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      Complete Genome Sequence of “ Candidatus Syntrophocurvum alkaliphilum” Strain B(2M), Obtained from the Metagenome of a Salt-Tolerant Alkaliphilic Anaerobic Syntrophic Butyrate-Degrading Consortium

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          Abstract

          A highly salt-tolerant and alkaliphilic syntrophic consortium that degrades butyrate under sulfate-reducing conditions was purified from a hypersaline soda lake in southwest Siberia. Here, we present the complete genome sequence of the syntrophic primary butyrate degrader in order to understand the molecular mechanisms of interaction between consortium members.

          ABSTRACT

          A highly salt-tolerant and alkaliphilic syntrophic consortium that degrades butyrate under sulfate-reducing conditions was purified from a hypersaline soda lake in southwest Siberia. Here, we present the complete genome sequence of the syntrophic primary butyrate degrader in order to understand the molecular mechanisms of interaction between consortium members.

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          Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation.

          Michael J. McInerney, Robert P. Gunsalus, Jessica Sieber (2011)
          Syntrophy is a tightly coupled mutualistic interaction between hydrogen-/formate-producing and hydrogen-/formate-using microorganisms that occurs throughout the microbial world. Syntrophy is essential for global carbon cycling, waste decomposition, and biofuel production. Reverse electron transfer, e.g., the input of energy to drive critical redox reactions, is a defining feature of syntrophy. Genomic analyses indicate multiple systems for reverse electron transfer, including ion-translocating ferredoxin:NAD(+) oxidoreductase and hydrogenases, two types of electron transfer flavoprotein:quinone oxidoreductases, and other quinone reactive complexes. Confurcating hydrogenases that couple the favorable production of hydrogen from reduced ferredoxin with the unfavorable production of hydrogen from NADH are present in almost all syntrophic metabolizers, implicating their critical role in syntrophy. Transcriptomic analysis shows upregulation of many genes without assigned functions in the syntrophic lifestyle. High-throughput technologies provide insight into the mechanisms used to establish and maintain syntrophic consortia and conserve energy from reactions that operate close to thermodynamic equilibrium.
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            A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

            Charlotte Vavourakis, Adrian-Ştefan Andrei, Maliheh Mehrshad … (2018)
            Background Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages. Results We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L−1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria. Conclusions Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments. Electronic supplementary material The online version of this article (10.1186/s40168-018-0548-7) contains supplementary material, which is available to authorized users.
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              A Proteomic View at the Biochemistry of Syntrophic Butyrate Oxidation in Syntrophomonas wolfei

              Alexander F. Schmidt, Nicolai Müller, Bernhard Schink … (2013)
              In syntrophic conversion of butyrate to methane and CO2, butyrate is oxidized to acetate by secondary fermenting bacteria such as Syntrophomonas wolfei in close cooperation with methanogenic partner organisms, e.g., Methanospirillum hungatei. This process involves an energetically unfavourable shift of electrons from the level of butyryl-CoA oxidation to the substantially lower redox potential of proton and/or CO2 reduction, in order to transfer these electrons to the methanogenic partner via hydrogen and/or formate. In the present study, all prominent membrane-bound and soluble proteins expressed in S. wolfei specifically during syntrophic growth with butyrate, in comparison to pure-culture growth with crotonate, were examined by one- and two-dimensional gel electrophoresis, and identified by peptide fingerprinting-mass spectrometry. A membrane-bound, externally oriented, quinone-linked formate dehydrogenase complex was expressed at high level specifically during syntrophic butyrate oxidation, comprising a selenocystein-linked catalytic subunit with a membrane-translocation pathway signal (TAT), a membrane-bound iron-sulfur subunit, and a membrane-bound cytochrome. Soluble hydrogenases were expressed at high levels specifically during growth with crotonate. The results were confirmed by native protein gel electrophoresis, by formate dehydrogenase and hydrogenase-activity staining, and by analysis of formate dehydrogenase and hydrogenase activities in intact cells and cell extracts. Furthermore, constitutive expression of a membrane-bound, internally oriented iron-sulfur oxidoreductase (DUF224) was confirmed, together with expression of soluble electron-transfer flavoproteins (EtfAB) and two previously identified butyryl-CoA dehydrogenases. Our findings allow to depict an electron flow scheme for syntrophic butyrate oxidation in S. wolfei. Electrons derived from butyryl-CoA are transferred through a membrane-bound EtfAB:quinone oxidoreductase (DUF224) to a menaquinone cycle and further via a b-type cytochrome to an externally oriented formate dehydrogenase. Hence, an ATP hydrolysis-driven proton-motive force across the cytoplasmatic membrane would provide the energy input for the electron potential shift necessary for formate formation.
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                Author and article information

                Contributors
                Irene L. G. Newton: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (hwp): ga
                Journal ID (pmc): mra
                Journal ID (publisher-id): MRA
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date Collection: February 2020
                Publication date (Electronic): 6 February 2020
                Volume: 9
                Issue: 6
                Electronic Location Identifier: e01511-19
                Affiliations
                [a ]Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
                [b ]Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
                [c ]Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
                Indiana University, Bloomington
                Author notes
                Address correspondence to Andrey V. Mardanov, mardanov@ 123456biengi.ac.ru .

                Citation Mardanov AV, Sorokin DY, Beletsky AV, Ravin NV. 2020. Complete genome sequence of “ Candidatus Syntrophocurvum alkaliphilum” strain B(2M), obtained from the metagenome of a salt-tolerant alkaliphilic anaerobic syntrophic butyrate-degrading consortium. Microbiol Resour Announc 9:e01511-19. https://doi.org/10.1128/MRA.01511-19.

                Author information
                https://orcid.org/0000-0002-8245-8757
                Article
                Publisher ID: MRA01511-19
                DOI: 10.1128/MRA.01511-19
                PMC ID: 7005122
                PubMed ID: 32029557
                SO-VID: a7f878f3-6d10-4f28-a2aa-2f128e51787a
                Copyright © Copyright © 2020 Mardanov et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 15 December 2019
                Date accepted : 14 January 2020
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 14, Pages: 3, Words: 1550
                Funding
                Funded by: Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO), https://doi.org/10.13039/501100003246;
                Award ID: 24002002
                Award Recipient :
                Funded by: Russian Foundation for Fundamental Investigations (RFFI), https://doi.org/10.13039/100012555;
                Award ID: 17-04-01740
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Custom metadata
                cover-date February 2020

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