Syntrophic Oxidation of Propionate in Rice Field Soil at 15 and 30°C under Methanogenic Conditions

Yan-lu, Gan; Qiu, Qiongfen; Liu, Pengfei; Rui, Junpeng; Lu, Yahai

doi:10.1128/aem.00688-12

Cited by 82 publications

(79 citation statements)

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“…In the investigations of syntrophic oxidations of acetate, propionate, and butyrate in Italian and Chinese rice soils, it was revealed that Methanocellales played the key role in H 2 consumption for the syntrophic interactions (10)(11)(12)(13)(14). These ecological studies reconfirm that Methanocellales are adapted to low-H 2 conditions.…”

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confidence: 51%

“…More evidence for the adaptation of Methanocellales to low H 2 came from the investigations of syntrophic oxidation of shortchain fatty acids (10)(11)(12)(13)(14). In the investigations of syntrophic oxidations of acetate, propionate, and butyrate in Italian and Chinese rice soils, it was revealed that Methanocellales played the key role in H 2 consumption for the syntrophic interactions (10)(11)(12)(13)(14).…”

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confidence: 99%

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Response of a Rice Paddy Soil Methanogen to Syntrophic Growth as Revealed by Transcriptional Analyses

Liu

Yang

Lü

et al. 2014

Appl Environ Microbiol

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Members of Methanocellales are widespread in paddy field soils and play the key role in methane production. These methanogens feature largely in these organisms' adaptation to low H 2 and syntrophic growth with anaerobic fatty acid oxidizers. The adaptive mechanisms, however, remain unknown. In the present study, we determined the transcripts of 21 genes involved in the key steps of methanogenesis and acetate assimilation of Methanocella conradii HZ254, a strain recently isolated from paddy field soil. M. conradii was grown in monoculture and syntrophically with Pelotomaculum thermopropionicum (a propionate syntroph) or Syntrophothermus lipocalidus (a butyrate syntroph). Comparison of the relative transcript abundances showed that three hydrogenase-encoding genes and all methanogenesis-related genes tested were upregulated in cocultures relative to monoculture. The genes encoding formylmethanofuran dehydrogenase (Fwd), heterodisulfide reductase (Hdr), and the membrane-bound energy-converting hydrogenase (Ech) were the most upregulated among the evaluated genes. The expression of the formate dehydrogenase (Fdh)-encoding gene also was significantly upregulated. In contrast, an acetate assimilation gene was downregulated in cocultures. The genes coding for Fwd, Hdr, and the D subunit of F 420 -nonreducing hydrogenase (Mvh) form a large predicted transcription unit; therefore, the Mvh/Hdr/Fwd complex, capable of mediating the electron bifurcation and connecting the first and last steps of methanogenesis, was predicted to be formed in M. conradii. We propose that Methanocella methanogens cope with low H 2 and syntrophic growth by (i) stabilizing the Mvh/Hdr/Fwd complex and (ii) activating formatedependent methanogenesis.T he 16S rRNA gene of a new type of methanogen, Methanocellales, was discovered in 1998 from the surface of rice root (1). The 16S rRNA gene sequences were found phylogenetically branching off between Methanosarcinaceae and Methanomicrobiales. An enrichment culture at 50°C revealed that these organisms contained the methyl-coenzyme M (CoM) reductase-encoding genes, confirming their nature as methanogenic archaea (2, 3). They were found to be widespread in rice field soils and the environment, including desert soil (4-7). Due to the difficulty of cultivation, many molecular studies were conducted to characterize their ecological functions prior to isolation into pure culture. The application of stable isotope probing technology showed that these organisms outcompeted other methanogens under low-H 2 conditions (8). This result suggested, for the first time, that these methanogens are intrinsically adaptive to low H 2 . Moreover, they were found to play the key role in CH 4 production from rootderived material in the rice rhizosphere in situ, illustrating their ecological significance and niche specificity (9).More evidence for the adaptation of Methanocellales to low H 2 came from the investigations of syntrophic oxidation of shortchain fatty acids (10-14). In the investigations of syntrophic oxidations...

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confidence: 51%

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confidence: 99%

Response of a Rice Paddy Soil Methanogen to Syntrophic Growth as Revealed by Transcriptional Analyses

Liu

Yang

Lü

et al. 2014

Appl Environ Microbiol

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“…Acidobacteriarelated bacteria have been proved in the degradation of petroleum [50], PAHs [33,50], and PCBs [32,50] in various habitats. To date, SIP has been successfully applied to investigate the ability of Acidobacterium to metabolize propionate [51], biocide [52], herbicide [53], and benzene [29]. Our recent SIP research also demonstrated that Acidobacteria-related bacteria were related to the degradation of PHE in forest soil [26].…”

Section: Discussionmentioning

confidence: 96%

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Song

Jiang

Zhang

et al. 2016

Journal of Hazardous Materials

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h i g h l i g h t s• Investigate PAHs degraders in forest carbon-rich soils via DNA-SIP.• Rhodanobacter is identified to metabolite anthracene for the first time.• The first fluoranthene degrader belongs to Acidobacteria.• Different functions of PAHs degraders in forest soils from contaminated soils. a r t i c l e i n f o a b s t r a c tInformation on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually 13 C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene-and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter-and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three-and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

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“…Microbial diversity studies in different methanogenic habitats, based on stable isotope probing (Lueders et al, 2004;Chauhan & Ogram, 2006;Hatamoto et al, 2007Liu et al, 2011Gan et al, 2012) and enrichment culturing (Shigematsu et al, 2006;Sousa et al, 2007;Tang et al, 2007;Narihiro et al, 2014), have confirmed Syntrophobacter, Smithella, Pelotomaculum and Syntrophomonas to be the major bacterial genera involved in VFA degradation under mesophilic conditions. While it is important to understand SFAB diversity, it would be extremely beneficial to measure their abundance in methanogenic habitats.…”

Section: Introductionmentioning

confidence: 99%

Quantitative detection of syntrophic fatty acid-degrading bacterial communities in methanogenic environments

2015

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In methanogenic habitats, volatile fatty acids (VFA), such as propionate and butyrate, are major intermediates in organic matter degradation. VFA are further metabolized to H 2 , acetate and CO 2 by syntrophic fatty acid-degrading bacteria (SFAB) in association with methanogenic archaea. Despite their indispensable role in VFA degradation, little is known about SFAB abundance and their environmental distribution. To facilitate ecological studies, we developed four novel genus-specific quantitative PCR (qPCR) assays, with primer sets targeting known SFAB: Syntrophobacter, Smithella, Pelotomaculum and Syntrophomonas. Primer set specificity was confirmed using in silico and experimental (target controls, clone libraries and melt-curve analysis) approaches. These qPCR assays were applied to quantify SFAB in a variety of mesophilic methanogenic habitats, including a laboratory propionate enrichment culture, pilotand full-scale anaerobic reactors, cow rumen, horse faeces, an experimental rice paddy soil, a bog stream and swamp sediments. The highest SFAB 16S rRNA gene copy numbers were found in the propionate enrichment culture and anaerobic reactors, followed by the bog stream and swamp sediment samples. In addition, it was observed that SFAB and methanogen abundance varied with reactor configuration and substrate identity. To our knowledge, this research represents the first comprehensive study to quantify SFAB in methanogenic habitats using qPCR-based methods. These molecular tools will help investigators better understand syntrophic microbial communities in engineered and natural environments.

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Syntrophic Oxidation of Propionate in Rice Field Soil at 15 and 30°C under Methanogenic Conditions

Cited by 82 publications

References 50 publications

Response of a Rice Paddy Soil Methanogen to Syntrophic Growth as Revealed by Transcriptional Analyses

Response of a Rice Paddy Soil Methanogen to Syntrophic Growth as Revealed by Transcriptional Analyses

Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil

Quantitative detection of syntrophic fatty acid-degrading bacterial communities in methanogenic environments

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