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Meier D, van Grinsven S, Michel A, Eickenbusch P, Glombitza C, Han X, Fiskal A, Bernasconi S, Schubert CJ, Lever MA. Hydrogen-independent CO 2 reduction dominates methanogenesis in five temperate lakes that differ in trophic states. ISME COMMUNICATIONS 2024; 4:ycae089. [PMID: 38988698 PMCID: PMC11235125 DOI: 10.1093/ismeco/ycae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/20/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024]
Abstract
Emissions of microbially produced methane (CH4) from lake sediments are a major source of this potent greenhouse gas to the atmosphere. The rates of CH4 production and emission are believed to be influenced by electron acceptor distributions and organic carbon contents, which in turn are affected by anthropogenic inputs of nutrients leading to eutrophication. Here, we investigate how eutrophication influences the abundance and community structure of CH4 producing Archaea and methanogenesis pathways across time-resolved sedimentary records of five Swiss lakes with well-characterized trophic histories. Despite higher CH4 concentrations which suggest higher methanogenic activity in sediments of eutrophic lakes, abundances of methanogens were highest in oligotrophic lake sediments. Moreover, while the methanogenic community composition differed significantly at the lowest taxonomic levels (OTU), depending on whether sediment layers had been deposited under oligotrophic or eutrophic conditions, it showed no clear trend in relation to in situ distributions of electron acceptors. Remarkably, even though methanogenesis from CO2-reduction was the dominant pathway in all sediments based on carbon isotope fractionation values, taxonomic identities, and genomes of resident methanogens, CO2-reduction with hydrogen (H2) was thermodynamically unfavorable based on measured reactant and product concentrations. Instead, strong correlations between genomic abundances of CO2-reducing methanogens and anaerobic bacteria with potential for extracellular electron transfer suggest that methanogenic CO2-reduction in lake sediments is largely powered by direct electron transfer from syntrophic bacteria without involvement of H2 as an electron shuttle.
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Affiliation(s)
- Dimitri Meier
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
- Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, Dr. Hans-Frisch-Straße 1-3, 95448 Bayreuth, Germany
| | - Sigrid van Grinsven
- Department of Surface Waters-Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Seestrasse 79, 6047 Kastanienbaum, Switzerland
- Geomicrobiology, Department of Geosciences, Eberhard Karls Universität Tübingen (Tübingen University), Schnarrenbergstraße 94-96, 72076 Tübingen, Germany
| | - Anja Michel
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Philip Eickenbusch
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Clemens Glombitza
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Xingguo Han
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Annika Fiskal
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Stefano Bernasconi
- Department of Earth Sciences, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Geological Institute, Sonneggstrasse 5, 8092 Zurich, Switzerland
| | - Carsten J Schubert
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
- Department of Surface Waters-Research and Management, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Mark A Lever
- Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology, Zurich (ETH Zurich), Universitätstrasse 16, 8092 Zurich, Switzerland
- Marine Science Institute, Department of Marine Sciences, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX 78373, United States
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Yu J, Park MJ, Lee J, Kwon SJ, Lim JK, Lee HS, Kang SG, Lee JH, Kwon KK, Kim YJ. Genomic potential and physiological characteristics of C1 metabolism in novel acetogenic bacteria. Front Microbiol 2023; 14:1279544. [PMID: 37933250 PMCID: PMC10625859 DOI: 10.3389/fmicb.2023.1279544] [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: 08/18/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023] Open
Abstract
Acetogenic bacteria can utilize C1 compounds, such as carbon monoxide (CO), formate, and methanol, via the Wood-Ljungdahl pathway (WLP) to produce biofuels and biochemicals. Two novel acetogenic bacteria of the family Eubacteriaceae ES2 and ES3 were isolated from Eulsukdo, a delta island in South Korea. We conducted whole genome sequencing of the ES strains and comparative genome analysis on the core clusters of WLP with Acetobacterium woodii DSM1030T and Eubacterium limosum ATCC8486T. The methyl-branch cluster included a formate transporter and duplicates or triplicates copies of the fhs gene, which encodes formyl-tetrahydrofolate synthetase. The formate dehydrogenase cluster did not include the hydrogenase gene, which might be replaced by a functional complex with a separate electron bifurcating hydrogenase (HytABCDE). Additionally, duplicated copies of the acsB gene, encoding acetyl-CoA synthase, are located within or close to the carbonyl-branch cluster. The serum bottle culture showed that ES strains can utilize a diverse range of C1 compounds, including CO, formate, and methanol, as well as CO2. Notably, ES2 exhibited remarkable resistance to high concentrations of C1 substrates, such as 100% CO (200 kPa), 700 mM formate, and 500 mM methanol. Moreover, ES2 demonstrated remarkable growth rates under 50% CO (0.45 h-1) and 200 mM formate (0.34 h-1). These growth rates are comparable to or surpassing those previously reported in other acetogenic bacteria. Our study introduces novel acetogenic ES strains and describes their genetic and physiological characteristics, which can be utilized in C1-based biomanufacturing.
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Affiliation(s)
- Jihyun Yu
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Mi-Jeong Park
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Joungmin Lee
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Soo Jae Kwon
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae Kyu Lim
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Hyun Sook Lee
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Sung Gyun Kang
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Jung-Hyun Lee
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Kae Kyoung Kwon
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
| | - Yun Jae Kim
- Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
- KIOST School, University of Science and Technology, Daejeon, Republic of Korea
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Wang Y, Gao Y, Lu X, Gadow SI, Zhuo G, Hu W, Song Y, Zhen G. Bioelectrochemical anaerobic membrane bioreactor enables high methane production from methanolic wastewater: Roles of microbial ecology and microstructural integrity of anaerobic biomass. CHEMOSPHERE 2023; 339:139676. [PMID: 37527740 DOI: 10.1016/j.chemosphere.2023.139676] [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: 05/06/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/03/2023]
Abstract
The disintegration of anaerobic sludge and blockage of membrane pores has impeded the practical application of anaerobic membrane bioreactor (AnMBR) in treating methanolic wastewater. In this study, bioelectrochemical system (BES) was integrated into AnMBR to alleviate sludge dispersion and membrane fouling as well as enhance bioconversion of methanol. Bioelectrochemical regulation effect induced by BES enhanced methane production rate from 4.94 ± 0.52 to 5.39 ± 0.37 L/Lreactor/d by accelerating the enrichment of electroactive microorganisms and the agglomeration of anaerobic sludge via the adhesive and chemical bonding force. 16 S rRNA gene high-throughput sequencing demonstrated that bioelectrochemical stimulation had modified the metabolic pathways by regulating the key functional microbial communities. Methanogenesis via the common methylotrophic Methanomethylovorans was partially substituted by the hydrogenotrophic Candidatus_Methanofastidiosum, etc. The metabolic behaviors of methanol are bioelectrochemistry-dependent, and controlling external voltage is thus an effective strategy for ensuring robust electron transfer, low membrane fouling, and long-term process stability.
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Affiliation(s)
- Yue Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China
| | - Yijing Gao
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China
| | - Xueqin Lu
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, PR China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing, 401120, China; Institute of Eco-Chongming (IEC), 3663 N. Zhongshan Rd, Shanghai, 200062, PR China
| | | | - Guihua Zhuo
- Fujian Provincial Academy of Environmental Science, Fuzhou, 350003, China
| | - Weijie Hu
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd, Shanghai, 200092, PR China
| | - Yu Song
- Shanghai Techase Environment Protection Co., Ltd., 1121 North Zhongshan No. 2 Road, Shanghai, 200092, China
| | - Guangyin Zhen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, 1515 North Zhongshan Rd. (No. 2), Shanghai, 200092, PR China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, 3663 N. Zhongshan Road, Shanghai, 200062, PR China.
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Barrera-Rojas J, Gurubel-Tun KJ, Ríos-Castro E, López-Méndez MC, Sulbarán-Rangel B. An Initial Proteomic Analysis of Biogas-Related Metabolism of Euryarchaeota Consortia in Sediments from the Santiago River, México. Microorganisms 2023; 11:1640. [PMID: 37512813 PMCID: PMC10384328 DOI: 10.3390/microorganisms11071640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
In this paper, sediments from the Santiago River were characterized to look for an alternative source of inoculum for biogas production. A proteomic analysis of methane-processing archaea present in these sediments was carried out. The Euryarchaeota superkingdom of archaea is responsible for methane production and methane assimilation in the environment. The Santiago River is a major river in México with great pollution and exceeded recovery capacity. Its sediments could contain nutrients and the anaerobic conditions for optimal growth of Euryarchaeota consortia. Batch bioreactor experiments were performed, and a proteomic analysis was conducted with current database information. The maximum biogas production was 266 NmL·L-1·g VS-1, with 33.34% of methane, and for proteomics, 3206 proteins were detected from 303 species of 69 genera. Most of them are metabolically versatile members of the genera Methanosarcina and Methanosarcinales, both with 934 and 260 proteins, respectively. These results showed a diverse euryarcheotic species with high potential to methane production. Although related proteins were found and could be feeding this metabolism through the methanol and acetyl-CoA pathways, the quality obtained from the biogas suggests that this metabolism is not the main one in carbon use, possibly the sum of several conditions including growth conditions and the pollution present in these sediments.
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Affiliation(s)
- Jesús Barrera-Rojas
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
| | - Kelly Joel Gurubel-Tun
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
| | - Emmanuel Ríos-Castro
- Laboratorios Nacionales de Servicios Experimentales, Centro de Investigación y Estudios Avanzados del IPN, Ciudad de México 07000, Mexico
| | - María Cristina López-Méndez
- Wetlands and Environmental Sustainability Laboratory, Division of Graduate Studies and Research, Tecnológico Nacional de México/ITS de Misantla, Veracruz 93850, Mexico
| | - Belkis Sulbarán-Rangel
- Department of Water and Energy, Campus Tonalá, University of Guadalajara, Tonalá 45425, Mexico
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Sun FS, Ma C, Yu GH, Kuzyakov Y, Lang YC, Fu PQ, Guo LJ, Teng HH, Liu CQ. Organic carbon preservation in wetlands: Iron oxide protection vs. thermodynamic limitation. WATER RESEARCH 2023; 241:120133. [PMID: 37262945 DOI: 10.1016/j.watres.2023.120133] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
The sequestration of organic carbon (OC) in wetland sediments is influenced by the presence of oxygen or lack thereof. The mechanisms of OC sequestration under redox fluctuations, particularly by the co-mediation of reactive iron (Fe) protection and thermodynamic limitation by the energetics of the OC itself, remain unclear. Over the past 26 years, a combination of field surveys and remote sensing images had revealed a strong decline in both natural and constructed wetland areas in Tianjin. This decline could be attributed to anthropogenic landfill practices and agricultural reclamation efforts, which may have significant impacts on the oxidation-reduction conditions for sedimentary OC. The Fe-bound OC (CBD extraction) decreased by 2 to 10-fold (from 8.3 to 10% to 0.7-4.5%) with increasing sediment depth at three sites with varying water depths (WD). The high-resolution spectro-microscopy analysis demonstrated that Fe (oxyhydr)oxides were colocalized with sedimentary OC. Corresponding to lower redox potential, the nominal oxidation state of C (NOSC), which corresponds to the energy content in OC, became more negative (energy content increased) with increasing sediment depth. Taken together, the preservation of sedimentary OC is contingent on the prevailing redox conditions: In environments where oxygen availability is high, reactive Fe provides protection for OC, while in anoxic environments, thermodynamic constraints (i.e., energetic constraints) limit the oxidation of OC.
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Affiliation(s)
- Fu-Sheng Sun
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China
| | - Chao Ma
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China
| | - Guang-Hui Yu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China.
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Gottingen, 37077 Gottingen, Germany; Peoples Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Yun-Chao Lang
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China
| | - Ping-Qing Fu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China
| | - Li-Jun Guo
- Tianjin Institute of Geological Survey, Tianjin 300191, China
| | - Hui Henry Teng
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China; Department of Chemistry, George Washington University, Washington, DC 20006, United States
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin Bohai Rim Coastal Earth Critical Zone National Observation and Research Station, Tianjin 300072, China
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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: 13] [Impact Index Per Article: 13.0] [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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Patidar P, Prakash T. Decoding the roles of extremophilic microbes in the anaerobic environments: Past, Present, and Future. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100146. [PMID: 35909618 PMCID: PMC9325894 DOI: 10.1016/j.crmicr.2022.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
Abstract
The inaccessible extreme environments harbor a large majority of anaerobic microbes which remain unknown. Anaerobic microbes are used in a variety of industrial applications. In the future, metagenomic-assisted techniques can be used to identify novel anaerobic microbes from the unexplored extreme environments. Genetic engineering can be used to enhance the efficiency of anaerobic microbes for various processes.
The genome of an organism is directly or indirectly correlated with its environment. Consequently, different microbes have evolved to survive and sustain themselves in a variety of environments, including unusual anaerobic environments. It is believed that their genetic material could have played an important role in the early evolution of their existence in the past. Presently, out of the uncountable number of microbes found in different ecosystems we have been able to discover only one percent of the total communities. A large majority of the microbial populations exists in the most unusual and extreme environments. For instance, many anaerobic bacteria are found in the gastrointestinal tract of humans, soil, and hydrothermal vents. The recent advancements in Metagenomics and Next Generation Sequencing technologies have improved the understanding of their roles in these environments. Presently, anaerobic bacteria are used in various industries associated with biofuels, fermentation, production of enzymes, vaccines, vitamins, and dairy products. This broad applicability brings focus to the significant contribution of their genomes in these functions. Although the anaerobic microbes have become an irreplaceable component of our lives, a major and important section of such anaerobic microbes still remain unexplored. Therefore, it can be said that unlocking the role of the microbial genomes of the anaerobes can be a noteworthy discovery not just for mankind but for the entire biosystem as well.
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Affiliation(s)
- Pratyusha Patidar
- School of Basic Sciences, Indian Institute of Technology (IIT) Mandi, HP, India
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology (IIT) Mandi, HP, India
- Corresponding author.
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