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Solchaga JI, Busalmen JP, Nercessian D. Unraveling Anaerobic Metabolisms in a Hypersaline Sediment. Front Microbiol 2022; 13:811432. [PMID: 35369499 PMCID: PMC8966722 DOI: 10.3389/fmicb.2022.811432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the microbial diversity inhabiting hypersaline sediments is still limited. In particular, existing data about anaerobic hypersaline archaea and bacteria are scarce and refer to a limited number of genera. The approach to obtain existing information has been almost exclusively attempting to grow every organism in axenic culture on the selected electron acceptor with a variety of electron donors. Here, a different approach has been used to interrogate the microbial community of submerged hypersaline sediment of Salitral Negro, Argentina, aiming at enriching consortia performing anaerobic respiration of different electron acceptor compounds, in which ecological associations can maximize the possibilities of successful growth. Growth of consortia was demonstrated on all offered electron acceptors, including fumarate, nitrate, sulfate, thiosulfate, dimethyl sulfoxide, and a polarized electrode. Halorubrum and Haloarcula representatives are here shown for the first time growing on lactate, using fumarate or a polarized electrode as the electron acceptor; in addition, they are shown also growing in sulfate-reducing consortia. Halorubrum representatives are for the first time shown to be growing in nitrate-reducing consortia, probably thanks to reduction of N2O produced by other consortium members. Fumarate respiration is indeed shown for the first time supporting growth of Halanaeroarchaeum and Halorhabdus belonging to the archaea, as well as growth of Halanaerobium, Halanaerobaculum, Sporohalobacter, and Acetohalobium belonging to the bacteria. Finally, evidence is presented suggesting growth of nanohaloarchaea in anaerobic conditions.
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Affiliation(s)
- Juan Ignacio Solchaga
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
| | - Juan Pablo Busalmen
- Laboratorio de Bioelectroquímica, INTEMA - CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
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2
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Sorokin DY, Messina E, Smedile F, La Cono V, Hallsworth JE, Yakimov MM. Carbohydrate‐dependent sulfur respiration in halo(alkali)philic archaea. Environ Microbiol 2021; 23:3789-3808. [DOI: 10.1111/1462-2920.15421] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/03/2021] [Accepted: 02/01/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Dimitry Y. Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology Russian Academy of Sciences Moscow Russia
- Department of Biotechnology Delft University of Technology Delft The Netherlands
| | - Enzo Messina
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Francesco Smedile
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - Violetta La Cono
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
| | - John E. Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, Northern Ireland BT9 5DL UK
| | - Michail M. Yakimov
- Institute of Biological Resources and Marine Biotechnology, IRBIM‐CNR Messina Italy
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3
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Abstract
Established in 2016, the family Pleolipoviridae comprises globally distributed archaeal viruses that produce pleomorphic particles. Pseudo-spherical enveloped virions of pleolipoviruses are membrane vesicles carrying a nucleic acid cargo. The cargo can be either a single-stranded or double-stranded DNA molecule, making this group the first family introduced in the 10th Report on Virus Taxonomy including both single-stranded and double-stranded DNA viruses. The length of the genomes is approximately 7–17 kilobase pairs, or kilonucleotides in the case of single-stranded molecules. The genomes are circular single-stranded DNA, circular double-stranded DNA, or linear double-stranded DNA molecules. Currently, eight virus species and seven proposed species are classified in three genera: Alphapleolipovirus (five species), Betapleolipovirus (nine species), and Gammapleolipovirus (one species). Here, we summarize the updated taxonomy of the family Pleolipoviridae to reflect recent advances in this field, with the focus on seven newly proposed species in the genus Betapleolipovirus: Betapleolipovirus HHPV3, HHPV4, HRPV9, HRPV10, HRPV11, HRPV12, and SNJ2.
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Affiliation(s)
- Tatiana A Demina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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Varrella S, Tangherlini M, Corinaldesi C. Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest. Mar Drugs 2020; 18:md18020091. [PMID: 32019162 PMCID: PMC7074082 DOI: 10.3390/md18020091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 12/18/2022] Open
Abstract
Deep-sea hypersaline anoxic basins (DHABs) are considered to be among the most extreme ecosystems on our planet, allowing only the life of polyextremophilic organisms. DHABs’ prokaryotes exhibit extraordinary metabolic capabilities, representing a hot topic for microbiologists and biotechnologists. These are a source of enzymes and new secondary metabolites with valuable applications in different biotechnological fields. Here, we review the current knowledge on prokaryotic diversity in DHABs, highlighting the biotechnological applications of identified taxa and isolated species. The discovery of new species and molecules from these ecosystems is expanding our understanding of life limits and is expected to have a strong impact on biotechnological applications.
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Affiliation(s)
- Stefano Varrella
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, 60131 Ancona, Italy;
| | | | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, 60131 Ancona, Italy;
- Correspondence:
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5
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Sorokin DY, Messina E, La Cono V, Ferrer M, Ciordia S, Mena MC, Toshchakov SV, Golyshin PN, Yakimov MM. Sulfur Respiration in a Group of Facultatively Anaerobic Natronoarchaea Ubiquitous in Hypersaline Soda Lakes. Front Microbiol 2018; 9:2359. [PMID: 30333814 PMCID: PMC6176080 DOI: 10.3389/fmicb.2018.02359] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/14/2018] [Indexed: 11/21/2022] Open
Abstract
The ubiquity of strictly anaerobic sulfur-respiring haloarchaea in hypersaline systems with circumneutral pH has shaken a traditional concept of this group as predominantly aerobic heterotrophs. Here, we demonstrated that this functional group of haloarchaea also has its representatives in hypersaline alkaline lakes. Sediments from various hypersaline soda lakes showed high activity of sulfur reduction only partially inhibited by antibiotics. Eight pure cultures of sulfur-reducing natronoarchaea were isolated from such sediments using formate and butyrate as electron donors and sulfur as an electron acceptor. Unlike strict anaerobic haloarchaea, these novel sulfur-reducing natronoarchaea are facultative anaerobes, whose metabolic capabilities were inferred from cultivation experiments and genomic/proteomic reconstruction. While sharing many physiological traits with strict anaerobic haloarchaea, following metabolic distinctions make these new organisms be successful in both anoxic and aerobic habitats: the recruiting of heme-copper quinol oxidases as terminal electron sink in aerobic respiratory chain and the utilization of formate, hydrogen or short-chain fatty acids as electron donors during anaerobic growth with elemental sulfur. Obtained results significantly advance the emerging concept of halo(natrono)archaea as important players in the anaerobic sulfur and carbon cycling in various salt-saturated habitats.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Enzo Messina
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Violetta La Cono
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Manuel Ferrer
- Institute of Catalysis, Spanish National Research Council, Madrid, Spain
| | - Sergio Ciordia
- Proteomics Unit, National Center for Biotechnology, Spanish National Research Council, Madrid, Spain
| | - Maria C Mena
- Proteomics Unit, National Center for Biotechnology, Spanish National Research Council, Madrid, Spain
| | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Peter N Golyshin
- School of Biological Sciences and The Centre for Environmental Biotechnology, Bangor University, Bangor, United Kingdom
| | - Michail M Yakimov
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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6
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Atanasova NS, Heiniö CH, Demina TA, Bamford DH, Oksanen HM. The Unexplored Diversity of Pleolipoviruses: The Surprising Case of Two Viruses with Identical Major Structural Modules. Genes (Basel) 2018; 9:genes9030131. [PMID: 29495629 PMCID: PMC5867852 DOI: 10.3390/genes9030131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 01/01/2023] Open
Abstract
Extremely halophilic Archaea are the only known hosts for pleolipoviruses which are pleomorphic non-lytic viruses resembling cellular membrane vesicles. Recently, pleolipoviruses have been acknowledged by the International Committee on Taxonomy of Viruses (ICTV) as the first virus family that contains related viruses with different DNA genomes. Genomic diversity of pleolipoviruses includes single-stranded and double-stranded DNA molecules and their combinations as linear or circular molecules. To date, only eight viruses belong to the family Pleolipoviridae. In order to obtain more information about the diversity of pleolipoviruses, further isolates are needed. Here we describe the characterization of a new halophilic virus isolate, Haloarcula hispanica pleomorphic virus 4 (HHPV4). All pleolipoviruses and related proviruses contain a conserved core of approximately five genes designating this virus family, but the sequence similarity among different isolates is low. We demonstrate that over half of HHPV4 genome is identical to the genome of pleomorphic virus HHPV3. The genomic regions encoding known virion components are identical between the two viruses, but HHPV4 includes unique genetic elements, e.g., a putative integrase gene. The co-evolution of these two viruses demonstrates the presence of high recombination frequency in halophilic microbiota and can provide new insights considering links between viruses, membrane vesicles, and plasmids.
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Affiliation(s)
- Nina S Atanasova
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
- Finnish Meteorological Institute; Erik Palménin aukio 1, FI-00101 Helsinki, Finland.
| | - Camilla H Heiniö
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Tatiana A Demina
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Dennis H Bamford
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
| | - Hanna M Oksanen
- Research Programme on Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
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Grand Challenges in Marine Biotechnology: Overview of Recent EU-Funded Projects. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_11] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Sorokin DY, Messina E, Smedile F, Roman P, Damsté JSS, Ciordia S, Mena MC, Ferrer M, Golyshin PN, Kublanov IV, Samarov NI, Toshchakov SV, La Cono V, Yakimov MM. Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats. ISME JOURNAL 2017; 11:1245-1260. [PMID: 28106880 PMCID: PMC5437934 DOI: 10.1038/ismej.2016.203] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/23/2016] [Accepted: 12/05/2016] [Indexed: 12/20/2022]
Abstract
Hypersaline anoxic habitats harbour numerous novel uncultured archaea whose metabolic and ecological roles remain to be elucidated. Until recently, it was believed that energy generation via dissimilatory reduction of sulfur compounds is not functional at salt saturation conditions. Recent discovery of the strictly anaerobic acetotrophic Halanaeroarchaeum compels to change both this assumption and the traditional view on haloarchaea as aerobic heterotrophs. Here we report on isolation and characterization of a novel group of strictly anaerobic lithoheterotrophic haloarchaea, which we propose to classify as a new genus Halodesulfurarchaeum. Members of this previously unknown physiological group are capable of utilising formate or hydrogen as electron donors and elemental sulfur, thiosulfate or dimethylsulfoxide as electron acceptors. Using genome-wide proteomic analysis we have detected the full set of enzymes required for anaerobic respiration and analysed their substrate-specific expression. Such advanced metabolic plasticity and type of respiration, never seen before in haloarchaea, empower the wide distribution of Halodesulfurarchaeum in hypersaline inland lakes, solar salterns, lagoons and deep submarine anoxic brines. The discovery of this novel functional group of sulfur-respiring haloarchaea strengthens the evidence of their possible role in biogeochemical sulfur cycling linked to the terminal anaerobic carbon mineralisation in so far overlooked hypersaline anoxic habitats.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Enzo Messina
- Institute for Coastal Marine Environment, CNR, Messina, Italy
| | | | - Pawel Roman
- Sub-department of Environmental Technology, Wageningen University, Wageningen, The Netherlands.,Wetsus, Centre of Excellence for Sustainable Water Technology, Leeuwarden, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Sergio Ciordia
- Proteomics Unit, National Center for Biotechnology, CSIC, Madrid, Spain
| | - Maria Carmen Mena
- Proteomics Unit, National Center for Biotechnology, CSIC, Madrid, Spain
| | | | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Bangor, UK.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nazar I Samarov
- Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | | | | | - Michail M Yakimov
- Institute for Coastal Marine Environment, CNR, Messina, Italy.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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9
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Williams TJ, Allen M, Tschitschko B, Cavicchioli R. Glycerol metabolism of haloarchaea. Environ Microbiol 2016; 19:864-877. [PMID: 27768817 DOI: 10.1111/1462-2920.13580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Haloarchaea are heterotrophic members of the Archaea that thrive in hypersaline environments, often feeding off the glycerol that is produced as an osmolyte by eucaryotic Dunaliella during primary production. In this study we analyzed glycerol metabolism genes in closed genomes of haloarchaea and examined published data describing the growth properties of haloarchaea and experimental data for the enzymes involved. By integrating the genomic data with knowledge from the literature, we derived an understanding of the ecophysiology and evolutionary properties of glycerol catabolic pathways in haloarchaea.
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Affiliation(s)
- Timothy J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Michelle Allen
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Bernhard Tschitschko
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, New South Wales, Australia
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Draft Genome Sequence of the Type Strain Desulfuribacillus alkaliarsenatis AHT28, an Obligately Anaerobic, Sulfidogenic Bacterium Isolated from Russian Soda Lake Sediments. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01244-16. [PMID: 27834702 PMCID: PMC5105095 DOI: 10.1128/genomea.01244-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Desulfuribacillus alkaliarsenatis AHT28T is an obligately anaerobic, sulfur- and arsenate-reducing haloalkaliphile that was isolated from Russian soda lake sediments. Here, we present the 3.1-Mb draft genome sequence for this strain, consisting of 36 contigs with a G+C content of 37.5% and 2,978 protein-coding sequences.
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