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Ou YF, Dong HP, McIlroy SJ, Crowe SA, Hallam SJ, Han P, Kallmeyer J, Simister RL, Vuillemin A, Leu AO, Liu Z, Zheng YL, Sun QL, Liu M, Tyson GW, Hou LJ. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. THE ISME JOURNAL 2022; 16:2373-2387. [PMID: 35810262 PMCID: PMC9478090 DOI: 10.1038/s41396-022-01281-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 05/28/2023]
Abstract
Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.
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Affiliation(s)
- Ya-Fei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Hong-Po Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Sean A Crowe
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Ping Han
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Jens Kallmeyer
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Rachel L Simister
- Ecosystem Services, Commercialization Platforms, and Entrepreneurship (ECOSCOPE) Training Program, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Aurele Vuillemin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Andy O Leu
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Zhanfei Liu
- Marine Science Institute, The University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Yan-Ling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Qian-Li Sun
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai, 200241, China
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Li-Jun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China.
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Liu Y, Beer LL, Whitman WB. Methanogens: a window into ancient sulfur metabolism. Trends Microbiol 2012; 20:251-8. [PMID: 22406173 DOI: 10.1016/j.tim.2012.02.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 01/29/2012] [Accepted: 02/06/2012] [Indexed: 11/26/2022]
Abstract
Methanogenesis is an ancient metabolism that originated on the early anoxic Earth. The buildup of O(2) about 2.4 billion years ago led to formation of a large oceanic sulfate pool, the onset of widespread sulfate reduction and the marginalization of methanogens to anoxic and sulfate-poor niches. Contemporary methanogens are restricted to anaerobic habitats and may have retained some metabolic relics that were common in early anaerobic life. Consistent with this hypothesis, methanogens do not utilize sulfate as a sulfur source, Cys is not utilized as a sulfur donor for Fe-S cluster and Met biosynthesis, and Cys biosynthesis uses an unusual tRNA-dependent pathway.
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Affiliation(s)
- Yuchen Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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González-Muñoz MT, Rodriguez-Navarro C, Martínez-Ruiz F, Arias JM, Merroun ML, Rodriguez-Gallego M. Bacterial biomineralization: new insights from Myxococcus-induced mineral precipitation. ACTA ACUST UNITED AC 2010. [DOI: 10.1144/sp336.3] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractBacteria have contributed to the formation of minerals since the advent of life on Earth. Bacterial biomineralization plays a critical role on biogeochemical cycles and has important technological and environmental applications. Despite the numerous efforts to better understand how bacteria induce/mediate or control mineralization, our current knowledge is far from complete. Considering that the number of recent publications on bacterial biomineralization has been overwhelming, here we attempt to show the importance of bacteria–mineral interactions by focusing in a single bacterial genus, Myxococcus, which displays an unusual capacity of producing minerals of varying compositions and morphologies. First, an overview of the recent history of bacterial mineralization, the most common bacteriogenic minerals and current models on bacterial biomineralization is presented. Afterwards a description of myxobacteria is presented, followed by a section where Myxococcus-induced precipitation of a number of phosphates, carbonates, sulphates, chlorides, oxalates and silicates is described and discussed in lieu of the information presented in the first part. As concluding remarks, implications of bacterial mineralization and perspectives for future research are outlined. This review strives to show that the mechanisms which control bacterial biomineralization are not mineral- or bacterial-specific. On the contrary, they appear to be universal and depend on the environment in which bacteria dwell.
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Affiliation(s)
| | - Carlos Rodriguez-Navarro
- Departamento de Mineralogía y Petrología, Universidad de Granada, Fuentenueva s/n, 18002, Granada, Spain
| | - Francisca Martínez-Ruiz
- Instituto Andaluz de Ciencias de la Tierra, CSIC – Universidad de Granada, Fuentenueva s/n, 18002, Granada, Spain
| | - Jose Maria Arias
- Departamento de Microbiología, Universidad de Granada, Fuentenueva s/n, 18002, Granada, Spain
| | - Mohamed L. Merroun
- Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, D–01314, Dresden, Germany; Present address: Departamento de Microbiología, Universidad de Granada, Granada, Spain
| | - Manuel Rodriguez-Gallego
- Departamento de Mineralogía y Petrología, Universidad de Granada, Fuentenueva s/n, 18002, Granada, Spain
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Abstract
Numerous hypotheses about how life on earth could have started can be found in the literature. In this article, we give an overview about the most widespread ones and try to point out which of them might have occurred on the primordial earth with highest probability from a chemical point of view. The idea that a very early stage of life was the "RNA world" encounters crucial problems concerning the formation of its building blocks and their stability in a prebiotic environment. Instead, it seems much more likely that a "peptide world" originated first and that RNA and DNA took up their part at a much later stage. It is shown that amino acids and peptides can be easily formed in a realistic primordial scenario and that these biomolecules can start chemical evolution without the help of RNA. The origin of biohomochirality seems strongly related to the most probable formation of the first peptides via the salt-induced peptide formation (SIPF) reaction.
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Rees DC, Howard JB. The interface between the biological and inorganic worlds: iron-sulfur metalloclusters. Science 2003; 300:929-31. [PMID: 12738849 DOI: 10.1126/science.1083075] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Complex iron-sulfur metalloclusters form the active sites of the enzymes that catalyze redox transformations of N2, CO, and H2, which are likely components of Earth's primordial atmosphere. Although these centers reflect the organizational principles of simpler iron-sulfur clusters, they exhibit extensive elaborations that confer specific ligand-binding and catalytic properties. These changes were probably achieved through evolutionary processes, including the fusion of small clusters, the addition of new metals, and the development of cluster assembly pathways, driven by selective pressures resulting from changes in the chemical composition of the biosphere.
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Affiliation(s)
- Douglas C Rees
- Division of Chemistry and Chemical Engineering 114-96, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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