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Prakash O, Dodsworth JA, Dong X, Ferry JG, L'Haridon S, Imachi H, Kamagata Y, Rhee SK, Sagar I, Shcherbakova V, Wagner D, Whitman WB. Proposed minimal standards for description of methanogenic archaea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37097839 DOI: 10.1099/ijsem.0.005500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.
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Affiliation(s)
- Om Prakash
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
- Symbiosis Centre for Climate Change and Sustainability, Symbiosis International (Deemed University), Lavale, Pune-412115, Maharashtra, India
| | - Jeremy A Dodsworth
- Department of Biology, California State University, San Bernardino, CA 92407, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephane L'Haridon
- CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, University of Brest, F-29280, Plouzané, France
| | - Hiroyuki Imachi
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Yoichi Kamagata
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8560, Japan
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Chungdae-ro 1, Cheongju 28644, Republic of Korea
| | - Isita Sagar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science, Ganeshkhind, Pune, 411007, Maharashtra, India
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, All-Russian Collection of Microorganisms (VKM), Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences, Prospect Nauki 3, Pushchino, Moscow, 142290, Russian Federation
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg A71-359, 14473 Potsdam, Germany
- Institut of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Li J, Ran X, Zhou M, Wang K, Wang H, Wang Y. Oxidative stress and antioxidant mechanisms of obligate anaerobes involved in biological waste treatment processes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156454. [PMID: 35667421 DOI: 10.1016/j.scitotenv.2022.156454] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
In-depth understanding of the molecular mechanisms and physiological consequences of oxidative stress is still limited for anaerobes. Anaerobic biotechnology has become widely accepted by the wastewater/sludge industry as a better alternative to more conventional but costly aerobic processes. However, the functional anaerobic microorganisms used in anaerobic biotechnology are frequently hampered by reactive oxygen/nitrogen species (ROS/RNS)-mediated oxidative stress caused by exposure to stressful factors (e.g., oxygen and heavy metals), which negatively impact treatment performance. Thus, identifying stressful factors and understanding antioxidative defense mechanisms of functional obligate anaerobes are crucial for the optimization of anaerobic bioprocesses. Herein, we present a comprehensive overview of oxidative stress and antioxidant mechanisms of obligate anaerobes involved in anaerobic bioprocesses; as examples, we focus on anaerobic ammonium oxidation bacteria and methanogenic archaea. We summarize the primary stress factors in anaerobic bioprocesses and the cellular antioxidant defense systems of functional anaerobes, a consortia of enzymatic and nonenzymatic mechanisms. The dual role of ROS/RNS in cellular processes is elaborated; at low concentrations, they have vital cell signaling functions, but at high concentrations, they cause oxidative damage. Finally, we highlight gaps in knowledge and future work to uncover antioxidant and damage repair mechanisms in obligate anaerobes. This review provides in-depth insights and guidance for future research on oxidative stress of obligate anaerobes to boost the accurate regulation of anaerobic bioprocesses in challenging and changing operating conditions.
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Affiliation(s)
- Jia Li
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Xiaochuan Ran
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Mingda Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Kaichong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Han Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China.
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
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Harris RL, Vetter MCYL, van Heerden E, Cason E, Vermeulen JG, Taneja A, Kieft TL, DeCoste CJ, Laevsky GS, Onstott TC. FISH-TAMB, a Fixation-Free mRNA Fluorescent Labeling Technique to Target Transcriptionally Active Members in Microbial Communities. MICROBIAL ECOLOGY 2022; 84:182-197. [PMID: 34406445 PMCID: PMC9250922 DOI: 10.1007/s00248-021-01809-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Keystone species or ecological engineers are vital to the health of an ecosystem; however, often, their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, the fast hybridization time of as short as 15 min at target cells' growth temperature, and the omission of washing steps. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB's ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A (mcrA) expressed in (1) Escherichia coli containing a plasmid with a partial mcrA gene of the methanogen Methanosarcina barkeri (E. coli mcrA+); (2) M. barkeri; and (3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA and thus is a versatile addition to the molecular ecologist's toolkit, with potentially widespread application in the field of environmental microbiology.
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Affiliation(s)
- Rachel L Harris
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
| | - Maggie C Y Lau Vetter
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA.
- Laboratory of Extraterrestrial Ocean Systems, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, Hainan, China.
| | - Esta van Heerden
- Centre for Water Sciences and Management, North West University, Potchefstroom, South Africa
- iWater Pty Ltd, 5 Walter Sisulu Rd, Park West, Bloemfontein, 9301, South Africa
| | - Errol Cason
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- Department of Animal-, Wildlife- and Grassland Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - Jan-G Vermeulen
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, 9301, South Africa
- Department of Virology, University of the Free State, Bloemfontein, 9301, South Africa
| | - Anjali Taneja
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
- McCourt School of Public Policy, Georgetown University, Washington, DC, 20057, USA
| | - Thomas L Kieft
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, 87801, USA
| | - Christina J DeCoste
- Flow Cytometry Resource Facility, Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Gary S Laevsky
- Confocal Imaging Facility, Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, 08544, USA
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Luo D, Li Y, Yao H, Chapman SJ. Effects of different carbon sources on methane production and the methanogenic communities in iron rich flooded paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153636. [PMID: 35124061 DOI: 10.1016/j.scitotenv.2022.153636] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/25/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Various carbon sources as substrates and electron donors can produce methane via different metabolic pathways. In particular, the methane produced by rice cultivation has a severe impact on climate change. However, how Fe3+, the most abundant oxide in paddy soil, mediates the methanogenesis of different carbon sources is unknown. In this study, we investigated the effect of four carbon sources with different chain lengths (acetate, glucose, nonanoate, and starch) on CH4 production and associated methanogens in iron-rich paddy soil over 90 days of anaerobic incubation. We found that glucose and starch were the more preferential substrates for liberating methane compared to acetate, and the rate was also faster. Nonanoate was unable to support methane production. Methanosarcinales and Methanobacteriales were the most predominant methanogenic archaea as shown by 16S rRNA gene sequencing, though their abundance changed over time. Additionally, a significantly higher content of iron-reducing bacteria was observed in the glucose and starch treatments, and it was significantly positively correlated with the copy number of the methanogenic mcrA gene. Together, we confirmed the methanogenic capacity of different carbon sources and their related microorganisms. We also showed that iron oxides play a central role in regulating methane emissions from paddy soils and need more attention to be paid to them.
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Affiliation(s)
- Dan Luo
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Institute of Urban Environment, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yaying Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Institute of Urban Environment, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China
| | - Huaiying Yao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Institute of Urban Environment, Chinese Academy of Sciences, Ningbo 315800, People's Republic of China; Research Center for Environmental Ecology and Engineering, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan 430073, People's Republic of China.
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Saha MK, Mia S, Abdul Ahad Biswas A, Sattar MA, Kader MA, Jiang Z. Potential methane emission reduction strategies from rice cultivation systems in Bangladesh: A critical synthesis with global meta-data. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 310:114755. [PMID: 35219203 DOI: 10.1016/j.jenvman.2022.114755] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/02/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Methane (CH4) is one of the dominant greenhouse gases (GHG) that is largely emitted from rice fields and thus, significantly contributes to global warming. Significant efforts have been made to find out suitable strategies to mitigate CH4 emission from rice culture. However, the effectiveness of these management practices is often diverse with negative, no, or positive impacts making it difficult to adopt under a particular condition. The diversity of rice cultivation in terms of agro-climatic conditions and cultivation practices makes it difficult for providing specific recommendations. Here, we collected data from a total of 198 studies reporting 1052 observations. The management practices are categorized into five different management practices i.e., water, organic and inorganic fertilizer management, crop establishment method, and agronomic practices while major categories were subdivided into different classes. To test statistically significant differences in the effectiveness between major management practices, an analysis of variance (ANOVA) was applied. The Gaussian and bootstrapping model were applied to find out the best estimate of the effectiveness of each practice. In addition, mechanisms controlling the CH4 emission reductions were synthesized. Next, the adoption potentials of these practices were assessed based on the existing rice cultivation systems in Bangladesh. Our results showed that water and organic matter management were the most effective methods irrespective of the growing conditions. When these technologies are customized to Bangladesh, water management and crop establishment methods seem most feasible. Among the rice-growing seasons in Bangladesh, there is a larger scope to adopt these management practices in the Boro season (December to May), while these scopes are minimal in the other two seasons due to their rain-fed nature of cultivation. Altogether, our study provides fundamental insights on CH4 reductions strategies from rice fields in Bangladesh.
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Affiliation(s)
- Milton Kumar Saha
- Department of Disaster Risk Management, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh
| | - Shamim Mia
- Department of Agronomy, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh.
| | - Akm Abdul Ahad Biswas
- Department of Disaster Risk Management, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh
| | - Md Abdus Sattar
- Department of Disaster Risk Management, Patuakhali Science and Technology University, Dumki, Patuakhali, Bangladesh
| | - Md Abdul Kader
- Agriculture and Food Technology Discipline, School of Agriculture, Geography, Environment, Ocean and Natural Sciences, University of the South Pacific, Apia, 1343, Samoa; Department of Soil Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh; Agriculture Discipline, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Zhixiang Jiang
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
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6
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Booth MT, Urbanic M, Wang X, Beaulieu JJ. Bioturbation frequency alters methane emissions from reservoir sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:148033. [PMID: 34323816 PMCID: PMC10825729 DOI: 10.1016/j.scitotenv.2021.148033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/09/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Inland aquatic systems are major global contributors to the atmospheric carbon budget through greenhouse gas (GHG) emissions, although the amount and form of carbon released varies widely across and within systems. Bioturbation of aquatic sediments can impact biogeochemical conditions and physically release sediment-bound bubbles containing GHGs, but variation in the frequency of such disturbance may modify the rate and composition of resulting GHG emissions. We hypothesized that an intermediate bioturbation frequency would result in the greatest methane (CH4) releases due to mechanical release of trapped bubbles, while frequent disturbance would result in greater diffusive carbon dioxide (CO2) releases relative to CH4, due to increased aeration of the sediment. We tested this bioturbation frequency hypothesis using laboratory mesocosms containing homogenized reservoir sediment. We used mechanical disturbance to simulate bioturbation at 3, 7, 14, or 21-day intervals; a control treatment was undisturbed for the duration of the experiment. We measured GHG emission (ebullition and diffusion) rates. An intermediate frequency of disturbance (7 days) produced the highest total GHG emission rate, while the most frequent disturbance interval (3 days) and least frequent interval (0 days) reduced overall GHG emissions relative to weekly disturbance by 24% and 15%, respectively. These patterns were primarily driven by differences in CH4 ebullition. Contrary to our hypothesis, there was no relationship between disturbance frequency and diffusive CO2 emissions. For all disturbance treatments, the majority of ebullition occurred during disturbance events, suggesting mechanical release of entrapped bubbles is an important emission mechanism. The frequency of disturbance has variable effects on GHG emissions and may explain conflicting results in prior studies of bioturbation. Our study provides insight into bioturbation as a driver of within-system variation in GHG emissions and highlights that variable bioturbation frequency results in non-linear responses in CH4 emissions, a globally important GHG, from reservoir sediments.
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Affiliation(s)
- Michael T Booth
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, United States of America.
| | - Megan Urbanic
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, United States of America
| | - Xia Wang
- Division of Statistics and Data Science, Department of Mathematical Sciences, University of Cincinnati, Cincinnati, OH 45221, United States of America.
| | - Jake J Beaulieu
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, United States of America.
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Putkinen A, Siljanen HMP, Laihonen A, Paasisalo I, Porkka K, Tiirola M, Haikarainen I, Tenhovirta S, Pihlatie M. New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing. THE NEW PHYTOLOGIST 2021; 231:524-536. [PMID: 33780002 DOI: 10.1111/nph.17365] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Methane (CH4 ) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH4 cycle. Recent studies have focused on quantifying tree stems as sources of CH4 and understanding abiotic CH4 emissions in plant canopies, with the role of microbial in situ CH4 formation receiving less attention. Moreover, despite initial reports revealing CH4 consumption, studies have not adequately evaluated the potential of microbial CH4 oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH4 exchange of plants, and particularly in boreal trees. We detected CH4 -producing methanogens and novel monooxygenases, potentially involved in CH4 consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH4 emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH4 exchange. Our findings, together with the emerging diversity of novel CH4 -producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH4 exchange.
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Affiliation(s)
- Anuliina Putkinen
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
| | - Henri M P Siljanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70200, Finland
- Department of Ecogenomics and Archaea Biology, University of Vienna, Vienna, A-1090, Austria
| | - Antti Laihonen
- Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä, FI-40014, Finland
| | - Inga Paasisalo
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70200, Finland
| | - Kaija Porkka
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
- Natural Resources Institute Finland, Savonlinna, FI-57200, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä, FI-40014, Finland
| | - Iikka Haikarainen
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
| | - Salla Tenhovirta
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
| | - Mari Pihlatie
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
- Department of Agricultural Sciences, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, 00014, Finland
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Methane Production in Soil Environments-Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation. Microorganisms 2020; 8:microorganisms8060881. [PMID: 32545191 PMCID: PMC7357154 DOI: 10.3390/microorganisms8060881] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 11/17/2022] Open
Abstract
Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O2, anaerobic processes such as CH4 production prevail. There is a substantial theoretical knowledge of the biogeochemistry and microbiology of processes in the absence of O2. Noteworthy are processes involved in the sequential degradation of organic matter coupled with the sequential reduction of electron acceptors, and, finally, the formation of CH4. These processes follow basic thermodynamic and kinetic principles, but also require the presence of microorganisms as catalysts. Meanwhile, there is a lot of empirical data that combines the observation of process function with the structure of microbial communities. While most of these observations confirmed existing theoretical knowledge, some resulted in new information. One important example was the observation that methanogens, which have been believed to be strictly anaerobic, can tolerate O2 to quite some extent and thus survive desiccation of flooded soil environments amazingly well. Another example is the strong indication of the importance of redox-active soil organic carbon compounds, which may affect the rates and pathways of CH4 production. It is noteworthy that drainage and aeration turns flooded soils, not generally, into sinks for atmospheric CH4, probably due to the peculiarities of the resident methanotrophic bacteria.
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Hernández M, Klose M, Claus P, Bastviken D, Marotta H, Figueiredo V, Enrich‐Prast A, Conrad R. Structure, function and resilience to desiccation of methanogenic microbial communities in temporarily inundated soils of the Amazon rainforest (Cunia Reserve, Rondonia). Environ Microbiol 2019; 21:1702-1717. [DOI: 10.1111/1462-2920.14535] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Marcela Hernández
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10, 35043, Marburg Germany
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10, 35043, Marburg Germany
| | - Peter Claus
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10, 35043, Marburg Germany
| | - David Bastviken
- Department of Thematic Studies ‐ Environmental ChangeLinköping University Linköping Sweden
| | - Humberto Marotta
- Ecosystems and Global Change Laboratory (LEMGUFF)/International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NABUFF), Graduate Program in Geosciences (Environmental Geochemistry), Universidade Federal Fluminense (UFF) Niteroi, Rio de Janeiro Brazil
- Sedimentary and Environmental Processes Laboratory (LAPSA‐UFF), Department of Geography, Graduate Program in GeographyUniversidade Federal Fluminense (UFF) Niteroi, Rio de Janeiro Brazil
| | - Viviane Figueiredo
- Departamento de BotânicaInstituto de Biologia, University Federal do Rio de Janeiro (UFRJ) Rio de Janeiro Brazil
| | - Alex Enrich‐Prast
- Department of Thematic Studies ‐ Environmental ChangeLinköping University Linköping Sweden
- Ecosystems and Global Change Laboratory (LEMGUFF)/International Laboratory of Global Change (LINCGlobal), Biomass and Water Management Research Center (NABUFF), Graduate Program in Geosciences (Environmental Geochemistry), Universidade Federal Fluminense (UFF) Niteroi, Rio de Janeiro Brazil
- Departamento de BotânicaInstituto de Biologia, University Federal do Rio de Janeiro (UFRJ) Rio de Janeiro Brazil
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology Karl‐von‐Frisch‐Str. 10, 35043, Marburg Germany
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Guerrero-Cruz S, Cremers G, van Alen TA, Op den Camp HJM, Jetten MSM, Rasigraf O, Vaksmaa A. Response of the Anaerobic Methanotroph " Candidatus Methanoperedens nitroreducens" to Oxygen Stress. Appl Environ Microbiol 2018; 84:e01832-18. [PMID: 30291120 PMCID: PMC6275348 DOI: 10.1128/aem.01832-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 11/20/2022] Open
Abstract
"Candidatus Methanoperedens nitroreducens" is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of "Ca Methanoperedens nitroreducens" could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a "Ca Methanoperedens nitroreducens" culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, "Candidatus Methanoperedens nitroreducens Verserenetto." RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of "Ca Methanoperedens nitroreducens" revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of "Ca Methanoperedens nitroreducens Verserenetto" to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion.IMPORTANCE "Candidatus Methanoperedens nitroreducens" is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, "Ca Methanoperedens nitroreducens" is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery "Ca Methanoperedens nitroreducens" possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.
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Affiliation(s)
- Simon Guerrero-Cruz
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Nijmegen, the Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Annika Vaksmaa
- Department of Microbiology, IWWR, Radboud University Nijmegen, Nijmegen, the Netherlands
- Royal Netherlands Institute for Sea Research, Texel, the Netherlands
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11
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Liu D, Nishida M, Takahashi T, Asakawa S. Transcription of mcrA Gene Decreases Upon Prolonged Non-flooding Period in a Methanogenic Archaeal Community of a Paddy-Upland Rotational Field Soil. MICROBIAL ECOLOGY 2018; 75:751-760. [PMID: 28890994 DOI: 10.1007/s00248-017-1063-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/24/2017] [Indexed: 06/07/2023]
Abstract
Methanogenic archaea survive under aerated soil conditions in paddy fields, and their community is stable under these conditions. Changes in the abundance and composition of an active community of methanogenic archaea were assessed by analyzing mcrA gene (encoding α subunit of methyl-coenzyme M reductase) and transcripts during a prolonged drained period in a paddy-upland rotational field. Paddy rice (Oryza sativa L.) was planted in the flooded field and rotated with soybean (Glycine max [L.] Merr.) under upland soil conditions. Soil samples were collected from the rotational plot in the first year, with paddy rice, and in the two successive years, with soybean, at six time points, before seeding, during cultivation, and after harvest as well as from a consecutive paddy (control) plot. By the time that soybean was grown in the second year, the methanogenic archaeal community in the rotational plot maintained high mcrA transcript levels, comparable with those of the control plot community, but the levels drastically decreased by over three orders of magnitude after 2 years of upland conversion. The composition of active methanogenic archaeal communities that survived upland conversion in the rotational plot was similar to that of the active community in the control plot. These results revealed that mcrA gene transcription of methanogenic archaeal community in the rotational field was affected by a prolonged non-flooding period, longer than 1 year, indicating that unknown mechanisms maintain the stability of methanogenic archaeal community in paddy fields last up to 1 year after the onset of drainage.
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Affiliation(s)
- Dongyan Liu
- Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi, 464-8601, Japan.
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Mizuhiko Nishida
- NARO Tohoku Agricultural Research Center, Daisen, Akita, 014-0120, Japan
| | - Tomoki Takahashi
- NARO Tohoku Agricultural Research Center, Daisen, Akita, 014-0120, Japan
| | - Susumu Asakawa
- Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi, 464-8601, Japan
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12
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Beblo-Vranesevic K, Bohmeier M, Perras AK, Schwendner P, Rabbow E, Moissl-Eichinger C, Cockell CS, Vannier P, Marteinsson VT, Monaghan EP, Ehrenfreund P, Garcia-Descalzo L, Gómez F, Malki M, Amils R, Gaboyer F, Westall F, Cabezas P, Walter N, Rettberg P. Lack of correlation of desiccation and radiation tolerance in microorganisms from diverse extreme environments tested under anoxic conditions. FEMS Microbiol Lett 2018; 365:4883205. [PMID: 29474542 PMCID: PMC5939664 DOI: 10.1093/femsle/fny044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/19/2018] [Indexed: 12/21/2022] Open
Abstract
Four facultative anaerobic and two obligate anaerobic bacteria were isolated from extreme environments (deep subsurface halite mine, sulfidic anoxic spring, mineral-rich river) in the frame MASE (Mars Analogues for Space Exploration) project. The isolates were investigated under anoxic conditions for their survivability after desiccation up to 6 months and their tolerance to ionizing radiation up to 3000 Gy. The results indicated that tolerances to both stresses are strain-specific features. Yersinia intermedia MASE-LG-1 showed a high desiccation tolerance but its radiation tolerance was very low. The most radiation-tolerant strains were Buttiauxella sp. MASE-IM-9 and Halanaerobium sp. MASE-BB-1. In both cases, cultivable cells were detectable after an exposure to 3 kGy of ionizing radiation, but cells only survived desiccation for 90 and 30 days, respectively. Although a correlation between desiccation and ionizing radiation resistance has been hypothesized for some aerobic microorganisms, our data showed that there was no correlation between tolerance to desiccation and ionizing radiation, suggesting that the physiological basis of both forms of tolerances is not necessarily linked. In addition, these results indicated that facultative and obligate anaerobic organisms living in extreme environments possess varied species-specific tolerances to extremes.
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Affiliation(s)
- Kristina Beblo-Vranesevic
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
| | - Maria Bohmeier
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
| | - Alexandra K Perras
- Department of Internal Medicine, Medical University of Graz, Auerbruggerplatz 15, 8010 Graz, Austria
- Department of Microbiology and Archaea, University of Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
| | - Petra Schwendner
- UK Center for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, EH9 3FD, Edinburgh, UK
| | - Elke Rabbow
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Auerbruggerplatz 15, 8010 Graz, Austria
- BioTechMed Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Charles S Cockell
- UK Center for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, EH9 3FD, Edinburgh, UK
| | | | - Viggo T Marteinsson
- MATISProkaria, Vinlandsleid 12, 113 Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Vatnsmýrarvegur 16, 101 Reykjavík, Iceland
| | - Euan P Monaghan
- Leiden Observatory, Universiteit Leiden, Niels Bohrweg 2, 2333 Leiden, Netherland
| | - Pascale Ehrenfreund
- Leiden Observatory, Universiteit Leiden, Niels Bohrweg 2, 2333 Leiden, Netherland
- Space Policy Institute, George Washington University, 1957 E Street, 20052 Washington DC, USA
| | - Laura Garcia-Descalzo
- Instituto Nacional de Técnica Aeroespacial-Centro de Astrobiología (INTA-CAB), Torrejón de Ardoz, 28850 Madrid, Spain
| | - Felipe Gómez
- Instituto Nacional de Técnica Aeroespacial-Centro de Astrobiología (INTA-CAB), Torrejón de Ardoz, 28850 Madrid, Spain
| | - Moustafa Malki
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM), Calle Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Frédéric Gaboyer
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Rue Charles Sadron, 45071 Orléans, France
| | - Frances Westall
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Rue Charles Sadron, 45071 Orléans, France
| | - Patricia Cabezas
- European Science Foundation (ESF), Quai Lezay-Marnésia, 67080 Strasbourg, France
| | - Nicolas Walter
- European Science Foundation (ESF), Quai Lezay-Marnésia, 67080 Strasbourg, France
| | - Petra Rettberg
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Linder Hoehe, 51147 Cologne, Germany
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13
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Lyu Z, Lu Y. Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. ISME JOURNAL 2017; 12:411-423. [PMID: 29135970 PMCID: PMC5776455 DOI: 10.1038/ismej.2017.173] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/31/2017] [Accepted: 08/09/2017] [Indexed: 11/09/2022]
Abstract
Methanogens have long been considered strictly anaerobic and oxygen-sensitive microorganisms, but their ability to survive oxygen stress has also been documented. Indeed, methanogens have been found in oxidative environments, and antioxidant genes have been detected in their genomes. How methanogens adapt to oxidative environments, however, remain poorly understood. Here, we systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders. Based on functional gene content involved in production of reactive oxygen species, Hierarchical Clustering analyses grouped methanogens into two distinct clusters, corresponding to the Class I and II methanogens, respectively. Comparative genomics suggested a systematic shift in metabolisms across the two classes, resulting in an enrichment of antioxidant features in the Class II. Moreover, meta-analysis of 16 S rRNA gene sequences obtained from EnvDB indicated that members of Class II were more frequently recovered from microaerophilic and even oxic environments than the Class I members. Phylogenomic analysis suggested that the Class I and II methanogens might have evolved before and around the Great Oxygenation Event, respectively. The enrichment of antioxidant features in the Class II methanogens may have played a key role in the adaption of this group to oxidative environments today and historically.
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Affiliation(s)
- Zhe Lyu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China.,Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Yahai Lu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, PR China.,College of Urban and Environmental Sciences, Peking University, Beijing, PR China
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14
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Jha P, Schmidt S. Reappraisal of chemical interference in anaerobic digestion processes. RENEWABLE AND SUSTAINABLE ENERGY REVIEWS 2017; 75:954-971. [DOI: 10.1016/j.rser.2016.11.076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
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15
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Reim A, Hernández M, Klose M, Chidthaisong A, Yuttitham M, Conrad R. Response of Methanogenic Microbial Communities to Desiccation Stress in Flooded and Rain-Fed Paddy Soil from Thailand. Front Microbiol 2017; 8:785. [PMID: 28529503 PMCID: PMC5418361 DOI: 10.3389/fmicb.2017.00785] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Rice paddies in central Thailand are flooded either by irrigation (irrigated rice) or by rain (rain-fed rice). The paddy soils and their microbial communities thus experience permanent or arbitrary submergence, respectively. Since methane production depends on anaerobic conditions, we hypothesized that structure and function of the methanogenic microbial communities are different in irrigated and rain-fed paddies and react differently upon desiccation stress. We determined rates and relative proportions of hydrogenotrophic and aceticlastic methanogenesis before and after short-term drying of soil samples from replicate fields. The methanogenic pathway was determined by analyzing concentrations and δ13C of organic carbon and of CH4 and CO2 produced in the presence and absence of methyl fluoride, an inhibitor of aceticlastic methanogenesis. We also determined the abundance (qPCR) of genes and transcripts of bacterial 16S rRNA, archaeal 16S rRNA and methanogenic mcrA (coding for a subunit of the methyl coenzyme M reductase) and the composition of these microbial communities by T-RFLP fingerprinting and/or Illumina deep sequencing. The abundances of genes and transcripts were similar in irrigated and rain-fed paddy soil. They also did not change much upon desiccation and rewetting, except the transcripts of mcrA, which increased by more than two orders of magnitude. In parallel, rates of CH4 production also increased, in rain-fed soil more than in irrigated soil. The contribution of hydrogenotrophic methanogenesis increased in rain-fed soil and became similar to that in irrigated soil. However, the relative microbial community composition on higher taxonomic levels was similar between irrigated and rain-fed soil. On the other hand, desiccation and subsequent anaerobic reincubation resulted in systematic changes in the composition of microbial communities for both Archaea and Bacteria. It is noteworthy that differences in the community composition were mostly detected on the level of operational taxonomic units (OTUs; 97% sequence similarity). The treatments resulted in change of the relative abundance of several archaeal OTUs. Some OTUs of Methanobacterium, Methanosaeta, Methanosarcina, Methanocella and Methanomassiliicoccus increased, while some of Methanolinea and Methanosaeta decreased. Bacterial OTUs within Firmicutes, Cyanobacteria, Planctomycetes and Deltaproteobacteria increased, while OTUs within other proteobacterial classes decreased.
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Affiliation(s)
- Andreas Reim
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Marcela Hernández
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany.,Centre for Biological Sciences, University of SouthamptonSouthampton, UK
| | - Melanie Klose
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
| | - Amnat Chidthaisong
- Joint Graduate School of Energy and Environment, King Mongkut's University of Technology ThonburiBangkok, Thailand
| | - Monthira Yuttitham
- Faculty of Environment and Resource Studies, Mahidol UniversitySalaya, Thailand
| | - Ralf Conrad
- Max Planck Institute for Terrestrial MicrobiologyMarburg, Germany
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16
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Archaea in Natural and Impacted Brazilian Environments. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2016; 2016:1259608. [PMID: 27829818 PMCID: PMC5086508 DOI: 10.1155/2016/1259608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/08/2016] [Indexed: 11/26/2022]
Abstract
In recent years, archaeal diversity surveys have received increasing attention. Brazil is a country known for its natural diversity and variety of biomes, which makes it an interesting sampling site for such studies. However, archaeal communities in natural and impacted Brazilian environments have only recently been investigated. In this review, based on a search on the PubMed database on the last week of April 2016, we present and discuss the results obtained in the 51 studies retrieved, focusing on archaeal communities in water, sediments, and soils of different Brazilian environments. We concluded that, in spite of its vast territory and biomes, the number of publications focusing on archaeal detection and/or characterization in Brazil is still incipient, indicating that these environments still represent a great potential to be explored.
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17
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Ji Y, Angel R, Klose M, Claus P, Marotta H, Pinho L, Enrich-Prast A, Conrad R. Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. Environ Microbiol 2016; 18:5082-5100. [PMID: 27507000 DOI: 10.1111/1462-2920.13491] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/06/2016] [Indexed: 11/28/2022]
Abstract
Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity.
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Affiliation(s)
- Yang Ji
- Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science & Technology, Ningliu Road 219, Nanjing, 210044, China.,Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Peter Claus
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Humberto Marotta
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Graduated Program in Geosciences (Geochemistry), Graduated Program in Geography, Research Center on Biomass and Water Management (NAB/UFF), Sedimentary Environmental Processes Laboratory (LAPSA/UFF), International Laboratory of Global Change (LINC-Global), Fluminense Federal University (UFF), Niterói, Brazil
| | - Luana Pinho
- Department of Chemical Oceanography, Rio de Janeiro State University, Pavilhão João Lyra Filho, sala 4008 Bloco E, Rua São Francisco Xavier, 524, Maracanã-RJ, 20550-900, Brazil
| | - Alex Enrich-Prast
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Department of Environmental Change, Linköping University, Linköping, Sweden
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
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18
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Estop-Aragonés C, Zając K, Blodau C. Effects of extreme experimental drought and rewetting on CO2 and CH4 exchange in mesocosms of 14 European peatlands with different nitrogen and sulfur deposition. GLOBAL CHANGE BIOLOGY 2016; 22:2285-300. [PMID: 26810035 DOI: 10.1111/gcb.13228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/14/2015] [Accepted: 12/11/2015] [Indexed: 05/27/2023]
Abstract
The quantitative impact of intense drought and rewetting on gas exchange in ombrotrophic bogs is still uncertain. In particular, we lack studies investigating multitudes of sites with different soil properties and nitrogen (N) and sulfur (S) deposition under consistent environmental conditions. We explored the timing and magnitude of change in CO2 (Respiration, Gross Primary Production - GPP, and Net Exchange - NE) and CH4 fluxes during an initial wet, a prolonged dry (~100 days), and a subsequent wet period (~230 days) at 12 °C in 14 Sphagnum peat mesocosms collected in hollows from bogs in the UK, Ireland, Poland, and Slovakia. The relationship of N and S deposition with GPP, respiration, and CH4 exchange was investigated. Nitrogen deposition increased CO2 fluxes and GPP more than respiration, at least up to about 15 kg N ha(-1) yr(-1) . All mesocosms became CO2 sources during drying and most of them when the entire annual period was considered. Response of GPP to drying was faster than that of respiration and contributed more to the change in NE; the effect was persistent and few sites recovered "predry" GPP by the end of the wet phase. Respiration was higher during the dry phase, but did not keep increasing as WT kept falling and peaked within the initial 33 days of drying; the change was larger when differences in humification with depth were small. CH4 fluxes strongly peaked during early drought and water table decline. After rewetting, methanogenesis recovered faster in dense peats, but CH4 fluxes remained low for several months, especially in peats with higher inorganic reduced sulfur content, where sulfate was generated and methanogenesis remained suppressed. Based on a range of European sites, the results support the idea that N and S deposition and intense drought can substantially affect greenhouse gas exchange on the annual scale.
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Affiliation(s)
- Cristian Estop-Aragonés
- Limnological Research Station and Department of Hydrology, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
- Department of Ecohydrology and Biogeochemistry, Institute of Landscape Ecology, University of Münster, Heisenbergstrasse 2, 48149, Münster, Germany
| | - Katarzyna Zając
- Limnological Research Station and Department of Hydrology, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Christian Blodau
- Limnological Research Station and Department of Hydrology, University of Bayreuth, Universitätsstrasse 30, 95447, Bayreuth, Germany
- Department of Ecohydrology and Biogeochemistry, Institute of Landscape Ecology, University of Münster, Heisenbergstrasse 2, 48149, Münster, Germany
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19
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Vijay A, Vaishnava M, Chhabra M. Microbial fuel cell assisted nitrate nitrogen removal using cow manure and soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7744-56. [PMID: 26755171 DOI: 10.1007/s11356-015-5934-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 12/07/2015] [Indexed: 04/15/2023]
Abstract
Microbial fuel cells (MFCs) are emerging wastewater treatment systems with a proven potential for denitrification. In this study, we have developed a high-rate denitrifying MFC. The anode consisted of cow manure and fruit waste and the cathode consisted of cow manure and soil. The initial chemical oxygen demand (COD)/nitrate nitrogen (NO3 (-)-N) was varied from 2 to 40 at the cathode while keeping the anode ratio fixed at 100. NO3 (-)-N removal rate of 7.1 ± 0.9 kg NO3 (-)-N/m(3) net cathodic compartment (NCC)/day was achieved at cathode COD/NO3 (-)-N ratio 7.31 with the current density of 190 ± 9.1 mA/m(2) and power density of 31.92 ± 4 mW/m(2) of electrode surface area. We achieved an open-circuit voltage (OCV) of 410 ± 20 mV at initial cathodic NO3 (-)-N of 0.345 g/l. The cathode COD/NO3 (-)-N ratio had a significant influence on MFC's OCV and nitrate removal rate. Lower OCV (<150 mV) and NO3 (-)-N removal rates were observed at COD/NO3 (-)-N ratio >12 and <7. Experiments done at different cathode pH values indicated that the optimum pH for denitrification was 7. Under optimized biochemical conditions, nitrate removal rate of 6.5 kg NO3 (-)-N/m(3) net cathodic compartment (NCC)/day and power density of 210 mW/m(2) were achieved in a low resistance MFC. The present study thus demonstrates the utility of MFCs for the treatment of high nitrate wastes.
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Affiliation(s)
- Ankisha Vijay
- Department of Biology, Indian Institute of Technology-Jodhpur, Rajasthan, 342011, India
| | - Monika Vaishnava
- Department of Biology, Indian Institute of Technology-Jodhpur, Rajasthan, 342011, India
| | - Meenu Chhabra
- Department of Biology, Indian Institute of Technology-Jodhpur, Rajasthan, 342011, India.
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20
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Abundance and potential metabolic activity of methanogens in well-aerated forest and grassland soils of an alpine region. FEMS Microbiol Ecol 2015; 92:fiv171. [DOI: 10.1093/femsec/fiv171] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2015] [Indexed: 11/12/2022] Open
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Kim J, Lee SH, Jang I, Jeong S, Kang H. Can abundance of methanogen be a good indicator for CH4 flux in soil ecosystems? ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2015; 37:1007-1015. [PMID: 26123992 DOI: 10.1007/s10653-015-9729-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 06/15/2015] [Indexed: 06/04/2023]
Abstract
Methane, which is produced by methanogenic archaea, is the second most abundant carbon compound in the atmosphere. Due to its strong radiative forcing, many studies have been conducted to determine its sources, budget, and dynamics. However, a mechanistic model of methane flux has not been developed thus far. In this study, we attempt to examine the relevance of the abundance of methanogen as a biological indicator of methane flux in three different types of soil ecosystems: permafrost, rice paddy, and mountainous wetland. We measured the annual average methane flux and abundance of methanogen in the soil ecosystems in situ. The correlation between methane flux and the abundance of methanogen exists only under a specific biogeochemical conditions such as SOM of higher than 60%, pH of 5.6-6.4, and water-saturated. Except for these conditions, significant correlations were absent. Therefore, microbial abundance information can be applied to a methane flux model selectively depending on the biogeochemical properties of the soil ecosystem.
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Affiliation(s)
- Jinhyun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, Korea
| | - Seung-Hoon Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, Korea
| | - Inyoung Jang
- National Institute of Ecology, Geumgang-ro, Maseo-Myeon, Seocheon-gun, Chungcheongnam-do, 325-318, Korea
| | - Sangseom Jeong
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, Korea
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 120-749, Korea.
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Sheehan R, McCarver AC, Isom CE, Karr EA, Lessner DJ. The Methanosarcina acetivorans thioredoxin system activates DNA binding of the redox-sensitive transcriptional regulator MsvR. J Ind Microbiol Biotechnol 2015; 42:965-9. [PMID: 25791378 DOI: 10.1007/s10295-015-1592-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/28/2015] [Indexed: 12/20/2022]
Abstract
The production of biogas (methane) by an anaerobic digestion is an important facet to renewable energy, but is subject to instability due to the sensitivity of strictly anaerobic methanogenic archaea (methanogens) to environmental perturbations, such as oxygen. An understanding of the oxidant-sensing mechanisms used by methanogens may lead to the development of more oxidant tolerant (i.e., stable) methanogen strains. MsvR is a redox-sensitive transcriptional regulator that is found exclusively in methanogens. We show here that oxidation of MsvR from Methanosarcina acetivorans (MaMsvR) with hydrogen peroxide oxidizes cysteine thiols, which inactivates MaMsvR binding to its own promoter (P(msvR)). Incubation of oxidized MaMsvR with the M. acetivorans thioredoxin system (NADPH, MaTrxR, and MaTrx7) results in reduction of the cysteines back to thiols and activation of P msvR binding. These data confirm that cysteines are critical for the thiol-disulfide regulation of P(msvR) binding by MaMsvR and support a role for the M. acetivorans thioredoxin system in the in vivo activation of MaMsvR. The results support the feasibility of using MaMsvR and P(msvR), along with the Methanosarcina genetic system, to design methanogen strains with oxidant-regulated gene expression systems, which may aid in stabilizing anaerobic digestion.
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Affiliation(s)
- Ryan Sheehan
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR, 72701, USA
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23
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Liu D, Ishikawa H, Nishida M, Tsuchiya K, Takahashi T, Kimura M, Asakawa S. Effect of paddy-upland rotation on methanogenic archaeal community structure in paddy field soil. MICROBIAL ECOLOGY 2015; 69:160-168. [PMID: 25113614 DOI: 10.1007/s00248-014-0477-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/31/2014] [Indexed: 06/03/2023]
Abstract
Methanogenic archaea are strict anaerobes and demand highly reduced conditions to produce methane in paddy field soil. However, methanogenic archaea survive well under upland and aerated conditions in paddy fields and exhibit stable community. In the present study, methanogenic archaeal community was investigated in fields where paddy rice (Oryza sativa L.) under flooded conditions was rotated with soybean (Glycine max [L.] Merr.) under upland conditions at different rotation histories, by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR methods targeting 16S rRNA and mcrA genes, respectively. Soil samples collected from the fields before flooding or seeding, during crop cultivation and after harvest of crops were analyzed. The abundance of the methanogenic archaeal populations decreased to about one-tenth in the rotational plots than in the consecutive paddy (control) plots. The composition of the methanogenic archaeal community also changed. Most members of the methanogenic archaea consisting of the orders Methanosarcinales, Methanocellales, Methanomicrobiales, and Methanobacteriales existed autochthonously in both the control and rotational plots, while some were strongly affected in the rotational plots, with fatal effect to some members belonging to the Methanosarcinales. This study revealed that the upland conversion for one or longer than 1 year in the rotational system affected the methanogenic archaeal community structure and was fatal to some members of methanogenic archaea in paddy field soil.
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Affiliation(s)
- Dongyan Liu
- Soil Biology and Chemistry, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi, 464-8601, Japan,
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24
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Jennings ME, Schaff CW, Horne AJ, Lessner FH, Lessner DJ. Expression of a bacterial catalase in a strictly anaerobic methanogen significantly increases tolerance to hydrogen peroxide but not oxygen. MICROBIOLOGY-SGM 2013; 160:270-278. [PMID: 24222618 DOI: 10.1099/mic.0.070763-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Haem-dependent catalase is an antioxidant enzyme that degrades H2O2, producing H2O and O2, and is common in aerobes. Catalase is present in some strictly anaerobic methane-producing archaea (methanogens), but the importance of catalase to the antioxidant system of methanogens is poorly understood. We report here that a survey of the sequenced genomes of methanogens revealed that the majority of species lack genes encoding catalase. Moreover, Methanosarcina acetivorans is a methanogen capable of synthesizing haem and encodes haem-dependent catalase in its genome; yet, Methanosarcina acetivorans cells lack detectable catalase activity. However, inducible expression of the haem-dependent catalase from Escherichia coli (EcKatG) in the chromosome of Methanosarcina acetivorans resulted in a 100-fold increase in the endogenous catalase activity compared with uninduced cells. The increased catalase activity conferred a 10-fold increase in the resistance of EcKatG-induced cells to H2O2 compared with uninduced cells. The EcKatG-induced cells were also able to grow when exposed to levels of H2O2 that inhibited or killed uninduced cells. However, despite the significant increase in catalase activity, growth studies revealed that EcKatG-induced cells did not exhibit increased tolerance to O2 compared with uninduced cells. These results support the lack of catalase in the majority of methanogens, since methanogens are more likely to encounter O2 rather than high concentrations of H2O2 in the natural environment. Catalase appears to be a minor component of the antioxidant system in methanogens, even those that are aerotolerant, including Methanosarcina acetivorans. Importantly, the experimental approach used here demonstrated the feasibility of engineering beneficial traits, such as H2O2 tolerance, in methanogens.
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Affiliation(s)
- Matthew E Jennings
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
| | - Cody W Schaff
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
| | - Alexandra J Horne
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
| | - Faith H Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
| | - Daniel J Lessner
- Department of Biological Sciences, University of Arkansas-Fayetteville, Fayetteville, AR 72701, USA
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Conrad R, Ji Y, Noll M, Klose M, Claus P, Enrich-Prast A. Response of the methanogenic microbial communities in Amazonian oxbow lake sediments to desiccation stress. Environ Microbiol 2013; 16:1682-94. [PMID: 24118927 DOI: 10.1111/1462-2920.12267] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/01/2013] [Accepted: 08/26/2013] [Indexed: 11/27/2022]
Abstract
Methanogenic microbial communities in soil and sediment function only when the environment is inundated and anoxic. In contrast to submerged soils, desiccation of lake sediments happens only rarely. However, some predictions suggest that extreme events of drying will become more common in the Amazon region, and this will promote an increase in sediments drying and exposure. We asked whether and how such methanogenic communities can withstand desiccation stress. Therefore, we determined the rates and pathways of CH(4) production (analysis of CH(4) and δ(13) C of CH(4), CO(2) and acetate), the copy numbers of bacterial and archaeal 16S rRNA genes and mcrA genes (quantitative PCR), and the community composition of Archaea and Bacteria (T-RFLP and pyrosequencing) in oxbow lake sediments of rivers in the Brazilian Amazon region. The rivers were of white water, black water and clear water type. The measurements were done with sediment in fresh state and after drying and rewetting. After desiccation and rewetting the composition of both, the archaeal and bacterial community changed. Since lake sediments from white water rivers exhibited only negligible methanogenic activity, probably because of relatively high iron and low organic matter content, they were not further analysed. The other sediments produced CH(4), with hydrogenotrophic methanogenesis usually accounting for > 50% of total activity. After desiccation and rewetting, archaeal and bacterial gene copy numbers decreased. The bacterial community showed a remarkable increase of Clostridiales from about 10% to > 30% of all Bacteria, partially caused by proliferation of specific taxa as the numbers of OTU shared with fresh sediment decreased from about 9% to 3%. Among the Archaea, desiccation specifically enhanced the relative abundance of either Methanocellales (black water) and/or Methanosarcinaceae (clear water). Despite the changes in gene copy numbers and composition of the microbial community, rates of CH(4) production even increased after desiccation-rewetting, demonstrating that the function of the methanogenic microbial community had not been impaired. This result indicates that the increase in extreme events of drying may increase methane production in flooded sediments.
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Affiliation(s)
- Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str.10, 35043, Marburg, Germany
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Manyi-Loh CE, Mamphweli SN, Meyer EL, Okoh AI, Makaka G, Simon M. Microbial anaerobic digestion (bio-digesters) as an approach to the decontamination of animal wastes in pollution control and the generation of renewable energy. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:4390-417. [PMID: 24048207 PMCID: PMC3799523 DOI: 10.3390/ijerph10094390] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 11/16/2022]
Abstract
With an ever increasing population rate; a vast array of biomass wastes rich in organic and inorganic nutrients as well as pathogenic microorganisms will result from the diversified human, industrial and agricultural activities. Anaerobic digestion is applauded as one of the best ways to properly handle and manage these wastes. Animal wastes have been recognized as suitable substrates for anaerobic digestion process, a natural biological process in which complex organic materials are broken down into simpler molecules in the absence of oxygen by the concerted activities of four sets of metabolically linked microorganisms. This process occurs in an airtight chamber (biodigester) via four stages represented by hydrolytic, acidogenic, acetogenic and methanogenic microorganisms. The microbial population and structure can be identified by the combined use of culture-based, microscopic and molecular techniques. Overall, the process is affected by bio-digester design, operational factors and manure characteristics. The purpose of anaerobic digestion is the production of a renewable energy source (biogas) and an odor free nutrient-rich fertilizer. Conversely, if animal wastes are accidentally found in the environment, it can cause a drastic chain of environmental and public health complications.
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Affiliation(s)
- Christy E. Manyi-Loh
- Fort Hare Institute of Technology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mails: (S.N.M.); (E.L.M.); (M.S.)
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mail:
| | - Sampson N. Mamphweli
- Fort Hare Institute of Technology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mails: (S.N.M.); (E.L.M.); (M.S.)
| | - Edson L. Meyer
- Fort Hare Institute of Technology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mails: (S.N.M.); (E.L.M.); (M.S.)
| | - Anthony I. Okoh
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mail:
| | - Golden Makaka
- Department of Physics, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mail:
| | - Michael Simon
- Fort Hare Institute of Technology, University of Fort Hare, Alice Campus, Alice 5700, Eastern Cape Province, South Africa; E-Mails: (S.N.M.); (E.L.M.); (M.S.)
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27
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Isom CE, Turner JL, Lessner DJ, Karr EA. Redox-sensitive DNA binding by homodimeric Methanosarcina acetivorans MsvR is modulated by cysteine residues. BMC Microbiol 2013; 13:163. [PMID: 23865844 PMCID: PMC3729527 DOI: 10.1186/1471-2180-13-163] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/12/2013] [Indexed: 11/16/2022] Open
Abstract
Background Methanoarchaea are among the strictest known anaerobes, yet they can survive exposure to oxygen. The mechanisms by which they sense and respond to oxidizing conditions are unknown. MsvR is a transcription regulatory protein unique to the methanoarchaea. Initially identified and characterized in the methanogen Methanothermobacter thermautotrophicus (Mth), MthMsvR displays differential DNA binding under either oxidizing or reducing conditions. Since MthMsvR regulates a potential oxidative stress operon in M. thermautotrophicus, it was hypothesized that the MsvR family of proteins were redox-sensitive transcription regulators. Results An MsvR homologue from the methanogen Methanosarcina acetivorans, MaMsvR, was overexpressed and purified. The two MsvR proteins bound the same DNA sequence motif found upstream of all known MsvR encoding genes, but unlike MthMsvR, MaMsvR did not bind the promoters of select genes involved in the oxidative stress response. Unlike MthMsvR that bound DNA under both non-reducing and reducing conditions, MaMsvR bound DNA only under reducing conditions. MaMsvR appeared as a dimer in gel filtration chromatography analysis and site-directed mutagenesis suggested that conserved cysteine residues within the V4R domain were involved in conformational rearrangements that impact DNA binding. Conclusions Results presented herein suggest that homodimeric MaMsvR acts as a transcriptional repressor by binding Ma PmsvR under non-reducing conditions. Changing redox conditions promote conformational changes that abrogate binding to Ma PmsvR which likely leads to de-repression.
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Affiliation(s)
- Catherine E Isom
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
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DeAngelis KM, Fortney JL, Borglin S, Silver WL, Simmons BA, Hazen TC. Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia. mBio 2012; 3:e00249-11. [PMID: 22354956 PMCID: PMC3374387 DOI: 10.1128/mbio.00249-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 01/17/2012] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED Tropical forest soils decompose litter rapidly with frequent episodes of anoxic conditions, making it likely that bacteria using alternate terminal electron acceptors (TEAs) play a large role in decomposition. This makes these soils useful templates for improving biofuel production. To investigate how TEAs affect decomposition, we cultivated feedstock-adapted consortia (FACs) derived from two tropical forest soils collected from the ends of a rainfall gradient: organic matter-rich tropical cloud forest (CF) soils, which experience sustained low redox, and iron-rich tropical rain forest (RF) soils, which experience rapidly fluctuating redox. Communities were anaerobically passed through three transfers of 10 weeks each with switchgrass as a sole carbon (C) source; FACs were then amended with nitrate, sulfate, or iron oxide. C mineralization and cellulase activities were higher in CF-FACs than in RF-FACs. Pyrosequencing of the small-subunit rRNA revealed members of the Firmicutes, Bacteroidetes, and Alphaproteobacteria as dominant. RF- and CF-FAC communities were not different in microbial diversity or biomass. The RF-FACs, derived from fluctuating redox soils, were the most responsive to the addition of TEAs, while the CF-FACs were overall more efficient and productive, both on a per-gram switchgrass and a per-cell biomass basis. These results suggest that decomposing microbial communities in fluctuating redox environments are adapted to the presence of a diversity of TEAs and ready to take advantage of them. More importantly, these data highlight the role of local environmental conditions in shaping microbial community function that may be separate from phylogenetic structure. IMPORTANCE After multiple transfers, we established microbial consortia derived from two tropical forest soils with different native redox conditions. Communities derived from the rapidly fluctuating redox environment maintained a capacity to use added terminal electron acceptors (TEAs) after multiple transfers, though they were not present during the enrichment. Communities derived from lower-redox soils were not responsive to TEA addition but were much more efficient at switchgrass decomposition. Though the communities were different, diversity was not, and both were dominated by many of the same species of clostridia. This reflects the inadequacy of rRNA for determining the function of microbial communities, in this case the retained ability to utilize TEAs that were not part of the selective growth conditions. More importantly, this suggests that microbial community function is shaped by life history, where environmental factors produce heritable traits through natural selection over time, creating variation in the community, a phenomenon not well documented for microbes.
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Affiliation(s)
- Kristen M DeAngelis
- Microbiology Department, University of Massachusetts, Amherst, Massachusetts, USA.
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Desiccation as a long-term survival mechanism for the archaeon Methanosarcina barkeri. Appl Environ Microbiol 2011; 78:1473-9. [PMID: 22194299 DOI: 10.1128/aem.06964-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viable methanogens have been detected in dry, aerobic environments such as dry reservoir sediment, dry rice paddies and aerobic desert soils, which suggests that methanogens have mechanisms for long-term survival in a desiccated state. In this study, we quantified the survival rates of the methanogenic archaeon Methanosarcina barkeri after desiccation under conditions equivalent to the driest environments on Earth and subsequent exposure to different stress factors. There was no significant loss of viability after desiccation for 28 days for cells grown with either hydrogen or the methylotrophic substrates, but recovery was affected by growth phase, with cells desiccated during the stationary phase of growth having a higher rate of recovery after desiccation. Synthesis of methanosarcinal extracellular polysaccharide (EPS) significantly increased the viability of desiccated cells under both anaerobic and aerobic conditions compared with that of non-EPS-synthesizing cells. Desiccated M. barkeri exposed to air at room temperature did not lose significant viability after 28 days, and exposure of M. barkeri to air after desiccation appeared to improve the recovery of viable cells compared with that of desiccated cells that were never exposed to air. Desiccated M. barkeri was more resistant to higher temperatures, and although resistance to oxidative conditions such as ozone and ionizing radiation was not as robust as in other desiccation-resistant microorganisms, the protection mechanisms are likely adequate to maintain cell viability during periodic exposure events. The results of this study demonstrate that after desiccation M. barkeri has the innate capability to survive extended periods of exposure to air and lethal temperatures.
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Angel R, Claus P, Conrad R. Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME JOURNAL 2011; 6:847-62. [PMID: 22071343 DOI: 10.1038/ismej.2011.141] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The prototypical representatives of the Euryarchaeota--the methanogens--are oxygen sensitive and are thought to occur only in highly reduced, anoxic environments. However, we found methanogens of the genera Methanosarcina and Methanocella to be present in many types of upland soils (including dryland soils) sampled globally. These methanogens could be readily activated by incubating the soils as slurry under anoxic conditions, as seen by rapid methane production within a few weeks, without any additional carbon source. Analysis of the archaeal 16S ribosomal RNA gene community profile in the incubated samples through terminal restriction fragment length polymorphism and quantification through quantitative PCR indicated dominance of Methanosarcina, whose gene copy numbers also correlated with methane production rates. Analysis of the δ(13)C of the methane further supported this, as the dominant methanogenic pathway was in most cases aceticlastic, which Methanocella cannot perform. Sequences of the key methanogenic enzyme methyl coenzyme M reductase retrieved from the soil samples before incubation confirmed that Methanosarcina and Methanocella are the dominant methanogens, though some sequences of Methanobrevibacter and Methanobacterium were also detected. The global occurrence of only two active methanogenic archaea supports the hypothesis that these are autochthonous members of the upland soil biome and are well adapted to their environment.
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Affiliation(s)
- Roey Angel
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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31
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Heavy-machinery traffic impacts methane emissions as well as methanogen abundance and community structure in oxic forest soils. Appl Environ Microbiol 2011; 77:6060-8. [PMID: 21742929 DOI: 10.1128/aem.05206-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Temperate forest soils are usually efficient sinks for the greenhouse gas methane, at least in the absence of significant amounts of methanogens. We demonstrate here that trafficking with heavy harvesting machines caused a large reduction in CH(4) consumption and even turned well-aerated forest soils into net methane sources. In addition to studying methane fluxes, we investigated the responses of methanogens after trafficking in two different forest sites. Trafficking generated wheel tracks with different impact (low, moderate, severe, and unaffected). We found that machine passes decreased the soils' macropore space and lowered hydraulic conductivities in wheel tracks. Severely compacted soils yielded high methanogenic abundance, as demonstrated by quantitative PCR analyses of methyl coenzyme M reductase (mcrA) genes, whereas these sequences were undetectable in unaffected soils. Even after a year after traffic compression, methanogen abundance in compacted soils did not decline, indicating a stability of methanogens here over time. Compacted wheel tracks exhibited a relatively constant community structure, since we found several persisting mcrA sequence types continuously present at all sampling times. Phylogenetic analysis revealed a rather large methanogen diversity in the compacted soil, and most mcrA gene sequences were mostly similar to known sequences from wetlands. The majority of mcrA gene sequences belonged either to the order Methanosarcinales or Methanomicrobiales, whereas both sites were dominated by members of the families Methanomicrobiaceae Fencluster, with similar sequences obtained from peatland environments. The results show that compacting wet forest soils by heavy machinery causes increases in methane production and release.
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Kitamura K, Fujita T, Akada S, Tonouchi A. Methanobacterium kanagiense sp. nov., a hydrogenotrophic methanogen, isolated from rice-field soil. Int J Syst Evol Microbiol 2011; 61:1246-1252. [DOI: 10.1099/ijs.0.026013-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pure culture of an obligately anaerobic, hydrogenotrophic, methanogenic archaeon, designated strain 169T, which grows with hydrogen and carbon dioxide as the sole energy and carbon sources, was isolated from an anaerobic propionate-oxidizing enrichment culture originally obtained as an inoculant from rice-field soil in Japan. Cells of strain 169T were non-motile, Gram-reaction-variable and rod-shaped or slightly curved rods with rounded ends (1.6–5.0×0.35–0.5 µm). Strain 169T had fimbriae at both ends of the cell (up to ~10 per cell) but did not possess flagella. Ultrathin sections showed a single-layered, electron-dense cell wall about 6 nm thick, which is typical of Gram-positive bacteria. Growth was observed at 15 °C–45 °C (optimum 40 °C), at pH 6.5–9.6 (optimum pH 7.5–8.5) and in 0–70 g NaCl l−1 (0–1.2 M) (optimum 5 g NaCl l−1; 0.086 M). Strain 169T utilized only hydrogen and carbon dioxide as energy and carbon sources. The DNA G+C content was 39.3 mol%. The results of 16S rRNA gene sequence analysis indicated that strain 169T was most closely related to Methanobacterium subterraneum DSM 11074T (96.8 % sequence similarity) and Methanobacterium formicicum DSM 1535T (96.4 %). On the basis of its morphological, physiological and phylogenetic characteristics, strain 169T ( = DSM 22026T = JCM 15797T) represents a novel species of the genus Methanobacterium, for which the name Methanobacterium kanagiense sp. nov. is proposed.
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Affiliation(s)
- Koji Kitamura
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
- The United Graduate School of Agricultural Sciences, Iwate University, 3-18-8, Ueda, Morioka, Iwate 020-8550, Japan
| | - Takashi Fujita
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Shinji Akada
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
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Yuan Y, Conrad R, Lu Y. Transcriptional response of methanogen mcrA genes to oxygen exposure of rice field soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:320-328. [PMID: 23761278 DOI: 10.1111/j.1758-2229.2010.00228.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Methane production in paddy soil is substantially suppressed after even a brief exposure of soil to oxygen. We hypothesized that the strong response of methanogen activity is reflected in the transcription of functional genes rather than in the composition of the community of methanogens. Therefore, we determined the community composition and the transcriptional response of methanogens in a rice field soil by targeting the mcrA gene (encoding the α subunit of methyl-coenzyme M reductase). Transcription of mcrA genes measured by quantitative PCR decreased by an order of magnitude after brief exposure to O2 . Terminal restriction fragment length polymorphism of mcrA genes and gene transcripts showed that although the community structure of methanogens did not change, the composition of transcripts dramatically responded to O2 exposure. In the beginning, transcripts of Methanocellales were the relatively most abundant, indicating resistance of these hydrogenotrophic methanogens against O2 stress. Later on, mcrA transcripts of acetoclastic methanogens became relatively more abundant coinciding with the turnover of acetate. The transcription of Methanosarcinaceae was relatively greater when acetate accumulated while Methanosaetaceae became more active when acetate concentrations decreased. In the presence of methyl fluoride, a specific inhibitor of acetoclastic methanogenesis, mcrA transcription by Methanosaetaceae was greatly suppressed while that of Methanosarcinaceae was less affected. Our study showed that in contrast to constant community structure as revealed by DNA-based fingerprinting the transcription of functional mcrA genes strongly responded to O2 stress and the presence of inhibitor CH3 F. The response patterns reflected the genomic and physiological traits of individual methanogens.
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Affiliation(s)
- Yanli Yuan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China. Max-Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str, 35043 Marburg, Germany
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Angel R, Matthies D, Conrad R. Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS One 2011; 6:e20453. [PMID: 21655270 PMCID: PMC3105065 DOI: 10.1371/journal.pone.0020453] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 04/26/2011] [Indexed: 11/20/2022] Open
Abstract
Methanogenesis is traditionally thought to occur only in highly reduced, anoxic environments. Wetland and rice field soils are well known sources for atmospheric methane, while aerated soils are considered sinks. Although methanogens have been detected in low numbers in some aerated, and even in desert soils, it remains unclear whether they are active under natural oxic conditions, such as in biological soil crusts (BSCs) of arid regions. To answer this question we carried out a factorial experiment using microcosms under simulated natural conditions. The BSC on top of an arid soil was incubated under moist conditions in all possible combinations of flooding and drainage, light and dark, air and nitrogen headspace. In the light, oxygen was produced by photosynthesis. Methane production was detected in all microcosms, but rates were much lower when oxygen was present. In addition, the δ(13)C of the methane differed between the oxic/oxygenic and anoxic microcosms. While under anoxic conditions methane was mainly produced from acetate, it was almost entirely produced from H(2)/CO(2) under oxic/oxygenic conditions. Only two genera of methanogens were identified in the BSC-Methanosarcina and Methanocella; their abundance and activity in transcribing the mcrA gene (coding for methyl-CoM reductase) was higher under anoxic than oxic/oxygenic conditions, respectively. Both methanogens also actively transcribed the oxygen detoxifying gene catalase. Since methanotrophs were not detectable in the BSC, all the methane produced was released into the atmosphere. Our findings point to a formerly unknown participation of desert soils in the global methane cycle.
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Affiliation(s)
- Roey Angel
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
| | - Diethart Matthies
- Plant Ecology, Department of Ecology, University of Marburg, Marburg, Germany
| | - Ralf Conrad
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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Oplinger RW, Wagner E. Disinfection of contaminated equipment: evaluation of benzalkonium chloride exposure time and solution age and the ability of air-drying to eliminate Flavobacterium psychrophilum. JOURNAL OF AQUATIC ANIMAL HEALTH 2010; 22:248-253. [PMID: 21413509 DOI: 10.1577/h10-003.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Disinfection of equipment that comes in contact with fish can help to minimize the spread of Flavobacterium psychrophilum (the etiological agent of bacterial coldwater disease) within and among fish culture facilities. We present the results of three studies that evaluated the potential use of benzalkonium chloride and air-drying to kill surface-attached F. psychrophilum. In the first study, we established a vat with a 600-mg/L benzalkonium chloride solution and sampled this solution 0, 14, 35, 56, 70, and 84 d after creation. The solution was kept outdoors and subjected to typical hatchery use. Plastic test strips were dipped in a solution containing F. psychrophilum and were then immersed in benzalkonium chloride for 0, 1, 10, 30, or 60 min. The strips were then rinsed with sterile water and streaked across a plate containing tryptone yeast extract salts (TYES) medium. No culturable bacteria were detected from any strips immersed for 10, 30, or 60 min. Bacteria were detected on 17% of the strips that were immersed for 1 min. The age of the benzalkonium chloride solution had no effect on disinfection ability. In the second study, plastic strips were immersed in a solution containing F. psychrophilum and then were dipped in a 600-mg/L benzalkonium chloride solution for 10 s. The strips were then air-dried for 1 h and were streaked onto TYES medium. No bacterial growth was observed from any strips in the second experiment. The third study determined whether air-drying alone was sufficient to kill F. psychrophilum. Plastic strips were dipped in a solution containing F. psychrophilum; were allowed to dry at room temperature for 0, 24, 48, or 96 h; and were then streaked across TYES medium. Bacteria were cultured from strips representing each drying interval, indicating that air-drying times of 96 h or less are insufficient to kill F. psychrophilum.
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Affiliation(s)
- Randall W Oplinger
- Utah Division of Wildlife Resources, Fisheries Experiment Station, 1465 West 200 North, Logan, Utah 8432, USA.
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Anaerobic digestion of renewable biomass: thermophilic temperature governs methanogen population dynamics. Appl Environ Microbiol 2010; 76:1842-50. [PMID: 20097828 DOI: 10.1128/aem.02397-09] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Beet silage and beet juice were digested continuously as representative energy crops in a thermophilic biogas fermentor for more than 7 years. Fluorescence microscopy of 15 samples covering a period of 650 days revealed that a decrease in temperature from 60 degrees C to 55 degrees C converted a morphologically uniform archaeal population (rods) into a population of methanogens exhibiting different cellular morphologies (rods and coccoid cells). A subsequent temperature increase back to 60 degrees C reestablished the uniform morphology of methanogens observed in the previous 60 degrees C period. In order to verify these observations, representative samples were investigated by amplified rRNA gene restriction analysis (ARDRA) and fluorescence in situ hybridization (FISH). Both methods confirmed the temperature-dependent population shift observed by fluorescence microscopy. Moreover, all samples investigated demonstrated that hydrogenotrophic Methanobacteriales dominated in the fermentor, as 29 of 34 identified operational taxonomic units (OTUs) were assigned to this order. This apparent discrimination of acetoclastic methanogens contradicts common models for anaerobic digestion processes, such as anaerobic digestion model 1 (ADM1), which describes the acetotrophic Euryarchaeota as predominant organisms.
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Yuan Y, Conrad R, Lu Y. Responses of methanogenic archaeal community to oxygen exposure in rice field soil. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:347-354. [PMID: 23765886 DOI: 10.1111/j.1758-2229.2009.00036.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Methanogens are regarded as strict anaerobes and hence sensitive to O2 exposure. It has been demonstrated that CH4 production and emission from rice field soil are substantially reduced when soil is drained or aerated even shortly. However, the response of different methanogenic populations to O2 stress remains unclear. Therefore, we determined CH4 production and structure of the methanogenic community in a Chinese rice field soil after short-term (24 h) and long-term (72 h) exposure to O2 under laboratory conditions. O2 stress strongly inhibited CH4 production, and the inhibitory effect increased with the duration of O2 exposure. O2 exposure also resulted in dramatic increase of ferric iron and sulfate concentrations. H2 partial pressures were significantly reduced, most probably due to the competitive consumption by iron and sulfate-reducing bacteria. However, substrate competition could not explain the inhibition of acetoclastic methanogenesis, since acetate accumulated after O2 exposure compared with the control. Quantitative (real-time) PCR analyses of both archaeal 16S rRNA and mcrA genes (coding for alpha subunit of the methyl coenzyme M reductase) revealed that growth of the methanogenic populations was suppressed after O2 exposure. However, terminal restriction fragment length polymorphism (T-RFLP) analyses of both 16S rDNA and 16S rRNA showed that the structure of the methanogenic archaeal community remained remarkably stable, and that acetoclastic Methanosarcinaceae were always dominant whether with or without O2 exposure. Thus, O2 stress apparently did not differentially affect the various methanogenic populations, but instead inhibited CH4 production by enabling competition, generally suppressing growth and differentially affecting existing enzyme activity.
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Affiliation(s)
- Yanli Yuan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China. Max-Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str, 35043 Marburg, Germany
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Beblo K, Rabbow E, Rachel R, Huber H, Rettberg P. Tolerance of thermophilic and hyperthermophilic microorganisms to desiccation. Extremophiles 2009; 13:521-31. [DOI: 10.1007/s00792-009-0239-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 03/16/2009] [Indexed: 11/27/2022]
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Summer H. Improved approach for transferring and cultivating Methanosarcina acetivorans C2A (DSM 2834). Lett Appl Microbiol 2009; 48:786-9. [PMID: 19413812 DOI: 10.1111/j.1472-765x.2009.02592.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM A method for cultivating Methanosarcina acetivorans was further developed to handle these anaerobic archaea without special equipment such as an anaerobic chamber. METHODS AND RESULTS Medium was filtered and oxygen removed under a nitrogen gas-phase. A dithiothreitol-filled syringe was used to transfer cells from high density grown cultures to new medium. Growth time and cell mass were determined, as well as cell viability was proven by light microscopy. CONCLUSION Cell transfer and growth was successful using this approach. SIGNIFICANCE AND IMPACT OF THE STUDY This updated technique allows almost every laboratory the opportunity to grow these methanogenic organisms for further studies. The described method could be used for proteomic analysis and is also interesting for further protein structure determination.
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Affiliation(s)
- H Summer
- ETH Zurich, Institute of Molecular Biology and Biophysics, CH-8093, Zurich, Switzerland.
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Liu Y, Whitman WB. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 2008; 1125:171-89. [PMID: 18378594 DOI: 10.1196/annals.1419.019] [Citation(s) in RCA: 639] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although of limited metabolic diversity, methanogenic archaea or methanogens possess great phylogenetic and ecological diversity. Only three types of methanogenic pathways are known: CO(2)-reduction, methyl-group reduction, and the aceticlastic reaction. Cultured methanogens are grouped into five orders based upon their phylogeny and phenotypic properties. In addition, uncultured methanogens that may represent new orders are present in many environments. The ecology of methanogens highlights their complex interactions with other anaerobes and the physical and chemical factors controlling their function.
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Affiliation(s)
- Yuchen Liu
- Department of Microbiology, University of Georgia, 541 Biological Sciences Building, Athens, GA 30605, USA
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Bardgett RD, Freeman C, Ostle NJ. Microbial contributions to climate change through carbon cycle feedbacks. ISME JOURNAL 2008; 2:805-14. [PMID: 18615117 DOI: 10.1038/ismej.2008.58] [Citation(s) in RCA: 382] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is considerable interest in understanding the biological mechanisms that regulate carbon exchanges between the land and atmosphere, and how these exchanges respond to climate change. An understanding of soil microbial ecology is central to our ability to assess terrestrial carbon cycle-climate feedbacks, but the complexity of the soil microbial community and the many ways that it can be affected by climate and other global changes hampers our ability to draw firm conclusions on this topic. In this paper, we argue that to understand the potential negative and positive contributions of soil microbes to land-atmosphere carbon exchange and global warming requires explicit consideration of both direct and indirect impacts of climate change on microorganisms. Moreover, we argue that this requires consideration of complex interactions and feedbacks that occur between microbes, plants and their physical environment in the context of climate change, and the influence of other global changes which have the capacity to amplify climate-driven effects on soil microbes. Overall, we emphasize the urgent need for greater understanding of how soil microbial ecology contributes to land-atmosphere carbon exchange in the context of climate change, and identify some challenges for the future. In particular, we highlight the need for a multifactor experimental approach to understand how soil microbes and their activities respond to climate change and consequences for carbon cycle feedbacks.
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Tholen A, Pester M, Brune A. Simultaneous methanogenesis and oxygen reduction by Methanobrevibacter cuticularis at low oxygen fluxes. FEMS Microbiol Ecol 2007; 62:303-12. [DOI: 10.1111/j.1574-6941.2007.00390.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Thummes K, Schäfer J, Kämpfer P, Jäckel U. Thermophilic methanogenic Archaea in compost material: Occurrence, persistence and possible mechanisms for their distribution to other environments. Syst Appl Microbiol 2007; 30:634-43. [DOI: 10.1016/j.syapm.2007.08.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 08/23/2007] [Indexed: 10/22/2022]
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Liu CT, Miyaki T, Aono T, Oyaizu H. Evaluation of methanogenic strains and their ability to endure aeration and water stress. Curr Microbiol 2007; 56:214-8. [PMID: 17990030 DOI: 10.1007/s00284-007-9059-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 09/08/2007] [Indexed: 10/22/2022]
Abstract
During periods of drainage, both water stress and oxygen can cause damage to indigenous methanogens. In the present study, we evaluated the tolerance of seven methanogenic strains (Methanobrevibacter arboriphilicus, Methanobacterium formicicum, Methanococcus vannielii, Methanospirillum hungatei, Methanoculleus olentangyi, Methanoplanus limicola, and Methanosarcina mazei) to long-term exposure to air/nitrogen and drying. We found that these methanogenic strains except for M. limicola and M. olentangyi in pre-dried cells offered more tenacious resistance to desiccation and oxygen exposure than those in enriched liquid cultures. In the case of M. formicicum, the liquid culture of this strain could remain viable when mixed well with fresh or sterile soil, but not when cultured without soil, or with agar slurry. These results suggest that indigenous methanogens localize within soil compartments to protect themselves from the damage caused by gradual drying under an oxic atmosphere.
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Affiliation(s)
- Chi-Te Liu
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Tokyo 113-8657, Japan
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Brioukhanov AL, Netrusov AI. Aerotolerance of strictly anaerobic microorganisms and factors of defense against oxidative stress: A review. APPL BIOCHEM MICRO+ 2007. [DOI: 10.1134/s0003683807060014] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Lessner DJ, Ferry JG. The archaeon Methanosarcina acetivorans contains a protein disulfide reductase with an iron-sulfur cluster. J Bacteriol 2007; 189:7475-84. [PMID: 17675382 PMCID: PMC2168450 DOI: 10.1128/jb.00891-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Methanosarcina acetivorans, a strictly anaerobic methane-producing species belonging to the domain Archaea, contains a gene cluster annotated with homologs encoding oxidative stress proteins. One of the genes (MA3736) is annotated as a gene encoding an uncharacterized carboxymuconolactone decarboxylase, an enzyme required for aerobic growth with aromatic compounds by species in the domain Bacteria. Methane-producing species are not known to utilize aromatic compounds, suggesting that MA3736 is incorrectly annotated. The product of MA3736, overproduced in Escherichia coli, had protein disulfide reductase activity dependent on a C(67)XXC(70) motif not found in carboxymuconolactone decarboxylase. We propose that MA3736 be renamed mdrA (methanosarcina disulfide reductase). Further, unlike carboxymuconolactone decarboxylase, MdrA contained an Fe-S cluster. Binding of the Fe-S cluster was dependent on essential cysteines C(67) and C(70), while cysteines C(39) and C(107) were not required. Loss of the Fe-S cluster resulted in conversion of MdrA from an inactive hexamer to a trimer with protein disulfide reductase activity. The data suggest that MdrA is the prototype of a previously unrecognized protein disulfide reductase family which contains an intermolecular Fe-S cluster that controls oligomerization as a mechanism to regulate protein disulfide reductase activity.
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Affiliation(s)
- Daniel J Lessner
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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Morozova D, Wagner D. Stress response of methanogenic archaea from Siberian permafrost compared with methanogens from nonpermafrost habitats. FEMS Microbiol Ecol 2007; 61:16-25. [PMID: 17428303 DOI: 10.1111/j.1574-6941.2007.00316.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We examined the survival potential of methanogenic archaea exposed to different environmental stress conditions such as low temperature (down to -78.5 degrees C), high salinity (up to 6 M NaCl), starvation (up to 3 months), long-term freezing (up to 2 years), desiccation (up to 25 days) and oxygen exposure (up to 72 h). The experiments were conducted with methanogenic archaea from Siberian permafrost and were complemented by experiments on well-studied methanogens from nonpermafrost habitats. Our results indicate a high survival potential of a methanogenic archaeon from Siberian permafrost when exposed to the extreme conditions tested. In contrast, these stress conditions were lethal for methanogenic archaea isolated from nonpermafrost habitats. A better adaptation to stress was observed at a low temperature (4 degrees C) compared with a higher one (28 degrees C). Given the unique metabolism of methanogenic archaea in general and the long-term survival and high tolerance to extreme conditions of the methanogens investigated in this study, methanogenic archaea from permafrost should be considered as primary candidates for possible subsurface Martian life.
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Affiliation(s)
- Daria Morozova
- Alfred Wegener Institute for Polar and Marine Research, Potsdam, Germany.
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Brioukhanov AL, Netrusov AI, Eggen RIL. The catalase and superoxide dismutase genes are transcriptionally up-regulated upon oxidative stress in the strictly anaerobic archaeon Methanosarcina barkeri. Microbiology (Reading) 2006; 152:1671-1677. [PMID: 16735730 DOI: 10.1099/mic.0.28542-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanosarcina barkeriis a strictly anaerobic methanogenic archaeon, which can survive oxidative stress. The oxidative stress agent paraquat (PQ) suppressed growth ofM. barkeriat concentrations of 50–200 μM. Hydrogen peroxide (H2O2) inhibited growth at concentrations of 0.4–1.6 mM. Catalase activity in cell-free extracts ofM. barkeriincreased about threefold during H2O2stress (1.3 mM H2O2, 2–4 h exposure) and nearly twofold during superoxide stress (160 μM PQ, 2 h exposure). PQ (160 μM, 2–4 h exposure) and H2O2(1.3 mM, 2 h exposure) also influenced superoxide dismutase activity in cell-free extracts ofM. barkeri. Dot-blot analysis was performed on total RNA isolated from H2O2- and PQ-exposed cultures, using labelled internal DNA fragments of thesodandkatgenes. It was shown that H2O2but not PQ strongly induced up-regulation of thekatgene. PQ and to a lesser degree H2O2induced the expression of superoxide dismutase. The results indicate the regulation of the adaptive response ofM. barkerito different oxidative stresses.
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Affiliation(s)
- Andrei L Brioukhanov
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
- Department of Microbiology, Biological Faculty, Lomonosov Moscow State University, Vorob'evy Hills 1/12, 119992 Moscow, Russia
| | - Alexander I Netrusov
- Department of Microbiology, Biological Faculty, Lomonosov Moscow State University, Vorob'evy Hills 1/12, 119992 Moscow, Russia
| | - Rik I L Eggen
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Überlandstrasse 133, 8600 Dübendorf, Switzerland
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Zhang W, Culley DE, Nie L, Brockman FJ. DNA microarray analysis of anaerobic Methanosarcina barkeri reveals responses to heat shock and air exposure. J Ind Microbiol Biotechnol 2006; 33:784-90. [PMID: 16604357 DOI: 10.1007/s10295-006-0114-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Accepted: 03/13/2006] [Indexed: 11/26/2022]
Abstract
Methanosarcina barkeri is a methanogenic archaeon that can digest cellulose and other polysaccharides to produce methane. It can only grow under strictly anoxic conditions, but which can survive air exposure. To obtain further knowledge of cellular changes occurring in M. barkeri in response to air exposure and other environmental stresses, we constructed the first oligonucleotide microarray for M. barkeri and used it to investigate the global transcriptomic responses of M. barkeri to air exposure and heat shock at 45 degrees C for 1 h. The results showed that various house-keeping genes, such as genes involved in DNA replication recombination and repair, energy production and conversion, and protein turnover were regulated by environmental stimuli. In response to air exposure, up-regulation of a large number of transposase encoding genes was observed. However, no differential expression of genes encoding superoxide dismutase, catalase, nonspecific peroxidases or thioredoxin reductase was observed in response to air exposure, implying that no significant level of reactive oxygen species has been formed under air exposure. In response to heat shock, both Hsp70 (DnaK-DnaJ-GrpE chaperone system) the Hsp60 (GroEL) systems were up-regulated, suggesting that they may play an important role in protein biogenesis in M. barkeri during heat stress.
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Affiliation(s)
- Weiwen Zhang
- Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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