15N2–DNA–stable isotope probing of diazotrophic methanotrophs in soil

Buckley, Daniel H.; Huangyutitham, Varisa; Hsu, Shi-Fang; Nelson, Tyrrell A.

doi:10.1016/j.soilbio.2007.05.006

Cited by 62 publications

(26 citation statements)

References 78 publications

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“…1), although the biomass of NE1115 was still lower than that of the WT in the SN field. This idea is partially consistent with previous findings obtained by the 15 N 2 -DNA stable isotope probing method that Methylocystis (a type II methanotroph) fixes N 2 in CH 4 -enriched soil (64) and that the N 2 fixation system of Methylococcus capsulatus (a type I methanotroph) is switched on under N-limited conditions (65).…”

Section: Discussionsupporting

confidence: 92%

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

Bao

Watanabe

Sasaki

et al. 2014

Appl Environ Microbiol

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Section: Discussionsupporting

confidence: 92%

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

Bao

Watanabe

Sasaki

et al. 2014

Appl Environ Microbiol

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“…This supposition is partially supported by the detection of nitrogenase of type II methanotrophs in rice root-associated microbes by transcriptome analysis (44), although the authors of that paper did not discuss this aspect of their findings. Moreover, this result is also consistent with the observation that type II methanotrophs fix N 2 in CH 4 -enriched soil (19).…”

Section: Discussionsupporting

confidence: 91%

“…Although N 2 fixation may lead to lowering methane oxidation via energy consumption as hypothesized earlier (18), in situ N 2 fixation in CH 4 -enriched soil by type II methanotrophs has previously been demonstrated (19,20). In support of possibility i, both type I and type II methanotrophs possess nif (nitrogen fixation) genes and both are able to fix N 2 under laboratory experiment conditions (21)(22)(23).…”

mentioning

confidence: 65%

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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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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“…These microorganisms are capable of fixing nitrogen and consuming CH 4 at both high and low concentrations, and a few strains are able to use acetate as an additional carbon source. The versatile metabolic capabilities of type II methanotrophs possibly represent an important part of their survival strategy in oligotrophic peatlands [12,37,38]. The deficiency of soil TOC and TN in Sanjiang wetland may create an oligotrophic environment which supports the growth of abundant Methylocystis.…”

Section: Discussionmentioning

confidence: 99%

Aerobic Methanotroph Diversity in Sanjiang Wetland, Northeast China

et al. 2014

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Aerobic methanotrophs present in wetlands can serve as a methane filter and thereby significantly reduce methane emissions. Sanjiang wetland is a major methane source and the second largest wetland in China, yet little is known about the characteristics of aerobic methanotrophs in this region. In the present study, we investigated the diversity and abundance of methanotrophs in marsh soils from Sanjiang wetland with three different types of vegetation by 16S ribosomal RNA (rRNA) and pmoA gene analysis. Quantitative polymerase chain reaction analysis revealed the highest number of pmoA gene copies in marsh soils vegetated with Carex lasiocarpa (10(9) g(-1) dry soil), followed by Carex meyeriana, and the least with Deyeuxia angustifolia (10(8) g(-1) dry soil). Consistent results were obtained using Sanger sequencing and pyrosequencing techniques, both indicating the codominance of Methylobacter and Methylocystis species in Sanjiang wetland. Other less abundant methanotrophy, including cultivated Methylomonas and Methylosinus genus, and uncultured clusters such as LP20 and JR-1, were also detected in the wetland. Methanotroph diversity was almost the same in three different vegetation covered soils, suggesting that vegetation types had very little influence on the methanotroph diversity. Our study gives an in-depth insight into the community composition of aerobic methanotrophs in the Sanjiang wetland.

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15N2–DNA–stable isotope probing of diazotrophic methanotrophs in soil

Cited by 62 publications

References 78 publications

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

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

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

Aerobic Methanotroph Diversity in Sanjiang Wetland, Northeast China

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15N2–DNA–stable isotope probing of diazotrophic methanotrophs in soil

Cited by 62 publications

References 78 publications

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

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

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

Aerobic Methanotroph Diversity in Sanjiang Wetland, Northeast China

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Product

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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

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