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Han Y, Li W, Gao Y, Cai T, Wang J, Liu Z, Yin J, Lu X, Zhen G. Biogas upgrading and membrane anti-fouling mechanisms in electrochemical anaerobic membrane bioreactor (EC-AnMBR): Focusing on spatio-temporal distribution of metabolic functionality of microorganisms. WATER RESEARCH 2024; 256:121557. [PMID: 38581982 DOI: 10.1016/j.watres.2024.121557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/23/2024] [Accepted: 03/29/2024] [Indexed: 04/08/2024]
Abstract
Electrochemical anaerobic membrane bioreactor (EC-AnMBR) by integrating a composite anodic membrane (CAM), represents an effective method for promoting methanogenic performance and mitigating membrane fouling. However, the development and formation of electroactive biofilm on CAM, and the spatio-temporal distribution of key functional microorganisms, especially the degradation mechanism of organic pollutants in metabolic pathways were not well documented. In this work, two AnMBR systems (EC-AnMBR and traditional AnMBR) were constructed and operated to identify the role of CAM in metabolic pathway on biogas upgrading and mitigation of membrane fouling. The methane yield of EC-AnMBR at HRT of 20 days was 217.1 ± 25.6 mL-CH4/g COD, about 32.1 % higher compared to the traditional AnMBR. The 16S rRNA analysis revealed that the EC-AnMBR significantly promoted the growth of hydrolysis bacteria (Lactobacillus and SJA-15) and methanogenic archaea (Methanosaeta and Methanobacterium). Metagenomic analysis revealed that the EC-AnMBR promotes the upregulation of functional genes involved in carbohydrate metabolism (gap and kor) and methane metabolism (mtr, mcr, and hdr), improving the degradation of soluble microbial products (SMPs)/extracellular polymeric substances (EPS) on the CAM and enhancing the methanogens activity on the cathode. Moreover, CAM biofilm exhibits heterogeneity in the degradation of organic pollutants along its vertical depth. The bacteria with high hydrolyzing ability accumulated in the upper part, driving the feedstock degradation for higher starch, sucrose and galactose metabolism. A three-dimensional mesh-like cake structure with larger pores was formed as a biofilter in the middle and lower part of CAM, where the electroactive Geobacter sulfurreducens had high capabilities to directly store and transfer electrons for the degradation of organic pollutants. This outcome will further contribute to the comprehension of the metabolic mechanisms of CAM module on membrane fouling control and organic solid waste treatment and disposal.
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Affiliation(s)
- Yule Han
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, PR China
| | - Wanjiang Li
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, PR China
| | - Yijing Gao
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, PR China
| | - Teng Cai
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, PR China
| | - Jiayi Wang
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, PR China
| | - Zhaobin Liu
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, PR China
| | - Jian Yin
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, PR China
| | - Xueqin Lu
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, 1515 North Zhongshan Rd. (No. 2), Shanghai 200092, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, PR China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, 3663N. Zhongshan Road, Shanghai, 200062, China
| | - Guangyin Zhen
- Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai 200241, PR China; Shanghai Institute of Pollution Control and Ecological Security, 1515 North Zhongshan Rd. (No. 2), Shanghai 200092, PR China; Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai 200241, PR China; Institute of Eco-Chongming (IEC), 3663N. Zhongshan Rd., Shanghai 200062, PR China.
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Mukherjee D, Selvi VA, Ganguly J, Masto RE. New insights into the coal-associated methane architect: the ancient archaebacteria. Arch Microbiol 2024; 206:234. [PMID: 38664262 DOI: 10.1007/s00203-024-03961-1] [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: 02/21/2024] [Revised: 04/04/2024] [Accepted: 04/13/2024] [Indexed: 05/20/2024]
Abstract
Exploration and marketable exploitation of coalbed methane (CBM) as cleaner fuel has been started globally. In addition, incidence of methane in coal basins is an imperative fraction of global carbon cycle. Significantly, subsurface coal ecosystem contains methane forming archaea. There is a rising attention in optimizing microbial coal gasification to exploit the abundant or inexpensive coal reserves worldwide. Therefore, it is essential to understand the coalbeds in geo-microbial perspective. Current review provides an in-depth analysis of recent advances in our understanding of how methanoarchaea are distributed in coal deposits globally. Specially, we highlight the findings on coal-associated methanoarchaeal existence, abundance, diversity, metabolic activity, and biogeography in diverse coal basins worldwide. Growing evidences indicates that we have arrived an exciting era of archaeal research. Moreover, gasification of coal into methane by utilizing microbial methanogenesis is a considerable way to mitigate the energy crisis for the rising world population.
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Affiliation(s)
- Diptangshu Mukherjee
- Industrial Biotechnology and Waste Utilization Research Group, CSIR-Central Institute of Mining and Fuel Research, Digwadih Campus, PO FRI, Dhanbad, Jharkhand, 828108, India
| | - Vetrivel Angu Selvi
- Industrial Biotechnology and Waste Utilization Research Group, CSIR-Central Institute of Mining and Fuel Research, Digwadih Campus, PO FRI, Dhanbad, Jharkhand, 828108, India.
| | - Jhuma Ganguly
- Department of Chemistry, Indian Institute of Engineering Science and Technology Shibpur, PO Botanical Garden, Howrah, West Bengal, 711103, India
| | - Reginald Ebhin Masto
- Industrial Biotechnology and Waste Utilization Research Group, CSIR-Central Institute of Mining and Fuel Research, Digwadih Campus, PO FRI, Dhanbad, Jharkhand, 828108, India
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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] [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).
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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
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Zhou J, Zhang H, Zhang CJ, Li M. Methanolobus mangrovi sp. nov. and Methanolobus sediminis sp. nov, two novel methylotrophic methanogens isolated from mangrove sediments in China. Int J Syst Evol Microbiol 2023; 73. [PMID: 37982371 DOI: 10.1099/ijsem.0.006169] [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] [Indexed: 11/21/2023] Open
Abstract
Two methylotrophic methanogens, designated strains FTZ2T and FTZ6T, were isolated from mangrove sediment sampled in Futian Mangrove Nature Reserve in Shenzhen, PR China. Cells of strains FTZ2T and FTZ6T were cocci, with diameters of 0.6-1.0 µm and 0.6-0.9 µm, respectively. Both strains grew on methanol, methylamine, dimethylamine and trimethylamine, but not on acetate, formate, H2/CO2, choline, betaine or dimethyl sulphide. Strain FTZ2T grew at 10-37 °C (optimally at 33 °C), pH 5.5-8.0 (optimally at pH 7.0) and 0-1.03 M NaCl (optimally at 0.17 M NaCl). In contrast, strain FTZ6T grew at 15-42 °C (optimally at 37 °C), pH 5.0-7.5 (optimally pH 6.5) and 0-1.03 M NaCl (optimally at 0.17 M NaCl). Both strains required magnesium for growth and were susceptible to sodium dodecyl sulphate. Biotin was required for the growth of strain FTZ2T but not of strain FTZ6T. The genomic G+C contents of strains FTZ2T and FTZ6T were 41.6 and 40.9 mol%, respectively. Phylogenetic analyses revealed that strain FTZ2T was mostly related to Methanolobus psychrotolerans YSF-03T, with 16S rRNA gene similarity of 98.6 %, an average nucleotide identity (ANI) of 82.5 %, and a digital DNA-DNA hybridization (dDDH) of 24.6 %. While strain FTZ6T was mostly related to Methanolobus vulcani PL-12/MT, with 16S rRNA gene similarity of 99.4 %, an ANI of 88.6% and a dDDH of 34.6 %. Based on phenotypic, phylogenetic and genotypic evidence, two novel species of the genus Methanolobus, Methanolobus mangrovi sp. nov. and Methanolobus sediminis sp. nov., are proposed. The type strain of M. mangrovi sp. nov. is FTZ2T (=CCAM 1276T=JCM 39396T) and the type strain of M. sediminis sp. nov. is FTZ6T (=CCAM 1277T=JCM 39397T).
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Affiliation(s)
- Jinjie Zhou
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Hanyun Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Cui-Jing Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
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Medina Caro D, Horstmann L, Ganzert L, Oses R, Friedl T, Wagner D. An improved method for intracellular DNA (iDNA) recovery from terrestrial environments. Microbiologyopen 2023; 12:e1369. [PMID: 37379428 DOI: 10.1002/mbo3.1369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023] Open
Abstract
The simultaneous extraction of intracellular DNA (iDNA) and extracellular DNA (eDNA) can help to separate the living in situ community (represented by iDNA) from background DNA that originated both from past communities and from allochthonous sources. As iDNA and eDNA extraction protocols require separating cells from the sample matrix, their DNA yields are generally lower than direct methods that lyse the cells within the sample matrix. We, therefore, tested different buffers with and without adding a detergent mix (DM) in the extraction protocol to improve the recovery of iDNA from surface and subsurface samples that covered a variety of terrestrial environments. The combination of a highly concentrated sodium phosphate buffer plus DM significantly improved iDNA recovery for almost all tested samples. Additionally, the combination of sodium phosphate and EDTA improved iDNA recovery in most of the samples and even allowed the successful extraction of iDNA from extremely low-biomass iron-bearing rock samples taken from the deep biosphere. Based on our results, we recommend using a protocol with sodium phosphate in combination with either a DM (NaP 300 mM + DM) or EDTA (NaP + EDTA 300 mM). Furthermore, for studies that rely on the eDNA pool, we recommend using buffers solely based on sodium phosphate because the addition of EDTA or a DM resulted in a decrease in eDNA for most of the tested samples. These improvements can help reduce community bias in environmental studies and contribute to better characterizations of both modern and past ecosystems.
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Affiliation(s)
- Diego Medina Caro
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Lucas Horstmann
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Department Experimental Phycology and Culture Collection of Algae (EPSAG), Albrecht-von-Haller-Institute for Plant Sciences, Georg August University Göttingen, Göttingen, Germany
| | - Lars Ganzert
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Marbio, UiT The Arctic University of Norway, Tromsø, Norway
| | - Romulo Oses
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Copiapó, Chile
| | - Thomas Friedl
- Department Experimental Phycology and Culture Collection of Algae (EPSAG), Albrecht-von-Haller-Institute for Plant Sciences, Georg August University Göttingen, Göttingen, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
- Institute of Geosciences, University of Potsdam, Potsdam, Germany
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Kawagucci S, Sakai S, Tasumi E, Hirai M, Takaki Y, Nunoura T, Saitoh M, Ueno Y, Yoshida N, Shibuya T, Clifford Sample J, Okumura T, Takai K. Deep Subseafloor Biogeochemical Processes and Microbial Populations Potentially Associated with the 2011 Tohoku-oki Earthquake at the Japan Trench Accretionary Wedge (IODP Expedition 343). Microbes Environ 2023; 38:n/a. [PMID: 37331792 DOI: 10.1264/jsme2.me22108] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023] Open
Abstract
Post-mega-earthquake geochemical and microbiological properties in subseafloor sediments of the Japan Trench accretionary wedge were investigated using core samples from Hole C0019E, which was drilled down to 851 m below seafloor (mbsf) at a water depth of 6,890 m. Methane was abundant throughout accretionary prism sediments; however, its concentration decreased close to the plate boundary decollement. Methane isotope systematics indicated a biogenic origin. The content of mole-cular hydrogen (H2) was low throughout core samples, but markedly increased at specific depths that were close to potential faults predicted by logging-while-drilling ana-lyses. Based on isotopic systematics, H2 appeared to have been abundantly produced via a low-temperature interaction between pore water and the fresh surface of crushed rock induced by earthquakes. Subseafloor microbial cell density remained constant at approximately 105 cells mL-1. Amplicon sequences revealed that predominant members at the phylum level were common throughout the units tested, which also included members frequently found in anoxic subseafloor sediments. Metabolic potential assays using radioactive isotopes as tracers revealed homoacetogenic activity in H2-enriched core samples collected near the fault. Furthermore, homoacetogenic bacteria, including Acetobacterium carbinolicum, were isolated from similar samples. Therefore, post-earthquake subseafloor microbial communities in the Japan Trench accretionary prism appear to be episodically dominated by homoacetogenic populations and potentially function due to the earthquake-induced low-temperature generation of H2. These post-earthquake microbial communities may eventually return to the steady-state communities dominated by oligotrophic heterotrophs and hydrogenotrophic and methylotrophic methanogens that are dependent on refractory organic matter in the sediment.
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Affiliation(s)
- Shinsuke Kawagucci
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Sanae Sakai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Eiji Tasumi
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Yuichiro Ueno
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology
- Earth-Life Science Institute, Tokyo Institute of Technology
| | - Naohiro Yoshida
- Earth-Life Science Institute, Tokyo Institute of Technology
- National Institute of Information and Communications Technology
| | - Takazo Shibuya
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Tomoyo Okumura
- Center for Advanced Marine Core Research, Kochi University
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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Chen Y, Wu N, Liu C, Mi T, Li J, He X, Li S, Sun Z, Zhen Y. Methanogenesis pathways of methanogens and their responses to substrates and temperature in sediments from the South Yellow Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152645. [PMID: 34998777 DOI: 10.1016/j.scitotenv.2021.152645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/19/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
Although coastal sediments are major contributors to the production of atmospheric methane, the effects of environmental conditions on methanogenesis and the community of methanogenic archaea are not well understood. Here, we investigated the methanogenesis pathways in nearshore and offshore sediments from the South Yellow Sea (SYS). Moreover, the effects of the supply of methanogenic substrates (H2/CO2, acetate, trimethylamine (TMA), and methanol) and temperature on methanogenesis and the community of methanogenic archaea were further determined. Methylotrophic, hydrogenotrophic and acetotrophic methanogenesis were found to be responsible for biogenic methane production in nearshore sediments. In the offshore sediments, methylotrophic methanogenesis was the predominant methanogenic pathway. The changes in methanogenic community structure under different substrate amendments were characterized. Lower diversities were detected in substrate-amended samples with methanogenic activity. Hydrogenotrophic Methanogenium, multitrophic Methanosarcina, methylotrophic Methanococcoide, Methanococcoide or methylotrophic Methanolobus were dominant in H2/CO2-, acetate-, TMA- and methanol-amended sediment slurries, respectively. PCoA showed that the methanogen community in H2/CO2 and acetate amendments exhibited greater differences than those in other treatments. Lower temperature (10 °C) limits hydrogenotrophic and acetoclastic methanogenesis, but methylotrophic methanogenesis is much less affected. The response of methanogen diversity to the incubation temperature varied among the different substrate-amended slurries. The multitrophic methanogen Methanosarcina became increasingly abundant in H2/CO2- and acetate-amended sediment slurries when the temperature increased from 10 to 30 °C.
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Affiliation(s)
- Ye Chen
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Nengyou Wu
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Changling Liu
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Tiezhu Mi
- Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Jing Li
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xingliang He
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Siqi Li
- Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
| | - Zhilei Sun
- Key Laboratory of Gas Hydrate, Ministry of Natural Resources, Qingdao Institute of Marine Geology, Qingdao 266237, China; Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Yu Zhen
- Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China; College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China.
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8
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Wang Y, Mairinger W, Raj SJ, Yakubu H, Siesel C, Green J, Durry S, Joseph G, Rahman M, Amin N, Hassan MZ, Wicken J, Dourng D, Larbi E, Adomako LAB, Senayah AK, Doe B, Buamah R, Tetteh-Nortey JNN, Kang G, Karthikeyan A, Roy S, Brown J, Muneme B, Sene SO, Tuffuor B, Mugambe RK, Bateganya NL, Surridge T, Ndashe GM, Ndashe K, Ban R, Schrecongost A, Moe CL. Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 763:143007. [PMID: 34718001 DOI: 10.1016/j.scitotenv.2020.143007] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal. OBJECTIVE Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities. METHODS In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods. RESULTS Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities). CONCLUSIONS Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.
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Affiliation(s)
- Yuke Wang
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Wolfgang Mairinger
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Suraja J Raj
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Habib Yakubu
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Casey Siesel
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jamie Green
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Sarah Durry
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - George Joseph
- Water Global Practice, The World Bank, Washington, DC, USA
| | - Mahbubur Rahman
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Nuhu Amin
- Environmental Interventions Unit, Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | | | - Eugene Larbi
- Training Research and Networking for Development (TREND), Accra, Ghana
| | | | | | - Benjamin Doe
- Training Research and Networking for Development (TREND), Accra, Ghana
| | - Richard Buamah
- Department of Civil Engineering, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Gagandeep Kang
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Arun Karthikeyan
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Sheela Roy
- Wellcome Research Laboratory, Christian Medical College, Vellore, India
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Bacelar Muneme
- Water Supply and Mapping, WE Consult, Maputo, Mozambique
| | - Seydina O Sene
- Initiative Prospective Agricole et Rurale (IPAR), Dakar, Senegal
| | - Benedict Tuffuor
- Training Research and Networking for Development (TREND), Accra, Ghana
| | - Richard K Mugambe
- Department of Disease Control and Environmental Health, Makerere University School of Public Health, Kampala, Uganda
| | - Najib Lukooya Bateganya
- Department of Environment and Public Health, Kampala Capital City Authority, Kampala, Uganda
| | - Trevor Surridge
- Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) GmbH, Lusaka, Zambia
| | | | - Kunda Ndashe
- Department of Environmental Health, Faculty of Health Science, Lusaka Apex Medical University, Lusaka, Zambia
| | - Radu Ban
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | | | - Christine L Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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9
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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] [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).
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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
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10
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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] [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).
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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
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11
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Rare Biosphere Archaea Assimilate Acetate in Precambrian Terrestrial Subsurface at 2.2 km Depth. GEOSCIENCES 2018. [DOI: 10.3390/geosciences8110418] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The deep biosphere contains a large portion of the total microbial communities on Earth, but little is known about the carbon sources that support deep life. In this study, we used Stable Isotope Probing (SIP) and high throughput amplicon sequencing to identify the acetate assimilating microbial communities at 2260 m depth in the bedrock of Outokumpu, Finland. The long-term and short-term effects of acetate on the microbial communities were assessed by DNA-targeted SIP and RNA targeted cell activation. The microbial communities reacted within hours to the amended acetate. Archaeal taxa representing the rare biosphere at 2260 m depth were identified and linked to the cycling of acetate, and were shown to have an impact on the functions and activity of the microbial communities in general through small key carbon compounds. The major archaeal lineages identified to assimilate acetate and metabolites derived from the labelled acetate were Methanosarcina spp., Methanococcus spp., Methanolobus spp., and unclassified Methanosarcinaceae. These archaea have previously been detected in the Outokumpu deep subsurface as minor groups. Nevertheless, their involvement in the assimilation of acetate and secretion of metabolites derived from acetate indicated an important role in the supporting of the whole community in the deep subsurface, where carbon sources are limited.
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12
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Chen SC, Huang HH, Lai MC, Weng CY, Chiu HH, Tang SL, Rogozin DY, Degermendzhy AG. Methanolobus psychrotolerans sp. nov., a psychrotolerant methanoarchaeon isolated from a saline meromictic lake in Siberia. Int J Syst Evol Microbiol 2018; 68:1378-1383. [DOI: 10.1099/ijsem.0.002685] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sheng-Chung Chen
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Hsing-Hua Huang
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Mei-Chin Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taiwan, ROC
- Department of Life Science, National Chung Hsing University, Taiwan, ROC
| | - Chieh-Yin Weng
- 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
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Andrey G. Degermendzhy
- Institute of Biophysics Siberian Branch of Russian Academy of Sciences, Krasnoyarsk 660036, Russia
- Siberian Federal University, Krasnoyarsk 660041, Russia
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13
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Abstract
Biogas production represents a fascinating process for the recovery of nutrients and renewable energy from various organic waste streams. The process is of interest for the production of value-added chemicals by mixed cultures and can also be applied in combined bioenergy production systems. Strategies and opportunities for optimization of biogas quality and quantity are presented.
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Affiliation(s)
- Caroline M Plugge
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.,Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands
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14
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Lindeboom REF, Shin SG, Weijma J, van Lier JB, Plugge CM. Piezo-tolerant natural gas-producing microbes under accumulating pCO 2. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:236. [PMID: 27826355 PMCID: PMC5097443 DOI: 10.1186/s13068-016-0634-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 10/06/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND It is known that a part of natural gas is produced by biogenic degradation of organic matter, but the microbial pathways resulting in the formation of pressurized gas fields remain unknown. Autogeneration of biogas pressure of up to 20 bar has been shown to improve the quality of biogas to the level of biogenic natural gas as the fraction of CO2 decreased. Still, the pCO2 is higher compared to atmospheric digestion and this may affect the process in several ways. In this work, we investigated the effect of elevated pCO2 of up to 0.5 MPa on Gibbs free energy, microbial community composition and substrate utilization kinetics in autogenerative high-pressure digestion. RESULTS In this study, biogas pressure (up to 2.0 MPa) was batch-wise autogenerated for 268 days at 303 K in an 8-L bioreactor, resulting in a population dominated by archaeal Methanosaeta concilii, Methanobacterium formicicum and Mtb. beijingense and bacterial Kosmotoga-like (31% of total bacterial species), Propioniferax-like (25%) and Treponema-like (12%) species. Related microorganisms have also been detected in gas, oil and abandoned coal-bed reservoirs, where elevated pressure prevails. After 107 days autogeneration of biogas pressure up to 0.50 MPa of pCO2, propionate accumulated whilst CH4 formation declined. Alongside the Propioniferax-like organism, a putative propionate producer, increased in relative abundance in the period of propionate accumulation. Complementary experiments showed that specific propionate conversion rates decreased linearly from 30.3 mg g-1 VSadded day-1 by more than 90% to 2.2 mg g-1 VSadded day-1 after elevating pCO2 from 0.10 to 0.50 MPa. Neither thermodynamic limitations, especially due to elevated pH2, nor pH inhibition could sufficiently explain this phenomenon. The reduced propionate conversion could therefore be attributed to reversible CO2-toxicity. CONCLUSIONS The results of this study suggest a generic role of the detected bacterial and archaeal species in biogenic methane formation at elevated pressure. The propionate conversion rate and subsequent methane production rate were inhibited by up to 90% by the accumulating pCO2 up to 0.5 MPa in the pressure reactor, which opens opportunities for steering carboxylate production using reversible CO2-toxicity in mixed-culture microbial electrosynthesis and fermentation.Graphical abstractThe role of pCO2 in steering product formation in autogenerative high pressure digestion.
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Affiliation(s)
- Ralph E. F. Lindeboom
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
- Section Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600 GA Delft, The Netherlands
| | - Seung Gu Shin
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
- Section Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600 GA Delft, The Netherlands
- School of Environmental Science and Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673 South Korea
| | - Jan Weijma
- Sub-Department of Environmental Technology, Wageningen University, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Jules B. van Lier
- Section Sanitary Engineering, Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600 GA Delft, The Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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15
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Holmes D, Smith J. Biologically Produced Methane as a Renewable Energy Source. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:1-61. [PMID: 27926429 DOI: 10.1016/bs.aambs.2016.09.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methanogens are a unique group of strictly anaerobic archaea that are more metabolically diverse than previously thought. Traditionally, it was thought that methanogens could only generate methane by coupling the oxidation of products formed by fermentative bacteria with the reduction of CO2. However, it has recently been observed that many methanogens can also use electrons extruded from metal-respiring bacteria, biocathodes, or insoluble electron shuttles as energy sources. Methanogens are found in both human-made and natural environments and are responsible for the production of ∼71% of the global atmospheric methane. Their habitats range from the human digestive tract to hydrothermal vents. Although biologically produced methane can negatively impact the environment if released into the atmosphere, when captured, it can serve as a potent fuel source. The anaerobic digestion of wastes such as animal manure, human sewage, or food waste produces biogas which is composed of ∼60% methane. Methane from biogas can be cleaned to yield purified methane (biomethane) that can be readily incorporated into natural gas pipelines making it a promising renewable energy source. Conventional anaerobic digestion is limited by long retention times, low organics removal efficiencies, and low biogas production rates. Therefore, many studies are being conducted to improve the anaerobic digestion process. Researchers have found that addition of conductive materials and/or electrically active cathodes to anaerobic digesters can stimulate the digestion process and increase methane content of biogas. It is hoped that optimization of anaerobic digesters will make biogas more readily accessible to the average person.
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16
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Shih CJ, Chen SC, Weng CY, Lai MC, Yang YL. Rapid identification of haloarchaea and methanoarchaea using the matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Sci Rep 2015; 5:16326. [PMID: 26541644 PMCID: PMC4635381 DOI: 10.1038/srep16326] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/13/2015] [Indexed: 12/23/2022] Open
Abstract
The aim of this study was to classify certain environmental haloarchaea and methanoarchaea using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and to expand the archaeal mass spectral database. A total of 69 archaea were collected including type strains and samples isolated locally from different environments. For extraction of the haloarchaeal total cell peptides/proteins, a simple method of acetonitrile extraction was developed. Cluster analysis conducted with the MALDI-TOF MS data overcame the high divergence in intragenomic 16S rRNA sequences in haloarchaea and clearly distinguished Methanohalophilus mahii from M. portucalensis. Putative biomarkers that can distinguish several particular archaeal genera were also assigned. In conclusion, this study expands the mass spectral database of peptide/protein fingerprints from bacteria and fungi to the archaea domain and provides a rapid identification platform for environmental archaeal samples.
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Affiliation(s)
- Chao-Jen Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan;,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.,Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.,Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan
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17
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Ng KK, Shi X, Ng HY. Evaluation of system performance and microbial communities of a bioaugmented anaerobic membrane bioreactor treating pharmaceutical wastewater. WATER RESEARCH 2015; 81:311-324. [PMID: 26086149 DOI: 10.1016/j.watres.2015.05.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/15/2015] [Accepted: 05/17/2015] [Indexed: 06/04/2023]
Abstract
In this study, a control anaerobic membrane bioreactor (C-AnMBR) and a bioaugmented anaerobic membrane bioreactor (B-AnMBR) were operated for 210 d to treat pharmaceutical wastewater. Both the bioreactors were fed with the pharmaceutical wastewater containing TCOD of 16,249 ± 714 mg/L and total dissolved solids (TDS) of 29,450 ± 2209 mg/L with an organic loading rate (OLR) of 13.0 ± 0.6 kgCOD/m(3)d. Under steady-state condition, an average total chemical oxygen demand (TCOD) removal efficiency of 46.1 ± 2.9% and 60.3 ± 2.8% was achieved by the C-AnMBR and the B-AnMBR, respectively. The conventional anaerobes in the C-AnMBR cannot tolerate the hypersaline conditions well, resulting in lower TCOD removal efficiency, biogas production and methane yield than the B-AnMBR seeded from the coastal shore. Pyrosequencing analysis indicated that marine bacterial species (Oliephilus sp.) and halophilic bacterial species (Thermohalobacter sp.) were only present in the B-AnMBR; these species could possibly degrade complex and recalcitrant organic matter and withstand hypersaline environments. Two different dominant archaeal communities, genus Methanosaeta (43.4%) and Methanolobus (61.7%), were identified as the dominant methanogens in the C-AnMBR and the B-AnMBR, respectively. The species of genus Methanolobus was reported resistant to penicillin and required sodium and magnesium for growth, which could enable it to thrive in the hypersaline environment.
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Affiliation(s)
- Kok Kwang Ng
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576, Singapore
| | - Xueqing Shi
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576, Singapore
| | - How Yong Ng
- Centre for Water Research, Department of Civil and Environmental Engineering, National University of Singapore, 1 Engineering Drive 2, 117576, Singapore.
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18
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Miura T, Kita A, Okamura Y, Aki T, Matsumura Y, Tajima T, Kato J, Nakashimada Y. Effect of salinity on methanogenic propionate degradation by acclimated marine sediment-derived culture. Appl Biochem Biotechnol 2015; 177:1541-52. [PMID: 26364311 DOI: 10.1007/s12010-015-1834-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/03/2015] [Indexed: 11/25/2022]
Abstract
Degradation of propionate under high salinity is needed for biomethane production from salt-containing feedstocks. In this study, marine sediment-derived culture was evaluated to determine the effect of salinity on methanogenic propionate degradation. Microbes in marine sediments were subjected to fed-batch cultivation on propionate for developing acclimatized cultures. The rate of propionate degradation increased eightfold during 10 rounds of cultivation. Microbial community composition was determined through pyrosequencing of 16S rRNA gene amplicons after 10 rounds of cultivation. Taxa analysis was conducted for the reads obtained by pyrosequencing. Known propionate degraders were undetectable in the acclimated culture. Comparison of bacterial taxa in the original sediment with those in the acclimated culture revealed that the populations of four bacterial taxa were significantly increased during acclimation. Methanolobus was the predominant archaea genus in the acclimated culture. The propionate degradation rate of the acclimated culture was not affected by salinity of up to equivalent of 1.9 % NaCl. The rate decreased at higher salinity levels and was more than 50 % of the maximum rate even at equivalent of 4.3 % NaCl.
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Affiliation(s)
- Toyokazu Miura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi, Hiroshima, 739-8530, Japan
- CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Akihisa Kita
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi, Hiroshima, 739-8530, Japan
- CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Yoshiko Okamura
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi, Hiroshima, 739-8530, Japan
- CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Tsunehiro Aki
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi, Hiroshima, 739-8530, Japan
- CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Yukihiko Matsumura
- Division of Energy and Environmental Engineering, Institute of Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi, Hiroshima, 739-8527, Japan
- CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Takahisa Tajima
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi, Hiroshima, 739-8530, Japan
- CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Junichi Kato
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi, Hiroshima, 739-8530, Japan
| | - Yutaka Nakashimada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi, Hiroshima, 739-8530, Japan.
- CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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19
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Chen SC, Chen MF, Lai MC, Weng CY, Wu SY, Lin S, Yang TF, Chen PC. Methanoculleus sediminis sp. nov., a methanogen from sediments near a submarine mud volcano. Int J Syst Evol Microbiol 2015; 65:2141-2147. [PMID: 25855623 DOI: 10.1099/ijs.0.000233] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, hydrogenotrophic methanogen, strain S3Fa(T), was isolated from sediments collected by Ocean Researcher I cruise ORI-934 in 2010 near the submarine mud volcano MV4 located at the upper slope of south-west Taiwan. The methanogenic substrates utilized by strain S3Fa(T) were formate and H2/CO2 but not acetate, secondary alcohols, methylamines, methanol or ethanol. Cells of strain S3Fa(T) were non-motile, irregular cocci, 0.5-1.0 μm in diameter. The surface-layer protein showed an Mr of 128,000.The optimum growth conditions were 37 °C, pH 7.1 and 0.17 M NaCl. The DNA G+C content of the genome of strain S3Fa(T) was 62.3 mol%. Phylogenetic analysis revealed that strain S3Fa(T) was most closely related to Methanoculleus marisnigri JR1(T) (99.3% 16S rRNA gene sequence similarity). Genome relatedness between strain S3Fa(T) and Methanoculleus marisnigri JR1(T) was computed using both genome-to-genome distance analysis (GGDA) and average nucleotide identity (ANI) with values of 46.3-55.5% and 93.08%, respectively. Based on morphological, phenotypic, phylogenetic and genomic relatedness data, it is evident that strain S3Fa(T) represents a novel species of the genus Methanoculleus, for which the name Methanoculleus sediminis sp. nov. is proposed. The type strain is S3Fa(T) ( = BCRC AR10044(T) = DSM 29354(T)).
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Affiliation(s)
- Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Fei Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC.,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan, ROC
| | - Tsanyao F Yang
- Department of Geosciences, National Taiwan University, Taipei, Taiwan, ROC
| | - Po-Chun Chen
- Central Geological Survey, MOEA, Taipei, Taiwan, ROC
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20
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Weng CY, Chen SC, Lai MC, Wu SY, Lin S, Yang TF, Chen PC. Methanoculleus taiwanensis sp. nov., a methanogen isolated from deep marine sediment at the deformation front area near Taiwan. Int J Syst Evol Microbiol 2015; 65:1044-1049. [DOI: 10.1099/ijs.0.000062] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A mesophilic, hydrogenotrophic methanogen, strain CYW4T, was isolated from deep-sea sediment obtained by the Ocean Researcher I cruiser, ORI-961, in 2011. The sediment was from the deformation front area offshore of south-western Taiwan. Here, seismic reflections indicated that methane hydrates were abundant. The methanogenic substrates utilized by strain CYW4T were formate and H2/CO2, but not acetate, secondary alcohols, methylamines, methanol and ethanol. Cells of strain CYW4T were non-motile, irregular cocci and 0.6–1.5 µm in diameter. The S-layer protein had an M
r of 112 000. The optimum growth conditions were at 37 °C, pH 8.1 and 0.08 M NaCl. Growth of the strain was stimulated by acetate. The G+C content of the chromosomal DNA of strain CYW4T was 61 mol%. Phylogenetic analysis revealed that strain CYW4T was most closely related to
Methanoculleus marisnigri
JR1T (96.82 % 16S rRNA gene sequence similarity). Based on the morphological, phenotypic and phylogenetic characteristics presented here, it is evident that strain CYW4T represents a novel species of the genus
Methanoculleus
, and the name Methanoculleus taiwanensis sp. nov. is proposed. The type strain is CYW4T ( = BCRC AR10043T = NBRC 110782T). The optical density of cultures of strain CYW4T dropped abruptly upon entering the stationary growth phase. During this time numerous particles of approximately 50 nm in diameter were observed on and around the cells. This suggests that strain CYW4T harbours a lytic virus that is induced in the stationary phase, which is of interest because only a few lytic viruses have been reported in methanogens.
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Affiliation(s)
- Chieh-Yin Weng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Sheng-Chung Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chin Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Sue-Yao Wu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Saulwood Lin
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Tsanyao F. Yang
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
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21
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2015. [DOI: 10.1099/ijs.0.000008-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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22
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Alawi M, Schneider B, Kallmeyer J. A procedure for separate recovery of extra- and intracellular DNA from a single marine sediment sample. J Microbiol Methods 2014; 104:36-42. [PMID: 24955890 DOI: 10.1016/j.mimet.2014.06.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/12/2014] [Accepted: 06/12/2014] [Indexed: 10/25/2022]
Abstract
Extracellular DNA (eDNA) is a ubiquitous biological compound in aquatic sediment and soil. Previous studies suggested that eDNA plays an important role in biogeochemical element cycling, horizontal gene transfer and stabilization of biofilm structures. Previous methods for eDNA extraction were either not suitable for oligotrophic sediments or only allowed quantification but no genetic analyses. Our procedure is based on cell detachment and eDNA liberation from sediment particles by sequential washing with an alkaline sodium phosphate buffer followed by a separation of cells and eDNA. The separated eDNA is then bound onto silica particles and purified, whereas the intracellular DNA from the separated cells is extracted using a commercial kit. The method provides extra- and intracellular DNA of high purity that is suitable for downstream applications like PCR. Extracellular DNA was extracted from organic-rich shallow sediment of the Baltic Sea, glacially influenced sediment of the Barents Sea and from the oligotrophic South Pacific Gyre. The eDNA concentration in these samples varied from 23 to 626ngg(-1) wet weight sediment. A number of experiments were performed to verify each processing step. Although extraction efficiency is higher than other published methods, it is not fully quantitative.
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Affiliation(s)
- Mashal Alawi
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, Potsdam, Germany.
| | - Beate Schneider
- University of Potsdam, Institute of Earth and Environmental Science, Geomicrobiology, Potsdam, Germany
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, Potsdam, Germany
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23
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Wang R, Zheng P, Xing YJ, Zhang M, Ghulam A, Zhao ZQ, Li W, Wang L. Anaerobic ferrous oxidation by heterotrophic denitrifying enriched culture. ACTA ACUST UNITED AC 2014; 41:803-9. [DOI: 10.1007/s10295-014-1424-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 01/23/2014] [Indexed: 12/01/2022]
Abstract
Abstract
Heterotrophic denitrifying enriched culture (DEC) from a lab-scale high-rate denitrifying reactor was discovered to perform nitrate-dependent anaerobic ferrous oxidation (NAFO). The DEC was systematically investigated to reveal their denitrification activity, their NAFO activity, and the predominant microbial population. The DEC was capable of heterotrophic denitrification with methanol as the electron donor, and autotrophic denitrification with ferrous salt as the electron donor named NAFO. The conversion ratios of ferrous-Fe and nitrate-N were 87.41 and 98.74 %, and the consumption Fe/N ratio was 2.3:1 (mol/mol). The maximum reaction velocity and half saturation constant of Fe were 412.54 mg/(l h) and 8,276.44 mg/l, and the counterparts of N were 20.87 mg/(l h) and 322.58 mg/l, respectively. The predominant bacteria were Hyphomicrobium, Thauera, and Flavobacterium, and the predominant archaea were Methanomethylovorans, Methanohalophilus, and Methanolobus. The discovery of NAFO by heterotrophic DEC is significant for the development of wastewater treatment and the biogeochemical iron cycle and nitrogen cycle.
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Affiliation(s)
- Ru Wang
- grid.13402.34 000000041759700X Department of Environmental Engineering Zhejiang University 310058 Hangzhou People’s Republic of China
| | - Ping Zheng
- grid.13402.34 000000041759700X Department of Environmental Engineering Zhejiang University 310058 Hangzhou People’s Republic of China
| | - Ya-Juan Xing
- grid.13402.34 000000041759700X Department of Environmental Engineering Zhejiang University 310058 Hangzhou People’s Republic of China
| | - Meng Zhang
- grid.13402.34 000000041759700X Department of Environmental Engineering Zhejiang University 310058 Hangzhou People’s Republic of China
| | - Abbas Ghulam
- grid.13402.34 000000041759700X Department of Environmental Engineering Zhejiang University 310058 Hangzhou People’s Republic of China
- grid.440562.1 Department of Chemical Engineering University of Gujrat Gujrat Pakistan
| | - Zhi-qing Zhao
- grid.469579.0 Quzhou College 324000 Quzhou People’s Republic of China
| | - Wei Li
- grid.13402.34 000000041759700X Department of Environmental Engineering Zhejiang University 310058 Hangzhou People’s Republic of China
| | - Lan Wang
- grid.13402.34 000000041759700X Department of Environmental Engineering Zhejiang University 310058 Hangzhou People’s Republic of China
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Shimizu S, Ueno A, Tamamura S, Naganuma T, Kaneko K. Methanoculleus horonobensis sp. nov., a methanogenic archaeon isolated from a deep diatomaceous shale formation. Int J Syst Evol Microbiol 2013; 63:4320-4323. [DOI: 10.1099/ijs.0.053520-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A methanogenic organism from the domain
Archaea
, designated strain T10T, was isolated from groundwater sampled from a deep diatomaceous shale formation located in Horonobe, Hokkaido, Japan. The strain utilized H2/CO2 and formate as substrates for methanogenesis. Cells were strictly anaerobic, Gram-negative-staining, flagellated, irregular coccoids, 0.7–1.6 µm in diameter, and occurred singly. The strain grew at 25–45 °C (optimum 37–42 °C), at pH 5.8–8.2 (optimum pH 6.7–6.8) and in the presence of 0–1.3 M NaCl (optimum 0.1–0.2 M NaCl). The G+C content of the genomic DNA was 62.9 mol%. 16S rRNA gene sequencing revealed that, although the strain is a member of the genus
Methanoculleus
, it clearly differed from all described species of this genus (95.5–98.3 % sequence similarity). Values for DNA–DNA hybridization with type strains of closely related
Methanoculleus
species were less than 50 %. Phenotypic and phylogenetic features of strain T10T clearly indicate that it represents a novel species of the genus
Methanoculleus
, for which the name Methanoculleus horonobensis sp. nov. is proposed. The type strain is T10T ( = DSM 21626T = JCM 15517T).
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Affiliation(s)
- Satoru Shimizu
- Horonobe Research Institute for the Subsurface Environment, Northern Advancement Center for Science and Technology, Horonobe-cho, Teshio-gun, Hokkaido 098-3221, Japan
| | - Akio Ueno
- Horonobe Research Institute for the Subsurface Environment, Northern Advancement Center for Science and Technology, Horonobe-cho, Teshio-gun, Hokkaido 098-3221, Japan
| | - Shuji Tamamura
- Horonobe Research Institute for the Subsurface Environment, Northern Advancement Center for Science and Technology, Horonobe-cho, Teshio-gun, Hokkaido 098-3221, Japan
| | - Takeshi Naganuma
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Katsuhiko Kaneko
- Horonobe Research Institute for the Subsurface Environment, Northern Advancement Center for Science and Technology, Horonobe-cho, Teshio-gun, Hokkaido 098-3221, Japan
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Unal B, Perry VR, Sheth M, Gomez-Alvarez V, Chin KJ, Nüsslein K. Trace elements affect methanogenic activity and diversity in enrichments from subsurface coal bed produced water. Front Microbiol 2012; 3:175. [PMID: 22590465 PMCID: PMC3349271 DOI: 10.3389/fmicb.2012.00175] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/20/2012] [Indexed: 12/01/2022] Open
Abstract
Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from coal bed methane (CBM) well produced water samples from the Powder River Basin, Wyoming. Methane production was shown to be limited both by a lack of additional trace elements as well as by the addition of an overly concentrated trace element mixture. Addition of trace elements at concentrations optimized for standard media enhanced methane production by 37%. After 7 days of incubation, the levels of mcrA transcripts in enrichment cultures with trace element amendment were much higher than in cultures without amendment. Transcript levels of mcrA correlated positively with elevated rates of methane production in supplemented enrichments (R2 = 0.95). Metabolically active methanogens, identified by clone sequences of mcrA mRNA retrieved from enrichment cultures, were closely related to Methanobacterium subterraneum and Methanobacterium formicicum. Enrichment cultures were dominated by M. subterraneum and had slightly higher predicted methanogenic richness, but less diversity than enrichment cultures without amendments. These results suggest that varying concentrations of trace elements in produced water from different subsurface coal wells may cause changing levels of CBM production and alter the composition of the active methanogenic community.
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Affiliation(s)
- Burcu Unal
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
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Guo H, Yu Z, Liu R, Zhang H, Zhong Q, Xiong Z. Methylotrophic methanogenesis governs the biogenic coal bed methane formation in Eastern Ordos Basin, China. Appl Microbiol Biotechnol 2012; 96:1587-97. [DOI: 10.1007/s00253-012-3889-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 12/29/2011] [Accepted: 01/02/2012] [Indexed: 10/14/2022]
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