C). The major cellular fatty acids were C 16 : 1 v5t, C 16 : 1 v8c, C 16 : 1 v7c and C 14 : 0 ; the DNA G+C content was 48.5 mol%. The isolate belongs to the family Methylococcaceae of the class Gammaproteobacteria and displayed 94.7-96.9 % 16S rRNA gene sequence similarity to members of the genus Methylomonas. However, strain MG30 T differed from all taxonomically characterized members of this genus by the absence of motility, the ability to grow in acidic conditions and low DNA G+C content. Therefore, we propose to classify this strain as representing a novel, acid-tolerant species of the genus Methylomonas, Methylomonas paludis sp. nov. Strain MG30 T (5DSM 24973 T 5VKM B-2745 T ) is the type strain.
Applied and Environmental Microbiology, 1999
The soluble MMO (sMMO) gene clusters from group I methanotrophs were characterized. An 8.1-kb Kpn I fragment from Methylomonas sp. strain KSWIII and a 7.5-kb Sal I fragment from Methylomonas sp. strain KSPIII which contained the sMMO gene clusters were cloned and sequenced. The sequences of these two fragments were almost identical. The sMMO gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described sMMO gene clusters of the group II and group X methanotrophs. The phylogenetic analysis of the predicted amino acid sequences of sMMO demonstrated that the sMMOs from these strains were closer to that from M. capsulatus Bath in the group X methanotrophs than to those from Methylosinus trichosporium OB3b and Methylocystis sp. strain M in the group II methanotrophs. Based on the sequence data of sMMO genes of our strains and other methanotrophs, we designed a new PCR primer to amplify sMMO gene fragment...
Isolation and some properties of methane-oxidizing bacteria from a subtropical paddy field
Soil Science and Plant Nutrition, 1997
Methane is the second most important greenhouse gas which contributes to global warming. As an important source of methane, rice paddy fields contribute an estimated lO% to the global methane emissions (IPCe 1992). Land use and agricultural practices significantly affect atmospheric methane fluxes (Bouwman 1989; Htitsch et al. 1994). Microbial oxidation of atmospheric methane in terrestrial environments is the only known net biological methane sink and the process consumes the equivalent of 1-lO% of the total global emission (Adamsen and King 1993). Methane-oxidizing bacteria (MOB, methanotrophic bacteria) are considered to be obligately or facultatively aerobic respiratory bacteria that can utilize methane as the sole source of carbon and energy for growth (Hanson et al. 1992; Roslev and King 1994). As a result, they are important regulators of atmospheric methane fluxes in nature (Mancinelli 1995). MOB have been isolated from a variety of environments including freshwater lakes, wetlands, and the open ocean (
Characterization of methanotrophic bacteria isolated from a subtropical paddy field
FEMS Microbiology Letters, 1999
The global methane cycle includes both terrestrial and atmospheric processes and may contribute to feedback regulation of the climate. Most oxic soils are a net sink for methane, and these soils consume approximately 20 to 60 Tg of methane per year. The soil sink for atmospheric methane is microbially mediated and sensitive to disturbance. A decrease in the capacity of this sink may have contributed to the ϳ1% ⅐ year ؊1 increase in the atmospheric methane level in this century. The organisms responsible for methane uptake by soils (the atmospheric methane sink) are not known, and factors that influence the activity of these organisms are poorly understood. In this study the soil methane-oxidizing population was characterized by both labelling soil microbiota with 14 CH 4 and analyzing a total soil monooxygenase gene library. Comparative analyses of [ 14 C]phospholipid ester-linked fatty acid profiles performed with representative methane-oxidizing bacteria revealed that the soil sink for atmospheric methane consists of an unknown group of methanotrophic bacteria that exhibit some similarity to type II methanotrophs. An analysis of monooxygenase gene libraries from the same soil samples indicated that an unknown group of bacteria belonging to the ␣ subclass of the class Proteobacteria was present; these organisms were only distantly related to extant methane-oxidizing strains. Studies on factors that affect the activity, population dynamics, and contribution to global methane flux of "atmospheric methane oxidizers" should be greatly facilitated by use of biomarkers identified in this study.
Systematic and Applied Microbiology, 1990
A numerical analysis of methane-utilizing isolates obtained from various locations in the north to northeastern region of Australia resulted in the recognition of two distinct but related taxa. Both species are orange, carotenoid-containing, obligate Type I methanotrophs. The first species-Methylomonas fodinarum sp. nov. has a mol% G+C of 58.4 ± 0.3% while the second species-Methylomonas aurantiaca sp. nov has a mol% G+C of 56.5 ± 0.4%. They are morphologically similar, polar-flagellated rods, which can be distinguished on biochemical and physiological properties. The DNA homology between the species ranges from 40 to 60%. Their phenotypic and genotypic characters and relationship to other Methylomonas species are shown.
KnE Life Sciences, 2022
Methane is a major greenhouse gas that contributes to climate change. Methanogen and methanotrophic group microbes play a role in methane emissions in lowland rice fields. Methane is produced by methanogenic bacteria that decompose organic matter in anaerobic conditions. These bacteria will be active if the soil is inundated for an extended period of time. Some of this methane will be oxidized by methanotrophic bacteria in the rhizosphere. The researchers aimed to isolate, screen, and characterize methane-utilizing bacteria in lowland rice sediment from several Indonesian provinces. 27 methane-utilizing bacteria were isolated from rice field sediments in Lampung, West Java, and East Nusa Tenggara Province. Six of them had the potential to reduce methane emissions by more than half. A pmoA-like gene could be found in all of the selected isolates. The bacterial isolates were identified as Mycobacterium senegalense, Bacillus marisflavi, Bacillus methylotrophicus, Flavobacterium tirrenicum, Providencia stuartii, and Rhizobium rhizoryzae after characterization and identification with the Biolog OmniLog® ID system. These were all capable of nitrogen fixation, phosphorus solubilization, and IAA production. These isolates have the potential to be used as biofertilizers and methane mitigation agents.