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Rao A, Driessen AJM. Unraveling the multiplicity of geranylgeranyl reductases in Archaea: potential roles in saturation of terpenoids. Extremophiles 2024; 28:14. [PMID: 38280122 PMCID: PMC10821996 DOI: 10.1007/s00792-023-01330-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/15/2023] [Indexed: 01/29/2024]
Abstract
The enzymology of the key steps in the archaeal phospholipid biosynthetic pathway has been elucidated in recent years. In contrast, the complete biosynthetic pathways for proposed membrane regulators consisting of polyterpenes, such as carotenoids, respiratory quinones, and polyprenols remain unknown. Notably, the multiplicity of geranylgeranyl reductases (GGRs) in archaeal genomes has been correlated with the saturation of polyterpenes. Although GGRs, which are responsible for saturation of the isoprene chains of phospholipids, have been identified and studied in detail, there is little information regarding the structure and function of the paralogs. Here, we discuss the diversity of archaeal membrane-associated polyterpenes which is correlated with the genomic loci, structural and sequence-based analyses of GGR paralogs.
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Affiliation(s)
- Alka Rao
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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2
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Xing T, Liu P, Ji M, Deng Y, Liu K, Wang W, Liu Y. Sink or Source: Alternative Roles of Glacier Foreland Meadow Soils in Methane Emission Is Regulated by Glacier Melting on the Tibetan Plateau. Front Microbiol 2022; 13:862242. [PMID: 35387086 PMCID: PMC8977769 DOI: 10.3389/fmicb.2022.862242] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Glacier foreland soils have long been considered as methane (CH4) sinks. However, they are flooded by glacial meltwater annually during the glacier melting season, altering their redox potential. The impacts of this annual flooding on CH4 emission dynamics and methane-cycling microorganisms are not well understood. Herein, we measured in situ methane flux in glacier foreland soils during the pre-melting and melting seasons on the Tibetan Plateau. In addition, high-throughput sequencing and qPCR were used to investigate the diversity, taxonomic composition, and the abundance of methanogenic archaea and methanotrophic bacteria. Our results showed that the methane flux ranged from -10.11 to 4.81 μg·m-2·h-1 in the pre-melting season, and increased to 7.48-22.57 μg·m-2·h-1 in the melting season. This indicates that glacier foreland soils change from a methane sink to a methane source under the impact of glacial meltwater. The extent of methane flux depends on methane production and oxidation conducted by methanogens and methanotrophs. Among all the environmental factors, pH (but not moisture) is dominant for methanogens, while both pH and moisture are not that strong for methanotrophs. The dominant methanotrophs were Methylobacter and Methylocystis, whereas the methanogens were dominated by methylotrophic Methanomassiliicoccales and hydrogenotrophic Methanomicrobiales. Their distributions were also affected by microtopography and environmental factor differences. This study reveals an alternative role of glacier foreland meadow soils as both methane sink and source, which is regulated by the annual glacial melt. This suggests enhanced glacial retreat may positively feedback global warming by increasing methane emission in glacier foreland soils in the context of climate change.
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Affiliation(s)
- Tingting Xing
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing, China.,Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Wenqiang Wang
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
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Tiwari BR, Rouissi T, Brar SK, Surampalli RY. Critical insights into psychrophilic anaerobic digestion: Novel strategies for improving biogas production. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 131:513-526. [PMID: 34280728 DOI: 10.1016/j.wasman.2021.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic digestion (AD) under psychrophilic temperature has only recently garnered deserved attention. In major parts of Europe, USA, Canada and Australia, climatic conditions are more suited for psychrophilic (<20 ℃) rather than mesophilic (35 - 37 ℃) and thermophilic (55 - 60 ℃) AD. Low temperature has adverse effects on important cellular processes which may render the cell biology inactive. Moreover, cold climate can also alter the physical and chemical properties of wastewater, thereby reducing the availability of substrate to microbes. Hence, the use of low temperature acclimated microbial biomass could overcome thermodynamic constraints and carry out flexible structural and conformational changes to proteins, membrane lipid composition, expression of cold-adapted enzymes through genotypic and phenotypic variations. Reduction in organic loading rate is beneficial to methane production under low temperatures. Moreover, modification in the design of existing reactors and the use of hybrid reactors have already demonstrated improved methane generation in the lab-scale. This review also discusses some novel strategies such as direct interspecies electron transfer (DIET), co-digestion of substrate, bioaugmentation, and bioelectrochemical system assisted AD which present promising prospects. While DIET can facilitate syntrophic electron exchange in diverse microbes, the addition of organic-rich co-substrate can help in maintaining suitable C/N ratio in the anaerobic digester which subsequently can enhance methane generation. Bioaugmentation with psychrophilic strains could reduce start-up time and ensure daily stable performance for wastewater treatment facilities at low temperatures. In addition to the technical discussion, the economic assessment and future outlook on psychrophilic AD are also highlighted.
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Affiliation(s)
- Bikash R Tiwari
- Institut National de la recherche scientifique - Centre Eau Terre Environnement, Université du Québec, Quebec City, Canada
| | - Tarek Rouissi
- Institut National de la recherche scientifique - Centre Eau Terre Environnement, Université du Québec, Quebec City, Canada
| | - Satinder Kaur Brar
- Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Canada.
| | - Rao Y Surampalli
- Global Institute for Energy, Environment and Sustainability, Lenexa, USA
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4
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Seasonal variations in culturable archaea and their plant growth promoting attributes to predict their role in establishment of vegetation in Rann of Kutch. Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00259-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Liu C, Mao L, Zheng X, Yuan J, Hu B, Cai Y, Xie H, Peng X, Ding X. Comparative proteomic analysis of Methanothermobacter thermautotrophicus reveals methane formation from H 2 and CO 2 under different temperature conditions. Microbiologyopen 2018; 8:e00715. [PMID: 30260585 PMCID: PMC6528648 DOI: 10.1002/mbo3.715] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 11/22/2022] Open
Abstract
The growth of all methanogens is limited to a specific temperature range. However, Methanothermobacter thermautotrophicus can be found in a variety of natural and artificial environments, the temperatures of which sometimes even exceed the temperature growth ranges of thermophiles. As a result, the extent to which methane production and survival are affected by temperature remains unclear. To investigate the mechanisms of methanogenesis that Archaea have evolved to cope with drastic temperature shifts, the responses of Methanothermobacter thermautotrophicus to temperature were investigated under a high temperature growth (71°C) and cold shock (4°C) using Isobaric tags for relative and absolute quantitation (iTRAQ). The results showed that methane formation is decreased and that protein folding and degradation are increased in both high‐ and low‐temperature treatments. In addition, proteins predicted to be involved in processing environmental information processing and in cell membrane/wall/envelope biogenesis may play key roles in affecting methane formation and enhancing the response of M. thermautotrophicus to temperature stress. Analysis of the genomic locations of the genes corresponding to these temperature‐dependent proteins predicted that 77 of the genes likely to form 32 gene clusters. Here, we assess the response of M. thermautotrophicus to different temperatures and provide a new level of understanding of methane formation and cellular putative adaptive responses.
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Affiliation(s)
- Cong Liu
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Lihui Mao
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Xiongmin Zheng
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Jiangan Yuan
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Beijuan Hu
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Xiaojue Peng
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China
| | - Xia Ding
- School of Life Sciences and Institute of Life Science, Nanchang University, Nanchang, Jiangxi, China.,Biology Experimental Teaching Demonstration, Nanchang University, Nanchang, Jiangxi, China
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6
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Psychrotrophic Microbiomes: Molecular Diversity and Beneficial Role in Plant Growth Promotion and Soil Health. MICROORGANISMS FOR SUSTAINABILITY 2018. [DOI: 10.1007/978-981-10-7146-1_11] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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7
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Dai Y, Yan Z, Jia L, Zhang S, Gao L, Wei X, Mei Z, Liu X. The composition, localization and function of low-temperature-adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils. J Appl Microbiol 2016; 121:163-76. [PMID: 27123875 DOI: 10.1111/jam.13164] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/26/2015] [Accepted: 01/18/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Y. Dai
- Key Laboratory of Environmental and Applied Microbiology; Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Sichuan China
| | - Z. Yan
- Key Laboratory of Environmental and Applied Microbiology; Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Sichuan China
| | - L. Jia
- The State Key Laboratory of Biotherapy; West China Hospital; Sichuan University; Sichuan China
| | - S. Zhang
- Key Laboratory of Environmental and Applied Microbiology; Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Sichuan China
| | - L. Gao
- Department of Agricultural Engineering; Chongqing Academy of Agricultural Sciences; Chongqing China
| | - X. Wei
- Department of Agricultural Engineering; Chongqing Academy of Agricultural Sciences; Chongqing China
| | - Z. Mei
- Center of Agricultural Engineering; Biogas Institute of Ministry of Agriculture; Chengdu China
| | - X. Liu
- Key Laboratory of Environmental and Applied Microbiology; Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Sichuan China
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Taubner RS, Schleper C, Firneis MG, Rittmann SKMR. Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies. Life (Basel) 2015; 5:1652-86. [PMID: 26703739 PMCID: PMC4695842 DOI: 10.3390/life5041652] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 10/15/2015] [Accepted: 11/10/2015] [Indexed: 12/31/2022] Open
Abstract
Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens.
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Affiliation(s)
- Ruth-Sophie Taubner
- Research Platform: ExoLife, University of Vienna, Türkenschanzstraße 17, 1180 Vienna, Austria.
- Institute of Astrophysics, University of Vienna, Türkenschanzstraße 17, 1180 Vienna, Austria.
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
| | - Maria G Firneis
- Research Platform: ExoLife, University of Vienna, Türkenschanzstraße 17, 1180 Vienna, Austria.
- Institute of Astrophysics, University of Vienna, Türkenschanzstraße 17, 1180 Vienna, Austria.
| | - Simon K-M R Rittmann
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
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Ding C, Ma T, Hu A, Dai L, He Q, Cheng L, Zhang H. Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions. MICROBIAL ECOLOGY 2015; 70:433-444. [PMID: 25783218 DOI: 10.1007/s00248-015-0590-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
Anaerobic alkane degradation via methanogenesis has been intensively studied under mesophilic and thermophilic conditions. While there is a paucity of information on the ability and composition of anaerobic alkane-degrading microbial communities under low temperature conditions. In this study, we investigated the ability of consortium Y15, enriched from Shengli oilfield, to degrade hydrocarbons under different temperature conditions (5-35 °C). The consortium could use hexadecane over a low temperature range (15-30 °C). No growth was detected below 10 °C and above 35 °C, indicating the presence of cold-tolerant species capable of alkane degradation. The preferential degradation of short chain n-alkanes from crude oil was observed by this consortium. The structure and dynamics of the microbial communities were examined using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and Sanger sequencing of 16S rRNA genes. The core archaeal communities were mainly composed of aceticlastic Methanosaeta spp. Syntrophaceae-related microorganisms were always detected during consecutive transfers and dominated the bacterial communities, sharing 94-96 % sequence similarity with Smithella propionica strain LYP(T). Phylogenetic analysis of Syntrophaceae-related clones in diverse methanogenic alkane-degrading cultures revealed that most of them were clustered into three sublineages. Syntrophaceae clones retrieved from this study were mainly clustered into sublineage I, which may represent psychrotolerant, syntrophic alkane degraders. These results indicate the wide geographic distribution and ecological function of syntrophic alkane degraders.
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Affiliation(s)
- Chen Ding
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041, People's Republic of China
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Protein adaptations in archaeal extremophiles. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:373275. [PMID: 24151449 PMCID: PMC3787623 DOI: 10.1155/2013/373275] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/26/2013] [Accepted: 08/14/2013] [Indexed: 12/25/2022]
Abstract
Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity under cold temperatures. Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity.
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