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Niya B, Yaakoubi K, Beraich FZ, Arouch M, Meftah Kadmiri I. Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches. Heliyon 2024; 10:e28221. [PMID: 38560681 PMCID: PMC10979216 DOI: 10.1016/j.heliyon.2024.e28221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.
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Affiliation(s)
- Btissam Niya
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Kaoutar Yaakoubi
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Fatima Zahra Beraich
- Biodome.sarl, Research and Development Design Office of Biogas Technology, Casablanca, Morocco
| | - Moha Arouch
- Engineering, Industrial Management & Innovation Laboratory IMII, Faculty of Science and Technics (FST), Hassan 1st University of Settat, Morocco
| | - Issam Meftah Kadmiri
- Plant and Microbial Biotechnology Center, Moroccan Foundation of Advanced Science Innovation and Research MAScIR, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
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Dengler L, Meier J, Klingl A, Nißl L, Bellack A, Grohmann D, Rachel R, Huber H. A novel interdomain consortium from a Costa Rican oil well composed of Methanobacterium cahuitense sp. nov. and Desulfomicrobium aggregans sp. nov. Arch Microbiol 2023; 205:189. [PMID: 37055657 PMCID: PMC10102059 DOI: 10.1007/s00203-023-03533-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/20/2023] [Accepted: 03/31/2023] [Indexed: 04/15/2023]
Abstract
A novel interdomain consortium composed of a methanogenic Archaeon and a sulfate-reducing bacterium was isolated from a microbial biofilm in an oil well in Cahuita National Park, Costa Rica. Both organisms can be grown in pure culture or as stable co-culture. The methanogenic cells were non-motile rods producing CH4 exclusively from H2/CO2. Cells of the sulfate-reducing partner were motile rods forming cell aggregates. They utilized hydrogen, lactate, formate, and pyruvate as electron donors. Electron acceptors were sulfate, thiosulfate, and sulfite. 16S rRNA sequencing revealed 99% gene sequence similarity of strain CaP3V-M-L2AT to Methanobacterium subterraneum and 98.5% of strain CaP3V-S-L1AT to Desulfomicrobium baculatum. Both strains grew from 20 to 42 °C, pH 5.0-7.5, and 0-4% NaCl. Based on our data, type strains CaP3V-M-L2AT (= DSM 113354 T = JCM 39174 T) and CaP3V-S-L1AT (= DSM 113299 T = JCM 39179 T) represent novel species which we name Methanobacterium cahuitense sp. nov. and Desulfomicrobium aggregans sp. nov.
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Affiliation(s)
- Linda Dengler
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
| | - Julia Meier
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Andreas Klingl
- Plant Development and Electron Microscopy, Biocenter LMU Munich, Planegg-Martinsried, Germany
| | - Laura Nißl
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Annett Bellack
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Reinhard Rachel
- Centre for Electron Microscopy, Faculty for Biology and Preclinical Medicine, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Harald Huber
- Institute of Microbiology and Archaea Centre, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany.
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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. Sci Total Environ 2022; 763:143007. [PMID: 34718001 DOI: 10.1016/j.scitotenv.2020.143007] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [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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Hirano S, Ihara S, Wakai S, Dotsuta Y, Otani K, Kitagaki T, Ueno F, Okamoto A. Novel Methanobacterium Strain Induces Severe Corrosion by Retrieving Electrons from Fe0 under a Freshwater Environment. Microorganisms 2022; 10:270. [PMID: 35208725 PMCID: PMC8880523 DOI: 10.3390/microorganisms10020270] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 02/06/2023] Open
Abstract
Methanogens capable of accepting electrons from Fe0 cause severe corrosion in anoxic conditions. In previous studies, all iron-corrosive methanogenic isolates were obtained from marine environments. However, the presence of methanogens with corrosion ability using Fe0 as an electron donor and their contribution to corrosion in freshwater systems is unknown. Therefore, to understand the role of methanogens in corrosion under anoxic conditions in a freshwater environment, we investigated the corrosion activities of methanogens in samples collected from groundwater and rivers. We enriched microorganisms that can grow with CO2/NaHCO3 and Fe0 as the sole carbon source and electron donor, respectively, in ground freshwater. Methanobacterium sp. TO1, which induces iron corrosion, was isolated from freshwater. Electrochemical analysis revealed that strain TO1 can uptake electrons from the cathode at lower than −0.61 V vs SHE and has a redox-active component with electrochemical potential different from those of other previously reported methanogens with extracellular electron transfer ability. This study indicated the corrosion risk by methanogens capable of taking up electrons from Fe0 in anoxic freshwater environments and the necessity of understanding the corrosion mechanism to contribute to risk diagnosis.
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Quéméneur M, Mei N, Monnin C, Postec A, Wils L, Bartoli M, Guasco S, Pelletier B, Erauso G. Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia). Microorganisms 2021; 9:1360. [PMID: 34201651 DOI: 10.3390/microorganisms9071360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 01/01/2023] Open
Abstract
(1) Background: The geothermal spring of La Crouen (New Caledonia) discharges warm (42 °C) alkaline water (pH~9) enriched in dissolved nitrogen with traces of methane, but its microbial diversity has not yet been studied. (2) Methods: Cultivation-dependent and -independent methods (e.g., Illumina sequencing and quantitative PCR based on 16S rRNA gene) were used to describe the prokaryotic diversity of this spring. (3) Results: Prokaryotes were mainly represented by Proteobacteria (57% on average), followed by Cyanobacteria, Chlorofexi, and Candidatus Gracilibacteria (GN02/BD1-5) (each > 5%). Both potential aerobes and anaerobes, as well as mesophilic and thermophilic microorganisms, were identified. Some of them had previously been detected in continental hyperalkaline springs found in serpentinizing environments (The Cedars, Samail, Voltri, and Zambales ophiolites). Gammaproteobacteria, Ca. Gracilibacteria and Thermotogae were significantly more abundant in spring water than in sediments. Potential chemolithotrophs mainly included beta- and gammaproteobacterial genera of sulfate-reducers (Ca. Desulfobacillus), methylotrophs (Methyloversatilis), sulfur-oxidizers (Thiofaba, Thiovirga), or hydrogen-oxidizers (Hydrogenophaga). Methanogens (Methanobacteriales and Methanosarcinales) were the dominant Archaea, as found in serpentinization-driven and deep subsurface ecosystems. A novel alkaliphilic hydrogenotrophic methanogen (strain CAN) belonging to the genus Methanobacterium was isolated, suggesting that hydrogenotrophic methanogenesis occurs at La Crouen.
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In 't Zandt MH, Kip N, Frank J, Jansen S, van Veen JA, Jetten MSM, Welte CU. High-Level Abundances of Methanobacteriales and Syntrophobacterales May Help To Prevent Corrosion of Metal Sheet Piles. Appl Environ Microbiol 2019; 85:e01369-19. [PMID: 31420342 DOI: 10.1128/AEM.01369-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/11/2019] [Indexed: 11/20/2022] Open
Abstract
Iron sheet piles are widely used in flood protection, dike construction, and river bank reinforcement. Their corrosion leads to gradual deterioration and often makes replacement necessary. Natural deposit layers on these sheet piles can prevent degradation and significantly increase their life span. However, little is known about the mechanisms of natural protective layer formation. Here, we studied the microbially diverse populations of corrosion-protective deposit layers on iron sheet piles at the Gouderak pumping station in Zuid-Holland, the Netherlands. Deposit layers, surrounding sediment and top sediment samples were analyzed for soil physicochemical parameters, microbially diverse populations, and metabolic potential. Methanogens appeared to be enriched 18-fold in the deposit layers. After sequencing, metagenome assembly and binning, we obtained four nearly complete draft genomes of microorganisms (Methanobacteriales, two Coriobacteriales, and Syntrophobacterales) that were highly enriched in the deposit layers, strongly indicating a potential role in corrosion protection. Coriobacteriales and Syntrophobacterales could be part of a microbial food web degrading organic matter to supply methanogenic substrates. Methane-producing Methanobacteriales could metabolize iron, which may initially lead to mild corrosion but potentially stimulates the formation of a carbonate-rich protective deposit layer in the long term. In addition, Methanobacteriales and Coriobacteriales have the potential to interact with metal surfaces via direct interspecies or extracellular electron transfer. In conclusion, our study provides valuable insights into microbial populations involved in iron corrosion protection and potentially enables the development of novel strategies for in situ screening of iron sheet piles in order to reduce risks and develop more sustainable replacement practices.IMPORTANCE Iron sheet piles are widely used to reinforce dikes and river banks. Damage due to iron corrosion poses a significant safety risk and has significant economic impact. Different groups of microorganisms are known to either stimulate or inhibit the corrosion process. Recently, natural corrosion-protective deposit layers were found on sheet piles. Analyses of the microbial composition indicated a potential role for methane-producing archaea. However, the full metabolic potential of the microbial communities within these protective layers has not been determined. The significance of this work lies in the reconstruction of the microbial food web of natural corrosion-protective layers isolated from noncorroding metal sheet piles. With this work, we provide insights into the microbiological mechanisms that potentially promote corrosion protection in freshwater ecosystems. Our findings could support the development of screening protocols to assess the integrity of iron sheet piles to decide whether replacement is required.
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Alpana S, Vishwakarma P, Adhya TK, Inubushi K, Dubey SK. Molecular ecological perspective of methanogenic archaeal community in rice agroecosystem. Sci Total Environ 2017; 596-597:136-146. [PMID: 28431358 DOI: 10.1016/j.scitotenv.2017.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/02/2017] [Accepted: 04/02/2017] [Indexed: 06/07/2023]
Abstract
Methane leads to global warming owing to its warming potential higher than carbon dioxide (CO2). Rice fields represent the major source of methane (CH4) emission as the recent estimates range from 34 to 112 Tg CH4 per year. Biogenic methane is produced by anaerobic methanogenic archaea. Advances in high-throughput sequencing technologies and isolation methodologies enabled investigators to decipher methanogens to be unexpectedly diverse in phylogeny and ecology. Exploring the link between biogeochemical methane cycling and methanogen community dynamics can, therefore, provide a more effective mechanistic understanding of CH4 emission from rice fields. In this review, we summarize the current knowledge on the diversity and activity of methanogens, factors controlling their ecology, possible interactions between rice plants and methanogens, and their potential involvement in the source relationship of greenhouse gas emissions from rice fields.
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Affiliation(s)
- Singh Alpana
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - P Vishwakarma
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - T K Adhya
- School of Biotechnology, KIIT University, Bhubaneshwar 751024, India
| | - K Inubushi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 2718510, Japan
| | - S K Dubey
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Xu J, Jia Z, Lin X, Feng Y. DNA-based stable isotope probing identifies formate-metabolizing methanogenic archaea in paddy soil. Microbiol Res 2017; 202:36-42. [DOI: 10.1016/j.micres.2017.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Fortney NW, He S, Converse BJ, Beard BL, Johnson CM, Boyd ES, Roden EE. Microbial Fe(III) oxide reduction potential in Chocolate Pots hot spring, Yellowstone National Park. Geobiology 2016; 14:255-275. [PMID: 26750514 DOI: 10.1111/gbi.12173] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 11/10/2015] [Indexed: 06/05/2023]
Abstract
Chocolate Pots hot springs (CP) is a unique, circumneutral pH, iron-rich, geothermal feature in Yellowstone National Park. Prior research at CP has focused on photosynthetically driven Fe(II) oxidation as a model for mineralization of microbial mats and deposition of Archean banded iron formations. However, geochemical and stable Fe isotopic data have suggested that dissimilatory microbial iron reduction (DIR) may be active within CP deposits. In this study, the potential for microbial reduction of native CP Fe(III) oxides was investigated, using a combination of cultivation dependent and independent approaches, to assess the potential involvement of DIR in Fe redox cycling and associated stable Fe isotope fractionation in the CP hot springs. Endogenous microbial communities were able to reduce native CP Fe(III) oxides, as documented by most probable number enumerations and enrichment culture studies. Enrichment cultures demonstrated sustained DIR driven by oxidation of acetate, lactate, and H2 . Inhibitor studies and molecular analyses indicate that sulfate reduction did not contribute to observed rates of DIR in the enrichment cultures through abiotic reaction pathways. Enrichment cultures produced isotopically light Fe(II) during DIR relative to the bulk solid-phase Fe(III) oxides. Pyrosequencing of 16S rRNA genes from enrichment cultures showed dominant sequences closely affiliated with Geobacter metallireducens, a mesophilic Fe(III) oxide reducer. Shotgun metagenomic analysis of enrichment cultures confirmed the presence of a dominant G. metallireducens-like population and other less dominant populations from the phylum Ignavibacteriae, which appear to be capable of DIR. Gene (protein) searches revealed the presence of heat-shock proteins that may be involved in increased thermotolerance in the organisms present in the enrichments as well as porin-cytochrome complexes previously shown to be involved in extracellular electron transport. This analysis offers the first detailed insight into how DIR may impact the Fe geochemistry and isotope composition of a Fe-rich, circumneutral pH geothermal environment.
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Affiliation(s)
- N W Fortney
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - S He
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - B J Converse
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - B L Beard
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - C M Johnson
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - E S Boyd
- Department of Microbiology and Immunology, NASA Astrobiology Institute, Montana State University, Bozeman, MT, USA
| | - E E Roden
- Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA
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Battumur U, Yoon YM, Kim CH. Isolation and Characterization of a New Methanobacterium formicicum KOR-1 from an Anaerobic Digester Using Pig Slurry. Asian-Australas J Anim Sci 2016; 29:586-93. [PMID: 26949961 PMCID: PMC4782095 DOI: 10.5713/ajas.15.0507] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/08/2015] [Accepted: 07/17/2015] [Indexed: 11/28/2022]
Abstract
A new methanogen was isolated from an anaerobic digester using pig slurry in South Korea. Only one strain, designated KOR-1, was characterized in detail. Cells of KOR-1 were straight or crooked rods, non-motile, 5 to 15 μm long and 0.7 μm wide. They stained Gram-positive and produced methane from H2+CO2 and formate. Strain KOR-1 grew optimally at 38°C. The optimum pH for growth was 7.0. The strain grew at 0.5% to 3.0% NaCl, with optimum growth at 2.5% NaCl. The G+C content of genomic DNA of strain KOR-1 was 41 mol%. The strain tolerated ampicillin, penicillin G, kanamycin and streptomycin but tetracycline inhibited cell growth. A large fragment of the 16S rRNA gene (~1,350 bp) was obtained from the isolate and sequenced. Comparison of 16S rRNA genes revealed that strain KOR–1 is related to Methanobacterium formicicum (98%, sequence similarity), Methanobacterium bryantii (95%) and Methanobacterium ivanovii (93%). Phylogenetic analysis of the deduced mcrA gene sequences confirmed the closest relative as based on mcrA gene sequence analysis was Methanobacterium formicicum strain (97% nucleic acid sequence identity). On the basis of physiological and phylogenetic characteristics, strain KOR-1 is proposed as a new strain within the genus Methanobacterium, Methanobacterium formicicum KOR-1.
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Affiliation(s)
| | - Young-Man Yoon
- Biogas Research Center, Hankyong National University, Anseong 456-749, Korea
| | - Chang-Hyun Kim
- Biogas Research Center, Hankyong National University, Anseong 456-749, Korea ; Department of Animal Life and Environment Science, Hankyong National University, Anseong 456-749, Korea
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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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Kern T, Linge M, Rother M. Methanobacterium aggregans sp. nov., a hydrogenotrophic methanogenic archaeon isolated from an anaerobic digester. Int J Syst Evol Microbiol 2015; 65:1975-1980. [PMID: 25807978 DOI: 10.1099/ijs.0.000210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, strictly anaerobic, hydrogenotrophic methanogen, strain E09F.3T, was isolated from a commercial biogas plant in Germany. Cells of E09F.3T were Gram-stain-negative, non-motile, slightly curved rods, long chains of which formed large aggregates consisting of intertwined bundles of chains. Cells utilized H2+CO2 and, to a lesser extent, formate as substrates for growth and methanogenesis. The optimal growth temperature was around 40 °C; maximum growth rate was obtained at pH around 7.0 with approximately 6.8 mM NaCl. The DNA G+C content of strain E09F.3T was 39.1 mol%. Phylogenetic analyses based on 16S rRNA and mcrA gene sequences placed strain E09F.3T within the genus Methanobacterium. On the basis of 16S rRNA gene sequence similarity, strain E09F.3T was closely related to Methanobacterium congolense CT but morphological, physiological and genomic characteristics indicated that strain E09F.3T represents a novel species. The name Methanobacterium aggregans sp. nov. is proposed for this novel species, with strain E09F.3T ( = DSM 29428T = JCM 30569T) as the type strain.
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Affiliation(s)
- Tobias Kern
- Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany
| | - Mary Linge
- Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany
| | - Michael Rother
- Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany
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Jabłoński S, Rodowicz P, Łukaszewicz M. Methanogenic archaea database containing physiological and biochemical characteristics. Int J Syst Evol Microbiol 2015; 65:1360-1368. [PMID: 25604335 DOI: 10.1099/ijs.0.000065] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The methanogenic archaea are a group of micro-organisms that have developed a unique metabolic pathway for obtaining energy. There are 150 characterized species in this group; however, novel species continue to be discovered. Since methanogens are considered a crucial part of the carbon cycle in the anaerobic ecosystem, characterization of these micro-organisms is important for understanding anaerobic ecology. A methanogens database (MDB; http://metanogen.biotech.uni.wroc.pl/), including physiological and biochemical characteristics of methanogens, was constructed based on the descriptions of isolated type strains. Analysis of the data revealed that methanogens are able to grow from 0 to 122 °C. Methanogens growing at the same temperature may have very different growth rates. There is no clear correlation between the optimal growth temperature and the DNA G+C content. The following substrate preferences are observed in the database: 74.5% of archaea species utilize H2+CO2, 33% utilize methyl compounds and 8.5% utilize acetate. Utilization of methyl compounds (mainly micro-organisms belonging to the genera Methanosarcina and Methanolobus ) is seldom accompanied by an ability to utilize H2+CO2. Very often, data for described species are incomplete, especially substrate preferences. Additional research leading to completion of missing information and development of standards, especially for substrate utilization, would be very helpful.
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Affiliation(s)
| | - Paweł Rodowicz
- Department of Information, Wrocław University of Technology, Wrocław, Poland.,Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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Cadillo-Quiroz H, Bräuer SL, Goodson N, Yavitt JB, Zinder SH. Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium lacus isolated from northern peatlands. Int J Syst Evol Microbiol 2014; 64:1473-1480. [DOI: 10.1099/ijs.0.059964-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two mesophilic, hydrogenotrophic methanogens, designated strains SWAN1T and AL-21, were isolated from two contrasting peatlands: a near circumneutral temperate minerotrophic fen in New York State, USA, and an acidic boreal poor fen site in Alaska, USA, respectively. Cells of the two strains were rod-shaped, non-motile, stained Gram-negative and resisted lysis with 0.1 % SDS. Cell size was 0.6×1.5–2.8 µm for strain SWAN1T and 0.45–0.85×1.5–35 µm for strain AL-21. The strains used H2/CO2 but not formate or other substrates for methanogenesis, grew optimally around 32–37 °C, and their growth spanned through a slightly low to neutral pH range (4.7–7.1). Strain AL-21 grew optimally closer to neutrality at pH 6.2, whereas strain SWAN1T showed a lower optimal pH at 5.4–5.7. The two strains were sensitive to NaCl with a maximal tolerance at 160 mM for strain SWAN1T and 50 mM for strain AL-21. Na2S was toxic at very low concentrations (0.01–0.8 mM), resulting in growth inhibition above these values. The DNA G+C content of the genomes was 35.7 mol% for strain SWAN1T and 35.8 mol% for strain AL-21. Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains are members of the genus
Methanobacterium
. Strain SWAN1T shared 94–97 % similarity with the type strains of recognized species of the genus
Methanobacterium
, whereas strain AL-21 shared 99 % similarity with
Methanobacterium lacus
17A1T. On the basis of phenotypic, genomic and phylogenetic characteristics, strain SWAN1T ( = DSM 25820T = JCM 18151T) is proposed as the type strain of a novel species, Methanobacterium paludis sp. nov., while strain AL-21 is proposed as a second strain of
Methanobacterium lacus
.
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Affiliation(s)
| | - Suzanna L. Bräuer
- Department of Biology, Appalachian State University, Boone, NC 28608, USA
| | - Noah Goodson
- Department of Biology, Appalachian State University, Boone, NC 28608, USA
| | - Joseph B. Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY 14853, USA
| | - Stephen H. Zinder
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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Schirmack J, Mangelsdorf K, Ganzert L, Sand W, Hillebrand-voiculescu A, Wagner D. Methanobacterium movilense sp. nov., a hydrogenotrophic, secondary-alcohol-utilizing methanogen from the anoxic sediment of a subsurface lake. Int J Syst Evol Microbiol 2014; 64:522-7. [DOI: 10.1099/ijs.0.057224-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain of methanogenic archaea, designated MC-20T, was isolated from the anoxic sediment of a subsurface lake in Movile Cave, Mangalia, Romania. Cells were non-motile, Gram-stain-negative rods 3.5–4.0 µm in length and 0.6–0.7 µm in width, and occurred either singly or in short chains. Strain MC-20T was able to utilize H2/CO2, formate, 2-propanol and 2-butanol as substrate, but not acetate, methanol, ethanol, dimethyl sulfide, monomethylamine, dimethylamine or trimethylamine. Neither trypticase peptone nor yeast extract was required for growth. The major membrane lipids of strain MC-20T were archaeol phosphatidylethanolamine and diglycosyl archaeol, while archaeol phosphatidylinositol and glycosyl archaeol were present only in minor amounts. Optimal growth was observed at 33 °C, pH 7.4 and 0.08 M NaCl. Based on phylogenetic analysis of 16S rRNA gene sequences, strain MC-20T was closely affiliated with
Methanobacterium oryzae
FPiT (similarity 97.1 %) and
Methanobacterium lacus
17A1T (97.0 %). The G+C content of the genomic DNA was 33.0 mol%. Based on phenotypic and genotypic differences, strain MC-20T was assigned to a novel species of the genus
Methanobacterium
for which the name Methanobacterium movilense sp. nov. is proposed. The type strain is MC-20T ( = DSM 26032T = JCM 18470T).
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Saini R, Kapoor R, Kumar R, Siddiqi TO, Kumar A. CO2 utilizing microbes — A comprehensive review. Biotechnol Adv 2011; 29:949-60. [PMID: 21856405 DOI: 10.1016/j.biotechadv.2011.08.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 08/04/2011] [Accepted: 08/05/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Rashmi Saini
- Department of Botany, North Campus, University of Delhi, New Delhi-110007, India
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Abstract
Two mesophilic methanogenic strains, designated TS-2(T) and GH(T), were isolated from sediments of Tuosu lake and Gahai lake, respectively, in the Qaidam basin, Qinghai province, China. Cells of both isolates were rods (about 0.3-0.5×2-5 µm) with blunt rounded ends and Gram-staining-positive. Strain TS-2(T) was motile with one or two polar flagella and used only H(2)/CO(2) for growth and methanogenesis. Strain GH(T) was non-motile, used both H(2)/CO(2) and formate and displayed a variable cell arrangement depending on the substrate: long chains when growing in formate (50 mM) or under high pressure H(2) and single cells under low pressure H(2). Phylogenetic analysis based on 16S rRNA gene sequences placed the two isolates in the genus Methanobacterium. Strain TS-2(T) was most closely related to Methanobacterium alcaliphilum NBRC 105226(T) (96% 16S rRNA gene sequence similarity). Phylogenetic analysis based on the alpha subunit of methyl-coenzyme M reductase also supported the affiliation of the two isolates with the genus Methanobacterium. DNA-DNA relatedness between the isolates and M. alcaliphilum DSM 3387(T) was 39-53%. Hence we propose two novel species, Methanobacterium movens sp. nov. (type strain TS-2(T)=AS 1.5093(T)=JCM 15415(T)) and Methanobacterium flexile sp. nov. (type strain GH(T)=AS 1.5092(T)=JCM 15416(T)).
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Affiliation(s)
- Jinxing Zhu
- Graduate University, Chinese Academy of Sciences, Beijing 100049, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiaoli Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Mori K, Harayama S. Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., mesophilic methanogens isolated from salty environments. Int J Syst Evol Microbiol 2011; 61:138-143. [DOI: 10.1099/ijs.0.022723-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two methane-producing archaea, designated Mic5c12T and Mic6c05T, were isolated from sludge deposited in a crude oil storage tank and a tubercle on the interior of a pipe transporting natural gas-containing brine, respectively. The isolates were Gram-staining-variable, non-motile rods and grew only on H2/CO2. Strain Mic6c05T produced methane from some alcohols without showing any growth; strain Mic5c12T did not utilize alcohols. The optimum growth conditions for strain Mic5c12T were 35 °C, pH 6.5 and 0–0.68 M NaCl and for strain Mic6c05T were 40 °C, pH 6.0–7.5 and 0.34 M NaCl. Strain Mic5c12T was halotolerant and strain Mic6c05T was halophilic. Comparative 16S rRNA gene sequence analysis revealed that strains Mic5c12T and Mic6c05T belonged to the genus Methanobacterium and their closest relative was Methanobacterium subterraneum A8pT (97.3 and 97.9 % 16S rRNA gene sequence similarity, respectively). The findings from the 16S rRNA gene sequence analyses were supported by analysis of McrA, the alpha subunit of methyl-coenzyme M reductase. On the basis of phylogenetic analyses and phenotypic characteristics, two novel species are proposed, Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., with type strains Mic5c12T (=NBRC 105198T =DSM 22353T) and Mic6c05T (=NBRC 105197T =DSM 21974T), respectively.
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Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shigeaki Harayama
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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Porat I, Vishnivetskaya TA, Mosher JJ, Brandt CC, Yang ZK, Brooks SC, Liang L, Drake MM, Podar M, Brown SD, Palumbo AV. Characterization of archaeal community in contaminated and uncontaminated surface stream sediments. Microb Ecol 2010; 60:784-95. [PMID: 20725722 PMCID: PMC2974187 DOI: 10.1007/s00248-010-9734-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 08/01/2010] [Indexed: 05/22/2023]
Abstract
Archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of Oak Ridge, TN, USA. The distribution of the Archaea was determined by pyrosequencing analysis of the V4 region of 16S rRNA amplified from 12 streambed surface sediments. Crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from Euryarchaeota. Phylogenetic analysis further classified the Crenarchaeota as a Freshwater Group, Miscellaneous Crenarchaeota group, Group I3, Rice Cluster VI and IV, Marine Group I and Marine Benthic Group B; and the Euryarchaeota into Methanomicrobiales, Methanosarcinales, Methanobacteriales, Rice Cluster III, Marine Benthic Group D, Deep Sea Hydrothermal Vent Euryarchaeota 1 and Eury 5. All groups were previously described. Both hydrogen- and acetate-dependent methanogens were found in all samples. Most of the groups (with 60% of the sequences) described in this study were not similar to any cultivated isolates, making it difficult to discern their function in the freshwater microbial community. A significant decrease in the number of sequences, as well as in the diversity of archaeal communities was found in the contaminated sites. The Marine Group I, including the ammonia oxidizer Nitrosopumilus maritimus, was the dominant group in both mercury and uranium/nitrate-contaminated sites. The uranium-contaminated site also contained a high concentration of nitrate, thus Marine Group I may play a role in nitrogen cycle.
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Affiliation(s)
- Iris Porat
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | | | - Jennifer J. Mosher
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Craig C. Brandt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Zamin K. Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Scott C. Brooks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Liyuan Liang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Meghan M. Drake
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Steven D. Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
| | - Anthony V. Palumbo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6342 USA
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Suryawanshi PC, Chaudhari AB, Kothari RM. Mesophilic anaerobic digestion: first option for waste treatment in tropical regions. Crit Rev Biotechnol 2010; 30:259-82. [DOI: 10.3109/07388551.2010.487047] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Krivushin KV, Shcherbakova VA, Petrovskaya LE, Rivkina EM. Methanobacterium veterum sp. nov., from ancient Siberian permafrost. Int J Syst Evol Microbiol 2009; 60:455-459. [PMID: 19654368 DOI: 10.1099/ijs.0.011205-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A methanogenic archaeon, strain MK4(T), was isolated from ancient permafrost after long-term selective anaerobic cultivation. The cells were rods, 2.0-8.0 microm long and 0.40-0.45 microm wide, and stained Gram-negative. Optimal growth was observed at 28 degrees C and pH 7.0-7.2 and in 0.05 M NaCl. The isolate used H(2) plus CO(2), methylamine plus H(2) and methanol plus H(2) as sources for growth and methanogenesis. Phylogenetic analysis of the 16S rRNA gene sequence of the strain showed close affinity with Methanobacterium bryantii (similarity >99 % to the type strain). On the basis of the level of DNA-DNA hybridization (62 %) between strain MK4(T) and Methanobacterium bryantii VKM B-1629(T) and phenotypic and phylogenetic differences, strain MK4(T) was assigned to a novel species of the genus Methanobacterium, Methanobacterium veterum sp. nov., with the type strain MK4(T) (=DSM 19849(T) =VKM B-2440(T)).
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Affiliation(s)
- Kirill V Krivushin
- Institute of Physicochemical and Biological Problems in Soil Sciences, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russian Federation
| | - Viktoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russian Federation
| | - Lada E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, 117997 GSP, Moscow V-437, Russian Federation
| | - Elizaveta M Rivkina
- Institute of Physicochemical and Biological Problems in Soil Sciences, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russian Federation
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Hwang K, Shin SG, Kim J, Hwang S. Methanogenic profiles by denaturing gradient gel electrophoresis using order-specific primers in anaerobic sludge digestion. Appl Microbiol Biotechnol 2008; 80:269-76. [PMID: 18536912 DOI: 10.1007/s00253-008-1544-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Revised: 05/14/2008] [Accepted: 05/15/2008] [Indexed: 10/22/2022]
Abstract
In the present study, the diversity of methanogenic populations was monitored for 25 days, together with the process data for an anaerobic batch reactor treating waste-activated sludge. To understand this microbial diversity and dynamics, 16S rRNA-gene-targeted denaturing gradient gel electrophoresis (DGGE) fingerprinting was conducted at two different taxonomic levels: the domain and order levels. The DGGE profiles of the domain Archaea and the three orders Methanosarcinales, Methanomicrobiales, and Methanobacteriales were comparatively analyzed after each DGGE band was sequenced to enable identification. The DGGE profiles of the three orders showed methanogens belonging to each order that were not detected in the DGGE profile of the Archaea. This discrepancy may have resulted from PCR bias or differences in the abundances of the three microbial orders in the anaerobic bioreactor. In conclusion, to fully understand the detailed methanogenic diversity and dynamics in an anaerobic bioreactor, it is necessary to conduct DGGE analysis with 16S rRNA gene primers that target lower taxonomic groups.
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Freeman SA, Sierra-Alvarez R, Altinbas M, Hollingsworth J, Stams AJM, Smidt H. Molecular characterization of mesophilic and thermophilic sulfate reducing microbial communities in expanded granular sludge bed (EGSB) reactors. Biodegradation 2007; 19:161-77. [PMID: 17479349 DOI: 10.1007/s10532-007-9123-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 04/10/2007] [Indexed: 10/23/2022]
Abstract
The microbial communities established in mesophilic and thermophilic expanded granular sludge bed reactors operated with sulfate as the electron acceptor were analyzed using 16S rRNA targeted molecular methods, including denaturing gradient gel electrophoresis, cloning, and phylogenetic analysis. Bacterial and archaeal communities were examined over 450 days of operation treating ethanol (thermophilic reactor) or ethanol and later a simulated semiconductor manufacturing wastewater containing citrate, isopropanol, and polyethylene glycol 300 (mesophilic reactor), with and without the addition of copper(II). Analysis, of PCR-amplified 16S rRNA gene fragments using denaturing gradient gel electrophoresis revealed a defined shift in microbial diversity in both reactors following a change in substrate composition (mesophilic reactor) and in temperature of operation from 30 degrees C to 55 degrees C (thermophilic reactor). The addition of copper(II) to the influent of both reactors did not noticeably affect the composition of the bacterial or archaeal communities, which is in agreement with the very low soluble copper concentrations (3-310 microg l(-1)) present in the reactor contents as a consequence of extensive precipitation of copper with biogenic sulfides. Furthermore, clone library analysis confirmed the phylogenetic diversity of sulfate-reducing consortia in mesophilic and thermophilic sulfidogenic reactors operated with simple substrates.
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Affiliation(s)
- Stephanie A Freeman
- Department of Chemical and Environmental Engineering, University of Arizona, P.O. Box 21001, Tucson, AZ 85721, USA
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Abstract
The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.
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Affiliation(s)
- Bonnie Chaban
- Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada
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26
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Kopp RE, Kirschvink JL, Hilburn IA, Nash CZ. The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis. Proc Natl Acad Sci U S A 2005; 102:11131-6. [PMID: 16061801 PMCID: PMC1183582 DOI: 10.1073/pnas.0504878102] [Citation(s) in RCA: 390] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Indexed: 11/18/2022] Open
Abstract
Although biomarker, trace element, and isotopic evidence have been used to claim that oxygenic photosynthesis evolved by 2.8 giga-annum before present (Ga) and perhaps as early as 3.7 Ga, a skeptical examination raises considerable doubt about the presence of oxygen producers at these times. Geological features suggestive of oxygen, such as red beds, lateritic paleosols, and the return of sedimentary sulfate deposits after a approximately 900-million year hiatus, occur shortly before the approximately 2.3-2.2 Ga Makganyene "snowball Earth" (global glaciation). The massive deposition of Mn, which has a high redox potential, practically requires the presence of environmental oxygen after the snowball. New age constraints from the Transvaal Supergroup of South Africa suggest that all three glaciations in the Huronian Supergroup of Canada predate the Snowball event. A simple cyanobacterial growth model incorporating the range of C, Fe, and P fluxes expected during a partial glaciation in an anoxic world with high-Fe oceans indicates that oxygenic photosynthesis could have destroyed a methane greenhouse and triggered a snowball event on time-scales as short as 1 million years. As the geological evidence requiring oxygen does not appear during the Pongola glaciation at 2.9 Ga or during the Huronian glaciations, we argue that oxygenic cyanobacteria evolved and radiated shortly before the Makganyene snowball.
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Affiliation(s)
- Robert E Kopp
- Division of Geological and Planetary Sciences, California Institute of Technology 170-25, Pasadena, CA 91125, USA.
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Abstract
Two methanogenic strains, 8-2T and 4-1, with rod-shaped (0·4–0·5×3–5 μm), non-motile cells, sometimes observed in chains, were isolated from two anaerobic digesters in Beijing, China. The two strains used H2/CO2 and formate for growth and produced methane. The temperature range for growth was 25–50 °C, with fastest growth at 37 °C. The pH ranges for growth and methane production were 6·5–8·0 for strain 8-2T and 6·8–8·6 for strain 4-1, with the fastest growth at pH 7·2 for strain 8-2T and pH 7·5–7·7 for strain 4-1. The G+C content of genomic DNA for strain 8-2T was 38·9 mol%. The similarity levels of the 16S rRNA sequence of strain 8-2T with other species of the genus Methanobacterium ranged from 93·8 to 96·0 %. Based on the phylogenetic analysis and phenotypic characteristics, the novel species Methanobacterium beijingense sp. nov. is proposed, with the type strain 8-2T (=DSM 15999T=CGMCC 1.5011T).
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Affiliation(s)
- Kai Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Xiaoli Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
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28
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Shlimon AG, Friedrich MW, Niemann H, Ramsing NB, Finster K. Methanobacterium aarhusense sp. nov., a novel methanogen isolated from a marine sediment (Aarhus Bay, Denmark). Int J Syst Evol Microbiol 2004; 54:759-763. [PMID: 15143021 DOI: 10.1099/ijs.0.02994-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain H2-LRT, a 5–18 μm long and 0·7 μm wide filamentous, mesophilic, moderately halophilic, non-motile hydrogenotrophic methanogen, was isolated from marine sediment of Aarhus Bay, Denmark, 1·7 m below the sediment surface. On the basis of 16S rRNA gene comparison with sequences of known methanogens, strain H2-LRT could be affiliated to the genus Methanobacterium. The strain forms a distinct line of descent within this genus, with Methanobacterium oryzae (95·9 % sequence identity) and Methanobacterium bryantii (95·7 % sequence identity) as its closest relatives. The 16S rRNA-based affiliation was supported by comparison of the mcrA gene, which encodes the α-subunit of methyl-coenzyme M reductase. Strain H2-LRT grew only on H2/CO2. The DNA G+C content is 34·9 mol%. Optimum growth temperature was 45 °C. The strain grew equally well at pH 7·5 and 8. No growth or methane production was observed below pH 5 or above pH 9. Strain H2-LRT grew well within an NaCl concentration range of 100 and 900 mM. No growth or methane production was observed at 1 M NaCl. At 50 mM NaCl, growth and methane production were reduced. Based on 16S rRNA gene sequence analysis, the isolate is proposed to represent a novel taxon within the genus Methanobacterium, namely Methanobacterium aarhusense sp. nov. The type strain is H2-LRT (=DSM 15219T=ATCC BAA-828T).
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Affiliation(s)
- Adris Georgis Shlimon
- Department of Microbiology, Institute of Biological Science, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Michael W Friedrich
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str, D-35043 Marburg, Germany
| | - Helge Niemann
- Max-Planck-Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Niels Birger Ramsing
- Department of Microbiology, Institute of Biological Science, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Kai Finster
- Department of Microbiology, Institute of Biological Science, Aarhus University, DK-8000 Aarhus C, Denmark
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Abstract
In the past two decades, a number of biotechnologies for anaerobic (methanogenic) wastewater treatment have been created, and practical applications of these processes are now being extended to more recalcitrant wastewaters and to wastewaters at extreme temperatures. Our knowledge of methanogenic organic degradation associated with bioreactors is also accumulating at a rapid rate. The recent advancement of such fundamental understanding is attributed to modern molecular biology techniques applied to the study of microbial communities and to continuous challenges to the cultivation of many important but recalcitrant anaerobes in bioreactors.
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Affiliation(s)
- Y Sekiguchi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, 940-2188, Niigata, Japan.
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