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Yan W, Wang D, Wang Y, Wang C, Chen X, Liu L, Wang Y, Li YY, Kamagata Y, Nobu MK, Zhang T. Metatranscriptomics-guided genome-scale metabolic reconstruction reveals the carbon flux and trophic interaction in methanogenic communities. MICROBIOME 2024; 12:121. [PMID: 38970122 PMCID: PMC11225162 DOI: 10.1186/s40168-024-01830-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/06/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry. RESULTS In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role. CONCLUSION Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. Video Abstract.
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Affiliation(s)
- Weifu Yan
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Dou Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yubo Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Chunxiao Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Xi Chen
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yulin Wang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Yu-You Li
- Laboratory of Environmental Protection Engineering, Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba Ward, Sendai, Miyagi, 980-8579, Japan
| | - Yoichi Kamagata
- Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Masaru K Nobu
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China.
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China.
- School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
- Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macao SAR, China.
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Ren Z, Li Y, Yin J, Zhao Z, Hu N, Zhao M, Wang Y, Wang L, Wu L. Regulation of nitrite-dependent anaerobic methane oxidation bacteria by available phosphorus and microbial communities in lake sediments of cold and arid regions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:172065. [PMID: 38556008 DOI: 10.1016/j.scitotenv.2024.172065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/11/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
As global anthropogenic nitrogen inputs continue to rise, nitrite-dependent anaerobic methane oxidation (N-DAMO) plays an increasingly significant role in CH4 consumption in lake sediments. However, there is a dearth of knowledge regarding the effects of anthropogenic activities on N-DAMO bacteria in lakes in the cold and arid regions. Sediment samples were collected from five sampling areas in Lake Ulansuhai at varying depth ranges (0-20, 20-40, and 40-60 cm). The ecological characterization and niche differentiation of N-DAMO bacteria were investigated using bioinformatics and molecular biology techniques. Quantitative PCR confirmed the presence of N-DAMO bacteria in Lake Ulansuhai sediments, with 16S rRNA gene abundances ranging from 1.72 × 104 to 5.75 × 105 copies·g-1 dry sediment. The highest abundance was observed at the farmland drainage outlet with high available phosphorus (AP). Anthropogenic disturbances led to a significant increase in the abundance of N-DAMO bacteria, though their diversity remained unaffected. The heterogeneous community of N-DAMO bacteria was affected by interactions among various environmental characteristics, with AP and oxidation-reduction potential identified as the key drivers in this study. The Mantel test indicated that the N-DAMO bacterial abundance was more readily influenced by the presence of the denitrification genes (nirS and nirK). Network analysis revealed that the community structure of N-DAMO bacteria generated numerous links (especially positive links) with microbial taxa involved in carbon and nitrogen cycles, such as methanogens and nitrifying bacteria. In summary, N-DAMO bacteria exhibited sensitivity to both environmental and microbial factors under various human disturbances. This study provides valuable insights into the distribution patterns of N-DAMO bacteria and their roles in nitrogen and carbon cycling within lake ecosystems.
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Affiliation(s)
- Zixuan Ren
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yingnan Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Jiahui Yin
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Ziwen Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Nan Hu
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Manping Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Yongman Wang
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Lixin Wang
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Linhui Wu
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle, Hohhot 010021, China.
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3
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Zhang B, Zhao Z, Ma R, Chen N, Kong Z, Lei Z, Zhang Z. Unveiling the mechanisms of Fe(III)-loaded chitosan composite (CTS-Fe) in enhancing anaerobic digestion of waste activated sludge. J Environ Sci (China) 2024; 138:200-211. [PMID: 38135389 DOI: 10.1016/j.jes.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 12/24/2023]
Abstract
Anaerobic digestion (AD) of waste activated sludge (WAS) is usually limited by the low generation efficiency of methane. Fe(III)-loaded chitosan composite (CTS-Fe) have been reported to effectively enhanced the digestion of WAS, but its role in promoting anaerobic sludge digestion remains unclear. In present study, the effects of CTS-Fe on the hydrolysis and methanogenesis stages of WAS anaerobic digestion were investigated. The addition of CTS-Fe increased methane production potential by 8%-23% under the tested conditions with the addition of 5-20 g/L CTS-Fe. Besides, the results demonstrate that the addition of CTS-Fe could effectively promote the hydrolysis of WAS, evidenced by lower protein or polysaccharides concentration, higher soluble organic carbon in rector adding CTS-Fe, as well as the increased activity of extracellular hydrolase with higher CTS-Fe concentration. Meanwhile, the enrichment of Clostridia abundance (iron-reducing bacteria (IRBs)) was observed in CTS-Fe adding reactor (8.9%-13.8%), which was higher than that in the control reactor (7.9%). The observation further suggesting the acceleration of hydrolysis through dissimilatory iron reduction (DIR) process, thus providing abundant substrates for methanogenesis. However, the presence of CTS-Fe was inhibited the acetoclastic and hydrogenotrophic methanogenesis process, which could be ascribed to the Fe(III) act as electron acceptor coupled to methane for anaerobic oxidation. Furthermore, coenzyme F420 activity in the CTS-Fe added reactor was 34.9% lower than in the blank, also abundance of microorganisms involved in hydrogenotrophic methanogenesis was decreased. Results from this study could provide theoretical support for the practical applications of CTS-Fe.
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Affiliation(s)
- Boaiqi Zhang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; The Key Laboratory of Water and Sediment Sciences, Ministry of Education; State Environmental Protection Key Laboratory of All Material Fluxes in River Ecosystems; College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Ziwen Zhao
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510345, China
| | - Rui Ma
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Nan Chen
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Zhe Kong
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Zhongfang Lei
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhenya Zhang
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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Xie F, Zhao S, Zhan X, Zhou Y, Li Y, Zhu W, Pope PB, Attwood GT, Jin W, Mao S. Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions. Genome Biol 2024; 25:32. [PMID: 38263062 PMCID: PMC10804542 DOI: 10.1186/s13059-024-03167-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains. RESULTS Here, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12 exchanges could enable them to occupy ecological niches that possibly alter the direction of H2 utilization. CONCLUSIONS We provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2 flow.
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Affiliation(s)
- Fei Xie
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shengwei Zhao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxiu Zhan
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yang Zhou
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yin Li
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Phillip B Pope
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Wei Jin
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
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5
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Treitli SC, Hanousková P, Beneš V, Brune A, Čepička I, Hampl V. Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti. THE ISME JOURNAL 2023; 17:1884-1894. [PMID: 37634049 PMCID: PMC10579272 DOI: 10.1038/s41396-023-01499-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/28/2023]
Abstract
Pelomyxa is a genus of anaerobic amoebae that live in consortia with multiple prokaryotic endosymbionts. Although the symbionts represent a large fraction of the cellular biomass, their metabolic roles have not been investigated. Using single-cell genomics and transcriptomics, we have characterized the prokaryotic community associated with P. schiedti, which is composed of two bacteria, Candidatus Syntrophus pelomyxae (class Deltaproteobacteria) and Candidatus Vesiculincola pelomyxae (class Clostridia), and a methanogen, Candidatus Methanoregula pelomyxae. Fluorescence in situ hybridization and electron microscopy showed that Ca. Vesiculincola pelomyxae is localized inside vesicles, whereas the other endosymbionts occur freely in the cytosol, with Ca. Methanoregula pelomyxae enriched around the nucleus. Genome and transcriptome-based reconstructions of the metabolism suggests that the cellulolytic activity of P. schiedti produces simple sugars that fuel its own metabolism and the metabolism of a Ca. Vesiculincola pelomyxae, while Ca. Syntrophus pelomyxae energy metabolism relies on degradation of butyrate and isovalerate from the environment. Both species of bacteria and the ameba use hydrogenases to transfer the electrons from reduced equivalents to hydrogen, a process that requires a low hydrogen partial pressure. This is achieved by the third endosymbiont, Ca. Methanoregula pelomyxae, which consumes H2 and formate for methanogenesis. While the bacterial symbionts can be successfully eliminated by vancomycin treatment without affecting the viability of the amoebae, treatment with 2-bromoethanesulfonate, a specific inhibitor of methanogenesis, killed the amoebae, indicating the essentiality of the methanogenesis for this consortium.
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Affiliation(s)
- Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42, Vestec, Czech Republic.
| | - Pavla Hanousková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00, Prague 2, Czech Republic
| | - Vladimír Beneš
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Brune
- RG Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00, Prague 2, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42, Vestec, Czech Republic.
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Goldman AD, Weber JM, LaRowe DE, Barge LM. Electron transport chains as a window into the earliest stages of evolution. Proc Natl Acad Sci U S A 2023; 120:e2210924120. [PMID: 37579147 PMCID: PMC10451490 DOI: 10.1073/pnas.2210924120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
The origin and early evolution of life is generally studied under two different paradigms: bottom up and top down. Prebiotic chemistry and early Earth geochemistry allow researchers to explore possible origin of life scenarios. But for these "bottom-up" approaches, even successful experiments only amount to a proof of principle. On the other hand, "top-down" research on early evolutionary history is able to provide a historical account about ancient organisms, but is unable to investigate stages that occurred during and just after the origin of life. Here, we consider ancient electron transport chains (ETCs) as a potential bridge between early evolutionary history and a protocellular stage that preceded it. Current phylogenetic evidence suggests that ancestors of several extant ETC components were present at least as late as the last universal common ancestor of life. In addition, recent experiments have shown that some aspects of modern ETCs can be replicated by minerals, protocells, or organic cofactors in the absence of biological proteins. Here, we discuss the diversity of ETCs and other forms of chemiosmotic energy conservation, describe current work on the early evolution of membrane bioenergetics, and advocate for several lines of research to enhance this understanding by pairing top-down and bottom-up approaches.
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Affiliation(s)
- Aaron D. Goldman
- Department of Biology, Oberlin College, Oberlin, OH44074
- Blue Marble Space Institute of Science, Seattle, WA98154
| | - Jessica M. Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
| | - Douglas E. LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA90089
| | - Laura M. Barge
- Blue Marble Space Institute of Science, Seattle, WA98154
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
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7
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Fu L, Lai S, Zhou Z, Chen Z, Cheng L. Seasonal variation of microbial community and methane metabolism in coalbed water in the Erlian Basin, China. Front Microbiol 2023; 14:1114201. [PMID: 36846781 PMCID: PMC9953142 DOI: 10.3389/fmicb.2023.1114201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023] Open
Abstract
Coalbed water is a semi-open system connecting underground coalbeds with the external environment. Microorganisms in coalbed water play an important role in coal biogasification and the carbon cycle. The community assemblages of microorganisms in such a dynamic system are not well understood. Here, we used high-throughput sequencing and metagenomic analysis to investigate microbial community structure and identify the potential functional microorganisms involved in methane metabolism in coalbed water in the Erlian Basin, a preferred low-rank coal bed methane (CBM) exploration and research area in China. The results showed that there were differences in the responses of bacteria and archaea to seasonal variation. Bacterial community structure was affected by seasonal variation but archaea was not. Methane oxidation metabolism dominated by Methylomonas and methanogenesis metabolism dominated by Methanobacterium may exist simultaneously in coalbed water.
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Affiliation(s)
- Li Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Shouchao Lai
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Zhuo Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Zhenhong Chen
- Research Institute of Petroleum Exploration and Development, Beijing, China,*Correspondence: Zhenhong Chen, ✉
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China,Lei Cheng, ✉
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Jiao Y, Yuan Y, He C, Liu L, Pan X, Li P. Enrichment culture combined with microbial electrochemical enhanced low-temperature anaerobic digestion of cow dung. BIORESOURCE TECHNOLOGY 2022; 360:127636. [PMID: 35853591 DOI: 10.1016/j.biortech.2022.127636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Enrichment culture combined with the microbial electrochemical system was used to co-enhance the low-temperature (20 °C) anaerobic digestion. The results showed that enrichment culture combined with microbial electrochemical system increased the cumulative methane production in low-temperature anaerobic digestion system by 39.64 % and 133.29 % compared to single and no enrichment culture, respectively. Enrichment culture combined with microbial electrochemical system increased the relative abundance of methanogenic archaea (Methanomassiliicoccus, Methanocorpusculum, unclassified Methanomicrobiaceae, Methanobacterium, Methanoculleus, Methanocalculus) and the relative abundance of cold-tolerant hydrolytic acidifying bacteria (unclassified Bacteroidetes, Treponema). The expressions of specific enzyme genes in the methanogenesis pathway were enhanced, including acetyl-CoA synthetase, formylmethanofuran dehydrogenase, methanol cobalamin methyltransferase, etc. These results indicated that enrichment culture combined with microbial electrochemical system enhanced low-temperature anaerobic digestion methanogenesis by altering microbial communities and stimulating enzyme gene expression to affect volatile fatty acids, pH, redox potential, and reducing sugar parameters.
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Affiliation(s)
- Youzhou Jiao
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy of Ministry of Agriculture and Rural Affairs, College of Mechanical & Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China; Henan International Joint Laboratory of Biomass Energy and Nanomaterials, Henan Agricultural University, Zhengzhou 450002, China
| | - Yongkang Yuan
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy of Ministry of Agriculture and Rural Affairs, College of Mechanical & Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China; Henan International Joint Laboratory of Biomass Energy and Nanomaterials, Henan Agricultural University, Zhengzhou 450002, China
| | - Chao He
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy of Ministry of Agriculture and Rural Affairs, College of Mechanical & Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China; Henan International Joint Laboratory of Biomass Energy and Nanomaterials, Henan Agricultural University, Zhengzhou 450002, China
| | - Liang Liu
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy of Ministry of Agriculture and Rural Affairs, College of Mechanical & Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China; Henan International Joint Laboratory of Biomass Energy and Nanomaterials, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaohui Pan
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy of Ministry of Agriculture and Rural Affairs, College of Mechanical & Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China; Henan International Joint Laboratory of Biomass Energy and Nanomaterials, Henan Agricultural University, Zhengzhou 450002, China
| | - Panpan Li
- Key Laboratory of New Materials and Facilities for Rural Renewable Energy of Ministry of Agriculture and Rural Affairs, College of Mechanical & Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China; Henan International Joint Laboratory of Biomass Energy and Nanomaterials, Henan Agricultural University, Zhengzhou 450002, China.
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9
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Brandau L, Jacksch S, Weis S, Schnell S, Egert M. Minority report: small-scale metagenomic analysis of the non-bacterial kitchen sponge microbiota. Arch Microbiol 2022; 204:363. [PMID: 35661258 PMCID: PMC9167186 DOI: 10.1007/s00203-022-02969-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Kitchen sponges are particularly well known to harbor a high number and diversity of bacteria, including pathogens. Viruses, archaea, and eukaryotes in kitchen sponges, however, have not been examined in detail so far. To increase knowledge on the non-bacterial kitchen sponge microbiota and its potential hygienic relevance, we investigated five used kitchen sponges by means of metagenomic shot-gun sequencing. Viral particles were sought to be enriched by a filter step during DNA extraction from the sponges. Data analysis revealed that ~ 2% of the sequences could be assigned to non-bacterial taxa. Each sponge harbored different virus (phage) species, while the present archaea were predominantly affiliated with halophilic taxa. Among the eukaryotic taxa, besides harmless algae, or amoebas, mainly DNA from food-left-overs was found. The presented work offers new insights into the complex microbiota of used kitchen sponges and contributes to a better understanding of their hygienic relevance.
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Affiliation(s)
- Lena Brandau
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Susanne Jacksch
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Severin Weis
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany
| | - Sylvia Schnell
- Research Centre for BioSystems, Land Use, and Nutrition (IFZ), Institute of Applied Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Microbiology and Hygiene Group, Furtwangen University, Villingen-Schwenningen, Germany.
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Wang B, Zheng X, Zhang H, Yu X, Lian Y, Yang X, Yu H, Hu R, He Z, Xiao F, Yan Q. Metagenomic insights into the effects of submerged plants on functional potential of microbial communities in wetland sediments. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:405-415. [PMID: 37073260 PMCID: PMC10077182 DOI: 10.1007/s42995-021-00100-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
Submerged plants in wetlands play important roles as ecosystem engineers to improve self-purification and promote elemental cycling. However, their effects on the functional capacity of microbial communities in wetland sediments remain poorly understood. Here, we provide detailed metagenomic insights into the biogeochemical potential of microbial communities in wetland sediments with and without submerged plants (i.e., Vallisneria natans). A large number of functional genes involved in carbon (C), nitrogen (N) and sulfur (S) cycling were detected in the wetland sediments. However, most functional genes showed higher abundance in sediments with submerged plants than in those without plants. Based on the comparison of annotated functional genes in the N and S cycling databases (i.e., NCycDB and SCycDB), we found that genes involved in nitrogen fixation (e.g., nifD/H/K/W), assimilatory nitrate reduction (e.g., nasA and nirA), denitrification (e.g., nirK/S and nosZ), assimilatory sulfate reduction (e.g., cysD/H/J/N/Q and sir), and sulfur oxidation (e.g., glpE, soeA, sqr and sseA) were significantly higher (corrected p < 0.05) in vegetated vs. unvegetated sediments. This could be mainly driven by environmental factors including total phosphorus, total nitrogen, and C:N ratio. The binning of metagenomes further revealed that some archaeal taxa could have the potential of methane metabolism including hydrogenotrophic, acetoclastic, and methylotrophic methanogenesis, which are crucial to the wetland methane budget and carbon cycling. This study opens a new avenue for linking submerged plants with microbial functions, and has further implications for understanding global carbon, nitrogen and sulfur cycling in wetland ecosystems. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00100-3.
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Affiliation(s)
- Binhao Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Hangjun Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Yingli Lian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Xueqin Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, Guangzhou, 510006 China
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11
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Cai W, Zhao M, Kong J, Riggio S, Finnigan T, Stuckey D, Guo M. Linkage of community composition and function over short response time in anaerobic digestion systems with food fermentation wastewater. iScience 2021; 24:102958. [PMID: 34466784 PMCID: PMC8384924 DOI: 10.1016/j.isci.2021.102958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/11/2021] [Accepted: 08/03/2021] [Indexed: 01/28/2023] Open
Abstract
We investigated the short-term dynamics of microbial composition and function in bioreactors with inocula collected from full-scale and laboratory-based anaerobic digestion (AD) systems. The Bray-Curtis dissimilarity of both inocula was approximately 10% of the predicted Kyoto Encyclopedia of Genes and Genomes pathway and 40% of the taxonomic composition and yet resulted in a similar performance in methane production, implying that the variation of community composition may be decoupled from performance. However, the significant correlation of volatile fatty acids with taxonomic variation suggested that the pathways of AD could be different because of the varying genus. The predicted function of the significantly varying genus was mostly related to fermentation, which strengthened the conclusion that most microbial variation occurred within the fermentative species and led to alternative routes to result in similar methane production in methanogenic bioreactors. This finding sheds some light on the understanding of AD community regulation, which depends on the aims to recover intermediates or methane.
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Affiliation(s)
- Weiwei Cai
- School of Civil Engineering, Beijing Jiaotong University, Beijing 100044, China.,Department of Engineering, King's College London, London WC2R 2LS, UK
| | - Mingxing Zhao
- Department of Civil and Environmental Engineering, Imperial College London, London SW7 2AZ, UK.,Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.,School of Environment and Civil Engineering, Jiangnan University, Wuxi, Jiangsu Province, China
| | - Jianyao Kong
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Silvio Riggio
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Tim Finnigan
- Quorn Foods, Station Road, Stokesley, North Yorkshire TS9 7AB, UK
| | - David Stuckey
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Miao Guo
- Department of Engineering, King's College London, London WC2R 2LS, UK.,Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK
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12
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Wu D, Zhao Y, Cheng L, Zhou Z, Wu Q, Wang Q, Yuan Q. Activity and structure of methanogenic microbial communities in sediments of cascade hydropower reservoirs, Southwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147515. [PMID: 33975103 DOI: 10.1016/j.scitotenv.2021.147515] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Freshwater reservoirs are an important source of the greenhouse gas methane (CH4). However, little is known about the activity and structure of microbial communities involved in methanogenic decomposition of sediment organic matter (SOM) in cascade hydropower reservoirs. In this study, we targeted on sediments of three cascade reservoirs in Wujiang River, Southwest China. Our results showed that the content of sediment organic carbon (SOC) was between 3% and 11%, and it's positively correlated with both C/N ratio and recalcitrant organic carbon content of SOM. Meanwhile, SOC content was positively correlated with CH4 production rates but had no significant correlation with total CO2 production rates of the sediments, when rates were normalized to sediment volume. Resultantly, the sediment anaerobic decomposition rates hardly significantly increase along with the SOC content. These results suggested that the terrestrial organic matter accumulated after damming stimulated CH4 production from the reservoir sediments even though its decomposition rate was limited. Meantime, high throughput sequencing of 16S rRNA genes indicated that not only the hydrogenotrophic and acetoclastic, but also the methylotrophic methanogens (Methanomassiliicoccus) are abundant in the reservoir sediments. Moreover, metagenomic sequencing also suggested that methylotrophic methanogenesis are potentially important in the sediment of cascade reservoirs. Finally, the hydraulic residence time of the reservoir could be the key controlling factor of the structures of bacterial and archaeal communities as well as the CH4 production rates of the reservoir sediments.
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Affiliation(s)
- Debin Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Zhao
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, China
| | - Zhuo Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, China
| | - Qiusheng Wu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Qian Wang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
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Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline. THE ISME JOURNAL 2021; 15:2351-2365. [PMID: 33649556 PMCID: PMC8319295 DOI: 10.1038/s41396-021-00931-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 02/08/2021] [Indexed: 02/03/2023]
Abstract
Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean's interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine-seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.
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Muriuki SW, Rengan MS, Budambula NLM. Prokaryotic diversity and potentially pathogenic bacteria in vended foods and environmental samples. ANN MICROBIOL 2021. [DOI: 10.1186/s13213-021-01640-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract
Purpose
Ready-to-eat fast food vending outlets provide a cheap and readily available food. Foodborne diseases have been previously reported in Embu, Kenya, but data on the prokaryotic metagenome in vended foods is scanty. This study aimed to determine the prokaryotic diversity in fruits, vegetable salad, African sausage, chips (potato fries), fried fish, roasted beef (meat), smokies, samosa, soil, and water collected from food vendors and the surrounding environment in Embu Town and Kangaru Market.
Methods
The study used 454 pyrosequencing, Illumina high-throughput sequencing of 16S rRNA gene in the analysis of total community DNA extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4-V7) of the extracted DNA was amplified and library construction performed. Sequence analysis was done using QIIME2. Hierarchical clustering of samples, diversity indices, rarefaction curves, and Venn diagrams were generated using the R programming language in R software version 3.6.3.
Results
Bacterial operational taxonomic units (OUTs) were distributed in Proteobacteria (52.81%), Firmicutes (31.16%), and Lentisphaerae (0.001%). The OTUs among archaea were Candidatus Nitrososphaera (63.56%) and Nitrososphaera spp. (8.77%). Brucella spp. and Bacillus cereus associated with foodborne diseases were detected. Potential pathogens, Rickettsia spp. in risk group 2 and Brucella spp. in risk group 3, were detected. Uncultured Candidatus Koribacter and Candidatus Solibacter were also detected in the food samples. There was a significant difference in the microbial community structure among the sample types (P<0.1).
Conclusion
The results demonstrated the presence of some prokaryotes that are associated with food spoilage or foodborne diseases in vended foods and environmental samples. This study also detected uncultured prokaryotes. The presence of potential pathogens calls for stringent hygiene measures in food vending operations.
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L. Bräuer S, Basiliko N, M. P. Siljanen H, H. Zinder S. Methanogenic archaea in peatlands. FEMS Microbiol Lett 2020; 367:5928548. [DOI: 10.1093/femsle/fnaa172] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
ABSTRACT
Methane emission feedbacks in wetlands are predicted to influence global climate under climate change and other anthropogenic stressors. Herein, we review the taxonomy and physiological ecology of the microorganisms responsible for methane production in peatlands. Common in peat soils are five of the eight described orders of methanogens spanning three phyla (Euryarchaeota, Halobacterota and Thermoplasmatota). The phylogenetic affiliation of sequences found in peat suggest that members of the thus-far-uncultivated group Candidatus Bathyarchaeota (representing a fourth phylum) may be involved in methane cycling, either anaerobic oxidation of methane and/or methanogenesis, as at least a few organisms within this group contain the essential gene, mcrA, according to metagenomic data. Methanogens in peatlands are notoriously challenging to enrich and isolate; thus, much remains unknown about their physiology and how methanogen communities will respond to environmental changes. Consistent patterns of changes in methanogen communities have been reported across studies in permafrost peatland thaw where the resulting degraded feature is thermokarst. However much remains to be understood regarding methanogen community feedbacks to altered hydrology and warming in other contexts, enhanced atmospheric pollution (N, S and metals) loading and direct anthropogenic disturbances to peatlands like drainage, horticultural peat extraction, forestry and agriculture, as well as post-disturbance reclamation.
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Affiliation(s)
- Suzanna L. Bräuer
- Appalachian State University, Department of Biology, ASU Box 32027, 572 Rivers Street, Boone, NC 28608-2027 USA
| | - Nathan Basiliko
- Laurentian University, Department of Biology and the Vale Living with Lakes Centre, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada
| | - Henri M. P. Siljanen
- Eastern Finland University, Department of Environmental and Biological Sciences, Biogeochemistry Research Group, Snellmania Room 4042, Yliopistonranta 1, Kuopio, 70210, Finland
| | - Stephen H. Zinder
- Cornell University, Department of Microbiology, 272 Wing Hall, Ithaca, NY 14850, USA
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Semiquantitative Detection of Hydrogen-Associated or Hydrogen-Free Electron Transfer within Methanogenic Biofilm of Microbial Electrosynthesis. Appl Environ Microbiol 2020; 86:AEM.01056-20. [PMID: 32561585 DOI: 10.1128/aem.01056-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/13/2020] [Indexed: 12/19/2022] Open
Abstract
Hydrogen-entangled electron transfer has been verified as an important extracellular pathway of sharing reducing equivalents to regulate biofilm activities within a diversely anaerobic environment, especially in microbial electrosynthesis systems. However, with a lack of useful methods for in situ hydrogen detection in cathodic biofilms, the role of hydrogen involvement in electron transfer is still debatable. Here, a cathodic biofilm was constructed in CH4-produced microbial electrosynthesis reactors, in which the hydrogen evolution dynamic was analyzed to confirm the presence of hydrogen-associated electron transfer near the cathode within a micrometer scale. Fluorescent in situ hybridization images indicated that a colocalized community of archaea and bacteria developed within a 58.10-μm-thick biofilm at the cathode, suggesting that the hydrogen gradient detected by the microsensor was consumed by the collaboration of bacteria and archaea. Coupling of a microsensor and cyclic voltammetry test further provided semiquantitative results of the hydrogen-associated contribution to methane generation (around 21.20% ± 1.57% at a potential of -0.5 V to -0.69 V). This finding provides deep insight into the mechanism of electron transfer in biofilm on conductive materials.IMPORTANCE Electron transfer from an electrode to biofilm is of great interest to the fields of microbial electrochemical technology, bioremediation, and methanogenesis. It has a promising potential application to boost more value-added products or pollutant degradation. Importantly, the ability of microbes to obtain electrons from electrodes and utilize them brings new insight into direct interspecies electron transfer during methanogenesis. Previous studies verified the direct pathway of electron transfer from the electrode to a pure-culture bacterium, but it was rarely reported how the methanogenic biofilm of mixed cultures shares electrons by a hydrogen-associated or hydrogen-free pathway. In the current study, a combination method of microsensor and cyclic voltammetry successfully semiquantified the role of hydrogen in electron transfer from an electrode to methanogenic biofilm.
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Zhang CJ, Pan J, Liu Y, Duan CH, Li M. Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments. MICROBIOME 2020; 8:94. [PMID: 32552798 PMCID: PMC7302380 DOI: 10.1186/s40168-020-00876-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/26/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Methanogens are crucial to global methane budget and carbon cycling. Methanogens from the phylum Euryarchaeota are currently classified into one class and seven orders, including two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales. The relative importance of the novel methanogens to methane production in the natural environment is poorly understood. RESULTS Here, we used a combined metagenomic and metatranscriptomic approach to investigate the metabolic activity of methanogens in mangrove sediments in Futian Nature Reserve, Shenzhen. We obtained 13 metagenome-assembled genomes (MAGs) representing one class (Methanofastidiosa) and five orders (Methanomassiliicoccales, Methanomicrobiales, Methanobacteriales, Methanocellales, and Methanosarcinales) of methanogens, including the two novel methanogens. Comprehensive annotation indicated the presence of an H2-dependent methylotrophic methanogenesis pathway in Methanofastidiosa and Methanomassiliicoccales. Based on the functional gene analysis, hydrogenotrophic and methylotrophic methanogenesis are the dominant pathways in mangrove sediments. MAG mapping revealed that hydrogenotrophic Methanomicrobiales were the most abundant methanogens and that methylotrophic Methanomassiliicoccales were the most active methanogens in the analyzed sediment profile, suggesting their important roles in methane production. CONCLUSIONS Partial or near-complete genomes of two novel methanogen taxa, Methanofastidiosa and Methanomassiliicoccales, in natural environments were recovered and analyzed here for the first time. The presented findings highlight the ecological importance of the two novel methanogens and complement knowledge of how methane is produced in mangrove ecosystem. This study implies that two novel methanogens play a vital role in carbon cycle. Video Abstract.
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Affiliation(s)
- Cui-Jing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Chang-Hai Duan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
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18
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Dinter T, Geihser S, Gube M, Daniel R, Kuzyakov Y. Impact of sea level change on coastal soil organic matter, priming effects and prokaryotic community assembly. FEMS Microbiol Ecol 2020; 95:5551479. [PMID: 31425573 DOI: 10.1093/femsec/fiz129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/18/2019] [Indexed: 01/09/2023] Open
Abstract
Salt marshes are coastal areas storing high amounts of soil organic matter (SOM) while simultaneously being prone to tidal changes. Here, SOM-decomposition and accompanied priming effects (PE), which describe interactions between labile and old SOM, were studied under controlled flooding conditions. Soil samples from two Wadden Sea salt marsh zones, pioneer (Pio), flooded two times/day, and lower salt marsh (Low), flooded ∼eight times/month, were measured for 56 days concerning CO2-efflux and prokaryotic community shifts during three different inundation-treatments: total-drained (Drained), all-time-flooded (Waterlogged) or temporal-flooding (Tidal). Priming was induced by 14C-glucose addition. CO2-efflux from soil followed Low>Pio and Tidal>Drained>Waterlogged, likely due to O2-depletion and moisture maintenance, two key factors governed by tidal inundation with regard to SOM mineralisation. PEs in both zones were positive (Drained) or absent (Waterlogged, Tidal), presumably as a result of prokaryotes switching from production of extracellular enzymes to direct incorporation of labile C. A doubled amount of prokaryotic biomass in Low compared to Pio probably induced higher chances of cometabolic effects and higher PE. 16S-rRNA-gene-amplicon-based analysis revealed differences in bacterial and archaeal community composition between both zones, revealing temporal niche adaptation with flooding treatment. Strongest alterations were found in Drained, likely due to inundation-mediated changes in C-binding capacities.
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Affiliation(s)
- Thomas Dinter
- Soil Science of Temperate Ecosystems, Büsgenweg 2, 37077 Göttingen, University of Göttingen, Germany
| | - Simone Geihser
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Grisebachstraße 8, 37077 Göttingen, University of Göttingen, Germany
| | - Matthias Gube
- Soil Science of Temperate Ecosystems, Büsgenweg 2, 37077 Göttingen, University of Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Grisebachstraße 8, 37077 Göttingen, University of Göttingen, Germany
| | - Yakov Kuzyakov
- Soil Science of Temperate Ecosystems, Büsgenweg 2, 37077 Göttingen, University of Göttingen, Germany
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Biderre-Petit C, Taib N, Gardon H, Hochart C, Debroas D. New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics. FEMS Microbiol Ecol 2020; 95:5092586. [PMID: 30203066 DOI: 10.1093/femsec/fiy183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/06/2018] [Indexed: 11/13/2022] Open
Abstract
Advances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in the microbial community, thereby providing an important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Hydrogenotrophs, the genes required for acetate activation in the methanogen genome, were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome.
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Affiliation(s)
- Corinne Biderre-Petit
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Najwa Taib
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Hélène Gardon
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Corentin Hochart
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
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Direct Electron Transfer between the frhAGB-Encoded Hydrogenase and Thioredoxin Reductase in the Nonmethanogenic Archaeon Thermococcus onnurineus NA1. Appl Environ Microbiol 2020; 86:AEM.02630-19. [PMID: 31924613 DOI: 10.1128/aem.02630-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/21/2019] [Indexed: 11/20/2022] Open
Abstract
To date, NAD(P)H, ferredoxin, and coenzyme F420 have been identified as electron donors for thioredoxin reductase (TrxR). In this study, we present a novel electron source for TrxR. In the hyperthermophilic archaeon Thermococcus onnurineus NA1, the frhAGB-encoded hydrogenase, a homolog of the F420-reducing hydrogenase of methanogens, was demonstrated to interact with TrxR in coimmunoprecipitation experiments and in vitro pulldown assays. Electrons derived from H2 oxidation by the frhAGB-encoded hydrogenase were transferred to TrxR and reduced Pdo, a redox partner of TrxR. Interaction and electron transfer were observed between TrxR and the heterodimeric hydrogenase complex (FrhAG) as well as the heterotrimeric complex (FrhAGB). Hydrogen-dependent reduction of TrxR was 7-fold less efficient than when NADPH was the electron donor. This study not only presents a different type of electron donor for TrxR but also reveals new functionality of the frhAGB-encoded hydrogenase utilizing a protein as an electron acceptor.IMPORTANCE This study has importance in that TrxR can use H2 as an electron donor with the aid of the frhAGB-encoded hydrogenase as well as NAD(P)H in T. onnurineus NA1. Further studies are needed to explore the physiological significance of this protein. This study also has importance as a significant step toward understanding the functionality of the frhAGB-encoded hydrogenase in a nonmethanogen; the hydrogenase can transfer electrons derived from oxidation of H2 to a protein target by direct contact without the involvement of an electron carrier, which is distinct from the mechanism of its homologs, F420-reducing hydrogenases of methanogens.
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Browne PD, Nielsen TK, Kot W, Aggerholm A, Gilbert MTP, Puetz L, Rasmussen M, Zervas A, Hansen LH. GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms. Gigascience 2020; 9:giaa008. [PMID: 32052832 PMCID: PMC7016772 DOI: 10.1093/gigascience/giaa008] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 11/25/2019] [Accepted: 01/14/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Metagenomic sequencing is a well-established tool in the modern biosciences. While it promises unparalleled insights into the genetic content of the biological samples studied, conclusions drawn are at risk from biases inherent to the DNA sequencing methods, including inaccurate abundance estimates as a function of genomic guanine-cytosine (GC) contents. RESULTS We explored such GC biases across many commonly used platforms in experiments sequencing multiple genomes (with mean GC contents ranging from 28.9% to 62.4%) and metagenomes. GC bias profiles varied among different library preparation protocols and sequencing platforms. We found that our workflows using MiSeq and NextSeq were hindered by major GC biases, with problems becoming increasingly severe outside the 45-65% GC range, leading to a falsely low coverage in GC-rich and especially GC-poor sequences, where genomic windows with 30% GC content had >10-fold less coverage than windows close to 50% GC content. We also showed that GC content correlates tightly with coverage biases. The PacBio and HiSeq platforms also evidenced similar profiles of GC biases to each other, which were distinct from those seen in the MiSeq and NextSeq workflows. The Oxford Nanopore workflow was not afflicted by GC bias. CONCLUSIONS These findings indicate potential sources of difficulty, arising from GC biases, in genome sequencing that could be pre-emptively addressed with methodological optimizations provided that the GC biases inherent to the relevant workflow are understood. Furthermore, it is recommended that a more critical approach be taken in quantitative abundance estimates in metagenomic studies. In the future, metagenomic studies should take steps to account for the effects of GC bias before drawing conclusions, or they should use a demonstrably unbiased workflow.
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Affiliation(s)
- Patrick Denis Browne
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, 4000, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, 4000, Denmark
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, 4000, Denmark
| | - Anni Aggerholm
- Department of Hematology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, Aarhus N, 8200, Denmark
| | - M Thomas P Gilbert
- The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen N, 2200, Denmark
| | - Lara Puetz
- The GLOBE Institute, Faculty of Health and Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen N, 2200, Denmark
| | - Morten Rasmussen
- Department of Genetics, School of Medicine, Stanford University, 291 Campus Drive, Stanford, CA 94305-5051, USA
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, 4000, Denmark
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, Roskilde, 4000, Denmark
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Murru F, Fliegerova K, Mura E, Mrázek J, Kopečný J, Moniello G. A comparison of methanogens of different regions of the equine hindgut. Anaerobe 2018; 54:104-110. [DOI: 10.1016/j.anaerobe.2018.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 08/20/2018] [Indexed: 11/17/2022]
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Yan Z, Ferry JG. Electron Bifurcation and Confurcation in Methanogenesis and Reverse Methanogenesis. Front Microbiol 2018; 9:1322. [PMID: 29973922 PMCID: PMC6019823 DOI: 10.3389/fmicb.2018.01322] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/30/2018] [Indexed: 12/27/2022] Open
Abstract
Reduction of the disulfide of coenzyme M and coenzyme B (CoMS–SCoB) by heterodisulfide reductases (HdrED and HdrABC) is the final step in all methanogenic pathways. Flavin-based electron bifurcation (FBEB) by soluble HdrABC homologs play additional roles in driving essential endergonic reactions at the expense of the exergonic reduction of CoMS–SCoM. In the first step of the CO2 reduction pathway, HdrABC complexed with hydrogenase or formate dehydrogenase generates reduced ferredoxin (Fdx2-) for the endergonic reduction of CO2 coupled to the exergonic reduction of CoMS–SCoB dependent on FBEB of electrons from H2 or formate. Roles for HdrABC:hydrogenase complexes are also proposed for pathways wherein the methyl group of methanol is reduced to methane with electrons from H2. The HdrABC complexes catalyze FBEB-dependent oxidation of H2 for the endergonic reduction of Fdx driven by the exergonic reduction of CoMS–SCoB. The Fdx2- supplies electrons for reduction of the methyl group to methane. In H2- independent pathways, three-fourths of the methyl groups are oxidized producing Fdx2- and reduced coenzyme F420 (F420H2). The F420H2 donates electrons for reduction of the remaining methyl groups to methane requiring transfer of electrons from Fdx2- to F420. HdrA1B1C1 is proposed to catalyze FBEB-dependent oxidation of Fdx2- for the endergonic reduction of F420 driven by the exergonic reduction of CoMS–SCoB. In H2- independent acetotrophic pathways, the methyl group of acetate is reduced to methane with electrons derived from oxidation of the carbonyl group mediated by Fdx. Electron transport involves a membrane-bound complex (Rnf) that oxidizes Fdx2- and generates a Na+ gradient driving ATP synthesis. It is postulated that F420 is reduced by Rnf requiring HdrA2B2C2 catalyzing FBEB-dependent oxidation of F420H2 for the endergonic reduction of Fdx driven by the exergonic reduction of CoMS–SCoB. The Fdx2- is recycled by Rnf and HdrA2B2C2 thereby conserving energy. The HdrA2B2C2 is also proposed to play a role in Fe(III)-dependent reverse methanogenesis. A flavin-based electron confurcating (FBEC) HdrABC complex is proposed for nitrate-dependent reverse methanogenesis in which the oxidation of CoM-SH/CoB-SH and Fdx2- is coupled to reduction of F420. The F420H2 donates electrons to a membrane complex that generates a proton gradient driving ATP synthesis.
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Affiliation(s)
- Zhen Yan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA, United States
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA, United States
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Gilmour CC, Bullock AL, McBurney A, Podar M, Elias DA. Robust Mercury Methylation across Diverse Methanogenic Archaea. mBio 2018; 9:e02403-17. [PMID: 29636434 PMCID: PMC5893877 DOI: 10.1128/mbio.02403-17] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/13/2018] [Indexed: 11/30/2022] Open
Abstract
Methylmercury (MeHg) production was compared among nine cultured methanogenic archaea that contain hgcAB, a gene pair that codes for mercury (Hg) methylation. The methanogens tested produced MeHg at inherently different rates, even when normalized to growth rate and Hg availability. Eight of the nine tested were capable of MeHg production greater than that of spent- and uninoculated-medium controls during batch culture growth. Methanococcoides methylutens, an hgcAB+ strain with a fused gene pair, was unable to produce more MeHg than controls. Maximal conversion of Hg to MeHg through a full batch culture growth cycle for each species (except M. methylutens) ranged from 2 to >50% of the added Hg(II) or between 0.2 and 17 pmol of MeHg/mg of protein. Three of the species produced >10% MeHg. The ability to produce MeHg was confirmed in several hgcAB+ methanogens that had not previously been tested (Methanocella paludicola SANAE, Methanocorpusculum bavaricum, Methanofollis liminatans GKZPZ, and Methanosphaerula palustris E1-9c). Maximal methylation was observed at low sulfide concentrations (<100 μM) and in the presence of 0.5 to 5 mM cysteine. For M. hollandica, the addition of up to 5 mM cysteine enhanced MeHg production and cell growth in a concentration-dependent manner. As observed for bacterial Hg methylators, sulfide inhibited MeHg production. An initial evaluation of sulfide and thiol impacts on bioavailability showed methanogens responding to Hg complexation in the same way as do Deltaproteobacteria The mercury methylation rates of several methanogens rival those of the better-studied Hg-methylating sulfate- and iron-reducing DeltaproteobacteriaIMPORTANCEArchaea, specifically methanogenic organisms, play a role in mercury methylation in nature, but their global importance to MeHg production and the subsequent risk to ecosystems are not known. Methanogenesis has been linked to Hg methylation in several natural habitats where methylmercury production incurs risk to people and ecosystems, including rice paddies and permafrost. In this study, we confirm that most methanogens carrying the hgcAB gene pair are capable of Hg methylation. We found that methylation rates vary inherently among hgcAB+ methanogens but that several species are capable of MeHg production at rates that rival those of the better-know Hg-methylating sulfate- and iron-reducing bacteria. Methanogens may need to be considered equally with sulfate and iron reducers in evaluations of MeHg production in nature.
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Affiliation(s)
| | | | - Alyssa McBurney
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Buckel W, Thauer RK. Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD + (Rnf) as Electron Acceptors: A Historical Review. Front Microbiol 2018; 9:401. [PMID: 29593673 PMCID: PMC5861303 DOI: 10.3389/fmicb.2018.00401] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme F420H2, H2, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of Clostridium kluyveri couples the endergonic reduction of ferredoxin (E0′ = −420 mV) with NADH (−320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (−10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Thermotoga maritima (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H2-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in Acetobacterium woodii (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in Clostridium acidi-urici (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in Clostridium autoethanogrenum (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in Moorella thermoacetica (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in A. woodii (2015), Fd- and F420H2-dependent heterodisulfide reductase (HdrA2B2C2) in Methanosarcina acetivorans (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in Azotobacter vinelandii (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms—in which they have been found—are strictly anaerobic microorganisms except for the aerobe A. vinelandii. The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO2 fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD+ reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.
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Affiliation(s)
- Wolfgang Buckel
- Laboratory for Microbiology, Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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