A Rice Gene for Microbial Symbiosis,
 Oryza sativa
 CCaMK
 , Reduces CH
 4
 Flux in a Paddy Field with Low Nitrogen Input

Bao, Zhihua; Watanabe, Aya; Sasaki, Kazuhiro; Okubo, Takashi; Tokida, Takeshi; Chen, Lingxin; Ikeda, Seishi; Imaizumi-Anraku, Haruko; Asakawa, Susumu; Satô, Tadashi; Mitsui, Hisayuki; Minamisawa, Kiwamu

doi:10.1128/aem.03646-13

Cited by 49 publications

(40 citation statements)

References 68 publications

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“…The rice roots were sampled at the flowering stage, on 22 August 2010. The CH 4 flux (14.8 to 15.4 mg C/h/m 2 ) and N 2 fixation (88.7 nmol h Ϫ1 g Ϫ1 root dry weight) values have been recorded in the same paddy field where Nipponbare was cultivated in the same stage in 2013 (17). The roots were washed well with tap water until no soil particles remained.…”

Section: Methodsmentioning

confidence: 99%

“…The rice (Oryza sativa L.) cultivar Nipponbare was planted in the Kashimadai experimental field of Tohoku University, Japan (38°27=39ЉN, 141°5=33ЉE), on 28 May 2010. Since 2004, the field had been treated with P-K fertilizer but without nitrogen fertilizer (17). The rice roots were sampled at the flowering stage, on 22 August 2010.…”

Section: Methodsmentioning

confidence: 99%

“…Nitrogen fertilization (13,14) and rice genotype (15,16) often influence the abundance of methanotrophs in rice fields. It was recently found that OsCCaMK, a microbial symbiosis gene of rice plants, simultaneously enhances CH 4 oxidation and N 2 fixation in a nitrogen-limited environment (17). However, little is known about the microbes in rice roots that are responsible for these processes.…”

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confidence: 99%

“…However, little is known about the microbes in rice roots that are responsible for these processes. There are two possibilities: (i) methanotrophs mediate both CH 4 oxidation and N 2 fixation, and (ii) methanotrophs simply mediate CH 4 oxidation, whereas other diazotrophs fix N 2 by using intermediate substrates such as methanol during CH 4 oxidation (17).…”

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confidence: 99%

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Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

Bao

Okubo

Kubota

et al. 2014

Appl Environ Microbiol

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108

105

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dIn a previous study by our group, CH 4 oxidation and N 2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH 4 oxidation and N 2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp. Minor nitrogenase proteins such as Methylocella, Bradyrhizobium, Rhodopseudomonas, and Anaeromyxobacter were also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of the Methylocystaceae. Because these results indicated that Methylocystaceae members mediate both CH 4 oxidation and N 2 fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH 4 oxidation and N 2 fixation are performed mainly by type II methanotrophs of the Methylocystaceae, including Methylosinus spp., inhabiting the vascular bundles and epidermal cells of rice roots.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

Bao

Okubo

Kubota

et al. 2014

Appl Environ Microbiol

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108

105

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“…On the other hand, methylotrophic bacteria including methanotrophs also increase where methane is available as a substrate. Growth of these methanotrophic and methylotrophic bacteria also depend on rice variety (Ma et al, 2010;Bao et al, 2014b), types of fertilizers (Mohanty et al, 2006;Zheng et al, 2014), and number of co-existing methanogens (Edwards et al, 2015). These studies suggest that methane emission system under rice paddy is very complicated, involving various microbial species and environmental factors.…”

Section: 미생물학회지 제52권 제2호mentioning

confidence: 99%

Metagenomics analysis of methane metabolisms in manure fertilized paddy soil

Nguyen¹,

Ho²,

Lee³

et al. 2016

The Korean Journal of Microbiology

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Under flooded rice fields, methanogens produce methane which comes out through rice stalks, thus rice fields are known as one of the anthropogenic sources of atmospheric methane. Studies have shown that use of manure increases amount of methane emission from rice. To investigate mechanisms by which manure boosts methane emission, comparative soil metagenomics between inorganically (NPK) and pig manure fertilized paddy soils (PIG) were conducted. Results from taxonomy analysis showed that more abundant methanogens, methanotrophs, methylotrophs, and acetogens were found in PIG than in NPK. In addition, BLAST results indicated more abundant carbohydrate mabolisetm functional genes in PIG. Among the methane metabolism related genes, PIG sample showed higher abundance of methyl-coenzyme M reductase (mcrB /mcrD /mcrG ) and trimethylamine-corrinoid protein Co-methyltransferase (mttB ) genes. In contrast, genes that down regulate methane emission, such as trimethylamine monooxygenase (tmm) and phosphoserine/ homoserine phosphotransferase (thrH ), were observed more in NPK sample. In addition, more methanotrophic genes (pmoB /amoB / mxaJ ), were found more abundant in PIG sample. Identifying key genes related to methane emission and methane oxidation may provide fundamental information regarding to mechanisms by which use of manure boosts methane emission from rice. The study presented here characterized molecular variation in rice paddy, introduced by the use of pig manure.

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Methylomagnum

Knief

2021

Bergey's Manual of Systematics of Archaea and Bacteria

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Me.thy.lo.mag'num, N.L. neut. n. methylum the methyl group; N.L. pref. methylo ‐ pertaining to the methyl radical; L. adj. magnus ‐a ‐um big, large, great; N.L. neut. n. Methylomagnum a large methylotroph. Proteobacteria / Gammaproteobacteria / Methylococcales / Methylococcaceae / Methylomagnum The genus Methylomagnum represents a group of aerobic obligately methanotrophic bacteria within the class Gammaproteobacteria . Their cells are Gram‐negative, motile short thick rods that are noticeably larger than those of other aerobic methanotrophic bacteria. Cells occur singly in young cultures and in short chains in older cultures on solidified media. They reproduce by binary fission. Colonies are opaque white, large, circular, and smooth. Cells have an intracellular membrane system and contain granules of different storage compounds including poly‐β‐hydroxybutyrate. Members of this genus are mesophilic and neutrophilic and use only methane or methanol as carbon and energy source. Methane oxidation is performed by the particulate or soluble methane monooxygenase. Formaldehyde is assimilated via the ribulose‐monophosphate pathway. In addition, CO 2 assimilation via ribulose‐bisphosphate carboxylase is possible. The major fatty acids are C 14:0 , C 16:0 , and C 16:1 ω7 c . A typical habitat of the genus is paddy soil. DNA G + C content (mol%) : 63.6–64.1 (HPLC and genome sequence analysis). Type species : Methylomagnum ishizawai Khalifa et al. 2015 VP emend. Frindte et al. 2017a.

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A Rice Gene for Microbial Symbiosis, Oryza sativa CCaMK , Reduces CH ₄ Flux in a Paddy Field with Low Nitrogen Input

Cited by 49 publications

References 68 publications

Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

Metagenomics analysis of methane metabolisms in manure fertilized paddy soil

Methylomagnum

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A Rice Gene for Microbial Symbiosis, Oryza sativa CCaMK , Reduces CH 4 Flux in a Paddy Field with Low Nitrogen Input

Cited by 49 publications

References 68 publications

Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

Metagenomics analysis of methane metabolisms in manure fertilized paddy soil

Methylomagnum

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A Rice Gene for Microbial Symbiosis, Oryza sativa CCaMK , Reduces CH ₄ Flux in a Paddy Field with Low Nitrogen Input