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Yi Y, Dolfing J, Jin G, Fang X, Han W, Liu L, Tang Y, Cheng L. Thermodynamic restrictions determine ammonia tolerance of methanogenic pathways in Methanosarcina barkeri. WATER RESEARCH 2023; 232:119664. [PMID: 36775717 DOI: 10.1016/j.watres.2023.119664] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 06/18/2023]
Abstract
Ammonia is a ubiquitous potential inhibitor of anaerobic digestion processes, mainly exhibiting inhibition towards methanogenic activity. However, knowledge as to how ammonia affects the methanogens is still limited. In this study, we cultured a multitrophic methanogen, Methanosarcina barkeri DSM 800, with acetate, H2/CO2, and methanol to evaluate the influence of ammonia on different methanogenic pathways. Aceticlastic methanogenesis was more sensitive to increased ammonia concentrations than hydrogenotrophic and methylotrophic methanogenesis. Theoretical maximum NH3 tolerances of M. barkeri fed with acetate, H2/CO2, and methanol were calculated to be 39.1 ± 9.0, 104.3 ± 7.4, and 85.7 ± 1.0 mg/L, respectively. The order of the ΔG range of M. barkeri under three methanogenic pathways reflected the order of ammonia tolerance of M. barkeri. Our results provide insights into the role of the thermodynamic potential of methanogenesis on the tolerance of ammonia stress; and shed light on the mechanism of ammonia inhibition on anaerobic digestion.
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Affiliation(s)
- Yue Yi
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China; College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Wynne Jones 2.11, Ellison Place, Newcastle-upon-Tyne NE1 8QH, UK
| | - Ge Jin
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - XiaoYu Fang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - WenHao Han
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - LaiYan Liu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China
| | - YueQin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China.
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin South Road, Chengdu, Sichuan 610041, China.
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2
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Feng G, Zeng Y, Wang HZ, Chen YT, Tang YQ. Proteiniphilum and Methanothrix harundinacea became dominant acetate utilizers in a methanogenic reactor operated under strong ammonia stress. Front Microbiol 2023; 13:1098814. [PMID: 36687577 PMCID: PMC9853277 DOI: 10.3389/fmicb.2022.1098814] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023] Open
Abstract
Microorganisms in anaerobic digestion (AD) are easily affected by ammonia, especially acetoclastic methanogens. Thus, in ammonia-suppressed AD systems, acetate degradation is reported to be carried out mainly by the cooperation of syntrophic acetate oxidizers and hydrogenotrophic methanogens. Previous studies have revealed ammonia inhibition on microbial flora by AD performance, but the effect mechanism of ammonia on microbial metabolism remains poorly understood. In this study, we constructed a mesophilic chemostat fed with acetate as the sole carbon source, gradually increased the total ammonia nitrogen (TAN) concentration from 1 g L-1 to 6 g L-1, and employed the 16S rRNA gene, metagenomics, and metatranscriptomics analysis to characterize the microbial community structure and metabolic behavior. The results showed that even at the TAN of 6 g L-1 (pH 7.5), the methanogenesis kept normal, the biogas production was approximately 92% of that at TAN of 1 g L-1 and the acetate degradation ratio reached 99%, suggesting the strong TAN tolerance of the microbial community enriched. 16S rRNA gene analysis suggested that the microbial community structure changed along with the TAN concentration. Methanothrix predominated in methanogens all the time, in which the dominant species was gradually replaced from M. soehngenii to M. harundinacea with the increased TAN. Dominant bacterial species also changed and Proteiniphilum showed a significant positive correlation with increased TAN. Meta-omics analysis showed that the absolute dominant microorganisms at TAN of 6 g L-1 were M. harundinacea and Proteiniphilum, both of which highly expressed genes for anti-oxidative stress. M. harundinacea and the second dominant methanogen Methanosarcina highly expressed both acetate cleavage and CO2 reduction pathways, suggesting the possibility that these two pathways contributed to methanogenesis together. Proteiniphilum and some other species in Firmicutes and Synergistetes were likely acetate oxidizers in the community as they highly expressed genes for syntrophic acetate oxidization, H2 generation, and electron transfer. These results suggested that Proteiniphilum as well as M. harundinacea have strong ammonia tolerance and played critical roles in acetate degradation under ammonia-suppressed conditions. The achievements of the study would contribute to the regulation and management of the AD process.
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Affiliation(s)
- Gao Feng
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Yan Zeng
- Institute of New Energy and Low-Carbon Technology, Sichuan University, Chengdu, Sichuan, China
| | - Hui-Zhong Wang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China
| | - Ya-Ting Chen
- Institute for Disaster Management and Reconstruction, Sichuan University, Chengdu, Sichuan, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, Sichuan, China,Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, Chengdu, Sichuan, China,Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, Chengdu, Sichuan, China,*Correspondence: Yue-Qin Tang,
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3
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Xie R, Takashino M, Igarashi K, Kitagawa W, Kato S. Transcriptional Regulation of Methanol Dehydrogenases in the Methanotrophic Bacterium Methylococcus capsulatus Bath by Soluble and Insoluble Lanthanides. Microbes Environ 2023; 38:ME23065. [PMID: 38092408 PMCID: PMC10728633 DOI: 10.1264/jsme2.me23065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023] Open
Abstract
The effects of soluble and insoluble lanthanides on gene expression in Methylococcus capsulatus Bath were investigated. Genes for lanthanide-containing methanol dehydrogenases (XoxF-MDHs) and their calcium-containing counterparts (MxaFI-MDHs) were up- and down-regulated, respectively, by supplementation with soluble lanthanide chlorides, indicating that M. capsulatus has the "lanthanide switch" observed in other methanotrophs. Insoluble lanthanide oxides also induced the lanthanide switch and were dissolved by the spent medium of M. capsulatus, suggesting the presence of lanthanide-chelating compounds. A transcriptome ana-lysis indicated that a gene cluster for the synthesis of an enterobactin-like metal chelator contributed to the dissolution of insoluble lanthanides.
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Affiliation(s)
- Ruoyun Xie
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060–8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Wataru Kitagawa
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060–8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
| | - Souichiro Kato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060–8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 2–17–2–1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062–8517, Japan
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4
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Jo Y, Cayetano RDA, Kim GB, Park J, Kim SH. The effects of ammonia acclimation on biogas recovery and the microbial population in continuous anaerobic digestion of swine manure. ENVIRONMENTAL RESEARCH 2022; 212:113483. [PMID: 35588770 DOI: 10.1016/j.envres.2022.113483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
This study investigated the ammonia toxicity and the acclimation of anaerobic microbiome in continuous anaerobic digestion of swine manure using unacclimated inoculum. When the total ammonia nitrogen concentration (TAN) reached 2.5 g N/L, the methane yield decreased from 254.1 ± 9.6 to 154.6 ± 9.9 mL/g COD. The free ammonia nitrogen concentration of the inhibited condition was 190 mg N/L. The methane yield was eventually recovered as 269.6 ± 3.6 mL/g COD with a further operation. Anaerobic toxicity assay (ATA) showed that mixed liquor from the recovered phase possessed enhanced tolerance to ammonia, not only within the exposed level in continuous operation (<2.5 g NH3/L) but also over the range (>2.5 g NH3/L). Microbial analysis revealed that continuous operation under ammonia stress resulted in the change of both bacterial and archaeal populations. The ammonia adaptation was concurrent with the archaeal population shift from Methanosaeta to Methanosarcina and Methanobacterium. The dominancy of Clostridia in bacterial population was found in the recovered phase. It is highly recommended to use an inoculum acclimated to a target ammonia level which can be pre-checked by ATA and to secure a start-up period for ammonia adaptation in the field application of anaerobic digestion for swine manure.
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Affiliation(s)
- Yura Jo
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Roent Dune A Cayetano
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Gi-Beom Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jungsu Park
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea.
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5
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Lopes HDFS, Tu Z, Sumi H, Yumoto I. Indigofera tinctoria L. leaf powder promotes initiation of indigo reduction by inducing of rapid transition of the microbial community. Front Microbiol 2022; 13:957809. [PMID: 36016790 PMCID: PMC9395713 DOI: 10.3389/fmicb.2022.957809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Water-insoluble indigo is solubilized by the reducing action of microorganisms which occurs during fermentation. In natural indigo fermentation, composted leaves of Polygonum tinctorium L. (sukumo) are the raw material that has been used as both the indigo source and the bacterial inoculum. Ideally, indigo reduction occurs shortly after preparation of the fermentation vat. The time-to-reduction depends on the quality of the sukumo and the methods for preparation and management of the fermentation batch. We estimated the effect of adding Indigofera tinctoria L. leaf powder (LP) to indigo fermentation in two fermentations originally exhibiting either rapid or slow time-to-reduction (T-sukumo and D-sukumo, respectively). Alkalihalobacillus spp. (97.7%–98.4% similarities with Alkalihalobacillus macyae) were observed only in the LP-added T-sukumo fermentation liquor. They appeared from day 1 (0.7%) and increased to 24.4% on day 6, and their presence was related to indigo reduction. Differences in functional ratio between LP-added and its control batches revealed enhancement of pathways related to reconstitution of cellular functions and substrate metabolisms, to all of which Alkalihalobacillus spp. contributed intensively. In D-sukumo batch, appearance of bacteria necessary to initiate indigo reduction (principally Anaerobacillus/Polygonibacillus) was comparatively slower. LP promotes earlier indigo reduction in both T- and D-sukumo-based batches, owing to its promotion of microbiota transition. The effect of the LP was intensified from day 1 to day 2 in both sukumo using batches according to the assumed function of the microbiota. The initial effect of LP on the T-sukumo batches was more intense than that in the D-sukumo batches and was continued until day 3, while the duration in the T-sukumo batches was continued until day 5. Based on these observations, we propose that the LP functions through its phytochemicals that eliminate oxygen, stimulate the microbiota, and accelerate its transitional changes toward a suitable function that opens the pathway for the extracellular electron transfer using carbohydrates as a substrate.
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Affiliation(s)
- Helena de Fátima Silva Lopes
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Zhihao Tu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hisako Sumi
- North-Indigo Textile Arts Studio, Otaru, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Laboratory of Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- *Correspondence: Isao Yumoto,
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Ye M, Zhu A, Sun B, Qin Y, Li YY. Methanogenic treatment of dairy product wastewater by thermophilic anaerobic membrane bioreactor: Ammonia inhibition and microbial community. BIORESOURCE TECHNOLOGY 2022; 357:127349. [PMID: 35605772 DOI: 10.1016/j.biortech.2022.127349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Dairy product wastewater contains high-strength organic matter suitable for anaerobic treatment, but excessive protein degradation may lead to an ammonia inhibition problem. This work studied protein-rich dairy product wastewater treatment in the anaerobic membrane bioreactor. The results showed that a temporary self-detoxification phase of ammonia inhibition from the change of pH buffer system was vital for rapid reactor recovery by substrate dilution. The ammonia washout from the reactor was simulated by a kinetic model. After ammonia inhibition, the relative abundance of syntrophic lactic and propionic acids oxidising bacteria significantly reduced along with fermentative bacteria involved in mixed organic acids production. Nevertheless, the relative abundance of the protein degradation bacteria producing acetic acid and H2/CO2 increased. A potential metabolic process change was proposed by profiling the functional community. To conclude, substrate dilution is essential for overcoming ammonia inhibition in the anaerobic treatment of protein-rich dairy product wastewater.
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Affiliation(s)
- Min Ye
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Aijun Zhu
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Borchen Sun
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu Qin
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aza, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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7
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Duan H, He P, Zhang H, Shao L, Lü F. Metabolic Regulation of Mesophilic Methanosarcina barkeri to Ammonium Inhibition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:8897-8907. [PMID: 35588324 DOI: 10.1021/acs.est.2c01212] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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.
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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
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Liu C, Huang H, Duan X, Chen Y. Integrated Metagenomic and Metaproteomic Analyses Unravel Ammonia Toxicity to Active Methanogens and Syntrophs, Enzyme Synthesis, and Key Enzymes in Anaerobic Digestion. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:14817-14827. [PMID: 34657430 DOI: 10.1021/acs.est.1c00797] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
During anaerobic digestion, the active microbiome synthesizes enzymes by transcription and translation, and then enzymes catalyze multistep bioconversions of substrates before methane being produced. However, little information is available on how ammonia affects truly active microbes containing the expressed enzymes, enzyme synthesis, and key enzymes. In this study, an integrated metagenomic and metaproteomic investigation showed that ammonia suppressed not only the obligate acetotrophic methanogens but also the syntrophic propionate and butyrate oxidation taxa and their assistant bacteria (genus Desulfovibrio), which declined the biotransformations of propionate and butyrate → acetate → methane. Although the total population of the hydrolyzing and acidifying bacteria was not affected by ammonia, the bacteria with ammonia resistance increased. Our study also revealed that ammonia restrained the enzyme synthesis process by inhibiting the RNA polymerase (subunits A' and D) during transcription and the ribosome (large (L3, L12, L13, L22, and L25) and small (S3, S3Ae, and S7) ribosomal subunits) and aminoacyl-tRNA synthesis (aspartate-tRNA synthetase) in translation. Further investigation suggested that methylmalonyl-CoA mutase, acetyl-CoA C-acetyltransferase, and CH3-CoM reductase, which regulate propionate and butyrate oxidation and acetoclastic methanation, were significantly downregulated by ammonia. This study provides intrinsic insights into the fundamental mechanisms of how ammonia inhibits anaerobic digestion.
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Affiliation(s)
- Chao Liu
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xu Duan
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
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Kato S, Takashino M, Igarashi K, Mochimaru H, Mayumi D, Tamaki H. An iron corrosion-assisted H 2-supplying system: a culture method for methanogens and acetogens under low H 2 pressures. Sci Rep 2020; 10:19124. [PMID: 33154519 PMCID: PMC7645788 DOI: 10.1038/s41598-020-76267-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/12/2020] [Indexed: 11/09/2022] Open
Abstract
H2 is an important fermentation intermediate in anaerobic environments. Although H2 occurs at very low partial pressures in the environments, the culture and isolation of H2-utilizing microorganisms is usually carried out under very high H2 pressures, which might have hampered the discovery and understanding of microorganisms adapting to low H2 environments. Here we constructed a culture system designated the "iron corrosion-assisted H2-supplying (iCH) system" by connecting the gas phases of two vials (one for the iron corrosion reaction and the other for culturing microorganisms) to achieve cultures of microorganisms under low H2 pressures. We conducted enrichment cultures for methanogens and acetogens using rice paddy field soil as the microbial source. In the enrichment culture of methanogens under canonical high H2 pressures, only Methanobacterium spp. were enriched. By contrast, Methanocella spp. and Methanoculleus spp., methanogens adapting to low H2 pressures, were specifically enriched in the iCH cultures. We also observed selective enrichment of acetogen species by the iCH system (Acetobacterium spp. and Sporomusa spp.), whereas Clostridium spp. predominated in the high H2 cultures. These results demonstrate that the iCH system facilitates culture of anaerobic microorganisms under low H2 pressures, which will enable the selective culture of microorganisms adapting to low H2 environments.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan. .,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan.
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido, 062-8517, Japan
| | - Hanako Mochimaru
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1 Higashi, Tsukuba, 305-8567, Japan
| | - Daisuke Mayumi
- Institute for Geo-Resources and Environment, Geological Survey of Japan, AIST, 1-1-1 Higashi, Tsukuba, 305-8567, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba, 305-8567, Japan
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Quaiyum S, Igarashi K, Narihiro T, Kato S. Microbial Community Analysis of Anaerobic Enrichment Cultures Supplemented with Bacterial Peptidoglycan as the Sole Substrate. Microbes Environ 2020; 35. [PMID: 32921647 PMCID: PMC7511781 DOI: 10.1264/jsme2.me20002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Methanogenic microbial communities were enriched from rice paddy soil and anaerobic digester sludge using peptidoglycan purified from gram-negative Escherichia coli or gram-positive Micrococcus luteus as the sole substrate. Methane production data suggested the anaerobic degradation of peptidoglycan and also that peptidoglycan from E. coli had lower degradability. The community structures of enrichment cultures fed peptidoglycan from E. coli or M. luteus were similar, but distinctly different. A number of phylogenetically novel and uncultured bacteria, particularly in the phyla Bacteroidetes, WWE1, Armatimonadetes, and Verrucomicrobia, dominated the enrichment cultures, suggesting their involvement in anaerobic peptidoglycan degradation.
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Affiliation(s)
- Samia Quaiyum
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
| | - Souichiro Kato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology
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11
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Kato S, Takashino M, Igarashi K, Kitagawa W. Isolation and Genomic Characterization of a Proteobacterial Methanotroph Requiring Lanthanides. Microbes Environ 2020; 35. [PMID: 32037377 PMCID: PMC7104280 DOI: 10.1264/jsme2.me19128] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Although the bioavailability of rare earth elements (REEs, including scandium, yttrium, and 15 lanthanides) has not yet been examined in detail, methane-oxidizing bacteria (methanotrophs) were recently shown to harbor specific types of methanol dehydrogenases (XoxF-MDHs) that contain lanthanides in their active site, whereas their well-characterized counterparts (MxaF-MDHs) were Ca2+-dependent. However, lanthanide dependency in methanotrophs has not been demonstrated, except in acidic environments in which the solubility of lanthanides is high. We herein report the isolation of a lanthanide-dependent methanotroph from a circumneutral environment in which lanthanides only slightly dissolved. Methanotrophs were enriched and isolated from pond sediment using mineral medium supplemented with CaCl2 or REE chlorides. A methanotroph isolated from the cerium (Ce) chloride-supplemented culture, Methylosinus sp. strain Ce-a6, was clearly dependent on lanthanide. Strain Ce-a6 only required approximately 30 nM lanthanide chloride for its optimal growth and exhibited the ability to utilize insoluble lanthanide oxides, which may enable survival in circumneutral environments. Genome and gene expression analyses revealed that strain Ce-a6 lost the ability to produce functional MxaF-MDH, and this may have been due to a large-scale deletion around the mxa gene cluster. The present results provide evidence for lanthanide dependency as a novel survival strategy by methanotrophs in circumneutral environments.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Wataru Kitagawa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST
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12
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Hackley RK, Schmid AK. Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response. J Mol Biol 2019; 431:4147-4166. [PMID: 31437442 PMCID: PMC7419163 DOI: 10.1016/j.jmb.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023]
Abstract
The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.
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Affiliation(s)
- Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA.
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13
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Kato S, Wada K, Kitagawa W, Mayumi D, Ikarashi M, Sone T, Asano K, Kamagata Y. Conductive Iron Oxides Promote Methanogenic Acetate Degradation by Microbial Communities in a High-Temperature Petroleum Reservoir. Microbes Environ 2019; 34:95-98. [PMID: 30773516 PMCID: PMC6440731 DOI: 10.1264/jsme2.me18140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Supplementation with conductive magnetite particles promoted methanogenic acetate degradation by microbial communities enriched from the production water of a high-temperature petroleum reservoir. A microbial community analysis revealed that Petrothermobacter spp. (phylum Deferribacteres), known as thermophilic Fe(III) reducers, predominated in the magnetite-supplemented enrichment, whereas other types of Fe(III) reducers, such as Thermincola spp. and Thermotoga spp., were dominant under ferrihydrite-reducing conditions. These results suggest that magnetite induced interspecies electron transfer via electric currents through conductive particles between Petrothermobacter spp. and methanogens. This is the first evidence for possible electric syntrophy in high-temperature subsurface environments.
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Affiliation(s)
- Souichiro Kato
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Kaoru Wada
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University
| | - Wataru Kitagawa
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | | | | | - Teruo Sone
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University
| | - Kozo Asano
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University
| | - Yoichi Kamagata
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST).,Bioproduction Research Institute, AIST
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14
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Zhang C, Yuan Q, Lu Y. Inhibitory effects of ammonia on syntrophic propionate oxidation in anaerobic digester sludge. WATER RESEARCH 2018; 146:275-287. [PMID: 30278382 DOI: 10.1016/j.watres.2018.09.046] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/30/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
Syntrophic propionate oxidation (SPO) coupled with methanogenesis is often inhibited under high ammonium concentrations in anaerobic digesters. However, the inhibitory mechanism remains poorly understood. We conducted two independent laboratory experiments with a swine manure digester sludge. In experiment I, RNA-based stable isotope probing (SIP) was applied to determine the active players of both bacteria and methanogens involved in SPO under different ammonium concentrations (0, 3 and 7 g NH4+N L-1). In experiment II, the dynamics of the bacterial community under ammonia stress was monitored using the 16S rRNA pyrosequencing and quantitative PCR under similar conditions as in experiment I but without the addition of external propionate. An additional higher ammonium treatment (10 g NH4+N L-1) was applied in experiment II to maximize the ammonia stress. We identified that the Smithella bacteria and the Methanosaetaceae and Methanospirillaceae archaea were the most active players involved in SPO and methanogenesis. We revealed that Smithella, Methanosaetaceae and Methanospirillaceae were moderately and severely inhibited at 3 and 7-10 g NH4+N L-1, respectively. However, the fermentative bacteria appeared to be more tolerant to ammonia stress. The microbial responses were corroborated with the accumulation of VFAs and the repression of methanogenesis under high ammonium conditions.
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Affiliation(s)
- Chen Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Quan Yuan
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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15
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Tanaka K, Yokoe S, Igarashi K, Takashino M, Ishikawa M, Hori K, Nakanishi S, Kato S. Extracellular Electron Transfer via Outer Membrane Cytochromes in a Methanotrophic Bacterium Methylococcus capsulatus (Bath). Front Microbiol 2018; 9:2905. [PMID: 30555443 PMCID: PMC6281684 DOI: 10.3389/fmicb.2018.02905] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/13/2018] [Indexed: 11/24/2022] Open
Abstract
Electron exchange reactions between microbial cells and solid materials, referred to as extracellular electron transfer (EET), have attracted attention in the fields of microbial physiology, microbial ecology, and biotechnology. Studies of model species of iron-reducing, or equivalently, current-generating bacteria such as Geobacter spp. and Shewanella spp. have revealed that redox-active proteins, especially outer membrane c-type cytochromes (OMCs), play a pivotal role in the EET process. Recent (meta)genomic analyses have revealed that diverse microorganisms that have not been demonstrated to have EET ability also harbor OMC-like proteins, indicating that EET via OMCs could be more widely preserved in microorganisms than originally thought. A methanotrophic bacterium Methylococcus capsulatus (Bath) was reported to harbor multiple OMC genes whose expression is elevated by Cu starvation. However, the physiological role of these genes is unknown. Therefore, in this study, we explored whether M. capsulatus (Bath) displays EET abilities via OMCs. In electrochemical analysis, M. capsulatus (Bath) generated anodic current only when electron donors such as formate were available, and could reduce insoluble iron oxides in the presence of electron donor compounds. Furthermore, the current-generating and iron-reducing activities of M. capsulatus (Bath) cells that were cultured in a Cu-deficient medium, which promotes high levels of OMC expression, were higher than those cultured in a Cu-supplemented medium. Anodic current production by the Cu-deficient cells was significantly suppressed by disruption of MCA0421, a highly expressed OMC gene, and by treatment with carbon monoxide (CO) gas (an inhibitor of c-type cytochromes). Our results provide evidence of EET in M. capsulatus (Bath) and demonstrate the pivotal role of OMCs in this process. This study raises the possibility that EET to solid compounds is a novel survival strategy of methanotrophic bacteria.
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Affiliation(s)
- Kenya Tanaka
- Graduate School of Engineering Science, Osaka University, Toyonaka, Japan
| | - Sho Yokoe
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Motoko Takashino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Masahito Ishikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Research Center for Solar Energy Chemistry, Osaka University, Toyonaka, Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Shuji Nakanishi
- Graduate School of Engineering Science, Osaka University, Toyonaka, Japan.,Research Center for Solar Energy Chemistry, Osaka University, Toyonaka, Japan
| | - Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Research Center for Solar Energy Chemistry, Osaka University, Toyonaka, Japan
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16
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Kato S, Igarashi K. Enhancement of methanogenesis by electric syntrophy with biogenic iron-sulfide minerals. Microbiologyopen 2018; 8:e00647. [PMID: 29877051 PMCID: PMC6436484 DOI: 10.1002/mbo3.647] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 02/13/2018] [Accepted: 04/05/2018] [Indexed: 01/29/2023] Open
Abstract
Recent studies have shown that interspecies electron transfer between chemoheterotrophic bacteria and methanogenic archaea can be mediated by electric currents flowing through conductive iron oxides, a process termed electric syntrophy. In this study, we conducted enrichment experiments with methanogenic microbial communities from rice paddy soil in the presence of ferrihydrite and/or sulfate to determine whether electric syntrophy could be enabled by biogenic iron sulfides. Although supplementation with either ferrihydrite or sulfate alone suppressed methanogenesis, supplementation with both ferrihydrite and sulfate enhanced methanogenesis. In the presence of sulfate, ferrihydrite was transformed into black precipitates consisting mainly of poorly crystalline iron sulfides. Microbial community analysis revealed that a methanogenic archaeon and iron- and sulfate-reducing bacteria (Methanosarcina, Geobacter, and Desulfotomaculum, respectively) predominated in the enrichment culture supplemented with both ferrihydrite and sulfate. Addition of an inhibitor specific for methanogenic archaea decreased the abundance of Geobacter, but not Desulfotomaculum, indicating that Geobacter acquired energy via syntrophic interaction with methanogenic archaea. Although electron acceptor compounds such as sulfate and iron oxides have been thought to suppress methanogenesis, this study revealed that coexistence of sulfate and iron oxide can promote methanogenesis by biomineralization of (semi)conductive iron sulfides that enable methanogenesis via electric syntrophy.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
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17
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Taubner RS, Pappenreiter P, Zwicker J, Smrzka D, Pruckner C, Kolar P, Bernacchi S, Seifert AH, Krajete A, Bach W, Peckmann J, Paulik C, Firneis MG, Schleper C, Rittmann SKMR. Biological methane production under putative Enceladus-like conditions. Nat Commun 2018; 9:748. [PMID: 29487311 PMCID: PMC5829080 DOI: 10.1038/s41467-018-02876-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 01/04/2018] [Indexed: 11/18/2022] Open
Abstract
The detection of silica-rich dust particles, as an indication for ongoing hydrothermal activity, and the presence of water and organic molecules in the plume of Enceladus, have made Saturn's icy moon a hot spot in the search for potential extraterrestrial life. Methanogenic archaea are among the organisms that could potentially thrive under the predicted conditions on Enceladus, considering that both molecular hydrogen (H2) and methane (CH4) have been detected in the plume. Here we show that a methanogenic archaeon, Methanothermococcus okinawensis, can produce CH4 under physicochemical conditions extrapolated for Enceladus. Up to 72% carbon dioxide to CH4 conversion is reached at 50 bar in the presence of potential inhibitors. Furthermore, kinetic and thermodynamic computations of low-temperature serpentinization indicate that there may be sufficient H2 gas production to serve as a substrate for CH4 production on Enceladus. We conclude that some of the CH4 detected in the plume of Enceladus might, in principle, be produced by methanogens.
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Affiliation(s)
- Ruth-Sophie Taubner
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, 1090, Vienna, Austria
- Department of Astrophysics, Universität Wien, 1180, Vienna, Austria
| | - Patricia Pappenreiter
- Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, 4040, Linz, Austria
| | - Jennifer Zwicker
- Department of Geodynamics and Sedimentology, Center for Earth Sciences, Universität Wien, 1090, Vienna, Austria
| | - Daniel Smrzka
- Department of Geodynamics and Sedimentology, Center for Earth Sciences, Universität Wien, 1090, Vienna, Austria
| | - Christian Pruckner
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, 1090, Vienna, Austria
| | - Philipp Kolar
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, 1090, Vienna, Austria
| | | | | | | | - Wolfgang Bach
- Geoscience Department, Universität Bremen, 28359, Bremen, Germany
| | - Jörn Peckmann
- Department of Geodynamics and Sedimentology, Center for Earth Sciences, Universität Wien, 1090, Vienna, Austria
- Institute for Geology, Center for Earth System Research and Sustainability, Universität Hamburg, 20146, Hamburg, Germany
| | - Christian Paulik
- Institute for Chemical Technology of Organic Materials, Johannes Kepler Universität Linz, 4040, Linz, Austria
| | - Maria G Firneis
- Department of Astrophysics, Universität Wien, 1180, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, 1090, Vienna, Austria
| | - Simon K-M R Rittmann
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, 1090, Vienna, Austria.
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18
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Affiliation(s)
- Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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19
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Jha P, Schmidt S. Reappraisal of chemical interference in anaerobic digestion processes. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2017; 75:954-971. [DOI: 10.1016/j.rser.2016.11.076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
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20
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Yu Z, Ma Y, Zhong W, Qiu J, Li J. Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles. Front Microbiol 2017; 8:1278. [PMID: 28744269 PMCID: PMC5504354 DOI: 10.3389/fmicb.2017.01278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/26/2017] [Indexed: 12/22/2022] Open
Abstract
Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.
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Affiliation(s)
- Zhiliang Yu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Yunting Ma
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Weihong Zhong
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Juanping Qiu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Jun Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China.,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong UniversityShanghai, China
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21
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Tian H, Fotidis IA, Mancini E, Angelidaki I. Different cultivation methods to acclimatise ammonia-tolerant methanogenic consortia. BIORESOURCE TECHNOLOGY 2017; 232:1-9. [PMID: 28214439 DOI: 10.1016/j.biortech.2017.02.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 06/06/2023]
Abstract
Bioaugmentation with ammonia tolerant-methanogenic consortia was proposed as a solution to overcome ammonia inhibition during anaerobic digestion process recently. However, appropriate technology to generate ammonia tolerant methanogenic consortia is still lacking. In this study, three basic reactors (i.e. batch, fed-batch and continuous stirred-tank reactors (CSTR)) operated at mesophilic (37°C) and thermophilic (55°C) conditions were assessed, based on methane production efficiency, incubation time, TAN/FAN (total ammonium nitrogen/free ammonia nitrogen) levels and maximum methanogenic activity. Overall, fed-batch cultivation was clearly the most efficient method compared to batch and CSTR. Specifically, by saving incubation time up to 150%, fed-batch reactors were acclimatised to nearly 2-fold higher FAN levels with a 37%-153% methanogenic activity improvement, compared to batch method. Meanwhile, CSTR reactors were inhibited at lower ammonia levels. Finally, specific methanogenic activity test showed that hydrogenotrophic methanogens were more active than aceticlastic methanogens in all FAN levels above 540mgNH3-NL-1.
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Affiliation(s)
- Hailin Tian
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet Bygning 115, DK-2800 Kgs. Lyngby, Denmark
| | - Ioannis A Fotidis
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet Bygning 115, DK-2800 Kgs. Lyngby, Denmark.
| | - Enrico Mancini
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet Bygning 115, DK-2800 Kgs. Lyngby, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Bygningstorvet Bygning 115, DK-2800 Kgs. Lyngby, Denmark
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22
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Mahmoud M, Parameswaran P, Torres CI, Rittmann BE. Electrochemical techniques reveal that total ammonium stress increases electron flow to anode respiration in mixed-species bacterial anode biofilms. Biotechnol Bioeng 2017; 114:1151-1159. [PMID: 28067404 DOI: 10.1002/bit.26246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/31/2016] [Accepted: 01/05/2017] [Indexed: 02/02/2023]
Abstract
When anode-respiring bacteria (ARB) respire electrons to an anode in microbial electrochemical cells (MXCs), they harvest only a small amount of free energy. This means that ARB must have a high substrate-oxidation rate coupled with a high ratio of electrons used for respiration compared to total electrons removed by substrate utilization. It also means that they are especially susceptible to inhibition that slows anode respiration or lowers their biomass yield. Using several electrochemical techniques, we show that a relatively high total ammonium-nitrogen (TAN) concentration (2.2 g TAN/L) induced significant stress on the ARB biofilms, lowering their true yield and forcing the ARB to boost the ratio of electrons respired per electrons consumed from the substrate. In particular, a higher respiration rate, measured as current density (j), was associated with slower growth and a lower net yield, compared to an ARB biofilm grown with a lower ammonium concentration (0.2 g TAN/L). Further increases in influent TAN (to 3 and then to 4.4 g TAN/L) caused nearly complete inhibition of anode respiration. However, the ARB could recover from high-TAN inhibition after a shift of the MXC's feed to 0.2 g TAN/L. In summary, ARB biofilms were inhibited by a high TAN concentration, but could divert more electron flow toward anode respiration with modest inhibition and recover when severe inhibition was relieved. Biotechnol. Bioeng. 2017;114: 1151-1159. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Mohamed Mahmoud
- Water Pollution Research Department, National Research Centre, 33 EL Bohouth St., Dokki, Cairo 12311, Egypt.,Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 727 Tyler Road, Tempe, Arizona 85287-5701.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona
| | - Prathap Parameswaran
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 727 Tyler Road, Tempe, Arizona 85287-5701.,Department of Civil Engineering, Kansas State University, Manhattan, Kansas
| | - César I Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 727 Tyler Road, Tempe, Arizona 85287-5701.,School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 727 Tyler Road, Tempe, Arizona 85287-5701.,School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona
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23
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Ranawat P, Rawat S. Stress response physiology of thermophiles. Arch Microbiol 2017; 199:391-414. [DOI: 10.1007/s00203-016-1331-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 12/07/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
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24
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Haruta S, Kanno N. Survivability of Microbes in Natural Environments and Their Ecological Impacts. Microbes Environ 2016; 30:123-5. [PMID: 26094633 PMCID: PMC4462920 DOI: 10.1264/jsme2.me3002rh] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University
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25
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Enrichment and isolation of Flavobacterium strains with tolerance to high concentrations of cesium ion. Sci Rep 2016; 6:20041. [PMID: 26883718 PMCID: PMC4756683 DOI: 10.1038/srep20041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/23/2015] [Indexed: 11/08/2022] Open
Abstract
Interest in the interaction of microorganisms with cesium ions (Cs+) has arisen, especially in terms of their potent ability for radiocesium bioaccumulation and their important roles in biogeochemical cycling. Although high concentrations of Cs+ display toxic effects on microorganisms, there have been only limited reports for Cs+-tolerant microorganisms. Here we report enrichment and isolation of Cs+-tolerant microorganisms from soil microbiota. Microbial community analysis revealed that bacteria within the phylum Bacteroidetes, especially Flavobacterium spp., dominated in enrichment cultures in the medium supplemented with 50 or 200 mM Cs+, while Gammaproteobacteria was dominant in the control enrichment cultures (in the presence of 50 and 200 mM K+ instead of Cs+). The dominant Flavobacterium sp. was successfully isolated from the enrichment culture and was closely related to Flavobacterium chungbukense with 99.5% identity. Growth experiments clearly demonstrated that the isolate has significantly higher tolerance to Cs+ compared to its close relatives, suggesting the Cs+-tolerance is a specific trait of this strain, but not a universal trait in the genus Flavobacterium. Measurement of intracellular K+ and Cs+ concentrations of the Cs+-tolerant isolate and its close relatives suggested that the ability to maintain low intracellular Cs+ concentration confers the tolerance against high concentrations of external Cs+.
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26
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Wang H, Tao Y, Gao D, Liu G, Chen C, Ren N, van Lier JB, de Kreuk M. Microbial population dynamics in response to increasing loadings of pre-hydrolyzed pig manure in an expanded granular sludge bed. WATER RESEARCH 2015; 87:29-37. [PMID: 26378729 DOI: 10.1016/j.watres.2015.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 08/26/2015] [Accepted: 09/05/2015] [Indexed: 06/05/2023]
Abstract
In recent years, pig manure (PM) has been regarded as a valuable substrate for energy and resource recovery via bioprocesses such as anaerobic digestion (AD), however, the efficiency of digesting raw PM is limited by the presence of refractory compounds. In this study, we applied a series of pretreatment on raw PM, consisting of subsequent thermochemical pretreatment, enzymatic hydrolysis, tyndallization and filtration. The liquid PM hydrolysates were fed to an expanded granular sludge bed (EGSB) for the production of biogas. The general performance and population dynamics of the EGSB reactor were assessed during an extended operational period of 339 days. An efficient and stable digestion process was achieved under high organic loading rates (OLRs) up to 21 kg-COD/(m(3)·d), agreeing with a sludge loading rate of 0.75 kg-COD/(kg-VSS·d), 1600 mg-NH4(+)-N/L and 17 mg/L of free ammonia nitrogen. The tyndallization decreased the total amount of active cells from 1 × 10(8) to 1 × 10(2) CFU/ml. Hence, bio-augmentation with pigs' intestinal microbiota was absent and the community dynamics were mainly credited to the composition of the substrate (i.e. PM hydrolysates) and the environmental conditions inside the reactor. The results showed the influence of both the seed community and the imposed loading rates on the evolutionary trajectory of the EGSB microbial community. Four bacterial genera (Clostridium, Cytophaga, Bacillus and Bacteroides) and two methanogenic genera (Methanosaeta and Methanobacterium) dominated the communities. An obvious shift from aceticlastic Methanosaeta to hydrogenotrophic Methanobacterium appeared when the OLR was increased to over 10 kg-COD/(m(3)·d).
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Affiliation(s)
- Haoyu Wang
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China; Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, 2628, CN Delft, The Netherlands
| | - Yu Tao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China; Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, 2628, CN Delft, The Netherlands; Department of Chemical Engineering, Imperial College London, South Kensington Campus, SW7 2AZ, UK
| | - Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China
| | - Gang Liu
- Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, 2628, CN Delft, The Netherlands
| | - Chunhong Chen
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China
| | - Nanqi Ren
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150090, Harbin, China.
| | - Jules B van Lier
- Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, 2628, CN Delft, The Netherlands
| | - Merle de Kreuk
- Section of Sanitary Engineering, Department of Water Management, Delft University of Technology, 2628, CN Delft, The Netherlands
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Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
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28
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Wang H, Fotidis IA, Angelidaki I. Ammonia effect on hydrogenotrophic methanogens and syntrophic acetate-oxidizing bacteria. FEMS Microbiol Ecol 2015; 91:fiv130. [DOI: 10.1093/femsec/fiv130] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2015] [Indexed: 11/12/2022] Open
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Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil. Sci Rep 2015; 5:14295. [PMID: 26399549 PMCID: PMC4585845 DOI: 10.1038/srep14295] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/24/2015] [Indexed: 11/08/2022] Open
Abstract
Anaerobic degradation of lignin-derived aromatics is an important metabolism for carbon and nutrient cycles in soil environments. Although there are some studies on degradation of lignin-derived aromatics by nitrate- and sulfate-reducing bacteria, knowledge on their degradation under methanogenic conditions are quite limited. In this study, methanogenic microbial communities were enriched from rice paddy field soil with lignin-derived methoxylated monoaromatics (vanillate and syringate) and their degradation intermediates (protocatechuate, catechol, and gallate) as the sole carbon and energy sources. Archaeal community analysis disclosed that both aceticlastic (Methanosarcina sp.) and hydrogenotrophic (Methanoculleus sp. and Methanocella sp.) methanogens dominated in all of the enrichments. Bacterial community analysis revealed the dominance of acetogenic bacteria (Sporomusa spp.) only in the enrichments on the methoxylated aromatics, suggesting that Sporomusa spp. initially convert vanillate and syringate into protocatechuate and gallate, respectively, with acetogenesis via O-demethylation. As the putative ring-cleavage microbes, bacteria within the phylum Firmicutes were dominantly detected from all of the enrichments, while the dominant phylotypes were not identical between enrichments on vanillate/protocatechuate/catechol (family Peptococcaceae bacteria) and on syringate/gallate (family Ruminococcaceae bacteria). This study demonstrates the importance of cooperation among acetogens, ring-cleaving fermenters/syntrophs and aceticlastic/hydrogenotrophic methanogens for degradation of lignin-derived aromatics under methanogenic conditions.
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Yamada C, Kato S, Ueno Y, Ishii M, Igarashi Y. Conductive iron oxides accelerate thermophilic methanogenesis from acetate and propionate. J Biosci Bioeng 2015; 119:678-82. [DOI: 10.1016/j.jbiosc.2014.11.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/20/2014] [Accepted: 11/04/2014] [Indexed: 12/19/2022]
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Kato S, Yoshida R, Yamaguchi T, Sato T, Yumoto I, Kamagata Y. The effects of elevated CO2 concentration on competitive interaction between aceticlastic and syntrophic methanogenesis in a model microbial consortium. Front Microbiol 2014; 5:575. [PMID: 25400628 PMCID: PMC4214200 DOI: 10.3389/fmicb.2014.00575] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/13/2014] [Indexed: 11/13/2022] Open
Abstract
Investigation of microbial interspecies interactions is essential for elucidating the function and stability of microbial ecosystems. However, community-based analyses including molecular-fingerprinting methods have limitations for precise understanding of interspecies interactions. Construction of model microbial consortia consisting of defined mixed cultures of isolated microorganisms is an excellent method for research on interspecies interactions. In this study, a model microbial consortium consisting of microorganisms that convert acetate into methane directly (Methanosaeta thermophila) and syntrophically (Thermacetogenium phaeum and Methanothermobacter thermautotrophicus) was constructed and the effects of elevated CO2 concentrations on intermicrobial competition were investigated. Analyses on the community dynamics by quantitative RT-PCR and fluorescent in situ hybridization targeting their 16S rRNAs revealed that high concentrations of CO2 have suppressive effects on the syntrophic microorganisms, but not on the aceticlastic methanogen. The pathways were further characterized by determining the Gibbs free energy changes (ΔG) of the metabolic reactions conducted by each microorganism under different CO2 concentrations. The ΔG value of the acetate oxidation reaction (T. phaeum) under high CO2 conditions became significantly higher than -20 kJ per mol of acetate, which is the borderline level for sustaining microbial growth. These results suggest that high concentrations of CO2 undermine energy acquisition of T. phaeum, resulting in dominance of the aceticlastic methanogen. This study demonstrates that investigation on model microbial consortia is useful for untangling microbial interspecies interactions, including competition among microorganisms occupying the same trophic niche in complex microbial ecosystems.
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Affiliation(s)
- Souichiro Kato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
- Research Center for Advanced Science and Technology, The University of TokyoTokyo, Japan
| | - Rina Yoshida
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Takashi Yamaguchi
- Department of Civil and Environmental Engineering, Nagaoka University of TechnologyNagaoka, Japan
| | - Tomoyuki Sato
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Isao Yumoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and TechnologySapporo, Japan
- Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido UniversitySapporo, Japan
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Isolation of acetogenic bacteria that induce biocorrosion by utilizing metallic iron as the sole electron donor. Appl Environ Microbiol 2014; 81:67-73. [PMID: 25304512 DOI: 10.1128/aem.02767-14] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Corrosion of iron occurring under anoxic conditions, which is termed microbiologically influenced corrosion (MIC) or biocorrosion, is mostly caused by microbial activities. Microbial activity that enhances corrosion via uptake of electrons from metallic iron [Fe(0)] has been regarded as one of the major causative factors. In addition to sulfate-reducing bacteria and methanogenic archaea in marine environments, acetogenic bacteria in freshwater environments have recently been suggested to cause MIC under anoxic conditions. However, no microorganisms that perform acetogenesis-dependent MIC have been isolated or had their MIC-inducing mechanisms characterized. Here, we enriched and isolated acetogenic bacteria that induce iron corrosion by utilizing Fe(0) as the sole electron donor under freshwater, sulfate-free, and anoxic conditions. The enriched communities produced significantly larger amounts of Fe(II) than the abiotic controls and produced acetate coupled with Fe(0) oxidation prior to CH4 production. Microbial community analysis revealed that Sporomusa sp. and Desulfovibrio sp. dominated in the enrichments. Strain GT1, which is closely related to the acetogen Sporomusa sphaeroides, was eventually isolated from the enrichment. Strain GT1 grew acetogenetically with Fe(0) as the sole electron donor and enhanced iron corrosion, which is the first demonstration of MIC mediated by a pure culture of an acetogen. Other well-known acetogenic bacteria, including Sporomusa ovata and Acetobacterium spp., did not grow well on Fe(0). These results indicate that very few species of acetogens have specific mechanisms to efficiently utilize cathodic electrons derived from Fe(0) oxidation and induce iron corrosion.
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