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Yan A, Pan Z, Liang Y, Mo X, Guo T, Li J. Archaea communities in aerobic granular sludge: A mini-review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174974. [PMID: 39053544 DOI: 10.1016/j.scitotenv.2024.174974] [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: 05/05/2024] [Revised: 06/27/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
Recent research on the archaea community in aerobic granular sludge (AGS) has attracted considerable attention. This review summarizes the existing literature on composition, distribution, and related functions of archaea community in AGS. Furthermore, the effects of granulation, substrate, temperature, process types, and aeration models on the archaea community were discussed. Significantly, the layered structure of AGS facilitates the enrichment of archaea, including methanogenic archaea and ammonia-oxidizing archaea. Archaea engage in metabolic interactions with other microorganisms, enhancing the ecological functionalities of AGS and its tolerance to adverse conditions. Future investigations should focus on minimizing greenhouse gas emissions and exploring the roles and interactive mechanisms of archaea and other microorganisms within AGS.
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Affiliation(s)
- Anqi Yan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zengrui Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yifan Liang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xinyan Mo
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Tao Guo
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jun Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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2
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Wu K, Zhou L, Tahon G, Liu L, Li J, Zhang J, Zheng F, Deng C, Han W, Bai L, Fu L, Dong X, Zhang C, Ettema TJG, Sousa DZ, Cheng L. Isolation of a methyl-reducing methanogen outside the Euryarchaeota. Nature 2024; 632:1124-1130. [PMID: 39048829 DOI: 10.1038/s41586-024-07728-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Methanogenic archaea are main contributors to methane emissions, and have a crucial role in carbon cycling and global warming. Until recently, methanogens were confined to Euryarchaeota, but metagenomic studies revealed the presence of genes encoding the methyl coenzyme M reductase complex in other archaeal clades1-4, thereby opening up the premise that methanogenesis is taxonomically more widespread. Nevertheless, laboratory cultivation of these non-euryarchaeal methanogens was lacking to corroborate their potential methanogenic ability and physiology. Here we report the isolation of a thermophilic archaeon LWZ-6 from an oil field. This archaeon belongs to the class Methanosuratincolia (originally affiliated with 'Candidatus Verstraetearchaeota') in the phylum Thermoproteota. Methanosuratincola petrocarbonis LWZ-6 is a strict hydrogen-dependent methylotrophic methanogen. Although previous metagenomic studies speculated on the fermentative potential of Methanosuratincolia members, strain LWZ-6 does not ferment sugars, peptides or amino acids. Its energy metabolism is linked only to methanogenesis, with methanol and monomethylamine as electron acceptors and hydrogen as an electron donor. Comparative (meta)genome analysis confirmed that hydrogen-dependent methylotrophic methanogenesis is a widespread trait among Methanosuratincolia. Our findings confirm that the diversity of methanogens expands beyond the classical Euryarchaeota and imply the importance of hydrogen-dependent methylotrophic methanogenesis in global methane emissions and carbon cycle.
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Affiliation(s)
- Kejia Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Lei Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Guillaume Tahon
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Laiyan Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jiang Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jianchao Zhang
- School of Earth System Science, Institute of Surface-Earth System Science, Tianjin University, Tianjin, China
| | - Fengfeng Zheng
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China
| | - Chengpeng Deng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Wenhao Han
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Liping Bai
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Lin Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Geo-Omics Research, Southern University of Science and Technology, Shenzhen, China
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China.
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Khan MI, Yoo K, Schwab L, Kümmel S, Nijenhuis I. Characterization of anaerobic biotransformation of hexachlorocyclohexanes by novel microbial consortia enriched from channel and river sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135198. [PMID: 39013321 DOI: 10.1016/j.jhazmat.2024.135198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/11/2024] [Accepted: 07/11/2024] [Indexed: 07/18/2024]
Abstract
The microbial biotransformation of hexachlorocyclohexane (HCH) by novel anaerobic microbial consortia enriched from sediments of an industrial effluent channel and the river Ravi in Pakistan was examined. The anaerobic consortia were capable of biotransforming α-, β-, γ-, and δ-HCH through reductive dichloroelimination, resulting in the formation of benzene and monochlorobenzene. Concerning γ-HCH biotransformation by the channel and river cultures, isotopic fractionations for carbon (εC) were - 5.3 ± 0.4 (‰) and - 10.6 ± 1.2 (‰), while isotopic fractionations for chlorine (εCl) were - 4.4 ± 0.4 (‰) and - 7.8 ± 0.9 (‰), respectively. Furthermore, lambda values (Λ), representing the correlation of δ13C and δ37Cl fractionation, were determined to be 1.1 ± 0.1 and 1.3 ± 0.1 for γ-HCH biotransformation, suggesting a reductive dichloroelimination as the initial step of HCH biotransformation in both cultures. Amplicon sequencing targeting the 16S rRNA genes revealed that Desulfomicrobium populations were considerably increased in both cultures, indicating their possible involvement in the degradation process. These findings suggest that Desulfomicrobium-like populations may have an important role in biotransformation of HCH and novel anaerobic HCH-degrading microbial consortia could be useful bioaugmentation agents for the bioremediation of HCH-contaminated sites in Pakistan.
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Affiliation(s)
- Muhammad Imran Khan
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Keunje Yoo
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan 49112, South Korea
| | - Laura Schwab
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Steffen Kümmel
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Ivonne Nijenhuis
- Department of Technical Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
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Padalko A, Nair G, Sousa FL. Fusion/fission protein family identification in Archaea. mSystems 2024; 9:e0094823. [PMID: 38700364 PMCID: PMC11237513 DOI: 10.1128/msystems.00948-23] [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] [Received: 09/05/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.
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Affiliation(s)
- Anastasiia Padalko
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Govind Nair
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Filipa L. Sousa
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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Ma Y, Qu Y, Yao X, Xia C, Lv M, Lin X, Zhang L, Zhang M, Hu B. Unveiling the unique role of iron in the metabolism of methanogens: A review. ENVIRONMENTAL RESEARCH 2024; 250:118495. [PMID: 38367837 DOI: 10.1016/j.envres.2024.118495] [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: 12/26/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Methanogens are the main participants in the carbon cycle, catalyzing five methanogenic pathways. Methanogens utilize different iron-containing functional enzymes in different methanogenic processes. Iron is a vital element in methanogens, which can serve as a carrier or reactant in electron transfer. Therefore, iron plays an important role in the growth and metabolism of methanogens. In this paper, we cast light on the types and functions of iron-containing functional enzymes involved in different methanogenic pathways, and the roles iron play in energy/substance metabolism of methanogenesis. Furthermore, this review provides certain guiding significance for lowering CH4 emissions, boosting the carbon sink capacity of ecosystems and promoting green and low-carbon development in the future.
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Affiliation(s)
- Yuxin Ma
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ying Qu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangwu Yao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chujun Xia
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengjie Lv
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao Lin
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lili Zhang
- Beijing Enterprises Water Group Limited, Beijing, China
| | - Meng Zhang
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China.
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6
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Ke T, Rajoo A, Tinkov AA, Skalny AV, Tizabi Y, Rocha JBT, Bowman AB, Aschner M. Intestinal microbiota protects against methylmercury-induced neurotoxicity. Biometals 2024; 37:561-576. [PMID: 37973679 DOI: 10.1007/s10534-023-00554-1] [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] [Received: 07/31/2023] [Accepted: 10/14/2023] [Indexed: 11/19/2023]
Abstract
Methylmercury (MeHg) remains a global public health issue because of its frequent presence in human food sources obtained from the water. The excretion of MeHg in humans occurs slowly with a biological half-time of 32-47 days. Short-term MeHg exposure may cause long-lasting neurotoxicity. The excretion through feces is a major route in the demethylation of MeHg. Accumulating evidence suggests that the intestinal microbiota plays an important role in the demethylation of MeHg, thereby protecting the host from neurotoxic effects. Here, we discuss recent developments on the role of intestinal microbiota in MeHg metabolism, based on in vitro cell culture experiments, experimental animal studies and human investigations. Demethylation by intestinal bacteria is the rate-limiting step in MeHg metabolism and elimination. The identity of bacteria strains responsible for this biotransformation is currently unknown; however, the non-homogenous distribution of intestinal microbiota may lead to different demethylation rates in the intestinal tract. The maintenance of intestinal barrier function by intestinal microbiota may afford protection against MeHg-induced neurotoxicity, which warrant future investigations. We also discuss studies investigating the effects of MeHg exposure on the population structural stability of intestinal microbiota in several host species. Although this is an emerging area in metal toxicity, current research suggests that a change in certain phyla in the intestinal microbiota may indicate MeHg overexposure.
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Affiliation(s)
- Tao Ke
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - André Rajoo
- Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL, 33458, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, 33431, USA
| | - Alexey A Tinkov
- IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia, 119991
- Yaroslavl State University, Yaroslavl, Russia, 150003
- Institute of Cellular and Intracellular Symbiosis, Russian Academy of Sciences, Orenburg, Russia, 460000
| | - Anatoly V Skalny
- IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia, 119991
- Department of Medical Elementology, Peoples' Friendship University of Russia (RUDN University), Moscow, Russia, 117198
| | - Yousef Tizabi
- Department of Pharmacology, Howard University College of Medicine, Washington, DC, 20059, USA
| | - Joao B T Rocha
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, 97105900, RS, Brazil
| | - Aaron B Bowman
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907-2051, USA
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, 1300 Morris Park Avenue Forchheimer Building, Room 209, Bronx, NY, 10461, USA.
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Candeliere F, Sola L, Raimondi S, Rossi M, Amaretti A. Good and bad dispositions between archaea and bacteria in the human gut: New insights from metagenomic survey and co-occurrence analysis. Synth Syst Biotechnol 2024; 9:88-98. [PMID: 38292760 PMCID: PMC10824687 DOI: 10.1016/j.synbio.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 02/01/2024] Open
Abstract
Archaea are an understudied component of the human microbiome. In this study, the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing. Archaea were ubiquitously found in a wide range of abundances, reaching up to 7.2 %. The dominant archaeal phylum was Methanobacteriota, specifically the family Methanobacteriaceae, encompassing more than 50 % of Archaea in 50 samples. The previously underestimated Thermoplasmatota, mostly composed of Methanomassiliicoccaceae, dominated in 10 subjects (>50 %) and was present in all others except one. Halobacteriota, the sole other archaeal phylum, occurred in negligible concentration, except for two samples (4.6-4.8 %). This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway: i) hydrogenotrophic reduction of CO2 is the predominant, being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples; ii) the second pathway, that involved Methanomassiliicoccales, was the hydrogenotrophic reduction of methyl-compounds; iii) dismutation of acetate or methyl-compounds seemed to be absent. Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community, allowing to depict a clearer picture of the human gut archaeome.
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Affiliation(s)
- Francesco Candeliere
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Laura Sola
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Biogest-Siteia, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Biogest-Siteia, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
- Biogest-Siteia, University of Modena and Reggio Emilia, 41125 Modena, Italy
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Bai Y, Wang Y, Shen L, Shang B, Ji Y, Ren B, Yang W, Yang Y, Ma Z, Feng Z. Equal importance of humic acids and nitrate in driving anaerobic oxidation of methane in paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169311. [PMID: 38103608 DOI: 10.1016/j.scitotenv.2023.169311] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
Methane (CH4) is both generated and consumed in paddy soils, where anaerobic oxidation of methane (AOM) serves as a crucial process for mitigating CH4 emissions. Although the participation of humic acids (HA) and nitrate in AOM has been recognized, their relative roles and significance in paddy soils remain insufficiently investigated. In this study, we explored the potential activity of AOM driven by HA and nitrate, as well as the composition of archaeal communities in paddy soils across different rice growth periods and fertilization treatments. AOM activity ranged from 0.81 to 1.33 and 1.26 to 2.38 nmol of 13CO2 g-1 (dry soil) day-1 with HA and nitrate, respectively. No significant differences (p < 0.05) were observed between the AOM activity driven by HA and nitrate across the three fertilization treatments. According to AOM activity, the annual consumption of CH4 was estimated at approximately 0.49 ± 0.06 and 0.83 ± 0.19 Tg for AOM processes driven by HA and nitrate in Chinese paddy soils. Nitrate-driven AOM activity exhibited a positive (p < 0.05) correlation with the abundance of the ANME-2d mcrA gene but a negative (p < 0.05) correlation with the content of dissolved organic carbon. Intriguingly, HA-driven AOM activity was only correlated positively with the nitrate-driven AOM activity. Soil water content, soil organic carbon, nitrate and nitrite contents were significantly correlated with the relative abundance of methanogenic and methanotrophic archaea. These results identified the potential importance of HA and nitrate in driving AOM processes within paddy soils, providing a comprehensive understanding of the complex microbial processes regulating greenhouse gas emissions from paddy soils.
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Affiliation(s)
- Yanan Bai
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yanping Wang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Lidong Shen
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.
| | - Bo Shang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yang Ji
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Bingjie Ren
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Wangting Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yuling Yang
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zhiguo Ma
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zhaozhong Feng
- Key Laboratory of Ecosystem Carbon Source and Sink, China Meteorological Administration (ECSS-CMA), School of Ecology and Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China
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9
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Pilliol V, Morsli M, Terlier L, Hassani Y, Malat I, Guindo CO, Davoust B, Lamglait B, Drancourt M, Aboudharam G, Grine G, Terrer E. Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos. Microbiol Spectr 2024; 12:e0514122. [PMID: 38189277 PMCID: PMC10845953 DOI: 10.1128/spectrum.05141-22] [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] [Received: 12/14/2022] [Accepted: 11/24/2023] [Indexed: 01/09/2024] Open
Abstract
Methanosphaera stadtmanae was the sole Methanosphaera representative to be cultured and detected by molecular methods in the human gut microbiota, further associated with digestive and respiratory diseases, leaving unknown the actual diversity of human-associated Methanosphaera species. Here, a novel Methanosphaera species, Candidatus Methanosphaera massiliense (Ca. M. massiliense) sp. nov. was isolated by culture using a hydrogen- and carbon dioxide-free medium from one human feces sample. Ca. M. massiliense is a non-motile, 850 nm Gram-positive coccus autofluorescent at 420 nm. Whole-genome sequencing yielded a 29.7% GC content, gapless 1,785,773 bp genome sequence with an 84.5% coding ratio, encoding for alcohol and aldehyde dehydrogenases promoting the growth of Ca. M. massiliense without hydrogen. Screening additional mammal and human feces using a specific genome sequence-derived DNA-polymerase RT-PCR system yielded a prevalence of 22% in pigs, 12% in red kangaroos, and no detection in 149 other human samples. This study, extending the diversity of Methanosphaera in human microbiota, questions the zoonotic sources of Ca. M. massiliense and possible transfer between hosts.IMPORTANCEMethanogens are constant inhabitants in the human gut microbiota in which Methanosphaera stadtmanae was the only cultivated Methanosphaera representative. We grew Candidatus Methanosphaera massiliense sp. nov. from one human feces sample in a novel culture medium under a nitrogen atmosphere. Systematic research for methanogens in human and animal fecal samples detected Ca. M. massiliense in pig and red kangaroo feces, raising the possibility of its zoonotic acquisition. Host specificity, source of acquisition, and adaptation of methanogens should be further investigated.
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Affiliation(s)
- Virginie Pilliol
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | - Madjid Morsli
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Laureline Terlier
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Yasmine Hassani
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ihab Malat
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Cheick Oumar Guindo
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard Davoust
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | | | - Michel Drancourt
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Gérard Aboudharam
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université, Ecole de Médecine Dentaire, Marseille, France
| | | | - Elodie Terrer
- Aix-Marseille Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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10
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Fagundes RR, Belt SC, Bakker BM, Dijkstra G, Harmsen HJM, Faber KN. Beyond butyrate: microbial fiber metabolism supporting colonic epithelial homeostasis. Trends Microbiol 2024; 32:178-189. [PMID: 37596118 DOI: 10.1016/j.tim.2023.07.014] [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: 05/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Human gut bacteria produce metabolites that support energy and carbon metabolism of colonic epithelial cells. While butyrate is commonly considered the primary fuel, it alone cannot meet all the carbon requirements for cellular synthetic functions. Glucose, delivered via circulation or microbial metabolism, serves as a universal carbon source for synthetic processes like DNA, RNA, protein, and lipid production. Detailed knowledge of epithelial carbon and energy metabolism is particularly relevant for epithelial regeneration in digestive and metabolic diseases, such as inflammatory bowel disease and type 2 diabetes. Here, we review the production and role of different colonic microbial metabolites in energy and carbon metabolism of colonocytes, also critically evaluating the common perception that butyrate is the preferred fuel.
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Affiliation(s)
- Raphael R Fagundes
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Saskia C Belt
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Barbara M Bakker
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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11
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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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12
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Zhao D, Zhang S, Chen J, Zhao J, An P, Xiang H. Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea. THE ISME JOURNAL 2024; 18:wrad033. [PMID: 38366248 PMCID: PMC10873845 DOI: 10.1093/ismejo/wrad033] [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: 10/08/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 02/18/2024]
Abstract
The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia, and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.
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Affiliation(s)
- Dahe Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengjie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Junyu Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Juanjuan Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Peng An
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Sichuan Normal University, Sichuan 610068, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
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13
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Guerra A. Human associated Archaea: a neglected microbiome worth investigating. World J Microbiol Biotechnol 2024; 40:60. [PMID: 38172371 DOI: 10.1007/s11274-023-03842-7] [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: 07/22/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The majority of research in the field of human microbiota has predominantly focused on bacterial and fungal communities. Conversely, the human archaeome has received scant attention and remains poorly studied, despite its potential role in human diseases. Archaea have the capability to colonize various human body sites, including the gastrointestinal tract, skin, vagina, breast milk, colostrum, urinary tract, lungs, nasal and oral cavities. This colonization can occur through vertical transmission, facilitated by the transfer of breast milk or colostrum from mother to child, as well as through the consumption of dairy products, organic produce, salty foods, and fermented items. The involvement of these microorganisms in diseases, such as periodontitis, might be attributed to their production of toxic compounds and the detoxification of growth inhibitors for pathogens. However, the precise mechanisms through which these contributions occur remain incompletely understood, necessitating further studies to assess their impact on human health.
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14
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Mir TUG, Manhas S, Khurshid Wani A, Akhtar N, Shukla S, Prakash A. Alterations in microbiome of COVID-19 patients and its impact on forensic investigations. Sci Justice 2024; 64:81-94. [PMID: 38182316 DOI: 10.1016/j.scijus.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 11/12/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
The human microbiome is vital for maintaining human health and has garnered substantial attention in recent years, particularly in the context of the coronavirus disease 2019 (COVID-19) outbreak. Studies have underscored significant alterations in the microbiome of COVID-19 patients across various body niches, including the gut, respiratory tract, oral cavity, skin, and vagina. These changes manifest as shifts in microbiota composition, characterized by an increase in opportunistic pathogens and a decrease in beneficial commensal bacteria. Such microbiome transformations may play a pivotal role in influencing the course and severity of COVID-19, potentially contributing to the inflammatory response. This ongoing relationship between COVID-19 and the human microbiome serves as a compelling subject of research, underscoring the necessity for further investigations into the underlying mechanisms and their implications for patient health. Additionally, these alterations in the microbiome may have significant ramifications for forensic investigations, given the microbiome's potential in establishing individual characteristics. Consequently, changes in the microbiome could introduce a level of complexity into forensic determinations. As research progresses, a more profound understanding of the human microbiome within the context of COVID-19 may offer valuable insights into disease prevention, treatment strategies, and its potential applications in forensic science. Consequently, this paper aims to provide an overarching review of microbiome alterations due to COVID-19 and the associated impact on forensic applications, bridging the gap between the altered microbiome of COVID-19 patients and the challenges forensic investigations may encounter when analyzing this microbiome as a forensic biomarker.
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Affiliation(s)
- Tahir Ul Gani Mir
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India; State Forensic Science Laboratory, Srinagar, Jammu and Kashmir 190001, India.
| | - Sakshi Manhas
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Saurabh Shukla
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India.
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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15
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Chen JS, Hussain B, Tsai HC, Nagarajan V, Kumar RS, Lin IC, Hsu BM. Deciphering microbial communities and their unique metabolic repertoire across rock-soil-plant continuum in the Dayoukeng fumarolic geothermal field of the Tatun Volcano Group. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:7330-7344. [PMID: 38158533 DOI: 10.1007/s11356-023-31313-x] [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: 05/08/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024]
Abstract
High temperature and sulfur concentrations in geothermal sulfur fumaroles host unique microbial ecosystems with niche-specific metabolic diversity and physiological functions. In this study, the microbial communities and their functionalities associated with the Dayoukeng geothermal field and the rock-soil-plant continuum were investigated to underpin the microbial modulation at different distances from the fumaroles source. At the phylum level, Bacteroidota, Planctomycetota, Armatimonadota, and Patescibacteria were abundant in plant samples; Elusimicrobiota and Desulfobacterota were in the rock samples while Nitrospirota, Micrarchaeota, and Deinococcota were dominant in the soil samples. Acidophilic thermophiles were enriched in samples within close proximity to the fumaroles, primarily at a distance of 1 m. The sulfur and iron-oxidizing acidophilic bacterial genera such as Acidothiobacillus and Sulfobacillus were abundant in the rock samples. The thermoacidophilic archaeon Acidianus and acidophilic bacteria Acidiphilium were abundant in the soil samples. Additionally, Thermosporothrix and Acidothermus were found abundant in the plant samples. The results of the functional annotation indicated that dark sulfur oxidation, iron oxidation, and hydrogen oxidation pathways were abundant in the soil samples up to 1 m from the fumaroles, while methanogenic and fermentation pathways were more prevalent in the soil samples located 10 m from the fumaroles. Interestingly, the results of this study indicated a higher microbial richness and abundance of acidophilic communities in the soils and plants compared to the rocks of the DYK fumarolic geothermal field.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
- Department of Biomedical Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - Rajendran Senthil Kumar
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan
| | - I-Ching Lin
- Department of Family Medicine, Asia University Hospital, Taichung, Taiwan
- Department of Kinesiology, Health and Leisure, Chienkuo Technology University, Chenghua, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Minxiong, Chiayi County, Taiwan.
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16
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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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17
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Borrel G, Fadhlaoui K, Ben Hania W, Gaci N, Pehau-Arnaudet G, Chaudhary PP, Vandekerckove P, Ballet N, Alric M, O’Toole PW, Fardeau ML, Ollivier B, Brugère JF. Methanomethylophilus alvi gen. nov., sp. nov., a Novel Hydrogenotrophic Methyl-Reducing Methanogenic Archaea of the Order Methanomassiliicoccales Isolated from the Human Gut and Proposal of the Novel Family Methanomethylophilaceae fam. nov. Microorganisms 2023; 11:2794. [PMID: 38004804 PMCID: PMC10673518 DOI: 10.3390/microorganisms11112794] [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: 10/28/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The methanogenic strain Mx-05T was isolated from the human fecal microbiome. A phylogenetic analysis based on the 16S rRNA gene and protein marker genes indicated that the strain is affiliated with the order Methanomassiliicoccales. It shares 86.9% 16S rRNA gene sequence identity with Methanomassiliicoccus luminyensis, the only member of this order previously isolated. The cells of Mx-05T were non-motile cocci, with a diameter range of 0.4-0.7 μm. They grew anaerobically and reduced methanol, monomethylamine, dimethylamine, and trimethylamine into methane, using H2 as an electron donor. H2/CO2, formate, ethanol, and acetate were not used as energy sources. The growth of Mx-05T required an unknown medium factor(s) provided by Eggerthella lenta and present in rumen fluid. Mx-05T grew between 30 °C and 40 °C (optimum 37 °C), over a pH range of 6.9-8.3 (optimum pH 7.5), and between 0.02 and 0.34 mol.L-1 NaCl (optimum 0.12 mol.L-1 NaCl). The genome is 1.67 Mbp with a G+C content of 55.5 mol%. Genome sequence annotation confirmed the absence of the methyl branch of the H4MPT Wood-Ljungdahl pathway, as described for other Methanomassiliicoccales members. Based on an average nucleotide identity analysis, we propose strain Mx-05T as being a novel representative of the order Methanomassiliicoccales, within the novel family Methanomethylophilaceae, for which the name Methanomethylophilus alvi gen. nov, sp. nov. is proposed. The type strain is Mx-05T (JCM 31474T).
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Affiliation(s)
- Guillaume Borrel
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell, 75015 Paris, France
| | - Khaled Fadhlaoui
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université Clermont Auvergne, INRA, MEDIS, 63000 Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS, UMR 6023 CNRS-UCA, Laboratoire Microorganismes: Génome et Environnement LMGE, 63000 Clermont-Ferrand, France
| | - Wajdi Ben Hania
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Nadia Gaci
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | - Gérard Pehau-Arnaudet
- Institut Pasteur, Université Paris Cité, Ultrastructural Bioimaging, 75015 Paris, France
| | - Prem Prashant Chaudhary
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
- Epithelial Therapeutics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Nathalie Ballet
- Lesaffre International, Lesaffre Group, 59700 Marcq-en-Barœul, France
| | - Monique Alric
- Université d’Auvergne, EA CIDAM, 63000 Clermont-Ferrand, France (J.-F.B.)
| | | | - Marie-Laure Fardeau
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
| | - Bernard Ollivier
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France; (K.F.); (B.O.)
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18
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Khairunisa BH, Heryakusuma C, Ike K, Mukhopadhyay B, Susanti D. Evolving understanding of rumen methanogen ecophysiology. Front Microbiol 2023; 14:1296008. [PMID: 38029083 PMCID: PMC10658910 DOI: 10.3389/fmicb.2023.1296008] [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: 09/17/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Production of methane by methanogenic archaea, or methanogens, in the rumen of ruminants is a thermodynamic necessity for microbial conversion of feed to volatile fatty acids, which are essential nutrients for the animals. On the other hand, methane is a greenhouse gas and its production causes energy loss for the animal. Accordingly, there are ongoing efforts toward developing effective strategies for mitigating methane emissions from ruminant livestock that require a detailed understanding of the diversity and ecophysiology of rumen methanogens. Rumen methanogens evolved from free-living autotrophic ancestors through genome streamlining involving gene loss and acquisition. The process yielded an oligotrophic lifestyle, and metabolically efficient and ecologically adapted descendants. This specialization poses serious challenges to the efforts of obtaining axenic cultures of rumen methanogens, and consequently, the information on their physiological properties remains in most part inferred from those of their non-rumen representatives. This review presents the current knowledge of rumen methanogens and their metabolic contributions to enteric methane production. It also identifies the respective critical gaps that need to be filled for aiding the efforts to mitigate methane emission from livestock operations and at the same time increasing the productivity in this critical agriculture sector.
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Affiliation(s)
| | - Christian Heryakusuma
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Kelechi Ike
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
- Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Dwi Susanti
- Microbial Discovery Research, BiomEdit, Greenfield, IN, United States
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19
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Chen C, Li L, Wang Y, Dong X, Zhao FJ. Methylotrophic methanogens and bacteria synergistically demethylate dimethylarsenate in paddy soil and alleviate rice straighthead disease. THE ISME JOURNAL 2023; 17:1851-1861. [PMID: 37604918 PMCID: PMC10579292 DOI: 10.1038/s41396-023-01498-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023]
Abstract
Microorganisms play a key role in arsenic (As) biogeochemistry, transforming As species between inorganic and organic forms and different oxidation states. Microbial As methylation is enhanced in anoxic paddy soil, producing primarily dimethylarsenic (DMAs), which can cause rice straighthead disease and large yield losses. DMAs can also be demethylated in paddy soil, but the microorganisms driving this process remain unclear. In this study, we showed that the enrichment culture of methylotrophic methanogens from paddy soil demethylated pentavalent DMAs(V) efficiently. DMAs(V) was reduced to DMAs(III) before demethylation. 16S rRNA gene diversity and metagenomic analysis showed that Methanomassiliicoccus dominated in the enrichment culture, with Methanosarcina and Methanoculleus also being present. We isolated Methanomassiliicoccus luminyensis CZDD1 and Methanosarcina mazei CZ1 from the enrichment culture; the former could partially demethylate trivalent DMAs(III) but not DMAs(V) and the latter could demethylate neither. Addition of strain CZDD1 to the enrichment culture greatly accelerated DMAs(V) demethylation. Demethylation of DMAs(V) in the enrichment culture was suppressed by ampicillin, suggesting the involvement of bacteria. We isolated three anaerobic bacterial strains including Clostridium from the enrichment culture, which could produce hydrogen and reduce DMAs(V) to DMAs(III). Furthermore, augmentation of the Methanomassiliicoccus-Clostridium coculture to a paddy soil decreased DMAs accumulation by rice and alleviated straighthead disease. The results reveal a synergistic relationship whereby anaerobic bacteria reduce DMAs(V) to DMAs(III) for demethylation by Methanomassiliicoccus and also produce hydrogen to promote the growth of Methanomassiliicoccus; enhancing their populations in paddy soil can help alleviate rice straighthead disease.
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Affiliation(s)
- Chuan Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lingyan Li
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China
| | - Xiuzhu Dong
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, 100049, Beijing, China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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20
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Dang H, Ewald JM, Mattes TE. Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16386-16398. [PMID: 37856784 PMCID: PMC10621002 DOI: 10.1021/acs.est.3c05439] [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: 07/10/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Growth of organohalide-respiring bacteria such as Dehalococcoides mccartyi on halogenated organics (e.g., polychlorinated biphenyls (PCBs)) at contaminated sites or in enrichment culture requires interaction and support from other microbial community members. To evaluate naturally occurring interactions between Dehalococcoides and key supporting microorganisms (e.g., production of H2, acetate, and corrinoids) in PCB-contaminated sediments, metagenomic and metatranscriptomic sequencing was conducted on DNA and RNA extracted from sediment microcosms, showing evidence of both Dehalococcoides growth and PCB dechlorination. Using a genome-resolved approach, 160 metagenome-assembled genomes (MAGs), including three Dehalococcoides MAGs, were recovered. A novel reductive dehalogenase gene, distantly related to the chlorophenol dehalogenase gene cprA (pairwise amino acid identity: 23.75%), was significantly expressed. Using MAG gene expression data, 112 MAGs were assigned functional roles (e.g., corrinoid producers, acetate/H2 producers, etc.). A network coexpression analysis of all 160 MAGs revealed correlations between 39 MAGs and the Dehalococcoides MAGs. The network analysis also showed that MAGs assigned with functional roles that support Dehalococcoides growth (e.g., corrinoid assembly, and production of intermediates required for corrinoid synthesis) displayed significant coexpression correlations with Dehalococcoides MAGs. This work demonstrates the power of genome-resolved metagenomic and metatranscriptomic analyses, which unify taxonomy and function, in investigating the ecology of dehalogenating microbial communities.
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Affiliation(s)
- Hongyu Dang
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
| | - Jessica M. Ewald
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
| | - Timothy E. Mattes
- Department of Civil and Environmental
Engineering, 4105 Seamans Center, University
of Iowa, Iowa City, Iowa 52242, United States
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21
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Meene A, Gierse L, Schwaiger T, Karte C, Schröder C, Höper D, Wang H, Groß V, Wünsche C, Mücke P, Kreikemeyer B, Beer M, Becher D, Mettenleiter TC, Riedel K, Urich T. Archaeome structure and function of the intestinal tract in healthy and H1N1 infected swine. Front Microbiol 2023; 14:1250140. [PMID: 37779690 PMCID: PMC10534045 DOI: 10.3389/fmicb.2023.1250140] [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: 06/29/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Background Methanogenic archaea represent a less investigated and likely underestimated part of the intestinal tract microbiome in swine. Aims/Methods This study aims to elucidate the archaeome structure and function in the porcine intestinal tract of healthy and H1N1 infected swine. We performed multi-omics analysis consisting of 16S rRNA gene profiling, metatranscriptomics and metaproteomics. Results and discussion We observed a significant increase from 0.48 to 4.50% of archaea in the intestinal tract microbiome along the ileum and colon, dominated by genera Methanobrevibacter and Methanosphaera. Furthermore, in feces of naïve and H1N1 infected swine, we observed significant but minor differences in the occurrence of archaeal phylotypes over the course of an infection experiment. Metatranscriptomic analysis of archaeal mRNAs revealed the major methanogenesis pathways of Methanobrevibacter and Methanosphaera to be hydrogenotrophic and methyl-reducing, respectively. Metaproteomics of archaeal peptides indicated some effects of the H1N1 infection on central metabolism of the gut archaea. Conclusions/Take home message Finally, this study provides the first multi-omics analysis and high-resolution insights into the structure and function of the porcine intestinal tract archaeome during a non-lethal Influenza A virus infection of the respiratory tract, demonstrating significant alterations in archaeal community composition and central metabolic functions.
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Affiliation(s)
- Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Laurin Gierse
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | | | | | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Verena Groß
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christine Wünsche
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Pierre Mücke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Martin Beer
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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22
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Volmer JG, McRae H, Morrison M. The evolving role of methanogenic archaea in mammalian microbiomes. Front Microbiol 2023; 14:1268451. [PMID: 37727289 PMCID: PMC10506414 DOI: 10.3389/fmicb.2023.1268451] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023] Open
Abstract
Methanogenic archaea (methanogens) represent a diverse group of microorganisms that inhabit various environmental and host-associated microbiomes. These organisms play an essential role in global carbon cycling given their ability to produce methane, a potent greenhouse gas, as a by-product of their energy production. Recent advances in culture-independent and -dependent studies have highlighted an increased prevalence of methanogens in the host-associated microbiome of diverse animal species. Moreover, there is increasing evidence that methanogens, and/or the methane they produce, may play a substantial role in human health and disease. This review addresses the expanding host-range and the emerging view of host-specific adaptations in methanogen biology and ecology, and the implications for host health and disease.
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Affiliation(s)
- James G. Volmer
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, Australia
| | - Harley McRae
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Mark Morrison
- Faculty of Medicine, University of Queensland Frazer Institute, Translational Research Institute, Woolloongabba, QLD, Australia
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23
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Yu Q, Mao H, Zhao Z, Quan X, Zhang Y. Electromotive force induced by dynamic magnetic field electrically polarized sediment to aggravate methane emission. WATER RESEARCH 2023; 240:120097. [PMID: 37224670 DOI: 10.1016/j.watres.2023.120097] [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: 11/05/2022] [Revised: 04/26/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023]
Abstract
As a primary driving force of global methane production, methanogens like other living organisms are exposed to an environment filled with dynamic electromagnetic waves, which might induce electromotive force (EMF) to potentially influence the metabolism of methanogens. However, no reports have been found on the effects of the induced electromotive force on methane production. In this study, we found that exposure to a dynamic magnetic field enhanced bio-methanogenesis via the induced electromotive force. When exposed to a dynamic magnetic field with 0.20 to 0.40 mT of intensity, the methane emission of the sediments increased by 41.71%. The respiration of methanogens and bacteria was accelerated by the EMF, as the ratios of F420H2/F420 and NAD+/NADH of the sediment increased by 44.12% and 55.56%, respectively. The respiratory enzymes in respiration chains might be polarized with the EMF to accelerate the proton-coupled electron transfer to enhance microbial metabolism. Together with the enriched exoelectrogens and electrotrophic methanogens, as well as the increased sediment electro-activities, this study indicated that the EMF could enhance the electron exchange among extracellular respiratory microorganisms to increase the methane emission from sediments.
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Affiliation(s)
- Qilin Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Haohao Mao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhiqiang Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xie Quan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yaobin Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Dalian University of Technology), Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
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24
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Khanthong K, Kadam R, Kim T, Park J. Synergetic effects of anaerobic co-digestion of food waste and algae on biogas production. BIORESOURCE TECHNOLOGY 2023; 382:129208. [PMID: 37217150 DOI: 10.1016/j.biortech.2023.129208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023]
Abstract
Anaerobic co-digestion of food waste and algae was assessed to offset the drawbacks of anaerobic mono-digestion of each substrate. Batch test results indicated that a food waste and algae mixture ratio of 8:2 facilitated the highest CH4 yield (334 mL CH4/g CODInput). This ratio was applied to the anaerobic co-digestion reactor, resulting in a CH4 yield that was twice that of the anaerobic mono-digestion reactors, thereby facilitating high operational stability. In contrast to the anaerobic mono-digestion, anaerobic co-digestion resulted in stable CH4 production by overcoming volatile fatty acid accumulation and a decreased pH, even under a high organic loading rate (3 kg COD/m3∙d). Furthermore, a comparative metagenomic analysis revealed that the abundance of volatile fatty acid-oxidizing bacteria and hydrogenotrophic and methylotrophic methanogens was significantly increased in the anaerobic co-digestion reactor. These findings indicate that the anaerobic co-digestion of food waste and algae significantly improves CH4 production and process stability.
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Affiliation(s)
- Kamonwan Khanthong
- Department of Advanced Energy Engineering, Chosun University, Gwangju 61457, Republic of Korea
| | - Rahul Kadam
- Department of Advanced Energy Engineering, Chosun University, Gwangju 61457, Republic of Korea
| | - Taeyoung Kim
- Department of Environmental Engineering, Chosun University, Gwangju 61457, Republic of Korea
| | - Jungyu Park
- Department of Advanced Energy Engineering, Chosun University, Gwangju 61457, Republic of Korea.
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25
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Lever MA, Alperin MJ, Hinrichs KU, Teske A. Zonation of the active methane-cycling community in deep subsurface sediments of the Peru trench. Front Microbiol 2023; 14:1192029. [PMID: 37250063 PMCID: PMC10213550 DOI: 10.3389/fmicb.2023.1192029] [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: 03/22/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
The production and anaerobic oxidation of methane (AOM) by microorganisms is widespread in organic-rich deep subseafloor sediments. Yet, the organisms that carry out these processes remain largely unknown. Here we identify members of the methane-cycling microbial community in deep subsurface, hydrate-containing sediments of the Peru Trench by targeting functional genes of the alpha subunit of methyl coenzyme M reductase (mcrA). The mcrA profile reveals a distinct community zonation that partially matches the zonation of methane oxidizing and -producing activity inferred from sulfate and methane concentrations and carbon-isotopic compositions of methane and dissolved inorganic carbon (DIC). McrA appears absent from sulfate-rich sediments that are devoid of methane, but mcrA sequences belonging to putatively methane-oxidizing ANME-1a-b occur from the zone of methane oxidation to several meters into the methanogenesis zone. A sister group of ANME-1a-b, referred to as ANME-1d, and members of putatively aceticlastic Methanothrix (formerly Methanosaeta) occur throughout the remaining methanogenesis zone. Analyses of 16S rRNA and mcrA-mRNA indicate that the methane-cycling community is alive throughout (rRNA to 230 mbsf) and active in at least parts of the sediment column (mRNA at 44 mbsf). Carbon-isotopic depletions of methane relative to DIC (-80 to -86‰) suggest mostly methane production by CO2 reduction and thus seem at odds with the widespread detection of ANME-1 and Methanothrix. We explain this apparent contradiction based on recent insights into the metabolisms of both ANME-1 and Methanothricaceae, which indicate the potential for methanogenetic growth by CO2 reduction in both groups.
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Affiliation(s)
- Mark A. Lever
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, United States
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Marc J. Alperin
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas Teske
- Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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26
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García-Maldonado JQ, Latisnere-Barragán H, Escobar-Zepeda A, Cadena S, Ramírez-Arenas PJ, Vázquez-Juárez R, Rojas-Contreras M, López-Cortés A. Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities. Microorganisms 2023; 11:microorganisms11030812. [PMID: 36985385 PMCID: PMC10059902 DOI: 10.3390/microorganisms11030812] [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: 01/31/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/30/2023] Open
Abstract
Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.
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Affiliation(s)
- José Q García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Mérida, Mérida 97310, Yucatán, Mexico
| | - Hever Latisnere-Barragán
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | | | - Santiago Cadena
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Patricia J Ramírez-Arenas
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Ricardo Vázquez-Juárez
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
| | - Maurilia Rojas-Contreras
- Departamento de Agronomía, Universidad Autónoma de Baja California Sur, La Paz 23080, Baja California Sur, Mexico
| | - Alejandro López-Cortés
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz 23205, Baja California Sur, Mexico
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27
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Zhang CJ, Liu YR, Cha G, Liu Y, Zhou XQ, Lu Z, Pan J, Cai M, Li M. Potential for mercury methylation by Asgard archaea in mangrove sediments. THE ISME JOURNAL 2023; 17:478-485. [PMID: 36639538 PMCID: PMC9938162 DOI: 10.1038/s41396-023-01360-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023]
Abstract
Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The conversion of MeHg from mercury (Hg) is mediated by a variety of anaerobic microorganisms carrying hgcAB genes. Mangrove sediments are potential hotspots of microbial Hg methylation; however, the microorganisms responsible for Hg methylation are poorly understood. Here, we conducted metagenomic and metatranscriptomic analyses to investigate the diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems. The highest hgcA abundance and expression occurred in surface sediments in Shenzhen, where the highest MeHg concentration was also observed. We reconstructed 157 metagenome-assembled genomes (MAGs) carrying hgcA and identified several putative novel Hg-methylators, including one Asgard archaea (Lokiarchaeota). Further analysis of MAGs revealed that Deltaproteobacteria, Euryarchaeota, Bacteroidetes, Chloroflexi, and Lokiarchaeota were the most abundant and active Hg-methylating groups, implying their crucial role in MeHg production. By screening publicly available MAGs, 104 additional Asgard MAGs carrying hgcA genes were identified from a wide range of coast, marine, permafrost, and lake sediments. Protein homology modelling predicts that Lokiarchaeota HgcAB proteins contained the highly conserved amino acid sequences and folding structures required for Hg methylation. Phylogenetic tree revealed that hgcA genes from Asgard clustered with fused hgcAB genes, indicating a transitional stage of Asgard hgcA genes. Our findings thus suggest that Asgard archaea are potential novel Hg-methylating microorganisms and play an important role in hgcA evolution.
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Affiliation(s)
- Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guihong Cha
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Xin-Quan Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
| | - Mingwei Cai
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China
- Chemical Biology Institute, Shenzhen Bay Laboratory, Shenzhen, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, 518060, Shenzhen, China.
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28
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Yu G, Chen J, Wang G, Chen H, Huang J, Li Y, Wang W, Song F, Ma Y, Wang Q, Wang M, Ling T, Shu Z, Sun J, Yu Z. Recent advances in constructed wetlands methane reduction: Mechanisms and methods. Front Microbiol 2023; 14:1106332. [PMID: 36819020 PMCID: PMC9936987 DOI: 10.3389/fmicb.2023.1106332] [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: 11/23/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Constructed wetlands (CWs) are artificial systems that use natural processes to treat wastewater containing organic pollutants. This approach has been widely applied in both developing and developed countries worldwide, providing a cost-effective method for industrial wastewater treatment and the improvement of environmental water quality. However, due to the large organic carbon inputs, CWs is produced in varying amounts of CH4 and have the potential to become an important contributor to global climate change. Subsequently, research on the mitigation of CH4 emissions by CWs is key to achieving sustainable, low-carbon dependency wastewater treatment systems. This review evaluates the current research on CH4 emissions from CWs through bibliometric analysis, summarizing the reported mechanisms of CH4 generation, transfer and oxidation in CWs. Furthermore, the important environmental factors driving CH4 generation in CW systems are summarized, including: temperature, water table position, oxidation reduction potential, and the effects of CW characteristics such as wetland type, plant species composition, substrate type, CW-coupled microbial fuel cell, oxygen supply, available carbon source, and salinity. This review provides guidance and novel perspectives for sustainable and effective CW management, as well as for future studies on CH4 reduction in CWs.
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Affiliation(s)
- Guanlong Yu
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Jundan Chen
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Guoliang Wang
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Huifang Chen
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Jiajun Huang
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Yifu Li
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Wenming Wang
- Technology Center, Hunan Pilot Yanghu Reclaimed Water Co., Ltd., Changsha, China,*Correspondence: Wenming Wang,
| | - Fengming Song
- Technology Center, Hunan Pilot Yanghu Reclaimed Water Co., Ltd., Changsha, China
| | - Yuanjun Ma
- Technology Department, Hunan Rongantai Ecological Technology Co., Ltd., Changsha, China
| | - Qi Wang
- Technology and Information Department, CCCC-TDC Environmental Engineering Co., Ltd., Tianjin, China
| | - Miaomiao Wang
- Technology and Information Department, CCCC-TDC Environmental Engineering Co., Ltd., Tianjin, China
| | - Tao Ling
- Engineering Department, China Railway Wuju Group the First Engineering Co., Ltd., Changsha, China
| | - Zhilai Shu
- Engineering Department, China Railway Wuju Group the First Engineering Co., Ltd., Changsha, China
| | - Julong Sun
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Zhi Yu
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
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Constantino-Jonapa LA, Espinoza-Palacios Y, Escalona-Montaño AR, Hernández-Ruiz P, Amezcua-Guerra LM, Amedei A, Aguirre-García MM. Contribution of Trimethylamine N-Oxide (TMAO) to Chronic Inflammatory and Degenerative Diseases. Biomedicines 2023; 11:biomedicines11020431. [PMID: 36830968 PMCID: PMC9952918 DOI: 10.3390/biomedicines11020431] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Trimethylamine N-oxide (TMAO) is a metabolite produced by the gut microbiota and has been mainly associated with an increased incidence of cardiovascular diseases (CVDs) in humans. There are factors that affect one's TMAO level, such as diet, drugs, age, and hormones, among others. Gut dysbiosis in the host has been studied recently as a new approach to understanding chronic inflammatory and degenerative diseases, including cardiovascular diseases, metabolic diseases, and Alzheimer's disease. These disease types as well as COVID-19 are known to modulate host immunity. Diabetic and obese patients have been observed to have an increase in their level of TMAO, which has a direct correlation with CVDs. This metabolite is attributed to enhancing the inflammatory pathways through cholesterol and bile acid dysregulation, promoting foam cell formation. Additionally, TMAO activates the transcription factor NF-κB, which, in turn, triggers cytokine production. The result can be an exaggerated inflammatory response capable of inducing endoplasmic reticulum stress, which is responsible for various diseases. Due to the deleterious effects that this metabolite causes in its host, it is important to search for new therapeutic agents that allow a reduction in the TMAO levels of patients and that, thus, allow patients to be able to avoid a severe cardiovascular event. The present review discussed the synthesis of TMAO and its contribution to the pathogenesis of various inflammatory diseases.
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Affiliation(s)
- Luis A. Constantino-Jonapa
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Yoshua Espinoza-Palacios
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Alma R. Escalona-Montaño
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Paulina Hernández-Ruiz
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Luis M. Amezcua-Guerra
- Departamento de Inmunología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
- Interdisciplinary Internal Medicine Unit, Careggi University Hospital, 50134 Florence, Italy
| | - María M. Aguirre-García
- Unidad de Investigación UNAM-INC, División de Investigación, Facultad de Medicina, UNAM, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico
- Correspondence: ; Tel.: +52-55-5573-2911 (ext. 27316)
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Tacconi E, Palma G, De Biase D, Luciano A, Barbieri M, de Nigris F, Bruzzese F. Microbiota Effect on Trimethylamine N-Oxide Production: From Cancer to Fitness-A Practical Preventing Recommendation and Therapies. Nutrients 2023; 15:nu15030563. [PMID: 36771270 PMCID: PMC9920414 DOI: 10.3390/nu15030563] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
Trimethylamine N-oxide (TMAO) is a microbial metabolite derived from nutrients, such as choline, L-carnitine, ergothioneine and betaine. Recently, it has come under the spotlight for its close interactions with gut microbiota and implications for gastrointestinal cancers, cardiovascular disease, and systemic inflammation. The culprits in the origin of these pathologies may be food sources, in particular, high fat meat, offal, egg yolk, whole dairy products, and fatty fish, but intercalated between these food sources and the production of pro-inflammatory TMAO, the composition of gut microbiota plays an important role in modulating this process. The aim of this review is to explain how the gut microbiota interacts with the conversion of specific compounds into TMA and its oxidation to TMAO. We will first cover the correlation between TMAO and various pathologies such as dysbiosis, then focus on cardiovascular disease, with a particular emphasis on pro-atherogenic factors, and then on systemic inflammation and gastrointestinal cancers. Finally, we will discuss primary prevention and therapies that are or may become possible. Possible treatments include modulation of the gut microbiota species with diets, physical activity and supplements, and administration of drugs, such as metformin and aspirin.
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Affiliation(s)
- Edoardo Tacconi
- Department of Human Science and Quality of Life Promotion, San Raffaele Roma Open University, 00166 Rome, Italy
| | - Giuseppe Palma
- S.S.D. Sperimentazione Animale, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
- Correspondence:
| | - Davide De Biase
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Antonio Luciano
- S.S.D. Sperimentazione Animale, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Massimiliano Barbieri
- S.S.D. Sperimentazione Animale, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Filomena de Nigris
- Department of Precision Medicine, School of Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Via De Crecchio 7, 80138 Naples, Italy
| | - Francesca Bruzzese
- S.S.D. Sperimentazione Animale, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
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Effect of Alkaline and Mechanical Pretreatment of Wheat Straw on Enrichment Cultures from Pachnoda marginata Larva Gut. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In order to partially mimic the efficient lignocellulose pretreatment process performed naturally in the gut system of Pachnoda marginata larvae, two wheat straw pretreatments were evaluated: a mechanical pretreatment via cutting the straw into two different sizes and an alkaline pretreatment with calcium hydroxide. After pretreatment, gut enrichment cultures on wheat straw at alkaline pH were inoculated and kept at mesophilic conditions over 45 days. The methanogenic community was composed mainly of the Methanomicrobiaceae and Methanosarcinaceae families. The combined pretreatment, size reduction and alkaline pretreatment, was the best condition for methane production. The positive effect of the straw pretreatment was higher in the midgut cultures, increasing the methane production by 192%, while for hindgut cultures the methane production increased only by 149% when compared to non-pretreated straw. Scanning electron microscopy (SEM) showed that the alkaline pretreatment modified the surface of the wheat straw fibers, which promoted biofilm formation and microbial growth. The enrichment cultures derived from larva gut microbiome were able to degrade larger 1 mm alkaline treated and smaller 250 µm but non-pretreated straw at the same efficiency. The combination of mechanical and alkaline pretreatments resulted in increased, yet not superimposed, methane yield.
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The Overlooked Microbiome-Considering Archaea and Eukaryotes Using Multiplex Nanopore-16S-/18S-rDNA-Sequencing: A Technical Report Focusing on Nasopharyngeal Microbiomes. Int J Mol Sci 2023; 24:ijms24021426. [PMID: 36674956 PMCID: PMC9863950 DOI: 10.3390/ijms24021426] [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: 09/23/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/15/2023] Open
Abstract
In contrast to bacteria, microbiome analyses often neglect archaea, but also eukaryotes. This is partly because they are difficult to culture due to their demanding growth requirements, or some even have to be classified as uncultured microorganisms. Consequently, little is known about the relevance of archaea in human health and diseases. Contemporary broad availability and spread of next generation sequencing techniques now enable a stronger focus on such microorganisms, whose cultivation is difficult. However, due to the enormous evolutionary distances between bacteria, archaea and eukaryotes, the implementation of sequencing strategies for smaller laboratory scales needs to be refined to achieve as a holistic view on the microbiome as possible. Here, we present a technical approach that enables simultaneous analyses of archaeal, bacterial and eukaryotic microbial communities to study their roles in development and courses of respiratory disorders. We thus applied combinatorial 16S-/18S-rDNA sequencing strategies for sequencing-library preparation. Considering the lower total microbiota density of airway surfaces, when compared with gut microbiota, we optimized the DNA purification workflow from nasopharyngeal swab specimens. As a result, we provide a protocol that allows the efficient combination of bacterial, archaeal, and eukaryotic libraries for nanopore-sequencing using Oxford Nanopore Technologies MinION devices and subsequent phylogenetic analyses. In a pilot study, this workflow allowed the identification of some environmental archaea, which were not correlated with airway microbial communities before. Moreover, we assessed the protocol's broader applicability using a set of human stool samples. We conclude that the proposed protocol provides a versatile and adaptable tool for combinatorial studies on bacterial, archaeal, and eukaryotic microbiomes on a small laboratory scale.
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Takizawa S, Shinkai T, Saito K, Fukumoto N, Arai Y, Hirai T, Maruyama M, Takeda M. Effect of rumen microbiota transfaunation on the growth, rumen fermentation, and microbial community of early separated Japanese Black cattle. Anim Sci J 2023; 94:e13876. [PMID: 37818871 DOI: 10.1111/asj.13876] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/20/2023] [Accepted: 09/07/2023] [Indexed: 10/13/2023]
Abstract
This study aimed to investigate the effect of rumen microbiota transfaunation on the growth, rumen fermentation, and the microbial community of Japanese Black cattle that were separated early from their dams. Here, 24 calves were separated from their dams immediately after calving, 12 of which were transfaunated via inoculation with rumen fluid from adult cattle at the age of 2 months while the remaining 12 were kept unfaunated (not-inoculated). Feed efficiency monitoring was performed during 7-10 months of age. Body weight and feed intake were not significantly different between the transfaunated and unfaunated cattle. Transfaunation increased the relative levels of acetate and butyrate but decreased those of propionate, which increased the non-glucogenic/glucogenic short-chain fatty acid ratio. Microbial 16S, 18S, and ITS ribosomal RNA gene amplicon analysis showed that rumen microbial diversity and composition differed between transfaunated and unfaunated cattle; transfaunation increased the abundance of acetate- and butyrate-producing bacteria, and decreased the abundance of bacterial genera associated with propionate production. Transfaunation also increased the abundance of Methanomassiliicoccaceae_group10 (1.94% vs. 0.05%) and Neocallimastix (27.1% vs. 6.8%) but decreased that of Methanomicrobium (<0.01% vs. 0.06%). Our findings indicate that rumen microbiota transfaunation shifts rumen fermentation toward acetate and butyrate production through a change in the rumen microbial composition in Japanese Black cattle.
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Affiliation(s)
- Shuhei Takizawa
- National Agriculture and Food Research Organization, Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Takumi Shinkai
- National Agriculture and Food Research Organization, Institute of Livestock and Grassland Science, Tsukuba, Japan
| | - Kunihiko Saito
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
| | - Natsuko Fukumoto
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
| | - Yukari Arai
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
- Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan
| | - Tomokazu Hirai
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
| | | | - Masayuki Takeda
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan
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Ai C, Tong A, Wen J, Chen R, Huang Y, Zhao C. Variations in the substrate composition and microbial community structure in the anaerobic fermentation process using the green algae Enteromorpha prolifera. FOOD PRODUCTION, PROCESSING AND NUTRITION 2022. [DOI: 10.1186/s43014-022-00110-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractEnteromorpha prolifera is a nutrient-rich green alga and abound in the Yellow Sea and the Bohai Sea of China. In this study, E. prolifera was anaerobically digested for biogas production. The variations of chemical compositions and microbial community structure as well as the physical structure of E. prolifera in anaerobic digestion process were investigated. This is the first report of multiple ways to deeply analysis the process of E. prolifera anaerobic digestion. Results from the present work showed that the biogas obtained from E. prolifera anaerobic digestion could achieve 409.7 mL•g− 1 TS with an average methane concentration of 53.2%, and the VFAs content in substrate played a vital role for driving the biogas production of flora. Moreover, S1 of Thermotogaceae and Cenarchaeum, the dominant bacteria and archaea in digestion flora, respectively, played important roles in degrading E. prolifera, acidizing slurry, and providing methanogenic substrate for methanogens.
Graphical Abstract
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Yong C, Huang G, Ge H, Zhu Y, Yang Y, Yu Y, Tian F, Gao K, Zhou E. Perilla frutescens
L. alleviates trimethylamine
N‐oxide
–induced apoptosis in the renal tubule by regulating
ASK1‐JNK
phosphorylation. Phytother Res 2022; 37:1274-1292. [PMID: 36420586 DOI: 10.1002/ptr.7684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/24/2022] [Accepted: 10/11/2022] [Indexed: 11/26/2022]
Abstract
Trimethylamine N-oxide (TMAO) is associated with overall mortality in patients with chronic kidney disease (CKD). Previous findings suggest that P. frutescens (L.) can alleviate renal injury, but its effects and mechanisms underlying alleviation of TMAO-induced kidney damage remain unclear. In this study, a TMAO injury model, in vivo and in vitro, was established to clarify the effects and mechanisms of P. frutescens in alleviating TMAO-induced kidney injury. The results show that TMAO (60 mM/L) can induce the activation of apoptosis signal-regulating kinase 1 (ASK1)-c-Jun N-terminal kinase (JNK), thus aggravating downstream cell apoptosis in vitro. The study also found that P. frutescens aqueous extract (PFAE) (5 mg/mL) can inhibit TMAO-induced apoptosis by downregulating ASK1-JNK phosphorylation. In the in vivo experiments, it was demonstrated that TMAO can increase the levels of blood urea nitrogen and cystatin C, aggravating renal tubular epithelial apoptosis. The results also show that PFAE can reduce TMAO-induced renal damage by inhibiting ASK1-JNK phosphorylation in vivo. Our findings confirmed that P. frutescens can alleviate TMAO-induced renal tubule apoptosis by regulating ASK1-JNK phosphorylation, indicating that P. frutescens may be an effective treatment for alleviating TMAO damage in CKD.
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Affiliation(s)
- Chen Yong
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
- No. 1 Clinical Medical College Nanjing University of Chinese Medicine Nanjing People's Republic of China
| | - Guoshun Huang
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
- No. 1 Clinical Medical College Nanjing University of Chinese Medicine Nanjing People's Republic of China
| | - Hongwei Ge
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
- No. 1 Clinical Medical College Nanjing University of Chinese Medicine Nanjing People's Republic of China
| | - Yiye Zhu
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
- No. 1 Clinical Medical College Nanjing University of Chinese Medicine Nanjing People's Republic of China
| | - Yang Yang
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
- No. 1 Clinical Medical College Nanjing University of Chinese Medicine Nanjing People's Republic of China
| | - Yongfei Yu
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
- No. 1 Clinical Medical College Nanjing University of Chinese Medicine Nanjing People's Republic of China
| | - Fang Tian
- Research Center of Chinese Medicine Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
| | - Kun Gao
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
- Inheritance Studio of Traditional Chinese Medicine Master Yanqin Zou Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
| | - Enchao Zhou
- Division of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
- Inheritance Studio of Traditional Chinese Medicine Master Yanqin Zou Jiangsu Province Hospital of Chinese Medicine Nanjing People's Republic of China
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Mudimela S, Vishwanath NK, Pillai A, Morales R, Marrelli SP, Barichello T, Giridharan VV. Clinical significance and potential role of trimethylamine N-oxide in neurological and neuropsychiatric disorders. Drug Discov Today 2022; 27:103334. [PMID: 35998800 PMCID: PMC10392962 DOI: 10.1016/j.drudis.2022.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/18/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022]
Abstract
In the past three decades, research on the gut microbiome and its metabolites, such as trimethylamines (TMA), trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), bile acids, tryptophan and indole derivatives, has attracted the attention of many scientists and industrialists. Among these metabolites, TMAO is produced from dietary choline, phosphatidylcholine, carnitine,andbetaine. TMAO and other gut metabolites, such as TMA and SCFAs, reach the brain by crossing the blood-brain barrier (BBB) and are involved in brain development, neurogenesis, and behavior. Gut-microbiota composition is influenced by diet, lifestyle, antibiotics, and age. Several studies have confirmed that altered TMAO levels contribute to metabolic, vascular, psychiatric, and neurodegenerative disorders. This review focuses on how altered TMAO levels impact oxidative stress, microglial activation, and the apoptosis of neurons, and may lead to neuroinflammation, which can subsequently result in the development of psychiatric, cognitive, and behavioral disorders.
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Affiliation(s)
- Sowjanya Mudimela
- Faculty of Pharmaceutical Sciences, PES University, HN-Campus, Bengaluru, Karnataka, India
| | | | - Anilkumar Pillai
- Pathophysiology of Neuropsychiatric Disorders Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center at Houston (UTHealth), Houston, TX, USA; Research and Development, Charlie Norwood VA Medical Center, Augusta, GA, USA; Department of Psychiatry and Health Behavior, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Rodrigo Morales
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O'Higgins, Santiago, Chile
| | - Sean P Marrelli
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Tatiana Barichello
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center at Houston (UTHealth), Houston, TX, USA; Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Experimental Physiopathology Laboratory, Graduate Program in Health Sciences, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Vijayasree V Giridharan
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
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Wang B, Liu W, Liang B, Jiang J, Wang A. Microbial fingerprints of methanation in a hybrid electric-biological anaerobic digestion. WATER RESEARCH 2022; 226:119270. [PMID: 36323204 DOI: 10.1016/j.watres.2022.119270] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/26/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Biomethane as a sustainable, alternative, and carbon-neutral renewable energy source to fossil fuels is highly needed to alleviate the global energy crisis and climate change. The conventional anaerobic digestion (AD) process for biomethane production from waste(water) streams has been widely employed while struggling with a low production rate, low biogas qualities, and frequent instability. The electric-biologically hybrid microbial electrochemical anaerobic digestion system (MEC-AD) prospects more stable and robust biomethane generation, which facilitates complex organic substrates degradation and mediates functional microbial populations by giving a small input power (commonly voltages < 1.0 V), mainly enhancing the communication between electroactive microorganisms and (electro)methanogens. Despite numerous bioreactor tests and studies that have been conducted, based on the MEC-AD systems, the integrated microbial fingerprints, and cooperation, accelerating substrate degradation, and biomethane production, have not been fully summarized. Herein, we present a comprehensive review of this novel developing biotechnology, beginning with the principles of MEC-AD. First, we examine the fundamentals, configurations, classifications, and influential factors of the whole system's performances (reactor types, applied voltages, temperatures, conductive materials, etc.,). Second, extracellular electron transfer either between diverse microbes or between microbes and electrodes for enhanced biomethane production are analyzed. Third, we further conclude (electro)methanogenesis, and microbial interactions, and construct ecological networks of microbial consortia in MEC-AD. Finally, future development and perspectives on MEC-AD for biomethane production are proposed.
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Affiliation(s)
- Bo Wang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China; Center for Electromicrobiology, Section for Microbiology, Department of Biology, Aarhus University, 8000 Aarhus C, Denmark; Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Wenzong Liu
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China.
| | - Bin Liang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China
| | - Jiandong Jiang
- Key Lab of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China
| | - Aijie Wang
- State Key Lab of Urban Water Resource and Environment, School of Civil and Environmental Engineering, Harbin Institute of Technology Shenzhen, 518055 Shenzhen, China; CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085 Beijing, China
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Sorokin DY, Merkel AY, Abbas B. Ecology of Methanonatronarchaeia. Environ Microbiol 2022; 24:5217-5229. [PMID: 35726892 PMCID: PMC9796771 DOI: 10.1111/1462-2920.16108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/19/2022] [Indexed: 01/07/2023]
Abstract
Methanonatronarchaeia represents a deep-branching phylogenetic lineage of extremely halo(alkali)philic and moderately thermophilic methyl-reducing methanogens belonging to the phylum Halobacteriota. It includes two genera, the alkaliphilic Methanonatronarchaeum and the neutrophilic Ca. Methanohalarchaeum. The former is represented by multiple closely related pure culture isolates from hypersaline soda lakes, while the knowledge about the latter is limited to a few mixed cultures with anaerobic haloarchaea. To get more insight into the distribution and ecophysiology of this enigmatic group of extremophilic methanogens, potential activity tests and enrichment cultivation with different substrates and at different conditions were performed with anaerobic sediment slurries from various hypersaline lakes in Russia. Methanonatronarchaeum proliferated exclusively in hypersaline soda lake samples mostly at elevated temperature, while at mesophilic conditions it coexisted with the extremely salt-tolerant methylotroph Methanosalsum natronophilum. Methanonatronarchaeum was also able to serve as a methylotrophic or hydrogenotrophic partner in several thermophilic enrichment cultures with fermentative bacteria. Ca. Methanohalarchaeum did not proliferate at mesophilic conditions and at thermophilic conditions it competed with extremely halophilic and moderately thermophilic methylotroph Methanohalobium, which it outcompeted at a combination of elevated temperature and methyl-reducing conditions. Overall, the results demonstrated that Methanonatronarchaeia are specialized extremophiles specifically proliferating in conditions of elevated temperature coupled with extreme salinity and simultaneous availability of a wide range of C1 -methylated compounds and H2 /formate.
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Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of BiotechnologyRussian Academy of SciencesMoscowRussia,Department of BiotechnologyDelft University of BiotechnologyDelftThe Netherlands
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Research Centre of BiotechnologyRussian Academy of SciencesMoscowRussia
| | - Ben Abbas
- Department of BiotechnologyDelft University of BiotechnologyDelftThe Netherlands
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Sari NF, Ray P, Rymer C, Kliem KE, Stergiadis S. Garlic and Its Bioactive Compounds: Implications for Methane Emissions and Ruminant Nutrition. Animals (Basel) 2022; 12:2998. [PMID: 36359121 PMCID: PMC9654579 DOI: 10.3390/ani12212998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Methane (CH4) emission from enteric fermentation of ruminant livestock is a source of greenhouse gases (GHG) and has become a significant concern for global warming. Enteric methane emission is also associated with poor feed efficiency. Therefore, research has focused on identifying dietary mitigation strategies to decrease CH4 emissions from ruminants. In recent years, plant-derived bioactive compounds have been investigated for their potential to reduce CH4 emissions from ruminant livestock. The organosulphur compounds of garlic have been observed to decrease CH4 emission and increase propionate concentration in anaerobic fermentations (in vitro) and in the rumen (in vivo). However, the mode of action of CH4 reduction is not completely clear, and the response in vivo is inconsistent. It might be affected by variations in the concentration and effect of individual substances in garlic. The composition of the diet that is being fed to the animal may also contribute to these differences. This review provides a summary of the effect of garlic and its bioactive compounds on CH4 emissions by ruminants. Additionally, this review aims to provide insight into garlic and its bioactive compounds in terms of enteric CH4 mitigation efficacy, consistency in afficacy, possible mode of action, and safety deriving data from both in vivo and in vitro studies.
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Affiliation(s)
- Nurul Fitri Sari
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK
- Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Cibinong 16911, West Java, Indonesia
| | - Partha Ray
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK
- The Nature Conservancy, Arlington, VA 22203, USA
| | - Caroline Rymer
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK
| | - Kirsty E. Kliem
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK
| | - Sokratis Stergiadis
- Department of Animal Sciences, School of Agriculture, Policy and Development, University of Reading, Reading RG6 6EU, UK
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Ou YF, Dong HP, McIlroy SJ, Crowe SA, Hallam SJ, Han P, Kallmeyer J, Simister RL, Vuillemin A, Leu AO, Liu Z, Zheng YL, Sun QL, Liu M, Tyson GW, Hou LJ. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. THE ISME JOURNAL 2022; 16:2373-2387. [PMID: 35810262 PMCID: PMC9478090 DOI: 10.1038/s41396-022-01281-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 05/28/2023]
Abstract
Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.
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Affiliation(s)
- Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Sean A Crowe
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Rachel L Simister
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aurele Vuillemin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Qian-Li Sun
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
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Dong Z, Ding Y, Chen F, Zhu X, Wang H, Cheng M, Liao Q. Enhanced carbon dioxide biomethanation with hydrogen using anaerobic granular sludge and metal-organic frameworks: Microbial community response and energy metabolism analysis. BIORESOURCE TECHNOLOGY 2022; 362:127822. [PMID: 36029983 DOI: 10.1016/j.biortech.2022.127822] [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: 06/28/2022] [Revised: 08/13/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
In this work, metal-organic frameworks (MOFs) were prepared to evaluate its impact on carbon dioxide (CO2) biomethanization during anaerobic degradation (AD). The results showed that MOFs significantly improved the CO2 biomethanation efficiency, especially in the AD reactors using a concentration of 1.0 g/L MOFs. Furthermore, MOFs promoted direct interspecific electron transfer and alleviated the hydrogen competition of bacteria. Meanwhile, hydrogenotrophic methanogens were enriched in the AD reactors with MOFs. After the addition of MOFs, there was 3.28 times and 3.41 times increase in the abundance of metabolic functions related to methanogenesis by CO2 reduction with hydrogen and dark hydrogen oxidation, respectively. There was an increased abundance of all genes that encode the key enzymes used in methane metabolism. However, functional genes involved in nitrate reduction had their expressions inhibited. The work may offer a contribution to helping the industry achieve the carbon capture and utilization policy.
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Affiliation(s)
- Zhiwei Dong
- Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400030, China
| | - Yudong Ding
- Key Laboratory of Low-Grade Energy Utilization Technologies and Systems, Ministry of Education, Chongqing University, Chongqing 400030, China; Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400030, China.
| | - Fei Chen
- Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400030, China
| | - Xun Zhu
- Key Laboratory of Low-Grade Energy Utilization Technologies and Systems, Ministry of Education, Chongqing University, Chongqing 400030, China; Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400030, China.
| | - Hong Wang
- Key Laboratory of Low-Grade Energy Utilization Technologies and Systems, Ministry of Education, Chongqing University, Chongqing 400030, China; Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400030, China.
| | - Min Cheng
- Key Laboratory of Low-Grade Energy Utilization Technologies and Systems, Ministry of Education, Chongqing University, Chongqing 400030, China; Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400030, China
| | - Qiang Liao
- Key Laboratory of Low-Grade Energy Utilization Technologies and Systems, Ministry of Education, Chongqing University, Chongqing 400030, China; Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400030, China.
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Zhuravleva EA, Shekhurdina SV, Kotova IB, Loiko NG, Popova NM, Kryukov E, Kovalev AA, Kovalev DA, Litti YV. Effects of various materials used to promote the direct interspecies electron transfer on anaerobic digestion of low-concentration swine manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156073. [PMID: 35618137 DOI: 10.1016/j.scitotenv.2022.156073] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 05/23/2023]
Abstract
The activation of direct interspecies electron transfer (DIET) by the supplementation of conductive materials is one of the effective and available methods to enhance anaerobic digestion (AD). Microorganisms that colonize the surface of these materials form biofilms, the study of which could provide new insights into the character of the DIET process and its effect on AD. The present study focused on AD performance, microbial community, as well as morphological and topological features of biofilms on various materials used to promote DIET during AD of low-concentration swine manure. The best AD characteristics were observed in stainless steel mesh (SM)/digested cow manure (CM) and polyester felt (PF)/digested sewage sludge (SS) combinations used as material/inoculum, respectively. Thus, potential methane yields in CM-SM and SS-PF were up to 26.4% and 26.2% higher compared to the corresponding controls. Microbial analysis of biofilms revealed the dominance of putatively syntrophic bacteria of the MBA03 group of the Limnochordia class in CM inoculated reactors, and syntrophic proteolytic bacteria of the genus Coprothermobacter and acetogenic Clostridium sensu stricto 1, known for their ability to carry out DIET, in SS inoculated reactors. Biofilms on non-conductive materials contained pili-like structures, which were observed only in SS inoculated reactors. Polyester felt tended to biofoul better than carbon felt, resulting in up to 2.8, 3.2 and 1.8 higher nucleic acid, extracellular polymeric substances, and total biomass content, respectively, depending on the inoculum. These results provide new insights into the different types of DIET that can occur in low-loaded AD systems with attached growth.
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Affiliation(s)
- Elena A Zhuravleva
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; Department of Biology, Lomonosov Moscow State University, Vorob'jovy gory, 119899 Moscow, Russia
| | - Svetlana V Shekhurdina
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; Department of Biology, Lomonosov Moscow State University, Vorob'jovy gory, 119899 Moscow, Russia
| | - Irina B Kotova
- Department of Biology, Lomonosov Moscow State University, Vorob'jovy gory, 119899 Moscow, Russia
| | - Natalia G Loiko
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia
| | - Nadezhda M Popova
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 31, bld.4, Leninsky prospect, 119071 Moscow, Russia
| | - Emil Kryukov
- Department of Physiology and Pharmacology, Karolinska Institute, 17165 Stockholm, Sweden; International School 'Future Medicine', IM Sechenov First Moscow State Medical University, 8-2 Trubetskaya str., 119435 Moscow, Russia
| | - Andrey A Kovalev
- Federal Scientific Agroengineering Center VIM, 1st Institutsky proezd, 5, 109428 Moscow, Russia
| | - Dmitriy A Kovalev
- Federal Scientific Agroengineering Center VIM, 1st Institutsky proezd, 5, 109428 Moscow, Russia
| | - Yuriy V Litti
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia.
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Sun C, Wang Z, Hu L, Zhang X, Chen J, Yu Z, Liu L, Wu M. Targets of statins intervention in LDL-C metabolism: Gut microbiota. Front Cardiovasc Med 2022; 9:972603. [PMID: 36158845 PMCID: PMC9492915 DOI: 10.3389/fcvm.2022.972603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing researches have considered gut microbiota as a new “metabolic organ,” which mediates the occurrence and development of metabolic diseases. In addition, the liver is an important organ of lipid metabolism, and abnormal lipid metabolism can cause the elevation of blood lipids. Among them, elevated low-density lipoprotein cholesterol (LDL-C) is related with ectopic lipid deposition and metabolic diseases, and statins are widely used to lower LDL-C. In recent years, the gut microbiota has been shown to mediate statins efficacy, both in animals and humans. The effect of statins on microbiota abundance has been deeply explored, and the pathways through which statins reduce the LDL-C levels by affecting the abundance of microbiota have gradually been explored. In this review, we discussed the interaction between gut microbiota and cholesterol metabolism, especially the cholesterol-lowering effect of statins mediated by gut microbiota, via AMPK-PPARγ-SREBP1C/2, FXR and PXR-related, and LPS-TLR4-Myd88 pathways, which may help to explain the individual differences in statins efficacy.
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Affiliation(s)
- ChangXin Sun
- Beijing University of Chinese Medicine, Beijing, China
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - ZePing Wang
- Beijing University of Chinese Medicine, Beijing, China
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - LanQing Hu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - XiaoNan Zhang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - JiYe Chen
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - ZongLiang Yu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - LongTao Liu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: LongTao Liu
| | - Min Wu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Min Wu
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Jin W, Dai Z, Wang L, Cai F, Song C, Liu G, Chen C. Recycling different textile wastes for methane production: Morphological and microstructural changes and microbial community dynamics. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 151:154-162. [PMID: 35952413 DOI: 10.1016/j.wasman.2022.07.018] [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: 03/02/2022] [Revised: 06/13/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
The dramatic increase of textile wastes has become a major global concern, which calls for alternative practices to alleviate severe environmental pollution and waste of resources due to their improper disposal and management. Anaerobic digestion (AD) is a cost-effective and eco-friendly technology that allows the bioconversion of organic wastes into clean energy (methane), which might be potentially useful for recycling textile wastes. In this study, AD was applied to 11 commonly available textile wastes in daily life to explore their feasibility, along with the methane production efficiency, biodegradability (BD), degradation mechanism, and microbial community dynamics during AD. The results showed that all textile wastes presented an obvious decomposition from an integrated shape to fragmented pieces within 18 days except blue denim. The highest experimental methane production (EMP) of 356.0 mL/g volatile solids (VS) and BD of 78.0 % were obtained with flax. The degradation mechanism could be concluded that predominant bacteria, especially Clostridium sensu stricto, first attached to the surface of textile waste and converted its main compositions cellulose and hemicellulose into acetate as the core intermediate. Then, acetate was utilized by the major methanogen, Methanothrix, through the acetoclastic methanogenesis pathway to produce methane. This study not only enriches the understanding of textile wastes degradation mechanisms during AD and provides very useful data on methane production from commonly available textile wastes but also proposes a promising method for efficiently recycling and utilizing the diverse range of textile wastes to reduce waste pollution and generate clean energy simultaneously.
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Affiliation(s)
- Wenxiong Jin
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhuangqiang Dai
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ligong Wang
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Fanfan Cai
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chao Song
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Guangqing Liu
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chang Chen
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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Low A, Lee JKY, Gounot JS, Ravikrishnan A, Ding Y, Saw WY, Tan LWL, Moong DKN, Teo YY, Nagarajan N, Seedorf H. Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative. Microbiol Spectr 2022; 10:e0084922. [PMID: 35699469 PMCID: PMC9431525 DOI: 10.1128/spectrum.00849-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Methanogenic Archaea (methanogens) are a phylogenetically diverse group of microorganisms and are considered to be the most abundant archaeal representatives in the human gut. However, the gut methanogen diversity of human populations in many global regions remains poorly investigated. Here, we report the abundance and diversity of gut methanogenic Archaea in a multi-ethnic cohort of healthy Singaporeans by using a concerted approach of metagenomic sequencing, 16S rRNA gene amplicon sequencing, and quantitative PCR. Our results indicate a mutual exclusion of Methanobrevibacter species, i.e., the highly prevalent Methanobrevibacter smithii and the less prevalent Candidatus Methanobrevibacter intestini in more than 80% of the samples when using an amplicon sequencing-based approach. Leveraging on this finding, we were able to select a fecal sample to isolate a representative strain, TLL-48-HuF1, for Candidatus Methanobrevibacter intestini. The analyzed physiological parameters of M. smithii DSM 861T and strain TLL-48-HuF1 suggest high similarity of the two species. Comparative genome analysis and the mutual exclusion of the Methanobrevibacter species indicate potentially different niche adaptation strategies in the human host, which may support the designation of Candidatus M. intestini as a novel species. IMPORTANCE Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents. While Methanobrevibacter smithii is the most prevalent and abundant methanogen in the human gut of local subjects, the recently proposed Candidatus Methanobrevibacter intestini is the abundant methanogen in a minority of individuals that harbor them. The observed potential mutual exclusion of M. smithii and Ca. M. intestini provides further support to the proposal that the two physiologically similar strains may belong to different Methanobrevibacter species.
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Affiliation(s)
- Adrian Low
- Temasek Life Sciences Laboratory, Singapore
| | | | | | | | | | - Woei-Yuh Saw
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Linda Wei Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yik Ying Teo
- Genome Institute of Singapore, A*STAR, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
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Prasitwuttisak W, Hoshiko Y, Maeda T, Haraguchi A, Yanagawa K. Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils. Microbes Environ 2022; 37. [PMID: 35851269 PMCID: PMC9530717 DOI: 10.1264/jsme2.me22004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key players in methane production, either well-known archaeal members or recently identified lineages, in peat soils collected from wetland areas in Japan. Based on an analysis of microbial communities using 16S rRNA gene sequencing and the molecular cloning of the functional gene, mcrA, a marker gene for methanogenesis, methanogenic archaea belonging to Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanomassiliicoccales were detected in anoxic peat soils, suggesting the potential of CH4 production in this natural wetland. “Candidatus Bathyarchaeia”, archaea with vast metabolic capabilities that is widespread in anoxic environments, was abundant in subsurface peat soils (up to 96% of the archaeal community) based on microbial gene quantification by qPCR. These results emphasize the importance of discovering archaea members outside of traditional methanogenic lineages that may have significant functions in the wetland biogeochemical cycle.
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Affiliation(s)
| | - Yuki Hoshiko
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology
| | - Akira Haraguchi
- Faculty of Environmental Engineering, The University of Kitakyushu
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Guindo CO, Amir L, Couderc C, Drancourt M, Grine G. Rapid identification of clinically interesting methanogens using an improved MALDI-TOF-MS assay. Access Microbiol 2022; 4:acmi000372. [PMID: 36003219 PMCID: PMC9394734 DOI: 10.1099/acmi.0.000372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
Methanogens, the archaea uniquely detoxifying fermentative hydrogen into methane in the digestive tract, are increasingly being detected in pathology situations, rendering their rapid identification mandatory. We improved the experimental protocol to identify broth-cultured methanogens by matrix-assisted laser desorption time-of-flight MS (MALDI-TOF-MS). A database incorporating 34 reference spectra derived from 16 methanogen reference strains representative of eight species supported further identification of 21 Methanobrevibacter smithii and 14 Methanobrevibacter oralis isolates broth-cultured from human stool and oral fluid, respectively, with scores >2. In addition, MALDI-TOF-MS differentiated five Methanobrevibacter smithii genotypes incorporated in the study. The data reported here found MALDI-TOF-MS as a first-line identification method for methanogens recovered from microbiota and clinical samples.
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Affiliation(s)
- Cheick Oumar Guindo
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Lynda Amir
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Carine Couderc
- Laboratoire de Microbiologie, Assistance Publique à Marseille, IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- Laboratoire de Microbiologie, Assistance Publique à Marseille, IHU Méditerranée Infection, Marseille, France
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ghiles Grine
- Aix-Marseille-Université, IRD, IHU Méditerranée, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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48
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Garcia PS, Gribaldo S, Borrel G. Diversity and Evolution of Methane-Related Pathways in Archaea. Annu Rev Microbiol 2022; 76:727-755. [PMID: 35759872 DOI: 10.1146/annurev-micro-041020-024935] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase (Mcr) complex. Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pierre Simon Garcia
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
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49
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Abdallah M, Greige S, Beyenal H, Harb M, Wazne M. Investigating microbial dynamics and potential advantages of anaerobic co-digestion of cheese whey and poultry slaughterhouse wastewaters. Sci Rep 2022; 12:10529. [PMID: 35732864 PMCID: PMC9217800 DOI: 10.1038/s41598-022-14425-1] [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: 04/05/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
Resource recovery and prevention of environmental pollution are key goals for sustainable development. It is widely reported that agro-industrial activities are responsible for the discharge of billions of liters of wastewater to the environment. Anaerobic digestion of these energy rich agro-industrial wastewaters can simultaneously mitigate environmental pollution and recover embedded energy as methane gas. In this study, an assessment of mono- and co-digestion of cheese whey wastewater (CWW) and poultry slaughterhouse wastewater (PSW) was conducted in 2.25-L lab-scale anaerobic digesters. Treatment combinations evaluated included CWW (R1), PSW (R2), 75:25 CWW:PSW (R3), 25:75 CWW:PSW (R4), and 50:50 CWW:PSW (R5). The digestion efficiencies of the mixed wastewaters were compared to the weighted efficiencies of the corresponding combined mono-digested samples. R4, with a mixture of 25% CWW and 75% PSW, achieved the greatest treatment efficiency. This corresponded with an average biodegradability of 84%, which was greater than for R1 and R2 at 68.5 and 71.9%, respectively. Similarly, R4 produced the highest average cumulative methane value compared to R1 and R2 at 1.22× and 1.39× for similar COD loading, respectively. The modified Gompertz model provided the best fit for the obtained methane production data, with lag time decreasing over progressive treatment cycles. PCoA and heatmap analysis of relative microbial abundances indicated a divergence of microbial communities based on feed type over the treatment cycles. Microbial community analysis showed that genus Petrimonas attained the highest relative abundance (RA) at up to 38.9% in the first two cycles, then subsequently decreased to near 0% for all reactors. Syntrophomonas was highly abundant in PSW reactors, reaching up to 36% RA. Acinetobacter was present mostly in CWW reactors with a RA reaching 56.5%. The methanogenic community was dominated by Methanothrix (84.3–99.9% of archaea). The presence of phosphate and Acinetobacter in CWW feed appeared to reduce the treatment efficiency of associated reactors. Despite Acinetobacter being strictly aerobic, previous and current results indicate its survival under anaerobic conditions, with the storage of phosphate likely playing a key role in its ability to scavenge acetate during the digestion process.
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Affiliation(s)
- M Abdallah
- Civil Engineering, Lebanese American University, 301 Bassil Building, Byblos, Lebanon
| | - S Greige
- Civil Engineering, Lebanese American University, 301 Bassil Building, Byblos, Lebanon
| | - H Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - M Harb
- Civil Engineering, Lebanese American University, 301 Bassil Building, Byblos, Lebanon
| | - M Wazne
- Civil Engineering, Lebanese American University, 301 Bassil Building, Byblos, Lebanon.
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50
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Biological Aspects, Advancements and Techno-Economical Evaluation of Biological Methanation for the Recycling and Valorization of CO2. ENERGIES 2022. [DOI: 10.3390/en15114064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Nowadays, sustainable and renewable energy production is a global priority. Over the past decade, several Power-to-X (PtX) technologies have been proposed to store and convert the surplus of renewable energies into chemical bonds of chemicals produced by different processes. CO2 is a major contributor to climate change, yet it is also an undervalued source of carbon that could be recycled and represents an opportunity to generate renewable energy. In this context, PtX technologies would allow for CO2 valorization into renewable fuels while reducing greenhouse gas (GHG) emissions. With this work we want to provide an up-to-date overview of biomethanation as a PtX technology by considering the biological aspects and the main parameters affecting its application and scalability at an industrial level. Particular attention will be paid to the concept of CO2-streams valorization and to the integration of the process with renewable energies. Aspects related to new promising technologies such as in situ, ex situ, hybrid biomethanation and the concept of underground methanation will be discussed, also in connection with recent application cases. Furthermore, the technical and economic feasibility will be critically analyzed to highlight current options and limitations for implementing a sustainable process.
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