Molecular characterization of methane-oxidizing bacteria associated with rice straw decomposition in a rice field

Jia, Zhongjun; Sugano, Atsuo; Asari, Naoko; Tun, Cho Cho; Ishihara, Rie; Asakawa, Susumu; Kimura, Makoto

doi:10.1111/j.1747-0765.2007.00198.x

Cited by 8 publications

(7 citation statements)

References 46 publications

(117 reference statements)

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“…This group showed no hybridization signal for the Indonesian and Vietnamese soils. Sequences forming this lineage were retrieved from various habitats including high methane environments such as paddy fields (Jia et al ., ; Lüke and Frenzel, ) and freshwater lakes (Kim et al ., ), but also from soils consuming atmospheric methane (e.g. Knief et al ., ).…”

Section: Resultsmentioning

confidence: 99%

“…Here, field studies on methanotroph diversity increased during the past years, revealing again a high abundance of type II methanotrophs (Zheng et al ., ; Vishwakarma et al ., ; Ma and Lu, ; Ho et al ., ). In Japanese rice fields, type II were found again to represent the dominant fraction (Jia et al ., ). Thus, a high proportion of the Methylocystis/Methylosinus group might be a common feature of wetland rice methanotrophs.…”

Section: Introductionmentioning

confidence: 97%

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Macroecology of methane‐oxidizing bacteria: the β‐diversity of pmoA genotypes in tropical and subtropical rice paddies

Lüke

Frenzel

et al. 2013

Environmental Microbiology

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SummaryStudies addressing microbial biogeography have increased during the past decade, but research on microbial distribution patterns is still in its infancies, and many aspects are only poorly understood. Here, we compared the methanotroph community in paddy soils sampled in Indonesia, Vietnam, China and Italy, focusing on the distance-decay relationship. We used the pmoA gene as marker for methanotroph diversity in terminal restriction fragment length polymorphism, microarray and pyrosequencing approaches. We could observe a significant increase of β-diversity with geographical distance across continents (12 000 km). Measured environmental parameters explained only a small amount of data variation, and we found no evidence for dispersal limitation. Thus, we propose historical contingencies being responsible for the observed patterns. Furthermore, we performed an in-depth analysis of type II methanotroph pmoA distribution at the sequence level. We used ordination analysis to project sequence dissimilarities into a three-dimensional space (multidimensional scaling). The ordination suggests that type II methanotrophs in paddy fields can be divided into five major groups. However, these groups were found to be distributed in all soils independent of the geographic origin. By including tropical field sites (Indonesia and Vietnam) into the analysis, we further observed the first paddy fields harbouring a methanotroph community depleted in type II methanotrophs.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Macroecology of methane‐oxidizing bacteria: the β‐diversity of pmoA genotypes in tropical and subtropical rice paddies

Lüke

Frenzel

et al. 2013

Environmental Microbiology

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“…Deduced amino acid sequences encoded by the pmoA gene derived from the same paddy field, i.e. paddy soil ( 32 ), rice straw ( 33 ), microcrustaceans in floodwater ( 43 ), and floodwater (Shibagaki-Shimizu et al , unpublished results) were included in the tree in Fig. 2 .…”

Section: Resultsmentioning

confidence: 99%

“…Although the presence of both types I and II MOB in rice paddy field compartments has been reported by many studies ( 18 , 20 , 21 , 29 , 31 – 33 , 35 , 38 , 40 , 50 ), only two type I strains ( Methylogaea oryzae [ 21 , 23 ] and Methylomonas koyamae [strain Fw12E-Y; 44 ]) have been isolated from this environment so far. What could be the limitations of a culture-dependent technique in isolating type I MOB from rice paddy fields?…”

Section: Discussionmentioning

confidence: 99%

Diversity of Cultivable Methane-Oxidizing Bacteria in Microsites of a Rice Paddy Field: Investigation by Cultivation Method and Fluorescence <i>in situ</i> Hybridization (FISH)

et al. 2012

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The diversity of cultivable methane-oxidizing bacteria (MOB) in the rice paddy field ecosystem was investigated by combined culture-dependent and fluorescence in situ hybridization (FISH) techniques. Seven microsites of a Japanese rice paddy field were the focus of the study: floodwater, surface soil, bulk soil, rhizosphere soil, root, basal stem of rice plant, and rice stumps of previous harvest. Based on pmoA gene analysis and transmission electron microscopy (TEM), four type I, and nine type II MOB isolates were obtained from the highest dilution series of enrichment cultures. The type I MOB isolates included a novel species in the genus Methylomonas from floodwater and this is the first type I MOB strain isolated from floodwater of a rice paddy field. In the type I MOB, two isolates from stumps were closely related to Methylomonas spp.; one isolate obtained from rhizosphere soil was most related to Methyloccocus-Methylocaldum-Methylogaea clade. Almost all the type II MOB isolates were related to Methylocystis methanotrophs. FISH confirmed the presence of both types I and II MOB in all the microsites and in the related enrichment cultures. The study reported, for the first time, the diversity of cultivable methanotrophs including a novel species of type I MOB in rice paddy field compartments. Refining growth media and culture conditions, in combination with molecular approaches, will allow us to broaden our knowledge on the MOB community in the rice paddy field ecosystem and consequently to implement strategies for mitigating CH 4 emission from this ecosystem.

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“…2008), sequencing of 16S rRNA genes and pmoA (Eller and Frenzel 2001; Eller et al . 2005; Jia et al . 2007; Kolb et al .…”

Section: Introductionmentioning

confidence: 99%

Characterization of cultivable methanotrophs from paddy soils and rice roots

Takeda

Tonouchi

Takada

et al. 2008

Soil Science and Plant Nutrition

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Characterization of methanotrophs isolated from paddy soils and rice (Oryza sativa) roots was investigated in the present study. The number of methanotrophs in root homogenates of the rice cultivar Mutsuhomare was 4.9 × 10 7 most-probable-number (MPN) g -1 dry roots, in Yumeakari it was 2.0 × 10 8 MPN g -1 dry roots and in Kirara it was 4.6 × 10 7 MPN g -1 dry roots. Although bacterial cells were observed infrequently on the surface and in the interiors of roots before incubation, a large number of colonies, measuring 0.5-5 mm in diameter, were observed on the sterilized roots after incubation on nitrate mineral agar plates under methane in air. In particular, a large number of colonies were observed at the emergence sites of lateral roots and root hairs. Strains MD5-1 and M1 were isolated from the roots of Mutsuhomare and strain R62 was isolated from the root homogenate of Yumeakari. All isolates were catalase-positive and oxidase-positive, Gram-negative, straight-rod-shaped and curved-rod-shaped bacteria, and formed exospores. The isolates were able to fix nitrogen and grew in the absence of copper. In addition, all were found to be positive for naphthalene-oxidizing activities (corresponding to soluble methane mono-oxygenase activities). Strains MD5-1, M1 and R62 were closely related to Methylosinus sporium. Methanotrophic strains W3-6, SD3-5 and 2-19, isolated previously from paddy field soils, were classified into Methylosinus (W3-6) and Methylocystis (SD3-5 and 2-19) type II methanotrophs. Isolates from the rice roots (MD5-1, R62 and M1) grew logarithmically when casamino acid was used as the nitrogen source; however, the growth of these strains was reduced on the nitrate medium. These strains preferred amino acids over inorganic nitrogen as a nitrogen source for growth.Methanotrophs in paddy soils and rice roots 877

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Molecular characterization of methane-oxidizing bacteria associated with rice straw decomposition in a rice field

Cited by 8 publications

References 46 publications

Macroecology of methane‐oxidizing bacteria: the β‐diversity of pmoA genotypes in tropical and subtropical rice paddies

Macroecology of methane‐oxidizing bacteria: the β‐diversity of pmoA genotypes in tropical and subtropical rice paddies

Diversity of Cultivable Methane-Oxidizing Bacteria in Microsites of a Rice Paddy Field: Investigation by Cultivation Method and Fluorescence <i>in situ</i> Hybridization (FISH)

Characterization of cultivable methanotrophs from paddy soils and rice roots

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