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Bueno de Mesquita CP, Wu D, Tringe SG. Methyl-Based Methanogenesis: an Ecological and Genomic Review. Microbiol Mol Biol Rev 2023; 87:e0002422. [PMID: 36692297 PMCID: PMC10029344 DOI: 10.1128/mmbr.00024-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.
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Affiliation(s)
| | - Dongying Wu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Alarcón-Vivero M, Moena NRT, Gonzalez F, Jopia-Contreras P, Aspé E, Briones HU, Fernandez KS. Anaerobic biofilm enriched with an ammonia tolerant methanogenic consortium to improve wastewater treatment in the fishing industry. Biotechnol Lett 2022; 44:239-251. [PMID: 35037233 DOI: 10.1007/s10529-021-03213-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/29/2021] [Indexed: 11/29/2022]
Abstract
The digestion efficiency of liquid industrial wastes increases when using bioreactors colonized by microbial biofilms. High concentrations of proteins derived from the fish processing industry lead to the production of ammonia, which inhibits methane production. Two bioreactors were constructed to compare methanogenic activity: one enriched with mMPA (methylaminotrofic methane production archaea) consortia (control bioreactor), and the second with NH3 tolerant consortia (treatment bioreactor). Ammonia tolerant activity was assessed by applying an ammonia shock (755 mg NH3/L). Methane production, consumption of total organic carbon (TOC) and the taxonomic composition of bacteria and archaea was evaluated using 16S rDNA in the acclimatization, ammonia shock, and recovery phases.The ammonia shock significantly affected both methane production and the consumption of TOC in the control reactor (p < 0.05) and taxonomical composition of the microbial consortia (OTU). These values remained constant in the treatment reactor. The analysis of biofilm composition showed a predominance of Methanosarcinaceae (Methanomethylovorans sp., and probably two different species of Methanosarcina sp.) in bioreactors. These results demonstrate that using acclimated biofilms enriched with ammonia tolerant methanogens control the inhibitory effect of ammonia on methanogenesis.
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Affiliation(s)
- Manuel Alarcón-Vivero
- Instituto de Acuicultura, Universidad Austral de Chile (UACh), Sede Puerto Montt, Puerto Montt, Chile
| | - Nathaly Ruiz-Tagle Moena
- Lab. Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | - Fidelina Gonzalez
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | | | - Estrella Aspé
- Departamento de Ingeniería Química, Facultad de Ingeniería, Universidad de Concepción, Concepción, Chile
| | - Homero Urrutia Briones
- Lab. Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile.,Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Katherine Sossa Fernandez
- Lab. Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile. .,Facultad de Ciencias Forestales, Universidad de Concepción, Concepción, Chile.
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Yang Y, Chen J, Chen X, Jiang Q, Liu Y, Xie S. Cyanobacterial bloom induces structural and functional succession of microbial communities in eutrophic lake sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117157. [PMID: 33892464 DOI: 10.1016/j.envpol.2021.117157] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 04/05/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Cyanobacterial blooms have considerable effects on lacustrine microbial communities. The current study explored the temporal pattern of sedimentary archaea and bacteria during cyanobacterial bloom in a eutrophic lake. With the sampling period divided into bloom phase, interval phase and end phase according to the variation of physicochemical parameters, the structures and functions of both kingdoms presented a significant difference among phases. Bloom phases could be characterized with the lowest diversity and up-regulated functions in biodegradation of cyanobacterial metabolites driven by bacteria. Archaeal community showed an increased metabolic function during interval phases, including active methanogenesis sensitive to carbon input. The highest diversity and an enrichment of hub genera in microbial network were both observed in end phase, allowing for closer cooperation among groups involved in cyanobacteria-derived organic matter transformation. Although the archaeal community was less variable or diverse than bacteria, methanogenic functions dramatically fluctuated with cyanobacterial dynamics. And microbial groups related to methane cycling played an important role in microbial network. The results provided new insights into temporal dynamics of lacustrine microbial communities and microbial co-occurrence, and highlighted the significant ecological role of methane cycling-related microbes in lake sediments under the influence of cyanobacterial blooms.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Xiuli Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Qingsong Jiang
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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