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Bueno de Mesquita CP, Wu D, Tringe SG. Methyl-Based Methanogenesis: an Ecological and Genomic Review. Microbiol Mol Biol Rev 2023; 87:e0002422. [PMID: 36692297 PMCID: PMC10029344 DOI: 10.1128/mmbr.00024-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.
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Affiliation(s)
| | - Dongying Wu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Li W, Feng D, Yang G, Deng Z, Rui J, Chen H. Soil water content and pH drive archaeal distribution patterns in sediment and soils of water-level-fluctuating zones in the East Dongting Lake wetland, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:29127-29137. [PMID: 31392608 DOI: 10.1007/s11356-019-06109-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Archaea play a vital role in Earth's geochemical cycles, but the factors that drive their distribution between sediments and water-level-fluctuating zones in the East Dongting Lake (EDL) wetland are poorly understood. Here, we used Illumina MiSeq to investigate the variation in the soil archaeal community structure and diversity among sediments and four water-level-fluctuating zones (mudflat, sedge, sedge-Phragmites, and Phragmites) in the EDL wetland. Diverse archaeal assemblages were found in our study, Crenarchaeota, Euryarchaeota, and ammonia-oxidizing and methanogenic subset were the dominant groups, and all their abundances shifted from sediment to water-level-fluctuating zones. The principal coordinates analysis and cluster analysis showed that the overall archaeal community structure was separated into two clusters: cluster I contained nine samples from sediment, mudflat, and sedge zones, whereas cluster II contained six samples from sedge-Phragmites and Phragmites zones. Archaeal diversity was significantly highest in sediment and lowest in Phragmites zone soils. The Mantel test showed that the variation in archaeal community structure was significantly positively correlated with soil water content and pH. The relative abundances of Crenarchaeota and Nitrososphaerales decreased with soil water content, while Euryarchaeota and Methanomicrobiales increased with soil water content. The relative abundance of Methanomicrobiales significantly decreased with pH (R2 = 0.34-0.48). Chao 1, observed operational taxonomic units, Shannon index, and Simpson index all correlated significantly positively with water content (R2 = 0.40-0.60), while Shannon and Simpson indexes both correlated significantly negatively with pH (R2 = 0.20-0.37). Our results demonstrated that the variations in the archaeal community structure were markedly driven by soil water content and pH in the EDL wetland. Our findings suggested that archaeal communities shifted among sediment and four water-level-fluctuating zones, highlighting that the spatiotemporal heterogeneity of greenhouse gas flux in small scale should be taken into account for accurate prediction of greenhouse gas emissions in the Dongting Lake area, especially on the background of climate change and human activities.
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Affiliation(s)
- Wei Li
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, 650091, China
| | - Defeng Feng
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, 650224, China
| | - Gang Yang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Zhengmiao Deng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Hunan, 410125, China
| | - Junpeng Rui
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Holmes D, Smith J. Biologically Produced Methane as a Renewable Energy Source. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:1-61. [PMID: 27926429 DOI: 10.1016/bs.aambs.2016.09.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methanogens are a unique group of strictly anaerobic archaea that are more metabolically diverse than previously thought. Traditionally, it was thought that methanogens could only generate methane by coupling the oxidation of products formed by fermentative bacteria with the reduction of CO2. However, it has recently been observed that many methanogens can also use electrons extruded from metal-respiring bacteria, biocathodes, or insoluble electron shuttles as energy sources. Methanogens are found in both human-made and natural environments and are responsible for the production of ∼71% of the global atmospheric methane. Their habitats range from the human digestive tract to hydrothermal vents. Although biologically produced methane can negatively impact the environment if released into the atmosphere, when captured, it can serve as a potent fuel source. The anaerobic digestion of wastes such as animal manure, human sewage, or food waste produces biogas which is composed of ∼60% methane. Methane from biogas can be cleaned to yield purified methane (biomethane) that can be readily incorporated into natural gas pipelines making it a promising renewable energy source. Conventional anaerobic digestion is limited by long retention times, low organics removal efficiencies, and low biogas production rates. Therefore, many studies are being conducted to improve the anaerobic digestion process. Researchers have found that addition of conductive materials and/or electrically active cathodes to anaerobic digesters can stimulate the digestion process and increase methane content of biogas. It is hoped that optimization of anaerobic digesters will make biogas more readily accessible to the average person.
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A diverse group of halophilic bacteria exist in Lunsu, a natural salt water body of Himachal Pradesh, India. SPRINGERPLUS 2015; 4:274. [PMID: 26090321 PMCID: PMC4469599 DOI: 10.1186/s40064-015-1028-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/12/2015] [Indexed: 11/10/2022]
Abstract
Five halophilic bacterial isolates namely SS1, SS2, SS3, SS5 and SS8 were isolated from soil sediments of Lunsu, a salty water body. All the bacterial isolates showed growth in LB medium containing up to 8.7% NaCl, pH 7-8 and at temperature range of 30-37°C. The bacterial isolates SS1 and SS3 require at least 3.8% NaCl for their growth, indicating their strict halophilic nature. Interestingly, bacterial isolates SS2, SS5 and SS8 but not SS1 and SS3 exhibited growth in medium supplemented with KCl. Accordingly, Na(+) and K(+) ions were detected at 1.39 and 0.0035%, respectively in Lunsu water. All the bacterial isolates were analyzed by random amplification of polymorphic DNA (RAPD) using four different random primers and produced PCR fragments ranging from 0.1 to 5 kb in size. Phylogenetic tree based on RAPD finger prints showed that SS1 and SS3 formed one group, while SS2 and SS5 formed the second group, whereas SS8 was out group. Sequence analysis of 16S rDNA identified SS1 and SS3 as Halobacillus trueperi, SS2 as Shewanella algae, SS5 as Halomonas venusta, and SS8 as Marinomonas sp. were deposited in GenBank with accession numbers of KM260166, KF751761, KF751760, KF751762 and KF751763, respectively. This is the first report on the presence of diverse halophilic bacteria in the foot hills of Himalayas.
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Chisti Y. Constraints to commercialization of algal fuels. J Biotechnol 2013; 167:201-14. [DOI: 10.1016/j.jbiotec.2013.07.020] [Citation(s) in RCA: 510] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/12/2013] [Accepted: 07/12/2013] [Indexed: 01/01/2023]
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Role of the fused corrinoid/methyl transfer protein CmtA during CO-dependent growth of Methanosarcina acetivorans. J Bacteriol 2012; 194:4161-8. [PMID: 22636775 DOI: 10.1128/jb.00593-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of Methanosarcina acetivorans encodes three homologs, initially annotated as hypothetical fused corrinoid/methyl transfer proteins, which are highly elevated in CO-grown cells versus cells grown with alternate substrates. Based only on phenotypic analyses of deletion mutants, it was previously concluded that the homologs are strictly dimethylsulfide:coenzyme M (CoM) methyltransferases not involved in the metabolism of CO (E. Oelgeschlager and M. Rother, Mol. Microbiol. 72:1260 -1272, 2009). The homolog encoded by MA4383 (here designated CmtA) was reexamined via biochemical characterization of the protein overproduced in Escherichia coli. Purified CmtA reconstituted with methylcob(III)alamin contained a molar ratio of cobalt to protein of 1.0 ± 0.2. The UV-visible spectrum was typical of methylated corrinoid-containing proteins, with absorbance maxima at 370 and 420 nm and a band of broad absorbance between 450 and 600 nm with maxima at 525, 490, and 550 nm. CmtA reconstituted with aquocobalamin showed methyl-tetrahydromethanopterin:CoM (CH(3)-THMPT:HS-CoM) methyltransferase activity (0.31 μmol/min/mg) with apparent K(m) values of 135 μM for CH(3)-THMPT and 277 μM for HS-CoM. The ratio of CH(3)-THMPT:HS-CoM methyltransferase activity in the soluble versus membrane cellular fractions was 15-fold greater in CO-grown versus methanol-grown cells. A mutant strain deleted for the CmtA gene showed lower growth rates and final yields when cultured with growth-limiting partial pressures of CO, demonstrating a role for CmtA during growth with this substrate. The results establish that CmtA is a soluble CH(3)-THSPT:HS-CoM methyltransferase postulated to supplement the membrane-bound CH(3)-THMPT:HS-CoM methyltransferase during CO-dependent growth of M. acetivorans. Thus, we propose that the name of the enzyme encoded by MA4384 be CmtA (for cytoplasmic methyltransferase).
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Antony CP, Murrell JC, Shouche YS. Molecular diversity of methanogens and identification of Methanolobus sp. as active methylotrophic Archaea in Lonar crater lake sediments. FEMS Microbiol Ecol 2012; 81:43-51. [PMID: 22150151 DOI: 10.1111/j.1574-6941.2011.01274.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 11/29/2011] [Accepted: 11/30/2011] [Indexed: 11/29/2022] Open
Abstract
Soda lakes constitute extreme aquatic ecosystems with remarkably high primary productivity rates, but information on the diversity and activity of methanogens in such environments is sparse. Using 16S rRNA and functional genes, we investigated the diversity of methanogens in the sediments of Lonar Lake, a unique saline and alkaline ecosystem formed by meteorite impact in the Deccan basalts. Although domain and phylum level 16S rRNA gene libraries were dominated by phylotypes related to Halobacteriales, sequences related to potentially novel Archaea within the orders Methanosarcinales and Methanomicrobiales were obtained together with a significant fraction of sequences representing uncultivated Euryarchaeota [Correction added after online publication 16 April 2012: orders 'Methanosarcina and Methanomicrobiaceae' changed to 'Methanosarcinales and Methanomicrobiales']. To identify the active methylotrophic Archaea involved in methanogenesis, mRNA transcripts of mcrA were retrieved from methanol consuming and methane emitting sediment microcosms at two different time points. Reverse-transcription PCR, qPCR, DGGE fingerprint, and clone library analysis showed that the active Archaea were closely related to Methanolobus oregonensis. To our knowledge, this is the first study identifying active methylotrophic methanogens in such an environment.
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Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T, Tice H, Copeland A, Cheng JF, Chen F, Nolan M, Saunders E, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Lykidis A, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Goodwin L, Detter JC, Brettin T, Rohde M, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. ARCHAEA (VANCOUVER, B.C.) 2010; 2010:690737. [PMID: 21234345 PMCID: PMC3017947 DOI: 10.1155/2010/690737] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 11/09/2010] [Indexed: 11/17/2022]
Abstract
Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLP(T) was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.
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Affiliation(s)
- Stefan Spring
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Carmen Scheuner
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | | | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Feng Chen
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Elizabeth Saunders
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | | | - Natalia Ivanova
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Yun-Juan Chang
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Cynthia D. Jeffries
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Oak Ridge National Laboratory, Oak Ridge, TN 37830-8026, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - Thomas Brettin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545-001, USA
| | - Manfred Rohde
- HZI—Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Markus Göker
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Jim Bristow
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, CA 94598-1632, USA
- Davis Genome Center, University of California, Davis, CA 95817, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | - Hans-Peter Klenk
- DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
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An engineered methanogenic pathway derived from the domains Bacteria and Archaea. mBio 2010; 1. [PMID: 21060738 PMCID: PMC2975365 DOI: 10.1128/mbio.00243-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 10/05/2010] [Indexed: 01/09/2023] Open
Abstract
A plasmid-based expression system wherein mekB was fused to a constitutive Methanosarcina acetivorans promoter was used to express MekB, a broad-specificity esterase from Pseudomonas veronii, in M. acetivorans. The engineered strain had 80-fold greater esterase activity than wild-type M. acetivorans. Methyl acetate and methyl propionate esters served as the sole carbon and energy sources, resulting in robust growth and methane formation, with consumption of >97% of the substrates. Methanol was undetectable at the end of growth with methyl acetate, whereas acetate accumulated, a result consistent with methanol as the more favorable substrate. Acetate was consumed, and growth continued after a period of adaptation. Similar results were obtained with methyl propionate, except propionate was not metabolized.
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Abstract
The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.
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Affiliation(s)
- Bonnie Chaban
- Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada
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Nercessian O, Prokofeva M, Lebedinski A, L'Haridon S, Cary C, Prieur D, Jeanthon C. Design of 16S rRNA-targeted oligonucleotide probes for detecting cultured and uncultured archaeal lineages in high-temperature environments. Environ Microbiol 2004; 6:170-82. [PMID: 14756881 DOI: 10.1046/j.1462-2920.2003.00560.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In order to facilitate the evaluation of archaeal community diversity and distribution in high-temperature environments, 14 16S rRNA oligonucleotide probes were designed. Adequate hybridization and wash conditions of the probes encompassing most known hyperthermophilic Archaea, members of the orders Thermococcales, Desulfurococcales and Sulfolobales, of the families Methanocaldococcaceae, Pyrodictiaceae and Thermoproteaceae, of the genera Archaeoglobus, Methanopyrus and Ignicoccus, and of the as yet uncultured lineages Korarchaeota, Crenarchaeota marine group I, deep-sea hydrothermal vent euryarchaeotic group 2 (DHVE 2), and deep-sea hydrothermal vent euryarchaeotic group 8 (DHVE 8) were determined by dot-blot hybridization from target and non-target reference organisms and environmental clones. The oligonucleotide probes were also used to evaluate the archaeal community composition in nine deep-sea hydrothermal vent samples. All probes, except those targeting members of Sulfolobales, Thermoproteaceae, Pyrodictiaceae and Korarchaeota, gave positive hybridization signals when hybridized against 16S rDNA amplification products obtained from hydrothermal DNA extracts. The results confirmed the widespread occurrence of Thermococcales, Desulfurococcales, Methanocaldococcaceae and Archaeoglobus in deep-sea hydrothermal vents, and extended the known ecological habitats of uncultured lineages. Despite their wide coverage, the probes were unable to resolve the archaeal communities associated with hydrothermally influenced sediments, suggesting that these samples may contain novel lineages. This suite of oligonucleotide probes may represent an efficient tool for rapid qualitative and quantitative characterization of archaeal communities. Their application would help to provide new insights in the future into the composition, distribution and abundance of Archaea in high-temperature environments.
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Affiliation(s)
- Olivier Nercessian
- Centre National de la Recherche Scientifique and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Technopole Brest-Iroise, Place Nicolas Copernic, 29280 Plouzané, France
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da Costa MS, Santos H, Galinski EA. An overview of the role and diversity of compatible solutes in Bacteria and Archaea. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 1998; 61:117-53. [PMID: 9670799 DOI: 10.1007/bfb0102291] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The accumulation of compatible solutes is a prerequisite for the adaptation of microorganisms to osmotic stress imposed by salt or organic solutes. Two types of strategies exist to cope with high external solute concentrations; one strategy is found in the extremely halophilic Archaea of the family Halobacteriaceae and the Bacteria of the order Haloanaerobiales involving the accumulation of inorganic ions. The other strategy of osmoadaptation involves the accumulation of specific organic solutes and is found in the vast majority of microorganisms. The organic osmolytes range from sugars, polyols, amino acids and their respective derivatives, ectoines and betaines. The diversity of these organic solutes has increased in the past few years as more organisms, especially thermophilic and hyperthermophilic Bacteria and Archaea, have been examined. The term compatible solute can also be applied to solutes that protect macromolecules and cells against stresses such as high temperature, desiccation and freezing. The mechanisms by which compatible solutes protect enzymes, cell components and cells are still a long way from being thoroughly elucidated, but there is a growing interest in the utilization of these solutes to protect macromolecules and cells from heating, freezing and desiccation.
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Affiliation(s)
- M S da Costa
- Departamento de Bioquímica, Universidade de Coimbra, Portugal.
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Abstract
New obligately anaerobic bacteria are being discovered at an accelerating rate and it is becoming very evident that the diversity of anoxic biotransformations has been greatly underestimated. Furthermore, among contemporary anaerobes there are many that thrive in extreme environments including, for example, an impressive array of both archaebacterial and eubacterial hyperthermophiles. Free energy for growth and reproduction may be conserved not only via fermentations but also by anoxygenic photophosphorylation and other modes of creating transmembrane proton potential. Thus forms of anaerobic respiration in which various inorganic oxidants (or indeed carbon dioxide) serve as terminal electron acceptors have greatly extended the natural habitats in which such organisms may predominate. Anaerobic bacteria are, however, often found in nature as members of close microbial communities (consortia) that, although sustained by syntrophic and other relations between component species, are liable to alter their composition and character in response to environmental changes, e.g., availability of terminal oxidants. It follows that the biotechnological exploitation of obligately anaerobic bacteria must be informed by knowledge both of their biochemical capacities and of their normal environmental roles. It is against this background that illustrative examples of the activities of anaerobic bacteria are considered under three heads: 1. Biodegradation/Bioremediation, with special reference to the anaerobic breakdown of aromatic and/or halogenated organic substances; 2. Biosynthesis/Bioproduction, encompassing normal and modified fermentations; and 3. Biotransformations, accomplished by whole or semipermeabilized organisms or by enzymes derived therefrom, with particular interest attaching to the production of chiral compounds by a number of procedures, including electromicrobial reduction.
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Affiliation(s)
- J G Morris
- Institute of Biological Sciences, University of Wales, Penglais, Aberystwyth, UK
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Abstract
Strictly anaerobic halophiles, namely fermentative, sulfate-reducing, homoacetogenic, phototrophic, and methanogenic bacteria are involved in the oxidation of organic carbon in hypersaline environments. To date, six anaerobic fermentative genera, containing nine species, have been described. Two of them are homoacetogens. Six species belong to the family Haloanaerobiaceae, as indicated by their unique 16S rRNA oligonucleotide sequences. Desulfohalobium retbaense and Desulfovibrio halophilus represent the only two moderately halophilic sulfate reducers so far reported. Among anoxygenic phototrophic anaerobes, a few purple bacteria with optimal growth at salinities between 6 and 11% NaCl have been isolated from hypersaline habitats. They belong to the genera Rhodospirillum, Chromatium, Thiocapsa, and Ectothiorhodospira. The commonest organisms isolated so far are Chromatium salexigens, Thiocapsa halophila, and Rhodospirillum salinarum. Extremely halophilic purple bacteria have most commonly been isolated from alkaline brines and require about 20 to 25% NaCl for optimal growth. They belong to the family Ectothiorodhospiraceae. Their osmoregulation involves synthesis or uptake of compatible solutes such as glycine-betaine that accumulate in their cytoplasm. The existence of methanogens in hypersaline environments is related to the presence of noncompetitive substrates such as methylamines, which originate mainly from the breakdown of osmoregulatory amines. Methanogenesis probably does not contribute to the mineralization of carbohydrates at NaCl concentrations higher than 15%. Above this concentration, sulfate reduction is probably the main way to oxidize H2 (although at rates too low to use up all the H2 formed) and occupies a terminal function kn the degradation of carbohydrates. Three genera and five species of halophilic methylotrophic methanogens have been reported. A bloom of phototrophic bacteria in the marine salterns of Salins-de-Giraud, located on the Mediterranean French coast in the Rhone Delta, is also described.
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Affiliation(s)
- B Ollivier
- Laboratoire de Microbiologie ORSTOM, Université de Provence, Marseille, France
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Kates M. Biology of halophilic bacteria, Part II. Membrane lipids of extreme halophiles: biosynthesis, function and evolutionary significance. EXPERIENTIA 1993; 49:1027-36. [PMID: 8270029 DOI: 10.1007/bf01929909] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Archaebacteria (archaea) are comprised of three groups of prokaryotes: extreme halophiles, methanogens and thermoacidophiles (extreme thermophiles). Their membrane phospholipids and glycolipids are derived entirely from a saturated, isopranoid glycerol diether, sn-2,3-diphytanylglycerol ('archaeol') and/or its dimer, dibiphytanyldiglyceroltetraether ('caldarchaeol'). In extreme halophiles, the major phospholipid is the archaeol analogue of phosphatidylglycerolmethylphosphate (PGP-Me); the glycolipids are sulfated and/or unsulfated glycosyl archaeols with diverse carbohydrate structure characteristic of taxons on the generic level. Biosynthesis of these archaeol-derived polar lipids occurs in a multienzyme, membrane-bound system that is absolutely dependent on high salt concentration (4 M). The highly complex biosynthetic pathways involve intermediates containing glycerol ether-linked C20-isoprenyl groups which are reduced to phytanyl groups to give the final saturated polar lipids. In methanogens, polar lipids are derived both from archaeol and caldarchaeol, and thermoacidophiles contain essentially only caldarchaeol-derived polar lipids. The function of these membrane polar lipids in maintaining the stability, fluidity and ionic properties of the cell membrane of extreme halophiles, as well as the evolutionary implications of the archaeol and caldarchaeol-derived structures will be discussed.
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Affiliation(s)
- M Kates
- Department of Biochemistry, University of Ottawa, Ontario, Canada
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17
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Clues from a halophilic methanogen about aromatic amino acid biosynthesis in archaebacteria. Arch Microbiol 1993. [DOI: 10.1007/bf00245304] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Menaia JAGF, Duarte JC, Boone DR. Osmotic adaptation of moderately halophilic methanogenic Archaeobacteria, and detection of cytosolicN,N-dimethylglycine. ACTA ACUST UNITED AC 1993. [DOI: 10.1007/bf01929912] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lowe SE, Jain MK, Zeikus JG. Biology, ecology, and biotechnological applications of anaerobic bacteria adapted to environmental stresses in temperature, pH, salinity, or substrates. Microbiol Rev 1993; 57:451-509. [PMID: 8336675 PMCID: PMC372919 DOI: 10.1128/mr.57.2.451-509.1993] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Anaerobic bacteria include diverse species that can grow at environmental extremes of temperature, pH, salinity, substrate toxicity, or available free energy. The first evolved archaebacterial and eubacterial species appear to have been anaerobes adapted to high temperatures. Thermoanaerobes and their stable enzymes have served as model systems for basic and applied studies of microbial cellulose and starch degradation, methanogenesis, ethanologenesis, acetogenesis, autotrophic CO2 fixation, saccharidases, hydrogenases, and alcohol dehydrogenases. Anaerobes, unlike aerobes, appear to have evolved more energy-conserving mechanisms for physiological adaptation to environmental stresses such as novel enzyme activities and stabilities and novel membrane lipid compositions and functions. Anaerobic syntrophs do not have similar aerobic bacterial counterparts. The metabolic end products of syntrophs are potent thermodynamic inhibitors of energy conservation mechanisms, and they require coordinated consumption by a second partner organism for species growth. Anaerobes adapted to environmental stresses and their enzymes have biotechnological applications in organic waste treatment systems and chemical and fuel production systems based on biomass-derived substrates or syngas. These kinds of anaerobes have only recently been examined by biologists, and considerably more study is required before they are fully appreciated by science and technology.
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Affiliation(s)
- S E Lowe
- Department of Biochemistry, Michigan State University, East Lansing 48824
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21
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Lai MC, Gunsalus RP. Glycine betaine and potassium ion are the major compatible solutes in the extremely halophilic methanogen Methanohalophilus strain Z7302. J Bacteriol 1992; 174:7474-7. [PMID: 1429470 PMCID: PMC207447 DOI: 10.1128/jb.174.22.7474-7477.1992] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Methanohalophilus strain Z7302 was previously isolated from a hypersaline environment and grows over a range of NaCl concentrations from 1.7 to 4.4 M. We examined the relationships between cell growth rate, cell volume, and intracellular solute concentrations with increasing salinity. This extremely halophilic methanogen synthesized three zwitterionic compounds, beta-glutamine, N epsilon-acetyl-beta-lysine, and glycine betaine, and also accumulated potassium ion as compatible solutes to balance the external and internal osmotic pressures. Potassium and glycine betaine were the predominant compatible solutes when Methanohalophilus strain Z7302 was grown at high external NaCl concentrations and approached intracellular levels of 3 and 4 M, respectively.
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Affiliation(s)
- M C Lai
- Department of Microbiology and Molecular Genetics, University of California, Los Angeles 90024
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22
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Smigán P, Rusnák P, Greksák M, Zhilina TN, Zavarzin GA. Mode of sodium ion action on methanogenesis and ATPase of the moderate halophilic methanogenis bacterium Methanohalophilus halophilus. FEBS Lett 1992; 300:193-6. [PMID: 1532942 DOI: 10.1016/0014-5793(92)80194-l] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cells of Methanohalophilus halophilus swelled when exposed to hypotonic solutions of NaCl at pH 7.0. The swelling of the cells ceased in the presence of Mg2+. Methane formation by non-growing cells was strongly dependent on the NaCl concentration. Among other monovalent and divalent cations only Li+ and Mg2+ could partly substitute for a specific function of sodium ions. The artificial Na+/H+ antiporter, monensin, exerted a strong inhibitory effect on methane formation from methylamine. The membrane-bound Mg(2+)-stimulated ATPase of these cells was enhanced at low (40 mM) NaCl concentration while higher concentrations of this solute were inhibitory. The results obtained show that sodium ions are a prerequisite for optimal methane formation and ATPase activity in these cells. However, both of these processes required different sodium ion concentrations.
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Affiliation(s)
- P Smigán
- Institute of Animal Biochemistry and Genetics, Slovak Academy of Sciences, Ivanka pri Dunaji, Czechoslovakia
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23
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Lai MC, Sowers KR, Robertson DE, Roberts MF, Gunsalus RP. Distribution of compatible solutes in the halophilic methanogenic archaebacteria. J Bacteriol 1991; 173:5352-8. [PMID: 1909318 PMCID: PMC208245 DOI: 10.1128/jb.173.17.5352-5358.1991] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Accumulation of compatible solutes, by uptake or de novo synthesis, enables bacteria to reduce the difference between osmotic potentials of the cell cytoplasm and the extracellular environment. To examine this process in the halophilic and halotolerant methanogenic archaebacteria, 14 strains were tested for the accumulation of compatible solutes in response to growth in various extracellular concentrations of NaCl. In external NaCl concentrations of 0.7 to 3.4 M, the halophilic methanogens accumulated K+ ion and low-molecular-weight organic compounds. beta-Glutamate was detected in two halotolerant strains that grew below 1.5 M NaCl. Two unusual beta-amino acids, N epsilon-acetyl-beta-lysine and beta-glutamine (3-aminoglutaramic acid), as well as L-alpha-glutamate were compatible solutes among all of these strains. De novo synthesis of glycine betaine was also detected in several strains of moderately and extremely halophilic methanogens. The zwitterionic compounds (beta-glutamine, N epsilon-acetyl-beta-lysine, and glycine betaine) and potassium were the predominant compatible solutes among the moderately and extremely halophilic methanogens. This is the first report of beta-glutamine as a compatible solute and de novo biosynthesis of glycine betaine in the methanogenic archaebacteria.
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Affiliation(s)
- M C Lai
- Department of Microbiology and Molecular Genetics, University of California, Los Angeles 90024
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24
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Ch. R-6 Isolation and Characterization of Anaerobic Halophilic Bacteria From Oil Reservoir Brines. ACTA ACUST UNITED AC 1991. [DOI: 10.1016/s0376-7361(09)70154-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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25
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Oren A. Formation and breakdown of glycine betaine and trimethylamine in hypersaline environments. Antonie Van Leeuwenhoek 1990; 58:291-8. [PMID: 2082817 DOI: 10.1007/bf00399342] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Glycine betaine is accumulated as a compatible solute in many photosynthetic and non-photosynthetic bacteria--the last being unable to synthesize the compound--and thus large pools of betaine can be expected to be present in hypersaline environments. A variety of aerobic and anaerobic microorganisms degrade betaine to among other products trimethylamine and methylamine, in a number of different pathways. Curiously, very few of these betaine breakdown processes have yet been identified in hypersaline environments. Trimethylamine can also be formed by bacterial reduction of trimethylamine N-oxide (also by extremely halophilic archaeobacteria). Degradation of trimethylamine in hypersaline environments by halophilic methanogenic bacteria is relatively well documented, and leads to the formation of methane, carbon dioxide and ammonia.
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Affiliation(s)
- A Oren
- Division of Microbial and Molecular Ecology, Hebrew University of Jerusalem, Israel
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Oremland RS, Kiene RP, Mathrani I, Whiticar MJ, Boone DR. Description of an Estuarine Methylotrophic Methanogen Which Grows on Dimethyl Sulfide. Appl Environ Microbiol 1989; 55:994-1002. [PMID: 16347900 PMCID: PMC184236 DOI: 10.1128/aem.55.4.994-1002.1989] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Characteristics of an obligately methylotrophic coccoid methanogen (strain GS-16) previously isolated from estuarine sediment are described. Growth was demonstrated on dimethyl sulfide (DMS) or trimethylamine (TMA), but not on methane thiol, methane thiol plus hydrogen, dimethyl disulfide, or methionine. DMS-grown cells were able to metabolize DMS and TMA simultaneously when inoculated into media containing substrate levels of these compounds. However, TMA-grown cells could not metabolize [
14
C]DMS to
14
CH
4
, although they could convert [
14
C]methanol to
14
CH
4
. These results suggest that metabolism of DMS proceeds along a somewhat different route than that of TMA and perhaps also that of methanol. The organism exhibited doubling times of 23 and 32 h for growth (25°C) in mineral media on TMA and DMS, respectively. Doubling times were more rapid (∼6 h) when the organisms were grown on TMA in complex broth. In mineral media, the fastest growth on DMS occurred between pH levels of 7.0 and 8.7, at 29°C, and with 0.2 to 0.4 M Na
+
and 0.04 M Mg
2+
. Somewhat different results occurred for growth on TMA in complex broth. Cells had a moles percent G+C value of 44.5% for their DNA. Growth on DMS, TMA, and methanol yielded stable carbon isotope fractionation factors of 1.044, 1.037, and 1.063, respectively. Fractionation factors for hydrogen were 1.203 (DMS) and 1.183 (TMA).
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Affiliation(s)
- R S Oremland
- United States Geological Survey, 345 Middlefield Road, Menlo Park, California 94025; University of Georgia Marine Institute, Sapelo Island, Georgia 31327 ; School of Public Health, University of California, Los Angeles, Los Angeles, California 90024 ; Federal Institute for Geosciences and Natural Resources, D-3000 Hannover 51, Hannover, Federal Republic of Germany ; and Department of Environmental Science and Engineering, Oregon Graduate Center, Beaverton, Oregon 97006-1999
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Yamaguchi M, Minami K, Tanimoto Y, Okamura K. Effects of volatile fatty acids on methanogenesis of methanol and of pregrowth with methanol on acetate utilization by methanogens. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/0922-338x(89)90099-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tomei FA, Rouse D, Maki JS, Mitchell R. Presence of an Unusual Methanogenic Bacterium in Coal Gasification Waste. Appl Environ Microbiol 1988; 54:2964-70. [PMID: 16347791 PMCID: PMC204412 DOI: 10.1128/aem.54.12.2964-2970.1988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanogenic bacteria growing on a pilot-scale, anaerobic filter processing coal gasification waste were enriched in a mineral salts medium containing hydrogen and acetate as potential energy sources. Transfer of the enrichments to methanol medium resulted in the initial growth of a strain of
Methanosarcina barkeri,
but eventually small cocci became dominant. The cocci growing on methanol produced methane and exhibited the typical fluorescence of methanogenic bacteria. They grew in the presence of the cell wall synthesis-inhibiting antibiotics
d
-cycloserine, fosfomycin, penicillin G, and vancomycin as well as in the presence of kanamycin, an inhibitor of protein synthesis in eubacteria. The optimal growth temperature was 37°C, and the doubling time was 7.5 h. The strain lysed after reaching stationary phase. The bacterium grew poorly with hydrogen as the energy source and failed to grow on acetate. Morphologically, the coccus shared similarities with
Methanosarcina
sp. Cells were 1 μm wide, exhibited the typical thick cell wall and cross-wall formation, and formed tetrads. Packets and cysts were not formed.
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Affiliation(s)
- F A Tomei
- Laboratory of Microbial Ecology, Division of Applied Sciences, Harvard University, Cambridge, Massachusetts 02138
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An extremely thermophilic Methanococcus from a deep sea hydrothermal vent and its plasmid. Arch Microbiol 1988. [DOI: 10.1007/bf00425159] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Methane ebullition and high rates of methane production were observed in sediments of a hypersaline pond (180 per thousand) which contained sulfate in excess of 100 mM. The highest rates of methane production were observed in surface sediments associated with an algal mat dominated by a Spirulina sp. The mat contained a methylated amine, glycine betaine (GBT), at levels which accounted for up to 20% of the total mat nitrogen. GBT was apparently the source of trimethylamine (TMA), which was also present in the sediment at relatively high concentrations. Patterns of substrate metabolism by the methanogenic populations in sediment slurries suggested that TMA was a major methane precursor. Neither exogenous hydrogen nor acetate stimulated methanogenesis, while addition of a variety of amines including TMA, trimethylamine oxide, GBT, and choline resulted in substantial increases with yields of >70%. The temperature optimum for methanogenesis in this system was 45 to 55 degrees C, which coincided with the observed sediment temperature. Patterns and rates of methane production in this and other hypersaline algal mats may be determined by a complex interaction between salinity, the use of methylated amines for osmoregulation by algae, and the formation of TMA by fermentation.
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Affiliation(s)
- Gary M King
- Darling Marine Center, University of Maine, Walpole, Maine 04573
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Oren A. Anaerobic degradation of organic compounds at high salt concentrations. Antonie Van Leeuwenhoek 1988; 54:267-77. [PMID: 3048206 DOI: 10.1007/bf00443585] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A number of obligately anaerobic fermentative bacteria are known to degrade a variety of organic substrates such as sugars, amino acids, and others, in the presence of high salt concentrations (up to 3-4 M) to products such as hydrogen, CO2, acetate and higher fatty acids, and ethanol. Our understanding of the fate of these products in hypersaline environments is still extremely limited. The occurrence of bacterial sulfate reduction is well established at salt concentrations of up to 24%; however, the bacteria involved have not yet been isolated in pure culture, and the range of electron donors used is unknown. Halophilic or halotolerant methanogenic bacteria using hydrogen/CO2 or acetate as energy source are notably absent; methanogenesis under hypersaline conditions is probably limited to such substrates as methanol and methylamines, which cannot be expected to be major products of anaerobic degradation of most organic compounds.
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Affiliation(s)
- A Oren
- Division of Microbial and Molecular Ecology, Hebrew University of Jerusalem, Israel
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