1
|
Palevich N, Jeyanathan J, Reilly K, Palevich FP, Maclean PH, Li D, Altermann E, Kelly WJ, Leahy SC, Attwood GT, Ronimus RS, Henderson G, Janssen PH. Complete genome sequence of Methanosphaera sp. ISO3-F5, a rumen methylotrophic methanogen. Microbiol Resour Announc 2024; 13:e0004324. [PMID: 38426731 PMCID: PMC11008217 DOI: 10.1128/mra.00043-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
Methanosphaera spp. are methylotrophic methanogenic archaea and members of the order Methanobacteriales with few cultured representatives. Methanosphaera sp. ISO3-F5 was isolated from sheep rumen contents in New Zealand. Here, we report its complete genome, consisting of a large chromosome and a megaplasmid (GenBank accession numbers CP118753 and CP118754, respectively).
Collapse
Affiliation(s)
- Nikola Palevich
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Jeyamalar Jeyanathan
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Kerri Reilly
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Faith P. Palevich
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
- AgResearch Ltd., Hopkirk Research Institute, Palmerston North, New Zealand
| | - Paul H. Maclean
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Dong Li
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Eric Altermann
- School of Veterinary Science and Centre for Bioparticle Applications, Massey University, Palmerston North, New Zealand
- Blue Barn Life Sciences Ltd., Feilding, New Zealand
| | - William J. Kelly
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Sinead C. Leahy
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
- New Zealand Agricultural Greenhouse Gas Research Centre (NZAGRC), Palmerston North, New Zealand
| | - Graeme T. Attwood
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Ron S. Ronimus
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| | - Gemma Henderson
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
- Bacthera AG, Basel, Switzerland
| | - Peter H. Janssen
- AgResearch Ltd., Grasslands Research Centre, Palmerston North, New Zealand
| |
Collapse
|
2
|
Zhang WL, Lai MC, Lin S, Chen WC, Deng YC, Lai SJ, Wu SY, Hung CC, Ding JY, Chen SC. Methanooceanicella nereidis gen. nov., sp. nov., the first oceanic Methanocellaceae methanogen, isolated from potential methane hydrate bearing area offshore southwestern Taiwan. Int J Syst Evol Microbiol 2024; 74. [PMID: 38634834 DOI: 10.1099/ijsem.0.006322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
A novel mesophilic, hydrogenotrophic methanogen, strain CWC-04T, was obtained from a sediment sample extracted from a gravity core retrieved at station 22 within the KP-9 area off the southwestern coast of Taiwan during the ORIII-1368 cruise in 2009. Cells of strain CWC-04T were rod-shaped, 1.4-2.9 µm long by 0.5-0.6 µm wide, and occurred singly. Strain CWC-04Tutilized formate, H2/CO2, 2-propanol/CO2 or 2-butanol/CO2 as catabolic substrates. The optimal growth conditions were 42 °C, 0.17 M NaCl and pH 5.35. The genomic DNA G+C content calculated from the genome sequence of strain CWC-04T was 46.19 mol%. Phylogenetic analysis of 16S rRNA gene revealed that strain CWC-04T is affiliated with the genus Methanocella. The 16S rRNA gene sequences similarities within strains Methanocella arvoryzae MRE50T, Methanocella paludicola SANAET and Methanocella conradii HZ254T were 93.7, 93.0 and 91.3 %, respectively. In addition, the optical density of CWC-04T culture dropped abruptly upon entering the late-log growth phase, with virus-like particles (150 nm in diameter) being observed on and around the cells. This observation suggests that strain CWC-04T harbours a lytic virus. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CWC-04T represents a novel species of a novel genus in the family Methanocellaceae, for which the name Methanooceanicella nereidis gen. nov., sp. nov. is proposed. The type strain is CWC-04T (=BCRC AR10050T=NBRC 113165T).
Collapse
Affiliation(s)
- Wei-Ling Zhang
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan, ROC
| | - Wen-Chieh Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Yu-Chen Deng
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Shu-Jung Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan, ROC
- Research Center for Cancer Biology, China Medical University, Taichung City, Taiwan, ROC
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Chuan-Chuan Hung
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Jiun-Yan Ding
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian, PR China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian, PR China
| |
Collapse
|
3
|
Xie LL, Wang SJ, Xiao B, Wang ZJ, Guo ZP, Guo XF, Luo S, Li R, Xia JH, Lan MJ, Yang SQ. Effects of ant nests on soil CH 4 emissions from Syzygium oblatum communities of a secondary tropical forest. Ying Yong Sheng Tai Xue Bao 2024; 35:678-686. [PMID: 38646755 DOI: 10.13287/j.1001-9332.202403.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Exploring the effects of ant nests on soil CH4 emissions in the secondary tropical forests is of great scientific significance to understand the contribution of soil faunal activities to greenhouse gas emissions. With static chamber-gas chromatography method, we measured the dry-wet seasonal dynamics of CH4 emissions from ant nests and control soils in the secondary forest of Syzygium oblatum communities in Xishuangbanna. We also examined the linkages of ant-mediated changes in functional microbial diversity and soil physicochemical properties with CH4 emissions. The results showed that: 1) Ant nests significantly accelerated soil CH4 emissions, with average CH4 emissions in the ant nests being 2.6-fold of that in the control soils. 2) The CH4 emissions had significant dry-wet seasonal variations, which was a carbon sink in the dry seasons (from -0.29±0.03 to -0.53±0.02 μg·m-2·h-1) and a carbon source in the wet seasons (from 0.098±0.02 to 0.041±0.009 μg·m-2·h-1). The CH4 emissions were significantly higher in ant nests than in control soils. The CH4 emissions from the ant nests had smaller dry-wet seasonal variation (from -0.38±0.01 to 0.12±0.02 μg·m-2·h-1) than those in the control soils (from -0.65±0.04 to 0.058±0.006 μg·m-2·h-1). 3) Ant nests significantly increased the values (6.2%-37.8%) of soil methanogen diversity (i.e., Ace and Shannon indices), temperature and humidity, carbon pools (i.e., total, easily oxidizable, and microbial carbon), and nitrogen pools (i.e., total, hydrolyzed, ammonium, and microbial biomass nitrogen), but decreased the diversity (i.e., Ace and Chao1 indices) of methane-oxidizing bacteria by 21.9%-23.8%. 4) Results of the structural equation modeling showed that CH4 emissions were promoted by soil methanogen diversity, temperature and humidity, and C and N pools, but inhibited by soil methane-oxidizing bacterial diversity. The explained extents of soil temperature, humidity, carbon pool, nitrogen pool, methanogen diversity, and methane-oxidizing bacterial diversity for the CH4 emission changes were 6.9%, 21.6%, 18.4%, 15.2%, 14.0%, and 10.8%, respectively. Therefore, ant nests regulated soil CH4 emission dynamics through altering soil functional bacterial diversities, micro-habitat, and carbon and nitrogen pools in the secondary tropical forests.
Collapse
Affiliation(s)
- Ling-Ling Xie
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Shao-Jun Wang
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Bo Xiao
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Zheng-Jun Wang
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Zhi-Peng Guo
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Xiao-Fei Guo
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Shuang Luo
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Rui Li
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Jia-Hui Xia
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Meng-Jie Lan
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| | - Sheng-Qiu Yang
- College of Ecology and environment, Southwest Forestry University, Kunming 650224, China
| |
Collapse
|
4
|
Pilliol V, Beye M, Terlier L, Balmelle J, Kacel I, Lan R, Aboudharam G, Grine G, Terrer E. Methanobrevibacter massiliense and Pyramidobacter piscolens Co-Culture Illustrates Transkingdom Symbiosis. Microorganisms 2024; 12:215. [PMID: 38276200 PMCID: PMC10819710 DOI: 10.3390/microorganisms12010215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
Among oral microbiota methanogens, Methanobrevibacter massiliense (M. massiliense) has remained less studied than the well-characterised and cultivated methanogens Methanobrevibacter oralis and Methanobrevibacter smithii. M. massiliense has been associated with different oral pathologies and was co-isolated with the Synergistetes bacterium Pyramidobacter piscolens (P. piscolens) in one case of severe periodontitis. Here, reporting on two additional necrotic pulp cases yielded the opportunity to characterise two co-cultivated M. massiliense isolates, both with P. piscolens, as non-motile, 1-2-µm-long and 0.6-0.8-µm-wide Gram-positive coccobacilli which were autofluorescent at 420 nm. The two whole genome sequences featured a 31.3% GC content, gapless 1,834,388-base-pair chromosome exhibiting an 85.9% coding ratio, encoding a formate dehydrogenase promoting M. massiliense growth without hydrogen in GG medium. These data pave the way to understanding a symbiotic, transkingdom association with P. piscolens and its role in oral pathologies.
Collapse
Affiliation(s)
- Virginie Pilliol
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
| | - Mamadou Beye
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Laureline Terlier
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Julien Balmelle
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Idir Kacel
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Romain Lan
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
- CNRS, EFS, ADES, Aix-Marseille University, 13385 Marseille, France
| | - Gérard Aboudharam
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
| | - Ghiles Grine
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- IHU Méditerranée Infection, 13005 Marseille, France; (M.B.); (I.K.)
| | - Elodie Terrer
- IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, 13005 Marseille, France; (V.P.); (L.T.); (J.B.); (G.A.)
- Ecole de Médecine Dentaire, Aix-Marseille University, 13385 Marseille, France;
| |
Collapse
|
5
|
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. ISME J 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
6
|
Fukuyama Y, Shimamura S, Sakai S, Michimori Y, Sumida T, Chikaraishi Y, Atomi H, Nunoura T. Development of a rapid and highly accurate method for 13C tracer-based metabolomics and its application on a hydrogenotrophic methanogen. ISME Commun 2024; 4:ycad006. [PMID: 38282645 PMCID: PMC10809761 DOI: 10.1093/ismeco/ycad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 01/30/2024]
Abstract
Microfluidic capillary electrophoresis-mass spectrometry (CE-MS) is a rapid and highly accurate method to determine isotopomer patterns in isotopically labeled compounds. Here, we developed a novel method for tracer-based metabolomics using CE-MS for underivatized proteinogenic amino acids. The method consisting of a ZipChip CE system and a high-resolution Orbitrap Fusion Tribrid mass spectrometer allows us to obtain highly accurate data from 1 μl of 100 nmol/l amino acids comparable to a mere 1 [Formula: see text] 104-105 prokaryotic cells. To validate the capability of the CE-MS method, we analyzed 16 protein-derived amino acids from a methanogenic archaeon Methanothermobacter thermautotrophicus as a model organism, and the mass spectra showed sharp peaks with low mass errors and background noise. Tracer-based metabolome analysis was then performed to identify the central carbon metabolism in M. thermautotrophicus using 13C-labeled substrates. The mass isotopomer distributions of serine, aspartate, and glutamate revealed the occurrence of both the Wood-Ljungdahl pathway and an incomplete reductive tricarboxylic acid cycle for carbon fixation. In addition, biosynthesis pathways of 15 amino acids were constructed based on the mass isotopomer distributions of the detected protein-derived amino acids, genomic information, and public databases. Among them, the presence of alternative enzymes of alanine dehydrogenase, ornithine cyclodeaminase, and homoserine kinase was suggested in the biosynthesis pathways of alanine, proline, and threonine, respectively. To our knowledge, the novel 13C tracer-based metabolomics using CE-MS can be considered the most efficient method to identify central carbon metabolism and amino acid biosynthesis pathways and is applicable to any kind of isolated microbe.
Collapse
Affiliation(s)
- Yuto Fukuyama
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Shigeru Shimamura
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Sanae Sakai
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yuta Michimori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomomi Sumida
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yoshito Chikaraishi
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| |
Collapse
|
7
|
Wang T, Leibrock N, Plugge CM, Smidt H, Zoetendal EG. In vitro interactions between Blautia hydrogenotrophica, Desulfovibrio piger and Methanobrevibacter smithii under hydrogenotrophic conditions. Gut Microbes 2023; 15:2261784. [PMID: 37753963 PMCID: PMC10538451 DOI: 10.1080/19490976.2023.2261784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Methanogens, reductive acetogens and sulfate-reducing bacteria play an important role in disposing of hydrogen in gut ecosystems. However, how they interact with each other remains largely unknown. This in vitro study cocultured Blautia hydrogenotrophica (reductive acetogen), Desulfovibrio piger (sulfate reducer) and Methanobrevibacter smithii (methanogen). Results revealed that these three species coexisted and did not compete for hydrogen in the early phase of incubations. Sulfate reduction was not affected by B. hydrogenotrophica and M. smithii. D. piger inhibited the growth of B. hydrogenotrophica and M. smithii after 10 h incubations, and the inhibition on M. smithii was associated with increased sulfide concentration. Remarkably, M. smithii growth lag phase was shortened by coculturing with B. hydrogenotrophica and D. piger. Formate was rapidly used by M. smithii under high acetate concentration. Overall, these findings indicated that the interactions of the hydrogenotrophic microbes are condition-dependent, suggesting their interactions may vary in gut ecosystems.
Collapse
Affiliation(s)
- Taojun Wang
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Nils Leibrock
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Wetsus European Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Erwin G. Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| |
Collapse
|
8
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
9
|
Jaberi Darmiyan S, Montazer Torbati MB, Ramin M, Ghiasi SE. Effects of wheat bran replacement with pomegranate seed pulp on rumen fermentation, gas production, methanogen and protozoa populations of camel and goat rumen using competitive PCR technique: An in vitro study. Vet Med Sci 2023; 9:2901-2911. [PMID: 37864580 PMCID: PMC10650269 DOI: 10.1002/vms3.1297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/25/2023] [Accepted: 10/05/2023] [Indexed: 10/23/2023] Open
Abstract
BACKGROUND Microbial populations in the rumen play an essential role in the degradation of Cellulosic dietary components and in providing nutrients to the host animal. OBJECTIVE This study aims to detect the effect of pomegranate seed pulp (PSP) on rumen fermentation, digestibility and methanogens and the protozoa population (by competitive polymerase chain reaction [PCR]) of the camel and goat rumen fluid. MATERIALS AND METHODS PSP was added to the experimental treatments and replaced by wheat bran (0%, 5% and 10%). Rumen fluid was collected from three goats and two camels according to the similarity of sex, breed, origin and time and used for three gas production studies. DNA extraction was performed by the RBB + c method, the ImageJ programme calculated band intensities (target and competing DNA), and line gradients were plotted based on the number of copies and intensity. RESULTS Our result showed that diets did not significantly affect the methanogen and protozoa population. Animal species affected microbial populations so that both populations in camels were less than goats. The production of gas and volatile fatty acids was not affected by diets. These two parameters and NH3 concentration and methane production in goats were higher than in camel. The pH of digested dry matter and microbial protein in camels was higher than in goats. CONCLUSIONS Therefore, the competitive PCR technique is an effective method for enumerating rumen microbiota. This supplementation can be considered a strategy to achieve performance and environmental benefits.
Collapse
Affiliation(s)
- Sanaz Jaberi Darmiyan
- Department of Animal Science, Faculty of AgricultureUniversity of BirjandBirjandIran
| | - Mohammad Bagher Montazer Torbati
- Department of Animal Science, Faculty of AgricultureUniversity of BirjandBirjandIran
- Research Group of Environmental Stress in Animal Science, Faculty of AgricultureUniversity of BirjandBirjandIran
| | - Mohammad Ramin
- Department of Animal Nutrition and ManagementSwedish University of Agricultural SciencesUmeåSweden
| | - Seyed Ehsan Ghiasi
- Department of Animal Science, Faculty of AgricultureUniversity of BirjandBirjandIran
- Research Group of Environmental Stress in Animal Science, Faculty of AgricultureUniversity of BirjandBirjandIran
| |
Collapse
|
10
|
Chien HH, Lai MC, Weng CY, Chen MF, Wu SY, Lin S, Chen SC. Methanovulcanius yangii gen. nov., sp. nov., a hydrogenotrophic methanogen, isolated from a submarine mud volcano in the offshore area of southwestern Taiwan. Int J Syst Evol Microbiol 2023; 73. [PMID: 37938098 DOI: 10.1099/ijsem.0.006164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A novel mesophilic, hydrogenotrophic methanogen, strain CYW5T, was isolated from a sediment sample of a piston core collected from submarine mud volcano MV5 located in the offshore area of southwestern Taiwan. Cells of strain CYW5T were irregular coccids, 0.5-1.0 µm in diameter and lysed easily by 0.01 % sodium dodecyl sulphate (SDS) treatment. Strain CYW5Tutilized formate or hydrogen plus carbon dioxide as catabolic substrates for methanogenesis. The optimal growth conditions were 37 °C, 0.043-0.085 M NaCl and pH 6.02-7.32. The genomic DNA G+C content calculated from the genome sequence of strain CYW5T was 56.2 mol%. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that strain CYW5T represented a member of the family Methanomicrobiaceae in the order Methanomicrobiales, and was closely related to the members of the genus Methanogenium. The most closely related species was Methanogenium cariaci JR1T (94.9 % of 16S rRNA gene sequence identity). The average nucleotide identity and average amino acid identity values between strain CYW5T and members of the family Methanomicrobiaceae were 74.7-78.5 % and 49.1-64.9%, respectively. Although many of the morphological and physiological characteristics of strain CYW5T and the species of the genus Methanogenium were similar, they were distinguishable by the differences in genomic G+C content and temperature, NaCl and pH ranges for growth. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CYW5T represents a novel species, of a novel genus, named Methanovulcanius yangii gen. nov., sp. nov. The type strain is CYW5T (=BCRC AR10048T=DSM 100756T=NBRC 111404T).
Collapse
Affiliation(s)
- Hsin-Hsin Chien
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Mei-Fei Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
- School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian 365004, PR China
- Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian 365004, PR China
| |
Collapse
|
11
|
Loughrin JH, Parekh RR, Agga GE, Silva PJ, Sistani KR. Microbiome Diversity of Anaerobic Digesters Is Enhanced by Microaeration and Low Frequency Sound. Microorganisms 2023; 11:2349. [PMID: 37764193 PMCID: PMC10535533 DOI: 10.3390/microorganisms11092349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
Biogas is produced by a consortium of bacteria and archaea. We studied how the microbiome of poultry litter digestate was affected by time and treatments that enhanced biogas production. The microbiome was analyzed at six, 23, and 42 weeks of incubation. Starting at week seven, the digesters underwent four treatments: control, microaeration with 6 mL air L-1 digestate per day, treatment with a 1000 Hz sine wave, or treatment with the sound wave and microaeration. Both microaeration and sound enhanced biogas production relative to the control, while their combination was not as effective as microaeration alone. At week six, over 80% of the microbiome of the four digesters was composed of the three phyla Actinobacteria, Proteobacteria, and Firmicutes, with less than 10% Euryarchaeota and Bacteroidetes. At week 23, the digester microbiomes were more diverse with the phyla Spirochaetes, Synergistetes, and Verrucomicrobia increasing in proportion and the abundance of Actinobacteria decreasing. At week 42, Firmicutes, Bacteroidetes, Euryarchaeota, and Actinobacteria were the most dominant phyla, comprising 27.8%, 21.4%, 17.6%, and 12.3% of the microbiome. Other than the relative proportions of Firmicutes being increased and proportions of Bacteroidetes being decreased by the treatments, no systematic shifts in the microbiomes were observed due to treatment. Rather, microbial diversity was enhanced relative to the control. Given that both air and sound treatment increased biogas production, it is likely that they improved poultry litter breakdown to promote microbial growth.
Collapse
Affiliation(s)
- John H. Loughrin
- United States Department of Agriculture, Agricultural Research Service, Food Animal Environmental Systems Research Unit, 2413 Nashville Road, Suite B5, Bowling Green, KY 42101, USA; (R.R.P.); (G.E.A.); (P.J.S.); (K.R.S.)
| | | | | | | | | |
Collapse
|
12
|
Rissanen AJ, Jilbert T, Simojoki A, Mangayil R, Aalto SL, Khanongnuch R, Peura S, Jäntti H. Organic matter lability modifies the vertical structure of methane-related microbial communities in lake sediments. Microbiol Spectr 2023; 11:e0195523. [PMID: 37698418 PMCID: PMC10581051 DOI: 10.1128/spectrum.01955-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/17/2023] [Indexed: 09/13/2023] Open
Abstract
Eutrophication increases the input of labile, algae-derived, organic matter (OM) into lake sediments. This potentially increases methane (CH4) emissions from sediment to water through increased methane production rates and decreased methane oxidation efficiency in sediments. However, the effect of OM lability on the structure of methane oxidizing (methanotrophic) and methane producing (methanogenic) microbial communities in lake sediments is still understudied. We studied the vertical profiles of the sediment and porewater geochemistry and the microbial communities (16S rRNA gene amplicon sequencing) at five profundal stations of an oligo-mesotrophic, boreal lake (Lake Pääjärvi, Finland), varying in surface sediment OM sources (assessed via sediment C:N ratio). Porewater profiles of methane, dissolved inorganic carbon (DIC), acetate, iron, and sulfur suggested that sites with more autochthonous OM showed higher overall OM lability, which increased remineralization rates, leading to increased electron acceptor (EA) consumption and methane emissions from sediment to water. When OM lability increased, the abundance of anaerobic nitrite-reducing methanotrophs (Candidatus Methylomirabilis) relative to aerobic methanotrophs (Methylococcales) in the methane oxidation layer of sediment surface decreased, suggesting that Methylococcales were more competitive than Ca. Methylomirabilis under decreasing redox conditions and increasing methane availability due to their more diverse metabolism (fermentation and anaerobic respiration) and lower affinity for methane. Furthermore, when OM lability increased, the abundance of methanotrophic community in the sediment surface layer, especially Ca. Methylomirabilis, relative to the methanogenic community decreased. We conclude that increasing input of labile OM, subsequently affecting the redox zonation of sediments, significantly modifies the methane producing and consuming microbial community of lake sediments. IMPORTANCE Lakes are important natural emitters of the greenhouse gas methane (CH4). It has been shown that eutrophication, via increasing the input of labile organic matter (OM) into lake sediments and subsequently affecting the redox conditions, increases methane emissions from lake sediments through increased sediment methane production rates and decreased methane oxidation efficiency. However, the effect of organic matter lability on the structure of the methane-related microbial communities of lake sediments is not known. In this study, we show that, besides the activity, also the structure of lake sediment methane producing and consuming microbial community is significantly affected by changes in the sediment organic matter lability.
Collapse
Affiliation(s)
- Antti J. Rissanen
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tom Jilbert
- Environmental Geochemistry Group, Department of Geosciences and Geography, Faculty of Science, Helsinki, Finland
| | - Asko Simojoki
- Department of Agricultural Sciences (Environmental Soil Science), Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Rahul Mangayil
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Sanni L. Aalto
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Ramita Khanongnuch
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Helena Jäntti
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Schöne C, Poehlein A, Rother M. Genetic and Physiological Probing of Cytoplasmic Bypasses for the Energy-Converting Methyltransferase Mtr in Methanosarcina acetivorans. Appl Environ Microbiol 2023; 89:e0216122. [PMID: 37347168 PMCID: PMC10370330 DOI: 10.1128/aem.02161-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
Methanogenesis is a unique energy metabolism carried out by members of the domain Archaea. Unlike most other methanogens, which reduce CO2 to methane with hydrogen as the electron donor, Methanosarcina acetivorans is able to grow on methylated compounds, on acetate, and on carbon monoxide (CO). These substrates are metabolized via distinct yet overlapping pathways. For the use of any single methanogenic substrate, the membrane-integral, energy-converting N5-methyl-tetrahydrosarcinapterin (H4SPT):coenzyme M (HS-CoM) methyltransferase (Mtr) is required. It was proposed that M. acetivorans can bypass the methyl transfer catalyzed by Mtr via cytoplasmic activities. To address this issue, conversion of different energy substrates by an mtr deletion mutant was analyzed. No significant methyl transfer from H4SPT to HS-CoM could be detected with CO as the electron donor. In contrast, formation of methane and CO2 in the presence of methanol or trimethylamine was indicative of an Mtr bypass in the oxidative direction. As methane thiol and dimethyl sulfide were transiently produced during methylotrophic methanogenesis in the mtr mutant, involvement in this process of methyl sulfide-dependent methyltransferases (Mts) was analyzed in a strain lacking both the Mts system and Mtr. It could be unequivocally demonstrated that the Mts system is not involved in bypassing Mtr, thereby ruling out previous proposals. Conversion of [13C]methanol indicated that in the absence of Mtr M. acetivorans provides the reducing equivalents for methyl-S-CoM reduction to methane by oxidizing (an) intracellular compound(s) to CO2 rather than disproportioning the source of methyl groups. Thus, no in vivo Mtr bypass appears to exist in M. acetivorans. IMPORTANCE Methanogenic archaea possess only a limited number of chemiosmotic coupling sites in their respiratory chains. Among them, N5-methyl-H4SPT:HS-CoM methyltransferase (Mtr) is the most widely distributed. Previous observations led to the conclusion that Methanosarcina acetivorans is able to bypass this reaction via methyl sulfide-dependent methyltransferases (Mts). However, strains lacking Mtr are not able to produce methane from CO. Also, these strains are unable to oxidize methylated substrates to CO2, in contrast to observations in the close relative Methanosarcina barkeri. The results also highlight the sole function of the Mts system in methyl sulfide metabolism. Thus, no in vivo Mtr bypass appears to exist in M. acetivorans.
Collapse
Affiliation(s)
- Christian Schöne
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Michael Rother
- Fakultät Biologie, Technische Universität Dresden, Dresden, Germany
| |
Collapse
|
15
|
Heryakusuma C, Johnson EF, Purwantini E, Mukhopadhyay B. Nitrite reductase activity in F 420-dependent sulphite reductase (Fsr) from Methanocaldococcus jannaschii. Access Microbiol 2023; 5:000482.v3. [PMID: 37223055 PMCID: PMC10202398 DOI: 10.1099/acmi.0.000482.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/25/2023] [Indexed: 05/25/2023] Open
Abstract
Methanocaldococcus jannaschii (Mj), a hyperthermophilic and evolutionarily deeply rooted methanogenic archaeon from a deep-sea hydrothermal vent, produces F420-dependent sulphite reductase (Fsr) in response to exposure to sulphite. This enzyme allows Mj to detoxify sulphite, a potent inhibitor of methyl coenzyme-M reductase (Mcr), by reducing it to sulphide with reduced coenzyme F420 (F420H2) as an electron donor; Mcr is essential for energy production for a methanogen. Fsr allows Mj to utilize sulphite as a sulphur source. Nitrite is another potent inhibitor of Mcr and is toxic to methanogens. It is reduced by most sulphite reductases. In this study, we report that MjFsr reduced nitrite to ammonia with F420H2 with physiologically relevant K m values (nitrite, 8.9 µM; F420H2, 9.7 µM). The enzyme also reduced hydroxylamine with a K m value of 112.4 µM, indicating that it was an intermediate in the reduction of nitrite to ammonia. These results open the possibility that Mj could use nitrite as a nitrogen source if it is provided at a low concentration of the type that occurs in its habitat.
Collapse
Affiliation(s)
- Christian Heryakusuma
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Eric F. Johnson
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Endang Purwantini
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Biswarup Mukhopadhyay
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
- Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| |
Collapse
|
16
|
Prakash O, Dodsworth JA, Dong X, Ferry JG, L'Haridon S, Imachi H, Kamagata Y, Rhee SK, Sagar I, Shcherbakova V, Wagner D, Whitman WB. Proposed minimal standards for description of methanogenic archaea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37097839 DOI: 10.1099/ijsem.0.005500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.
Collapse
Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
- Symbiosis Centre for Climate Change and Sustainability, Symbiosis International (Deemed University), Lavale, Pune-412115, Maharashtra, India
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephane L'Haridon
- CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, University of Brest, F-29280, Plouzané, France
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoichi Kamagata
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8560, Japan
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
| | - Isita Sagar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 3, Pushchino, Moscow, 142290, Russian Federation
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg A71-359, 14473 Potsdam, Germany
- Institut of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
17
|
Wang H, Jurasinski G, Täumer J, Kuß AW, Groß V, Köhn D, Günther A, Urich T. Linking Transcriptional Dynamics of Peat Microbiomes to Methane Fluxes during a Summer Drought in Two Rewetted Fens. Environ Sci Technol 2023; 57:5089-5101. [PMID: 36926875 DOI: 10.1021/acs.est.2c07461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Rewetted peatlands are reestablished hot spots for CH4 emissions, which are subject to increased drought events in the course of climate change. However, the dynamics of soil methane-cycling microbiomes in rewetted peatlands during summer drought are still poorly characterized. Using a quantitative metatranscriptomic approach, we investigated the changes in the transcript abundances of methanogen and methanotroph rRNA, as well as mcrA and pmoA mRNA before, during, and after the 2018 summer drought in a coastal and a percolation fen in northern Germany. Drought changed the community structure of methane-cycling microbiomes and decreased the CH4 fluxes as well as the rRNA and mRNA transcript abundances of methanogens and methanotrophs, but they showed no recovery or increase after the drought ended. The rRNA transcript abundance of methanogens was not correlated with CH4 fluxes in both fens. In the percolation fen, however, the mcrA transcript abundance showed a positive and significant correlation with CH4 fluxes. Importantly, when integrating pmoA abundance, a stronger correlation was observed between CH4 fluxes and mcrA/pmoA, suggesting that relationships between methanogens and methanotrophs are the key determinant of CH4 turnover. Our study provides a comprehensive understanding of the methane-cycling microbiome feedbacks to drought events in rewetted peatlands.
Collapse
Affiliation(s)
- Haitao Wang
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Gerald Jurasinski
- Landscape Ecology, University of Rostock, 18059 Rostock, Germany
- Interdisciplinary Faculty, University of Rostock, 18059 Rostock, Germany
- Peatland Science, University of Greifswald, 17489 Greifswald, Germany
| | - Jana Täumer
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Andreas W Kuß
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Verena Groß
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Daniel Köhn
- Landscape Ecology, University of Rostock, 18059 Rostock, Germany
| | - Anke Günther
- Landscape Ecology, University of Rostock, 18059 Rostock, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| |
Collapse
|
18
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
19
|
Cui H, Wang Y, Su X, Wei S, Pang S, Zhu Y, Zhang S, Ma C, Hou W, Jiang H. Response of methanogenic community and their activity to temperature rise in alpine swamp meadow at different water level of the permafrost wetland on Qinghai-Tibet Plateau. Front Microbiol 2023; 14:1181658. [PMID: 37213493 PMCID: PMC10198574 DOI: 10.3389/fmicb.2023.1181658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/17/2023] [Indexed: 05/23/2023] Open
Abstract
Wetlands are an important source of atmospheric methane (CH4) and are sensitive to global climate change. Alpine swamp meadows, accounting for ~50% of the natural wetlands on the Qinghai-Tibet Plateau, were considered one of the most important ecosystems. Methanogens are important functional microbes that perform the methane producing process. However, the response of methanogenic community and the main pathways of CH4 production to temperature rise remains unknown in alpine swamp meadow at different water level in permafrost wetlands. In this study, we investigated the response of soil CH4 production and the shift of methanogenic community to temperature rise in the alpine swamp meadow soil samples with different water levels collected from the Qinghai-Tibet Plateau through anaerobic incubation at 5°C, 15°C and 25°C. The results showed that the CH4 contents increased with increasing incubation temperature, and were 5-10 times higher at the high water level sites (GHM1 and GHM2) than that at the low water level site (GHM3). For the high water level sites (GHM1 and GHM2), the change of incubation temperatures had little effect on the methanogenic community structure. Methanotrichaceae (32.44-65.46%), Methanobacteriaceae (19.30-58.86%) and Methanosarcinaceae (3.22-21.24%) were the dominant methanogen groups, with the abundance of Methanotrichaceae and Methanosarcinaceae having a significant positive correlation with CH4 production (p < 0.01). For the low water level site (GHM3), the methanogenic community structure changed greatly at 25°C. The Methanobacteriaceae (59.65-77.33%) was the dominant methanogen group at 5°C and 15°C; In contrast, the Methanosarcinaceae (69.29%) dominated at 25°C, and its abundance showed a significant positive correlation with CH4 production (p < 0.05). Collectively, these findings enhance the understanding of methanogenic community structures and CH4 production in permafrost wetlands with different water levels during the warming process.
Collapse
Affiliation(s)
- Hongpeng Cui
- Key Laboratory of Marine Mineral Resources and Polar Geology, Ministry of Education, China University of Geosciences, Beijing, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Yanfa Wang
- Key Laboratory of Marine Mineral Resources and Polar Geology, Ministry of Education, China University of Geosciences, Beijing, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Xin Su
- Key Laboratory of Marine Mineral Resources and Polar Geology, Ministry of Education, China University of Geosciences, Beijing, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Ocean Sciences, China University of Geosciences, Beijing, China
- Xin Su,
| | - Shiping Wei
- Key Laboratory of Marine Mineral Resources and Polar Geology, Ministry of Education, China University of Geosciences, Beijing, China
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Shouji Pang
- Oil and Gas Survey, China Geological Survey, Beijing, China
| | - Youhai Zhu
- Oil and Gas Survey, China Geological Survey, Beijing, China
| | - Shuai Zhang
- Oil and Gas Survey, China Geological Survey, Beijing, China
| | - Chenjie Ma
- Key Laboratory of Marine Mineral Resources and Polar Geology, Ministry of Education, China University of Geosciences, Beijing, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Ocean Sciences, China University of Geosciences, Beijing, China
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
| | - Hongchen Jiang
- Key Laboratory of Marine Mineral Resources and Polar Geology, Ministry of Education, China University of Geosciences, Beijing, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, China
- School of Ocean Sciences, China University of Geosciences, Beijing, China
- *Correspondence: Hongchen Jiang,
| |
Collapse
|
20
|
Ginsbach LF, Gonzalez JM. Understanding Life at High Temperatures: Relationships of Molecular Channels in Enzymes of Methanogenic Archaea and Their Growth Temperatures. Int J Mol Sci 2022; 23. [PMID: 36499474 DOI: 10.3390/ijms232315149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
Analyses of protein structures have shown the existence of molecular channels in enzymes from Prokaryotes. Those molecular channels suggest a critical role of spatial voids in proteins, above all, in those enzymes functioning under high temperature. It is expected that these spaces within the protein structure are required to access the active site and to maximize availability and thermal stability of their substrates and cofactors. Interestingly, numerous substrates and cofactors have been reported to be highly temperature-sensitive biomolecules. Methanogens represent a singular phylogenetic group of Archaea that performs anaerobic respiration producing methane during growth. Methanogens inhabit a variety of environments including the full range of temperatures for the known living forms. Herein, we carry out a dimensional analysis of molecular tunnels in key enzymes of the methanogenic pathway from methanogenic Archaea growing optimally over a broad temperature range. We aim to determine whether the dimensions of the molecular tunnels are critical for those enzymes from thermophiles. Results showed that at increasing growth temperature the dimensions of molecular tunnels in the enzymes methyl-coenzyme M reductase and heterodisulfide reductase become increasingly restrictive and present strict limits at the highest growth temperatures, i.e., for hyperthermophilic methanogens. However, growth at lower temperature allows a wide dimensional range for the molecular spaces in these enzymes. This is in agreement with previous suggestions on a potential major role of molecular tunnels to maintain biomolecule stability and activity of some enzymes in microorganisms growing at high temperatures. These results contribute to better understand archaeal growth at high temperatures. Furthermore, an optimization of the dimensions of molecular tunnels would represent an important adaptation required to maintain the activity of key enzymes of the methanogenic pathway for those methanogens growing optimally at high temperatures.
Collapse
|
21
|
Palabikyan H, Ruddyard A, Pomper L, Novak D, Reischl B, Rittmann SKMR. Scale-up of biomass production by Methanococcus maripaludis. Front Microbiol 2022; 13:1031131. [PMID: 36504798 PMCID: PMC9727139 DOI: 10.3389/fmicb.2022.1031131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/13/2022] [Indexed: 11/24/2022] Open
Abstract
The development of a sustainable energy economy is one of the great challenges in the current times of climate crisis and growing energy demands. Industrial production of the fifth-generation biofuel methane by microorganisms has the potential to become a crucial biotechnological milestone of the post fossil fuel era. Therefore, reproducible cultivation and scale-up of methanogenic archaea (methanogens) is essential for enabling biomass generation for fundamental studies and for defining peak performance conditions for bioprocess development. This study provides a comprehensive revision of established and optimization of novel methods for the cultivation of the model organism Methanococcus maripaludis S0001. In closed batch mode, 0.05 L serum bottles cultures were gradually replaced by 0.4 L Schott bottle cultures for regular biomass generation, and the time for reaching peak optical density (OD578) values was reduced in half. In 1.5 L reactor cultures, various agitation, harvesting and transfer methods were compared resulting in a specific growth rate of 0.16 h-1 and the highest recorded OD578 of 3.4. Finally, a 300-fold scale-up from serum bottles was achieved by growing M. maripaludis for the first time in a 22 L stainless steel bioreactor with 15 L working volume. Altogether, the experimental approaches described in this study contribute to establishing methanogens as essential organisms in large-scale biotechnology applications, a crucial stage of an urgently needed industrial evolution toward sustainable biosynthesis of energy and high value products.
Collapse
Affiliation(s)
- Hayk Palabikyan
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria
| | - Aquilla Ruddyard
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria
| | - Lara Pomper
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria
| | - David Novak
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czechia
| | - Barbara Reischl
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, Vienna, Austria,Arkeon GmbH, Tulln a.d. Donau, Austria,*Correspondence: Simon K.-M. R. Rittmann,
| |
Collapse
|
22
|
Mei N, Postec A, Bartoli M, Vandecasteele C, Wils L, Gil L, Monnin C, Pelletier B, Erauso G, Quéméneur M. Methanobacterium alkalithermotolerans sp. nov., a novel alkaliphilic and hydrogen-utilizing methanogen isolated from an alkaline geothermal spring (La Crouen, New Caledonia). Int J Syst Evol Microbiol 2022; 72. [PMID: 36260502 DOI: 10.1099/ijsem.0.005554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
An anaerobic, hydrogenotrophic methane-producing archaeon was isolated from an alkaline thermal spring (42 °C, pH 9.0) in New Caledonia. This methanogen, designated strain CANT, is alkaliphilic, thermotolerant, with Gram-positive staining non-motile cells. Strain CANT grows autotrophically using hydrogen exclusively as an energy source and carbon dioxide as the sole carbon source (without the requirement of yeast extract or other organic compounds). It grows at 20-45 °C (optimum, 45 °C) and pH 7.3-9.7 (optimum, pH 9.0). NaCl is not required for growth (optimum 0 %) but is tolerated up to 1.5 %. It resists novobiocin, streptomycin and vancomycin but is inhibited by ampicillin and penicillin, among other antibiotics. The genome consists of a circular chromosome (2.2 Mb) containing 2126 predicted protein-encoding genes with a G+C content of 36.4 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CANT is a member of the genus Methanobacterium, most closely related to the alkaliphilic Methanobacterium alcaliphilum WeN4T with 98.5 % 16S rRNA gene sequence identity. The genomes of strain CANT and M. alcaliphilum DSM 3459, sequenced in this study, share 71.6 % average nucleotide identity and 14.0 % digital DNA-DNA hybridization. Therefore, phylogenetic and physiological results indicate that strain CANT represents a novel species, for which the name Methanobacterium alkalithermotolerans sp. nov. is proposed, and strain CANT (=DSM 102889T= JCM 31304T) is assigned as the type strain.
Collapse
Affiliation(s)
- Nan Mei
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
- Present address: School of Chemistry, Chemical Engineering, and Life Science, Wuhan University of Technology, Wuhan 430070, PR China
| | - Anne Postec
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Manon Bartoli
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Laura Wils
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Lisa Gil
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Christophe Monnin
- GET UMR5563 (CNRS/UPS/IRD/CNES), Géosciences Environnement Toulouse, 14 Avenue Edouard Belin, 31400 Toulouse, France
| | - Bernard Pelletier
- UMR Géoazur, Centre IRD de Nouméa, 101 Promenade Roger Laroque, BP A5 - 98848 Nouméa cedex, New Caledonia
| | - Gael Erauso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Marianne Quéméneur
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| |
Collapse
|
23
|
Subedi BP, Schofield LR, Carbone V, Wolf M, Martin WF, Ronimus RS, Sutherland-Smith AJ. Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases. Microbiology (Reading) 2022; 168. [PMID: 36178458 DOI: 10.1099/mic.0.001235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Archaea have diverse cell wall types, yet none are identical to bacterial peptidoglycan (murein). Methanogens Methanobacteria and Methanopyrus possess cell walls of pseudomurein, a structural analogue of murein. Pseudomurein differs from murein in containing the unique archaeal sugar N-acetyltalosaminuronic acid instead of N-acetylmuramic acid, β-1,3 glycosidic bonds in place of β-1,4 bonds and only l-amino acids in the peptide cross-links. We have determined crystal structures of methanogen pseudomurein peptide ligases (termed pMurE) from Methanothermus fervidus (Mfer762) and Methanothermobacter thermautotrophicus (Mth734) that are structurally most closely related to bacterial MurE peptide ligases. The homology of the archaeal pMurE and bacterial MurE enzymes is clear both in the overall structure and at the level of each of the three domains. In addition, we identified two UDP-binding sites in Mfer762 pMurE, one at the exterior surface of the interface of the N-terminal and middle domains, and a second site at an inner surface continuous with the highly conserved interface of the three domains. Residues involved in ATP binding in MurE are conserved in pMurE, suggesting that a similar ATP-binding pocket is present at the interface of the middle and the C-terminal domains of pMurE. The presence of pMurE ligases in members of the Methanobacteriales and Methanopyrales, that are structurally related to bacterial MurE ligases, supports the idea that the biosynthetic origins of archaeal pseudomurein and bacterial peptidoglycan cell walls are evolutionarily related.
Collapse
Affiliation(s)
- Bishwa P Subedi
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,School of Natural Sciences, Massey University, Palmerston North 4442, New Zealand.,Present address: Faculty of Medicine, Nursing and Health Sciences, Monash Biomedicine Discovery Institute, Monash University, Victoria 3800, Australia
| | - Linley R Schofield
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Vincenzo Carbone
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Maximilian Wolf
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand.,Present address: Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany
| | - William F Martin
- Institute for Molecular Evolution, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ron S Ronimus
- AgResearch Ltd, Grasslands, Tennent Drive, Palmerston North, 4442, New Zealand
| | | |
Collapse
|
24
|
Steward KF, Payne D, Kincannon W, Johnson C, Lensing M, Fausset H, Németh B, Shepard EM, Broderick WE, Broderick JB, Dubois J, Bothner B. Proteomic Analysis of Methanococcus voltae Grown in the Presence of Mineral and Nonmineral Sources of Iron and Sulfur. Microbiol Spectr 2022; 10:e0189322. [PMID: 35876569 PMCID: PMC9431491 DOI: 10.1128/spectrum.01893-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
Iron sulfur (Fe-S) proteins are essential and ubiquitous across all domains of life, yet the mechanisms underpinning assimilation of iron (Fe) and sulfur (S) and biogenesis of Fe-S clusters are poorly understood. This is particularly true for anaerobic methanogenic archaea, which are known to employ more Fe-S proteins than other prokaryotes. Here, we utilized a deep proteomics analysis of Methanococcus voltae A3 cultured in the presence of either synthetic pyrite (FeS2) or aqueous forms of ferrous iron and sulfide to elucidate physiological responses to growth on mineral or nonmineral sources of Fe and S. The liquid chromatography-mass spectrometry (LCMS) shotgun proteomics analysis included 77% of the predicted proteome. Through a comparative analysis of intra- and extracellular proteomes, candidate proteins associated with FeS2 reductive dissolution, Fe and S acquisition, and the subsequent transport, trafficking, and storage of Fe and S were identified. The proteomic response shows a large and balanced change, suggesting that M. voltae makes physiological adjustments involving a range of biochemical processes based on the available nutrient source. Among the proteins differentially regulated were members of core methanogenesis, oxidoreductases, membrane proteins putatively involved in transport, Fe-S binding ferredoxin and radical S-adenosylmethionine proteins, ribosomal proteins, and intracellular proteins involved in Fe-S cluster assembly and storage. This work improves our understanding of ancient biogeochemical processes and can support efforts in biomining of minerals. IMPORTANCE Clusters of iron and sulfur are key components of the active sites of enzymes that facilitate microbial conversion of light or electrical energy into chemical bonds. The proteins responsible for transporting iron and sulfur into cells and assembling these elements into metal clusters are not well understood. Using a microorganism that has an unusually high demand for iron and sulfur, we conducted a global investigation of cellular proteins and how they change based on the mineral forms of iron and sulfur. Understanding this process will answer questions about life on early earth and has application in biomining and sustainable sources of energy.
Collapse
Affiliation(s)
- Katherine F. Steward
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Will Kincannon
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Christina Johnson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Malachi Lensing
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Hunter Fausset
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Brigitta Németh
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Eric M. Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - William E. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Joan B. Broderick
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jen Dubois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| |
Collapse
|
25
|
Abstract
Undesirable ammonium concentrations can lead to unstable anaerobic digestion processes, and Methanosarcina spp. are the representative methanogens under inhibition. However, no known work seems to exist for directly exploring the detailed metabolic regulation of pure cultured representative Methanosarcina spp. to ammonium inhibition. We used transcriptomics and proteomics to profile the metabolic regulation of Methanosarcina barkeri to 1, 4, and 7 g N/L of total ammoniacal nitrogen (TAN), where free ammonia concentrations were between 1.5 and 36.1 mg N/L. At the initial stages of ammonium inhibition, the genes participating in the acquisition and assimilation of reduced nitrogen sources showed significant upregulation where the minimal fold change of gene transcription was about 2. Apart from nitrogen metabolism, the transcription of some genes in methanogenesis also significantly increased at the initial stages. For example, the genes encoding alternative heterodisulfide reductase subunits (HdrAB), energy-converting hydrogenase subunit (EchC), and methanophenazine-dependent hydrogenase subunits (VhtAC) were significantly upregulated by at least 2.05 times. For the element translocation at the initial stages, the genes participating in the uptake of ferrous iron, potassium ion, and molybdate were significantly upregulated with a minimal fold change of 2.10. As the cultivation proceeded, the gene encoding the cell division protein subunit (FtsH) was significantly upregulated by 13.0 times at 7 g N/L of TAN; meanwhile, an increment in OD600 was observed at the terminal sampling point of 7 g N/L of TAN. The present study explored the metabolic regulation of M. barkeri in stress response, protein synthesis, signal transduction, nitrogen metabolism, methanogenesis, and element translocation. The results would contribute to the understanding of the metabolic effects of ammonium inhibition on methanogens and have significant practical implication in inhibited anaerobic digestion.
Collapse
Affiliation(s)
- Haowen Duan
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China
- Shanghai Multi-Source Solid Waste Collaborative Treatment and Energy Engineering Technology Research Center, Shanghai 200092, China
| | - Hua Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai 200092, China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| |
Collapse
|
26
|
Heryakusuma C, Susanti D, Yu H, Li Z, Purwantini E, Hettich RL, Orphan VJ, Mukhopadhyay B. A Reduced F 420-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon. J Bacteriol 2022;:e0007822. [PMID: 35695516 DOI: 10.1128/jb.00078-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anaerobic methanotrophic archaea (ANME), which oxidize methane in marine sediments through syntrophic associations with sulfate-reducing bacteria, carry homologs of coenzyme F420-dependent sulfite reductase (Fsr) of Methanocaldococcus jannaschii, a hyperthermophilic methanogen from deep-sea hydrothermal vents. M. jannaschii Fsr (MjFsr) and ANME-Fsr belong to two phylogenetically distinct groups, FsrI and FsrII, respectively. MjFsrI reduces sulfite to sulfide with reduced F420 (F420H2), protecting methyl coenzyme M reductase (Mcr), an essential enzyme for methanogens, from sulfite inhibition. However, the function of FsrIIs in ANME, which also rely on Mcr and live in sulfidic environments, is unknown. We have determined the catalytic properties of FsrII from a member of ANME-2c. Since ANME remain to be isolated, we expressed ANME2c-FsrII in a closely related methanogen, Methanosarcina acetivorans. Purified recombinant FsrII contained siroheme, indicating that the methanogen, which lacks a native sulfite reductase, produced this coenzyme. Unexpectedly, FsrII could not reduce sulfite or thiosulfate with F420H2. Instead, it acted as an F420H2-dependent nitrite reductase (FNiR) with physiologically relevant Km values (nitrite, 5 μM; F420H2, 14 μM). From kinetic, thermodynamic, and structural analyses, we hypothesize that in FNiR, F420H2-derived electrons are delivered at the oxyanion reduction site at a redox potential that is suitable for reducing nitrite (E0' [standard potential], +440 mV) but not sulfite (E0', -116 mV). These findings and the known nitrite sensitivity of Mcr suggest that FNiR may protect nondenitrifying ANME from nitrite toxicity. Remarkably, by reorganizing the reductant processing system, Fsr transforms two analogous oxyanions in two distinct archaeal lineages with different physiologies and ecologies. IMPORTANCE Coenzyme F420-dependent sulfite reductase (Fsr) protects methanogenic archaea inhabiting deep-sea hydrothermal vents from the inactivation of methyl coenzyme M reductase (Mcr), one of their essential energy production enzymes. Anaerobic methanotrophic archaea (ANME) that oxidize methane and rely on Mcr, carry Fsr homologs that form a distinct clade. We show that a member of this clade from ANME-2c functions as F420-dependent nitrite reductase (FNiR) and lacks Fsr activity. This specialization arose from a distinct feature of the reductant processing system and not the substrate recognition element. We hypothesize FNiR may protect ANME Mcr from inactivation by nitrite. This is an example of functional specialization within a protein family that is induced by changes in electron transfer modules to fit an ecological need.
Collapse
|
27
|
Cai C, Ni G, Xia J, Zhang X, Zheng Y, He B, Marcellin E, Li W, Pu J, Yuan Z, Hu S. Response of the Anaerobic Methanotrophic Archaeon Candidatus " Methanoperedens nitroreducens" to the Long-Term Ferrihydrite Amendment. Front Microbiol 2022; 13:799859. [PMID: 35509320 PMCID: PMC9058156 DOI: 10.3389/fmicb.2022.799859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/10/2022] [Indexed: 11/30/2022] Open
Abstract
Anaerobic methanotrophic (ANME) archaea can drive anaerobic oxidation of methane (AOM) using solid iron or manganese oxides as the electron acceptors, hypothetically via direct extracellular electron transfer (EET). This study investigated the response of Candidatus "Methanoperedens nitroreducens TS" (type strain), an ANME archaeon previously characterized to perform nitrate-dependent AOM, to an Fe(III)-amended condition over a prolonged period. Simultaneous consumption of methane and production of dissolved Fe(II) were observed for more than 500 days in the presence of Ca. "M. nitroreducens TS," indicating that this archaeon can carry out Fe(III)-dependent AOM for a long period. Ca. "M. nitroreducens TS" possesses multiple multiheme c-type cytochromes (MHCs), suggesting that it may have the capability to reduce Fe(III) via EET. Intriguingly, most of these MHCs are orthologous to those identified in Candidatus "Methanoperedens ferrireducens," an Fe(III)-reducing ANME archaeon. In contrast, the population of Ca. "M. nitroreducens TS" declined and was eventually replaced by Ca. "M. ferrireducens," implying niche differentiation between these two ANME archaea in the environment.
Collapse
Affiliation(s)
- Chen Cai
- CAS Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, China
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Gaofeng Ni
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Jun Xia
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Xueqin Zhang
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Yue Zheng
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Bingqing He
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Weiwei Li
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, China
| | - Jiaoyang Pu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Shihu Hu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St Lucia, QLD, Australia
| |
Collapse
|
28
|
Holmes DE, Zhou J, Ueki T, Woodard T, Lovley DR. Mechanisms for Electron Uptake by Methanosarcina acetivorans during Direct Interspecies Electron Transfer. mBio 2021; 12:e0234421. [PMID: 34607451 PMCID: PMC8546582 DOI: 10.1128/mbio.02344-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022] Open
Abstract
Direct interspecies electron transfer (DIET) between bacteria and methanogenic archaea appears to be an important syntrophy in both natural and engineered methanogenic environments. However, the electrical connections on the outer surface of methanogens and the subsequent processing of electrons for carbon dioxide reduction to methane are poorly understood. Here, we report that the genetically tractable methanogen Methanosarcina acetivorans can grow via DIET in coculture with Geobacter metallireducens serving as the electron-donating partner. Comparison of gene expression patterns in M. acetivorans grown in coculture versus pure-culture growth on acetate revealed that transcripts for the outer-surface multiheme c-type cytochrome MmcA were higher during DIET-based growth. Deletion of mmcA inhibited DIET. The high aromatic amino acid content of M. acetivorans archaellins suggests that they might assemble into electrically conductive archaella. A mutant that could not express archaella was deficient in DIET. However, this mutant grew in DIET-based coculture as well as the archaellum-expressing parental strain in the presence of granular activated carbon, which was previously shown to serve as a substitute for electrically conductive pili as a conduit for long-range interspecies electron transfer in other DIET-based cocultures. Transcriptomic data suggesting that the membrane-bound Rnf, Fpo, and HdrED complexes also play a role in DIET were incorporated into a charge-balanced model illustrating how electrons entering the cell through MmcA can yield energy to support growth from carbon dioxide reduction. The results are the first genetics-based functional demonstration of likely outer-surface electrical contacts for DIET in a methanogen. IMPORTANCE The conversion of organic matter to methane plays an important role in the global carbon cycle and is an effective strategy for converting wastes to a useful biofuel. The reduction of carbon dioxide to methane accounts for approximately a third of the methane produced in anaerobic soils and sediments as well as waste digesters. Potential electron donors for carbon dioxide reduction are H2 or electrons derived from direct interspecies electron transfer (DIET) between bacteria and methanogens. Elucidating the relative importance of these electron donors has been difficult due to a lack of information on the electrical connections on the outer surfaces of methanogens and how they process the electrons received from DIET. Transcriptomic patterns and gene deletion phenotypes reported here provide insight into how a group of Methanosarcina organisms that play an important role in methane production in soils and sediments participate in DIET.
Collapse
Affiliation(s)
- Dawn E. Holmes
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Department of Physical and Biological Science, Western New England University, Springfield, Massachusetts, USA
| | - Jinjie Zhou
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
| | - Trevor Woodard
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
| |
Collapse
|
29
|
Long F, Cheung CY, Whitman WB, Cook GM, Ronimus RS. Using genome comparisons of wild-type and resistant mutants of Methanococcus maripaludis to help understand mechanisms of resistance to methane inhibitors. Access Microbiol 2021; 3:000244. [PMID: 34595395 PMCID: PMC8479958 DOI: 10.1099/acmi.0.000244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 06/08/2021] [Indexed: 11/24/2022] Open
Abstract
Methane emissions from enteric fermentation in the ruminant digestive system generated by methanogenic archaea are a significant contributor to anthropogenic greenhouse gas emissions. Additionally, methane produced as an end-product of enteric fermentation is an energy loss from digested feed. To control the methane emissions from ruminants, extensive research in the last decades has been focused on developing viable enteric methane mitigation practices, particularly, using methanogen-specific inhibitors. We report here the utilization of two known inhibitors of methanogenic archaea, neomycin and chloroform, together with a recently identified inhibitor, echinomycin, to produce resistant mutants of Methanococcus maripaludis S2 and S0001. Whole-genome sequencing at high coverage (> 100-fold) was performed subsequently to investigate the potential targets of these inhibitors at the genomic level. Upon analysis of the whole-genome sequencing data, we identified mutations in a number of genetic loci pointing to potential mechanisms of inhibitor action and their underlying mechanisms of resistance.
Collapse
Affiliation(s)
- Feng Long
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
- Present address: Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH, USA
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Ron S Ronimus
- Rumen Microbiology, AgResearch Ltd., Palmerston North, New Zealand
| |
Collapse
|
30
|
Hoffert M, Anderson RE, Reveillaud J, Murphy LG, Stepanauskas R, Huber JA. Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems. Front Microbiol 2021; 12:714920. [PMID: 34489903 PMCID: PMC8417812 DOI: 10.3389/fmicb.2021.714920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/31/2021] [Indexed: 11/13/2022] Open
Abstract
Hydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five Methanothermococcus single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some Methanothermococcus lineages and their transcripts were more abundant than others in individual vent sites, indicating differential fitness among lineages. The relative abundances of lineages represented by SAGs in each of the samples matched phylogenetic relationships based on single-copy universal genes, and genes related to nitrogen fixation and the CRISPR/Cas immune system were among those differentiating the clades. Lineages possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of Methanothermococcus were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of Methanothermococcus co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems.
Collapse
Affiliation(s)
- Michael Hoffert
- Biology Department, Carleton College, Northfield, MN, United States.,Finch Therapeutics Group, Somerville, MA, United States
| | - Rika E Anderson
- Biology Department, Carleton College, Northfield, MN, United States
| | - Julie Reveillaud
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Institut de Recherche Pour le Développement, Montpellier, France
| | | | | | - Julie A Huber
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| |
Collapse
|
31
|
Park T, Cheong H, Yoon J, Kim A, Yun Y, Unno T. Comparison of the Fecal Microbiota of Horses with Intestinal Disease and Their Healthy Counterparts. Vet Sci 2021; 8:vetsci8060113. [PMID: 34204317 PMCID: PMC8234941 DOI: 10.3390/vetsci8060113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022] Open
Abstract
(1) Background: The intestinal microbiota plays an essential role in maintaining the host's health. Dysbiosis of the equine hindgut microbiota can alter the fermentation patterns and cause metabolic disorders. (2) Methods: This study compared the fecal microbiota composition of horses with intestinal disease and their healthy counterparts living in Korea using 16S rRNA sequencing from fecal samples. A total of 52 fecal samples were collected and divided into three groups: horses with large intestinal disease (n = 20), horses with small intestinal disease (n = 8), and healthy horses (n = 24). (3) Results: Horses with intestinal diseases had fewer species and a less diverse bacterial population than healthy horses. Lactic acid bacteria, Lachnospiraceae, and Lactobacillaceae were overgrown in horses with large intestinal colic. The Firmicutes to Bacteroidetes ratio (F/B), which is a relevant marker of gut dysbiosis, was 1.94, 2.37, and 1.74 for horses with large intestinal colic, small intestinal colic, and healthy horses, respectively. (4) Conclusions: The overgrowth of two lactic acid bacteria families, Lachnospiraceae and Lactobacillaceae, led to a decrease in hindgut pH that interfered with normal fermentation, which might cause large intestinal colic. The overgrowth of Streptococcus also led to a decrease in pH in the hindgut, which suppressed the proliferation of the methanogen and reduced methanogenesis in horses with small intestinal colic.
Collapse
Affiliation(s)
- Taemook Park
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju 63346, Korea; (T.P.); (J.Y.); (A.K.)
- College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Korea
| | - Heetae Cheong
- College of Veterinary Medicine and Institute of Veterinary Science, Kangwon National University, Chuncheon 24341, Korea;
| | - Jungho Yoon
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju 63346, Korea; (T.P.); (J.Y.); (A.K.)
| | - Ahram Kim
- Equine Clinic, Jeju Stud Farm, Korea Racing Authority, Jeju 63346, Korea; (T.P.); (J.Y.); (A.K.)
| | - Youngmin Yun
- College of Veterinary Medicine and Veterinary Medical Research Institute, Jeju National University, Jeju 63243, Korea
- Correspondence: (Y.Y.); (T.U.); Tel.: +82-64-754-3376 (Y.Y.); +82-64-754-3354 (T.U.)
| | - Tatsuya Unno
- Faculty of Biotechnology, School of Life Sciences, SARI, Jeju 63243, Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju 63243, Korea
- Correspondence: (Y.Y.); (T.U.); Tel.: +82-64-754-3376 (Y.Y.); +82-64-754-3354 (T.U.)
| |
Collapse
|
32
|
Zhou J, Holmes DE, Tang HY, Lovley DR. Correlation of Key Physiological Properties of Methanosarcina Isolates with Environment of Origin. Appl Environ Microbiol 2021; 87:e0073121. [PMID: 33931421 DOI: 10.1128/AEM.00731-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
It is known that the physiology of Methanosarcina species can differ significantly, but the ecological impact of these differences is unclear. We recovered two strains of Methanosarcina from two different ecosystems with a similar enrichment and isolation method. Both strains had the same ability to metabolize organic substrates and participate in direct interspecies electron transfer but also had major physiological differences. Strain DH-1, which was isolated from an anaerobic digester, used H2 as an electron donor. Genome analysis indicated that it lacks an Rnf complex and conserves energy from acetate metabolism via intracellular H2 cycling. In contrast, strain DH-2, a subsurface isolate, lacks hydrogenases required for H2 uptake and cycling and has an Rnf complex for energy conservation when growing on acetate. Further analysis of the genomes of previously described isolates, as well as phylogenetic and metagenomic data on uncultured Methanosarcina in anaerobic digesters and diverse soils and sediments, revealed a physiological dichotomy that corresponded with environment of origin. The physiology of type I Methanosarcina revolves around H2 production and consumption. In contrast, type II Methanosarcina species eschew H2 and have genes for an Rnf complex and the multiheme, membrane-bound c-type cytochrome MmcA, shown to be essential for extracellular electron transfer. The distribution of Methanosarcina species in diverse environments suggests that the type I H2-based physiology is well suited for high-energy environments, like anaerobic digesters, whereas type II Rnf/cytochrome-based physiology is an adaptation to the slower, steady-state carbon and electron fluxes common in organic-poor anaerobic soils and sediments. IMPORTANCE Biogenic methane is a significant greenhouse gas, and the conversion of organic wastes to methane is an important bioenergy process. Methanosarcina species play an important role in methane production in many methanogenic soils and sediments as well as anaerobic waste digesters. The studies reported here emphasize that the genus Methanosarcina is composed of two physiologically distinct groups. This is important to recognize when interpreting the role of Methanosarcina in methanogenic environments, especially regarding H2 metabolism. Furthermore, the finding that type I Methanosarcina species predominate in environments with high rates of carbon and electron flux and that type II Methanosarcina species predominate in lower-energy environments suggests that evaluating the relative abundance of type I and type II Methanosarcina may provide further insights into rates of carbon and electron flux in methanogenic environments.
Collapse
|
33
|
Yoshikawa M, Zhang M, Kawabe Y, Katayama T. Effects of ferrous iron supplementation on reductive dechlorination of tetrachloroethene and on methanogenic microbial community. FEMS Microbiol Ecol 2021; 97:6274675. [PMID: 33979429 PMCID: PMC8139862 DOI: 10.1093/femsec/fiab069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/10/2021] [Indexed: 11/14/2022] Open
Abstract
Chloroethenes are common soil and groundwater pollutants. Their dechlorination is impacted by environmental factors, such as the presence of metal ions. We here investigated the effect of ferrous iron on bacterial reductive dechlorination of chloroethenes and on methanogen community. Reductive dechlorination of tetrachloroethene was assayed with a groundwater sample originally containing 6.3 × 103 copies mL−1 of Dehalococcoides 16S rRNA gene and 2 mg L−1 of iron. Supplementation with 28 mg L−1 of ferrous iron enhanced the reductive dechlorination of cis-dichloroethene (cis-DCE) and vinyl chloride in the presence of methanogens. The supplementation shortened the time required for complete dechlorination of 1 mg L−1 of tetrachloroethene to ethene and ethane from 84 to 49 d. Methanogens, such as Candidatus ‘Methanogranum’, Methanomethylovorans and Methanocorpusculum, were significantly more abundant in iron-supplemented cultures than in non-supplemented cultures (P < 0.01). Upon methanogen growth inhibition by 2-bromoethanesulfonate and in the absence of iron supplementation, cis-DCE was not dechlorinated. Further, iron supplementation induced 71.3% dechlorination of cis-DCE accompanied by an increase in Dehalococcoides 16S rRNA and dehalogenase vcrA gene copies but not dehalogenase tceA gene copies. These observations highlight the cooperative effect of iron and methanogens on the reductive dechlorination of chloroethenes by Dehalococcoides spp.
Collapse
Affiliation(s)
- Miho Yoshikawa
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Ming Zhang
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Yoshishige Kawabe
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
| | - Taiki Katayama
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8567, Japan
| |
Collapse
|
34
|
Rupp DL, Lamit LJ, Techtmann SM, Kane ES, Lilleskov EA, Turetsky MR. The Rhizosphere Responds: Rich Fen Peat and Root Microbial Ecology after Long-Term Water Table Manipulation. Appl Environ Microbiol 2021; 87:e0024121. [PMID: 33811029 DOI: 10.1128/AEM.00241-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrologic shifts due to climate change will affect the cycling of carbon (C) stored in boreal peatlands. Carbon cycling in these systems is carried out by microorganisms and plants in close association. This study investigated the effects of experimentally manipulated water tables (lowered and raised) and plant functional groups on the peat and root microbiomes in a boreal rich fen. All samples were sequenced and processed for bacterial, archaeal (16S DNA genes; V4), and fungal (internal transcribed spacer 2 [ITS2]) DNA. Depth had a strong effect on microbial and fungal communities across all water table treatments. Bacterial and archaeal communities were most sensitive to the water table treatments, particularly at the 10- to 20-cm depth; this area coincides with the rhizosphere or rooting zone. Iron cyclers, particularly members of the family Geobacteraceae, were enriched around the roots of sedges, horsetails, and grasses. The fungal community was affected largely by plant functional group, especially cinquefoils. Fungal endophytes (particularly Acephala spp.) were enriched in sedge and grass roots, which may have underappreciated implications for organic matter breakdown and cycling. Fungal lignocellulose degraders were enriched in the lowered water table treatment. Our results were indicative of two main methanogen communities, a rooting zone community dominated by the archaeal family Methanobacteriaceae and a deep peat community dominated by the family Methanomicrobiaceae. IMPORTANCE This study demonstrated that roots and the rooting zone in boreal fens support organisms likely capable of methanogenesis, iron cycling, and fungal endophytic association and are directly or indirectly affecting carbon cycling in these ecosystems. These taxa, which react to changes in the water table and associate with roots and, particularly, graminoids, may gain greater biogeochemical influence, as projected higher precipitation rates could lead to an increased abundance of sedges and grasses in boreal fens.
Collapse
|
35
|
Okada M, Unno H, Emi KI, Matsumoto M, Hemmi H. A versatile cis-prenyltransferase from Methanosarcina mazei catalyzes both C- and O-prenylations. J Biol Chem 2021; 296:100679. [PMID: 33872599 PMCID: PMC8131916 DOI: 10.1016/j.jbc.2021.100679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022] Open
Abstract
Polyprenyl groups, products of isoprenoid metabolism, are utilized in peptidoglycan biosynthesis, protein N-glycosylation, and other processes. These groups are formed by cis-prenyltransferases, which use allylic prenyl pyrophosphates as prenyl-donors to catalyze the C-prenylation of the general acceptor substrate, isopentenyl pyrophosphate. Repetition of this reaction forms (Z,E-mixed)-polyprenyl pyrophosphates, which are converted later into glycosyl carrier lipids, such as undecaprenyl phosphate and dolichyl phosphate. MM_0014 from the methanogenic archaeon Methanosarcina mazei is known as a versatile cis-prenyltransferase that accepts both isopentenyl pyrophosphate and dimethylallyl pyrophosphate as acceptor substrates. To learn more about this enzyme’s catalytic activity, we determined the X-ray crystal structures of MM_0014 in the presence or absence of these substrates. Surprisingly, one structure revealed a complex with O-prenylglycerol, suggesting that the enzyme catalyzed the prenylation of glycerol contained in the crystallization buffer. Further analyses confirmed that the enzyme could catalyze the O-prenylation of small alcohols, such as 2-propanol, expanding our understanding of the catalytic ability of cis-prenyltransferases.
Collapse
Affiliation(s)
- Miyako Okada
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hideaki Unno
- Graduate School of Engineering, Nagasaki University, Nagasaki, Nagasaki, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki, Nagasaki, Japan
| | - Koh-Ichi Emi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Mayuko Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hisashi Hemmi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan.
| |
Collapse
|
36
|
Müller AL, Gu W, Patsalo V, Deutzmann JS, Williamson JR, Spormann AM. An alternative resource allocation strategy in the chemolithoautotrophic archaeon Methanococcus maripaludis. Proc Natl Acad Sci U S A 2021; 118:e2025854118. [PMID: 33879571 DOI: 10.1073/pnas.2025854118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most microorganisms in nature spend the majority of time in a state of slow or zero growth and slow metabolism under limited energy or nutrient flux rather than growing at maximum rates. Yet, most of our knowledge has been derived from studies on fast-growing bacteria. Here, we systematically characterized the physiology of the methanogenic archaeon Methanococcus maripaludis during slow growth. M. maripaludis was grown in continuous culture under energy (formate)-limiting conditions at different dilution rates ranging from 0.09 to 0.002 h-1, the latter corresponding to 1% of its maximum growth rate under laboratory conditions (0.23 h-1). While the specific rate of methanogenesis correlated with growth rate as expected, the fraction of cellular energy used for maintenance increased and the maintenance energy per biomass decreased at slower growth. Notably, proteome allocation between catabolic and anabolic pathways was invariant with growth rate. Unexpectedly, cells maintained their maximum methanogenesis capacity over a wide range of growth rates, except for the lowest rates tested. Cell size, cellular DNA, RNA, and protein content as well as ribosome numbers also were largely invariant with growth rate. A reduced protein synthesis rate during slow growth was achieved by a reduction in ribosome activity rather than via the number of cellular ribosomes. Our data revealed a resource allocation strategy of a methanogenic archaeon during energy limitation that is fundamentally different from commonly studied versatile chemoheterotrophic bacteria such as E. coli.
Collapse
|
37
|
Sogodogo E, Doumbo O, Kouriba B, Aboudharam G. Microbial biodiversity of natural toothbrushes in Mali. New Microbes New Infect 2021; 40:100844. [PMID: 33796319 PMCID: PMC7995651 DOI: 10.1016/j.nmni.2021.100844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/13/2021] [Accepted: 01/20/2021] [Indexed: 11/26/2022] Open
Abstract
Different oral hygiene practices are used to overcome endemic diseases such as dental caries and oral infections. In Mali (Africa), natural plant-based toothbrushes are used for eliminating bacterial biofilm. The repertoire of microorganisms associated with natural toothbrushes is unknown. The aim of our study is to study microbial flora in particular the methanogenic archaea associated with natural toothbrushes recently recognized as responsible for periodontitis and peri-implantitis. We investigated the methanogens and bacteria associated with 15 different natural plant toothbrushes collected in Bamako local market (Mali). Microbiological investigations consisted in culturing the bacteria on agar plates and searching archaea using molecular techniques. No archaea were demonstrated by molecular biology but 50 bacterial species, including 33 aero-anaerobic and 17 aerobic species, were isolated from natural toothbrushes. We isolated Pseudomonas sp., Staphylococcus sp. and Klebsiella pneumoniae, which are acknowledged as opportunistic human pathogens. This study has highlighted the likely impact of the use of natural toothbrushes in the spread of potentially pathogenic bacteria in the human oral cavity.
Collapse
Affiliation(s)
- E Sogodogo
- Aix Marseille Université. IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - O Doumbo
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - B Kouriba
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali.,Centre d'infectiologie Charles-Mérieux (CICM), Bamako, Mali
| | - G Aboudharam
- Aix Marseille Université. IRD, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille Université, UFR Odontology, Marseille, France
| |
Collapse
|
38
|
Susanti D, Frazier MC, Mukhopadhyay B. Corrigendum: A Genetic System for Methanocaldococcus jannaschii: An Evolutionary Deeply Rooted Hyperthermophilic Methanarchaeon. Front Microbiol 2021; 12:649127. [PMID: 33767687 PMCID: PMC7986713 DOI: 10.3389/fmicb.2021.649127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 01/26/2021] [Indexed: 11/23/2022] Open
Affiliation(s)
- Dwi Susanti
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Mary C Frazier
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States.,Biocomplexity Institute, Virginia Tech, Blacksburg, VA, United States.,Virginia Tech Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
| |
Collapse
|
39
|
McDaniel MD, Hernández M, Dumont MG, Ingram LJ, Adams MA. Disproportionate CH 4 Sink Strength from an Endemic, Sub-Alpine Australian Soil Microbial Community. Microorganisms 2021; 9:606. [PMID: 33804229 DOI: 10.3390/microorganisms9030606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/27/2021] [Accepted: 03/09/2021] [Indexed: 11/17/2022] Open
Abstract
Soil-to-atmosphere methane (CH4) fluxes are dependent on opposing microbial processes of production and consumption. Here we use a soil–vegetation gradient in an Australian sub-alpine ecosystem to examine links between composition of soil microbial communities, and the fluxes of greenhouse gases they regulate. For each soil/vegetation type (forest, grassland, and bog), we measured carbon dioxide (CO2) and CH4 fluxes and their production/consumption at 5 cm intervals to a depth of 30 cm. All soils were sources of CO2, ranging from 49 to 93 mg CO2 m−2 h−1. Forest soils were strong net sinks for CH4, at rates of up to −413 µg CH4 m−2 h−1. Grassland soils varied, with some soils acting as sources and some as sinks, but overall averaged −97 µg CH4 m−2 h−1. Bog soils were net sources of CH4 (+340 µg CH4 m−2 h−1). Methanotrophs were dominated by USCα in forest and grassland soils, and Candidatus Methylomirabilis in the bog soils. Methylocystis were also detected at relatively low abundance in all soils. Our study suggests that there is a disproportionately large contribution of these ecosystems to the global soil CH4 sink, which highlights our dependence on soil ecosystem services in remote locations driven by unique populations of soil microbes. It is paramount to explore and understand these remote, hard-to-reach ecosystems to better understand biogeochemical cycles that underpin global sustainability.
Collapse
|
40
|
Aldridge J, Carr S, Weber KA, Buan NR. Anaerobic Production of Isoprene by Engineered Methanosarcina Species Archaea. Appl Environ Microbiol 2021; 87:e02417-20. [PMID: 33452028 DOI: 10.1128/AEM.02417-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/25/2020] [Indexed: 01/14/2023] Open
Abstract
Isoprene is a valuable petrochemical used for a wide variety of consumer goods, such as adhesives and synthetic rubber. We were able to achieve a high yield of renewable isoprene by taking advantage of the naturally high-flux mevalonate lipid synthesis pathway in anaerobic methane-producing archaea (methanogens). Our study illustrates that by genetically manipulating Methanosarcina species methanogens, it is possible to create organisms that grow by producing the hemiterpene isoprene. Mass balance measurements show that engineered methanogens direct up to 4% of total carbon flux to isoprene, demonstrating that methanogens produce higher isoprene yields than engineered yeast, bacteria, or cyanobacteria, and from inexpensive feedstocks. Expression of isoprene synthase resulted in increased biomass and changes in gene expression that indicate that isoprene synthesis depletes membrane precursors and redirects electron flux, enabling isoprene to be a major metabolic product. Our results demonstrate that methanogens are a promising engineering chassis for renewable isoprene synthesis.IMPORTANCE A significant barrier to implementing renewable chemical technologies is high production costs relative to those for petroleum-derived products. Existing technologies using engineered organisms have difficulty competing with petroleum-derived chemicals due to the cost of feedstocks (such as glucose), product extraction, and purification. The hemiterpene monomer isoprene is one such chemical that cannot currently be produced using cost-competitive renewable biotechnologies. To reduce the cost of renewable isoprene, we have engineered methanogens to synthesize it from inexpensive feedstocks such as methane, methanol, acetate, and carbon dioxide. The "isoprenogen" strains we developed have potential to be used for industrial production of inexpensive renewable isoprene.
Collapse
|
41
|
Solomon J, Rasekh MF, Hiller CJ, Lee CC, Tanifuji K, Ribbe MW, Hu Y. Probing the All-Ferrous States of Methanogen Nitrogenase Iron Proteins. JACS Au 2021; 1:119-123. [PMID: 34467276 PMCID: PMC8395668 DOI: 10.1021/jacsau.0c00072] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Fe protein of nitrogenase reduces two C1 substrates, CO2 and CO, under ambient conditions when its [Fe4S4] cluster adopts the all-ferrous [Fe4S4]0 state. Here, we show disparate reactivities of the nifH- and vnf-encoded Fe proteins from Methanosarcina acetivorans (designated MaNifH and MaVnfH) toward C1 substrates in the all-ferrous state, with the former capable of reducing both CO2 and CO to hydrocarbons, and the latter only capable of reducing CO to hydrocarbons at substantially reduced yields. EPR experiments conducted at varying solution potentials reveal that MaVnfH adopts the all-ferrous state at a more positive reduction potential than MaNifH, which could account for the weaker reactivity of the MaVnfH toward C1 substrates than MaNifH. More importantly, MaVnfH already displays the g = 16.4 parallel-mode EPR signal that is characteristic of the all-ferrous [Fe4S4]0 cluster at a reduction potential of -0.44 V, and the signal reaches 50% maximum intensity at a reduction potential of -0.59 V, suggesting the possibility of this Fe protein to access the all-ferrous [Fe4S4]0 state under physiological conditions. These results bear significant relevance to the long-lasting debate of whether the Fe protein can utilize the [Fe4S4]0/2+ redox couple to support a two-electron transfer during substrate turnover which, therefore, is crucial for expanding our knowledge of the reaction mechanism of nitrogenase and the cellular energetics of nitrogenase-based processes.
Collapse
Affiliation(s)
- Joseph
B. Solomon
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Mahtab F. Rasekh
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Caleb J. Hiller
- Department
of Physical Science, Southern Utah University, Cedar City, Utah 84720, United States
| | - Chi Chung Lee
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
| | - Kazuki Tanifuji
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
| | - Markus W. Ribbe
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697-3900, United States
| |
Collapse
|
42
|
Wang H, Larson RA, Borchardt M, Spencer S. Effect of mixing duration on biogas production and methanogen distribution in an anaerobic digester. Environ Technol 2021; 42:93-99. [PMID: 31159681 DOI: 10.1080/09593330.2019.1621951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Mixing has been shown to have effect on biogas production in anaerobic digestion systems. To further examine this impact, a study was designed to evaluate nearly continuous mixing (mixing for 15 min followed by no mixing for 15 min, CON), intermediate mixing (mixing for 15 min followed by no mixing for 45 min, INT) and no mixing (unmixed, NO) on biogas production in three 208 L pilot-scale tank reactors. The experiments were conducted in triplicates at a controlled temperature of 37 ± 1°C, with a total solids percentage of 5%, a hydraulic retention time (HRT) of 21 days, and an organic loading rate (OLR) of 2 kg VS m-3 d- 1. Digesters with NO mixing had greater solids build up in the bottom quarter of the digester after four weeks' retention time. The methane percentage in biogas produced from digesters with INT and CON mixing were 63% and 62%, respectively, which were 4% and 5% higher than that from digesters with NO mixing (58%). The specific methane yield for digesters with NO, INT and CON mixing was 1.15, 1.15, and 1.49 m3-methane per kg-VS destroyed, however, those differences were not statistically significant (p > 0.05). Digesters had the least amount of Methanosarcinales of the methanogens measured under all treatments. However, the Methanosarcinales, Methanosarcinaceae, Methanomicrobiales, and the total amount of methanogens were less in digesters with INT mixing compared to NO and CON mixing treatments.
Collapse
Affiliation(s)
- Hui Wang
- Department of Biological Systems Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Rebecca A Larson
- Department of Biological Systems Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Mark Borchardt
- USDA Agricultural Research Service - Institute for Environmentally Integrated Dairy Management, Marshfield, WI, USA
| | - Susan Spencer
- USDA Agricultural Research Service - Institute for Environmentally Integrated Dairy Management, Marshfield, WI, USA
| |
Collapse
|
43
|
Christman GD, León-Zayas RI, Summers ZM, Biddle JF. Methanogens Within a High Salinity Oil Reservoir From the Gulf of Mexico. Front Microbiol 2020; 11:570714. [PMID: 33042074 PMCID: PMC7530209 DOI: 10.3389/fmicb.2020.570714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/26/2020] [Indexed: 11/18/2022] Open
Abstract
Oil reservoirs contain microbial populations that are both autochthonously and allochthonously introduced by industrial development. These microbial populations are greatly influenced by external factors including, but not limited to, salinity and temperature. In this study, we used metagenomics to examine the microbial populations within five wells of the same hydrocarbon reservoir system in the Gulf of Mexico. These elevated salinity (149–181 ppt salinity, 4–5× salinity of seawater) reservoirs have limited taxonomic and functional microbial diversity dominated by methanogens, Halanaerobium and other Firmicutes lineages, and contained less abundant lineages such as Deltaproteobacteria. Metagenome assembled genomes (MAGs) were generated and analyzed from the various wells. Methanogen MAGs were closely related to Methanohalophilus euhalobius, a known methylotrophic methanogen from a high salinity oil environment. Based on metabolic reconstruction of genomes, the Halanaerobium perform glycine betaine fermentation, potentially produced by the methanogens. Industrial introduction of methanol to prevent methane hydrate formation to this environment is likely to be consumed by these methanogens. As such, this subsurface oil population may represent influences from industrial processes.
Collapse
Affiliation(s)
- Glenn D Christman
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Rosa I León-Zayas
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States.,Department of Biology, Willamette University, Salem, OR, United States
| | - Zarath M Summers
- ExxonMobil Research & Engineering Company, Annandale, NJ, United States
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| |
Collapse
|
44
|
Shen Y, Chen SC, Lai MC, Huang HH, Chiu HH, Tang SL, Rogozin DY, Degermendzhy AG. Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia. Int J Syst Evol Microbiol 2020; 70:5586-5593. [PMID: 32915124 DOI: 10.1099/ijsem.0.004453] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A halotolerant, psychrotolerant and methylotrophic methanogen, strain SY-01T, was isolated from the saline Lake Tus in Siberia. Cells of strain SY-01T were non-motile, cocci and 0.8-1.0 µm in diameter. The only methanogenic substrate utilized by strain SY-01T was methanol. The temperature range of growth for strain SY-01T was from 4 to 40 °C and the optimal temperature for growth was 30 °C. The pH range of growth was from pH 7.2 to 9.0, with optimal growth at pH 8.0. The NaCl range of growth was 0-1.55 M with optimal growth at 0.51 M NaCl. The G+C content of the genome of strain SY-01T was 43.6 mol % as determined by genome sequencing. Phylogenetic analysis revealed that strain SY-01T was most closely related to Methanolobus zinderi SD1T (97.3 % 16S rRNA gene sequence similarity), and had 95.5-97.2 % similarities to other Methanolobus species with valid names. Genome relatedness between strain SY-01T and DSM 21339T was computed using average nucleotide identity and digital DNA-DNAhybridization, which yielded values of 79.7 and 21.7 %, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain SY-01T represents a novel species of the genus Methanolobus, and the name Methanolobus halotolerans sp. nov. is proposed. The type strain is SY-01T (=BCRC AR10051T=NBRC 113166 T=DSM 107642T).
Collapse
Affiliation(s)
- Ya Shen
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Sheng-Chung Chen
- Department of Life Science, National Chung Hsing University, Taiwan, ROC.,Fujian Provincial Key Laboratory of Resources and Environmental Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian 365004, PR China.,School of Resources and Chemical Engineering, Sanming University, Sanming, Fujian 365004, PR China
| | - Mei-Chin Lai
- Department of Life Science, National Chung Hsing University, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taiwan, ROC
| | - Hsing-Hua Huang
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taiwan, ROC
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taiwan, ROC
| | - Denis Yu Rogozin
- Siberian Federal University, Krasnoyarsk 660041, Russia.,Institute of Biophysics Siberian Branch of Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| | - Andrey G Degermendzhy
- Siberian Federal University, Krasnoyarsk 660041, Russia.,Institute of Biophysics Siberian Branch of Russian Academy of Sciences, Krasnoyarsk 660036, Russia
| |
Collapse
|
45
|
Chen SC, Teng NH, Lin YS, Lai MC, Chen HH, Wang CC. Methanofollis fontis sp. nov., a methanogen isolated from marine sediment near a cold seep at Four-Way Closure Ridge offshore southwestern Taiwan. Int J Syst Evol Microbiol 2020; 70:5497-5502. [PMID: 32897849 DOI: 10.1099/ijsem.0.004440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, hydrogenotrophic methanogen, strain FWC-SCC2T, was isolated from deep-sea sediments collected by a real-time video multiple-corer at the C5-6 station near a cold seep at Four-Way Closure Ridge region during R/V Ocean Researcher III ORIII-1900 cruise in 2015. The cells were irregular cocci, non-motile and 0.8-1.2 µm in diameter. The methanogenic substrates utilized by strain FWC-SCC2T were formate or H2+CO2, but not acetate, methanol, ethanol or methylamines. Strain FWC-SCC2T was lysed in SDS (0.01 %, w/v). The M r of surface-layer protein was 116 400. The optimum growth conditions of strain FWC-SCC2T were 37 °C, 0.17 M NaCl and pH 6.7-7.0. The genomic DNA G+C content calculated from the genome sequence of strain FWC-SCC2T was 59.5 mol %. Phylogenetic analysis revealed that strain FWC-SCC2T was a member of the genus Methanofollis, and was most closely related to Methanofollis tationis Chile 9T (97.6 % similarity of 16S rRNA gene sequence) and shared 97.4, 95.9, 95.9 and 95.4 % with Methanofollis liminatans GKZPZT, Methanofollis formosanus ML15T, Methanofollis aquaemaris N2F9704T and Methanofollis ethanolicus HASUT, respectively. The genome relatedness values between strain FWC-SCC2T and M. tationis DSM 2702T were estimated by average nucleotide identity and digital DNA-DNA hybridization analyses and the results were 79.4 and 21.2 %, respectively. Based on the differences in physiological and biochemical properties, 16S rRNA gene phylogeny and genome relatedness presented here, it is suggested that strain FWC-SCC2T represents a novel species of the genus Methanofollis, and the name Methanofollis fontis sp. nov. is proposed. The type strain is FWC-SCC2T (=BCRC AR10052T=DSM 107935T= NBRC 113164T).
Collapse
Affiliation(s)
- Sheng-Chung Chen
- School of Resources and Chemical Engineering, Sanming University, Sanming City, Fujian, PR China.,Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Nai-Hsuan Teng
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Yu-Shih Lin
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Mei-Chin Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, ROC.,Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan, ROC
| | - Hsin-Hung Chen
- Institute of Undersea Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Chau-Chang Wang
- Institute of Undersea Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| |
Collapse
|
46
|
Li Y, Hou Z, Shi Q, Cheng Y, Zhu W. Methane Production From Different Parts of Corn Stover via a Simple Co-culture of an Anaerobic Fungus and Methanogen. Front Bioeng Biotechnol 2020; 8:314. [PMID: 32426337 PMCID: PMC7204275 DOI: 10.3389/fbioe.2020.00314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/23/2020] [Indexed: 12/27/2022] Open
Abstract
To determine ways to improve the utilization of corn stover, this study investigated methane production from different parts of corn stover using a simple co-culture of an anaerobic fungus (Pecoramyces species) and methanogen (Methanobrevibacter species). The simple co-culture was incubated with the stem pith, leaf blade, or stem bark of corn stover (as substrates) at 39°C for 72 h. The results showed that the stem bark had the lowest (P < 0.05) digestibility (38.0 ± 1.36%) and neutral detergent solubles, that is, cell solubles (31.6 ± 0.45%), and the highest (P < 0.05) lignin content (4.8 ± 0.56%). The leaf blade had a significantly higher methane conversion rate (56.6 ± 0.76 mL/g digested substrate) than the stem pith (49.2 ± 1.60 mL/g digested substrate), even though they showed similar levels of methane production (42.4 ± 1.0 mL and 40.9 ± 1.35 mL, respectively). Both the leaf blade and stem pith of corn stover have the potential to produce methane in a simple co-culture of an anaerobic fungus and methanogen.
Collapse
Affiliation(s)
- Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| | - Zhesheng Hou
- College of Mechanical and Electrical Engineering, Jilin Institute of Chemical Technology, Jilin, China
| | - Qicheng Shi
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing, China.,Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agriculture University, Nanjing, China
| |
Collapse
|
47
|
An BA, Kleinbub S, Ozcan O, Koerdt A. Iron to Gas: Versatile Multiport Flow-Column Revealed Extremely High Corrosion Potential by Methanogen-Induced Microbiologically Influenced Corrosion (Mi-MIC). Front Microbiol 2020; 11:527. [PMID: 32296410 PMCID: PMC7136402 DOI: 10.3389/fmicb.2020.00527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/11/2020] [Indexed: 01/01/2023] Open
Abstract
Currently, sulfate-reducing bacteria (SRB) is regarded as the main culprit of microbiologically influenced corrosion (MIC), mainly due to the low reported corrosion rates of other microorganisms. For example, the highest reported corrosion rate for methanogens is 0.065 mm/yr. However, by investigating methanogen-induced microbiologically influenced corrosion (Mi-MIC) using an in-house developed versatile multiport flow test column, extremely high corrosion rates were observed. We analyzed a large set of carbon steel beads, which were sectionally embedded into the test columns as substrates for iron-utilizing methanogen Methanobacterium IM1. After 14 days of operation using glass beads as fillers for section separation, the highest average corrosion rate of Methanobacterium IM1 was 0.2 mm/yr, which doubled that of Desulfovibrio ferrophilus IS5 and Desulfovibrio alaskensis 16109 investigated at the same conditions. At the most corroded region, nearly 80% of the beads lost 1% of their initial weight (fast-corrosion), resulting in an average corrosion rate of 0.2 mm/yr for Methanobacterium IM1-treated columns. When sand was used as filler material to mimic sediment conditions, average corrosion rates for Methanobacterium IM1 increased to 0.3 mm/yr (maximum 0.52 mm/yr) with over 83% of the beads having corrosion rates above 0.3 mm/yr. Scanning electron images of metal coupons extracted from the column showed methanogenic cells were clustered close to the metal surface. Methanobacterium IM1 is a hydrogenotrophic methanogen with higher affinity to metal than H2. Unlike SRB, Methanobacterium IM1 is not restricted to the availability of sulfate concentration in the environment. Thus, the use of the multiport flow column provided a new insight on the corrosion potential of methanogens, particularly in dynamic conditions, that offers new opportunities for monitoring and development of mitigation strategies. Overall, this study shows (1) under certain conditions methanogenic archaea can cause higher corrosion than SRB, (2) specific quantifications, i.e., maximum, average, and minimum corrosion rates can be determined, and (3) that spatial statistical evaluations of MIC can be carried out.
Collapse
Affiliation(s)
| | | | | | - Andrea Koerdt
- Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
| |
Collapse
|
48
|
Gilbert RA, Townsend EM, Crew KS, Hitch TCA, Friedersdorff JCA, Creevey CJ, Pope PB, Ouwerkerk D, Jameson E. Rumen Virus Populations: Technological Advances Enhancing Current Understanding. Front Microbiol 2020; 11:450. [PMID: 32273870 PMCID: PMC7113391 DOI: 10.3389/fmicb.2020.00450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/02/2020] [Indexed: 01/07/2023] Open
Abstract
The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often out-numbering the microbial populations that they both predate on and co-exist with. To date the research effort devoted to understanding rumen-associated viral populations has been considerably less than that given to the other microbial populations, yet their contribution to maintaining microbial population balance, intra-ruminal microbial lysis, fiber breakdown, nutrient cycling and genetic transfer may be highly significant. This review follows the technological advances which have contributed to our current understanding of rumen viruses and drawing on knowledge from other environmental and animal-associated microbiomes, describes the known and potential roles and impacts viruses have on rumen function and speculates on the future directions of rumen viral research.
Collapse
Affiliation(s)
- Rosalind A. Gilbert
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor M. Townsend
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Kathleen S. Crew
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
| | - Thomas C. A. Hitch
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Jessica C. A. Friedersdorff
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Christopher J. Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Phillip B. Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Diane Ouwerkerk
- Department of Agriculture and Fisheries, Brisbane, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eleanor Jameson
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| |
Collapse
|
49
|
Yoshida R, Yoshimura T, Hemmi H. Reconstruction of the "Archaeal" Mevalonate Pathway from the Methanogenic Archaeon Methanosarcina mazei in Escherichia coli Cells. Appl Environ Microbiol 2020; 86:e02889-19. [PMID: 31924615 DOI: 10.1128/AEM.02889-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022] Open
Abstract
The mevalonate pathway is a well-known metabolic route that provides biosynthetic precursors for myriad isoprenoids. An unexpected variety of the pathway has been discovered from recent studies on microorganisms, mainly on archaea. The most recently discovered example, called the "archaeal" mevalonate pathway, is a modified version of the canonical eukaryotic mevalonate pathway and was elucidated in our previous study using the hyperthermophilic archaeon Aeropyrum pernix This pathway comprises four known enzymes that can produce mevalonate 5-phosphate from acetyl coenzyme A, two recently discovered enzymes designated phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase, and two more known enzymes, i.e., isopentenyl phosphate kinase and isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase. To show its wide distribution in archaea and to confirm if its enzyme configuration is identical among species, the putative genes of a lower portion of the pathway-from mevalonate to isopentenyl pyrophosphate-were isolated from the methanogenic archaeon Methanosarcina mazei, which is taxonomically distant from A. pernix, and were introduced into an engineered Escherichia coli strain that produces lycopene, a red carotenoid pigment. Lycopene production, as a measure of isoprenoid productivity, was enhanced when the cells were grown semianaerobically with the supplementation of mevalonolactone, which demonstrates that the archaeal pathway can function in bacterial cells to convert mevalonate into isopentenyl pyrophosphate. Gene deletion and complementation analysis using the carotenogenic E. coli strain suggests that both phosphomevalonate dehydratase and anhydromevalonate phosphate decarboxylase from M. mazei are required for the enhancement of lycopene production.IMPORTANCE Two enzymes that have recently been identified from the hyperthermophilic archaeon A. pernix as components of the archaeal mevalonate pathway do not require ATP for their reactions. This pathway, therefore, might consume less energy than other mevalonate pathways to produce precursors for isoprenoids. Thus, the pathway might be applicable to metabolic engineering and production of valuable isoprenoids that have application as pharmaceuticals. The archaeal mevalonate pathway was successfully reconstructed in E. coli cells by introducing several genes from the methanogenic or hyperthermophilic archaeon, which demonstrated that the pathway requires the same components even in distantly related archaeal species and can function in bacterial cells.
Collapse
|
50
|
Boyd ES, Amenabar MJ, Poudel S, Templeton AS. Bioenergetic constraints on the origin of autotrophic metabolism. Philos Trans A Math Phys Eng Sci 2020; 378:20190151. [PMID: 31902344 PMCID: PMC7015307 DOI: 10.1098/rsta.2019.0151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/02/2019] [Indexed: 06/07/2023]
Abstract
Autotrophs form the base of all complex food webs and seemingly have done so since early in Earth history. Phylogenetic evidence suggests that early autotrophs were anaerobic, used CO2 as both an oxidant and carbon source, were dependent on H2 as an electron donor, and used iron-sulfur proteins (termed ferredoxins) as a primary electron carrier. However, the reduction potential of H2 is not typically low enough to efficiently reduce ferredoxin. Instead, in modern strictly anaerobic and H2-dependent autotrophs, ferredoxin reduction is accomplished using one of several recently evolved enzymatic mechanisms, including electron bifurcating and coupled ion translocating mechanisms. These observations raise the intriguing question of why anaerobic autotrophs adopted ferredoxins as central electron carriers only to have to evolve complex machinery to reduce them. Here, we report calculated reduction potentials for H2 as a function of observed environmental H2 concentration, pH and temperature. Results suggest that a combination of alkaline pH and high H2 concentration yield H2 reduction potentials low enough to efficiently reduce ferredoxins. Hyperalkaline, H2 rich environments have existed in discrete locations throughout Earth history where ultramafic minerals are undergoing hydration through the process of serpentinization. These results suggest that serpentinizing systems, which would have been common on early Earth, naturally produced conditions conducive to the emergence of H2-dependent autotrophic life. The primitive process of hydrogenotrophic methanogenesis is used to examine potential changes in methanogenesis and Fd reduction pathways as these organisms diversified away from serpentinizing environments. This article is part of a discussion meeting issue 'Serpentinite in the earth system'.
Collapse
Affiliation(s)
- Eric S. Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | | | - Saroj Poudel
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Alexis S. Templeton
- Department of Geological Sciences, University of Colorado, Boulder, CO 80309, USA
| |
Collapse
|