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Liébana R, Viver T, Ramos-Barbero MD, Bustos-Caparros E, Urdiain M, López C, Amoozegar MA, Antón J, Rossello-Mora R. Extremely halophilic brine community manipulation shows higher robustness of microbiomes inhabiting human-driven solar saltern than naturally driven lake. mSystems 2024; 9:e0053824. [PMID: 38934645 DOI: 10.1128/msystems.00538-24] [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: 04/16/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Hypersaline ecosystems display taxonomically similar assemblages with low diversities and highly dense accompanying viromes. The ecological implications of viral infection on natural microbial populations remain poorly understood, especially at finer scales of diversity. Here, we sought to investigate the influence of changes in environmental physicochemical conditions and viral predation pressure by autochthonous and allochthonous viruses on host dynamics. For this purpose, we transplanted two microbiomes coming from distant hypersaline systems (solar salterns of Es Trenc in Spain and the thalassohaline lake of Aran-Bidgol lake in Iran), by exchanging the cellular fractions with the sterile-filtered accompanying brines with and without the free extracellular virus fraction. The midterm exposure (1 month) of the microbiomes to the new conditions showed that at the supraspecific taxonomic range, the assemblies from the solar saltern brine more strongly resisted the environmental changes and viral predation than that of the lake. The metagenome-assembled genomes (MAGs) analysis revealed an intraspecific transition at the ecotype level, mainly driven by changes in viral predation pressure, by both autochthonous and allochthonous viruses. IMPORTANCE Viruses greatly influence succession and diversification of their hosts, yet the effects of viral infection on the ecological dynamics of natural microbial populations remain poorly understood, especially at finer scales of diversity. By manipulating the viral predation pressure by autochthonous and allochthonous viruses, we uncovered potential phage-host interaction, and their important role in structuring the prokaryote community at an ecotype level.
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Affiliation(s)
- Raquel Liébana
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - María Dolores Ramos-Barbero
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
| | - Cristina López
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Esporles, Spain
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2
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Chibani CM, Shah SA, Schmitz RA, Nayfach S. Inaccurate viral prediction leads to overestimated diversity of the archaeal virome in the human gut. Nat Commun 2024; 15:5976. [PMID: 39019907 PMCID: PMC11255274 DOI: 10.1038/s41467-024-49902-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 06/24/2024] [Indexed: 07/19/2024] Open
Affiliation(s)
- Cynthia M Chibani
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, D-24118, Kiel, Germany
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Gentofte, Denmark
| | - Ruth A Schmitz
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, D-24118, Kiel, Germany
| | - Stephen Nayfach
- Profluent Bio, Berkeley, CA, USA.
- Joint Genome Institute, Berkeley, CA, USA.
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3
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Sensevdi ER, Sourrouille ZA, Quax TE. Host range and cell recognition of archaeal viruses. Curr Opin Microbiol 2024; 77:102423. [PMID: 38232492 DOI: 10.1016/j.mib.2023.102423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
Archaea are members of a separate domain of life that have unique properties, such as the composition of their cell walls and the structure of their lipid bilayers. Consequently, archaeal viruses face different challenges to infect host cells in comparison with viruses of bacteria and eukaryotes. Despite their significant impact on shaping microbial communities, our understanding of infection processes of archaeal viruses remains limited. Several receptors used by archaeal viruses to infect cells have recently been identified. The interactions between viruses and receptors are one of the determinants of the host range of viruses. Here, we review the current literature on host ranges of archaeal viruses and factors that might impact the width of these host ranges.
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Affiliation(s)
- Emine Rabia Sensevdi
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands
| | - Zaloa Aguirre Sourrouille
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands
| | - Tessa Ef Quax
- Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty of Science and Engineering, University of Groningen, 9747 Groningen AG, the Netherlands.
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4
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Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. Archaeal virus entry and egress. MICROLIFE 2024; 5:uqad048. [PMID: 38234448 PMCID: PMC10791045 DOI: 10.1093/femsml/uqad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these viruses enter and exit their host cells. Research on archaeal viruses has lately made significant progress due to advances in genetic tools and imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, a steady output of newly identified archaeal viral receptors and egress mechanisms has offered the first insight into how archaeal viruses interact with the archaeal cell envelope. As more details about archaeal viral entry and egress are unravelled, patterns are starting to emerge. This helps to better understand the interactions between viruses and the archaeal cell envelope and how these compare to infection strategies of viruses in other domains of life. Here, we provide an overview of recent developments in the field of archaeal viral entry and egress, shedding light onto the most elusive part of the virosphere.
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Affiliation(s)
- Bastiaan P Kuiper
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna M C Schöntag
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Bertram Daum
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Tessa E F Quax
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
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5
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Alarcón-Schumacher T, Lücking D, Erdmann S. Revisiting evolutionary trajectories and the organization of the Pleolipoviridae family. PLoS Genet 2023; 19:e1010998. [PMID: 37831715 PMCID: PMC10599561 DOI: 10.1371/journal.pgen.1010998] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Archaeal pleomorphic viruses belonging to the Pleolipoviridae family represent an enigmatic group as they exhibit unique genomic features and are thought to have evolved through recombination with different archaeal plasmids. However, most of our understanding of the diversity and evolutionary trajectories of this clade comes from a handful of isolated representatives. Here we present 164 new genomes of pleolipoviruses obtained from metagenomic data of Australian hypersaline lakes and publicly available metagenomic data. We perform a comprehensive analysis on the diversity and evolutionary relationships of the newly discovered viruses and previously described pleolipoviruses. We propose to classify the viruses into five genera within the Pleolipoviridae family, with one new genus represented only by virus genomes retrieved in this study. Our data support the current hypothesis that pleolipoviruses reshaped their genomes through recombining with multiple different groups of plasmids, which is reflected in the diversity of their predicted replication strategies. We show that the proposed genus Epsilonpleolipovirus has evolutionary ties to pRN1-like plasmids from Sulfolobus, suggesting that this group could be infecting other archaeal phyla. Interestingly, we observed that the genome size of pleolipoviruses is correlated to the presence or absence of an integrase. Analyses of the host range revealed that all but one virus exhibit an extremely narrow range, and we show that the predicted tertiary structure of the spike protein is strongly associated with the host family, suggesting a specific adaptation to the host S-layer glycoprotein organization.
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Affiliation(s)
| | - Dominik Lücking
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Susanne Erdmann
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
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6
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Overton MS, Manuel RD, Lawrence CM, Snyder JC. Viruses of the Turriviridae: an emerging model system for studying archaeal virus-host interactions. Front Microbiol 2023; 14:1258997. [PMID: 37808280 PMCID: PMC10551542 DOI: 10.3389/fmicb.2023.1258997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Viruses have played a central role in the evolution and ecology of cellular life since it first arose. Investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. As well, the discovery of viral lineages that infect members of all three domains suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. Archaeal viruses have only recently become a subject of intense study, but investigations have already produced intriguing and exciting results. STIV was originally discovered in Yellowstone National Park and has been the focus of concentrated research. Through this research, a viral genetic system was created, a novel lysis mechanism was discovered, and the interaction of the virus with cellular ESCRT machinery was revealed. This review will summarize the discoveries within this group of viruses and will also discuss future work.
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Affiliation(s)
- Michael S. Overton
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Robert D. Manuel
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
| | - C. Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Jamie C. Snyder
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
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7
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Mercier C, Thies D, Zhong L, Raftery MJ, Erdmann S. Characterization of an archaeal virus-host system reveals massive genomic rearrangements in a laboratory strain. Front Microbiol 2023; 14:1274068. [PMID: 37789858 PMCID: PMC10544981 DOI: 10.3389/fmicb.2023.1274068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
Halophilic archaea (haloarchaea) are known to exhibit multiple chromosomes, with one main chromosome and one or several smaller secondary chromosomes or megaplasmids. Halorubrum lacusprofundi, a model organism for studying cold adaptation, exhibits one secondary chromosome and one megaplasmid that include a large arsenal of virus defense mechanisms. We isolated a virus (Halorubrum tailed virus DL1, HRTV-DL1) infecting Hrr. lacusprofundi, and present an in-depth characterization of the virus and its interactions with Hrr. lacusprofundi. While studying virus-host interactions between Hrr. lacusprofundi and HRTV-DL1, we uncover that the strain in use (ACAM34_UNSW) lost the entire megaplasmid and about 38% of the secondary chromosome. The loss included the majority of virus defense mechanisms, making the strain sensitive to HRTV-DL1 infection, while the type strain (ACAM34_DSMZ) appears to prevent virus replication. Comparing infection of the type strain ACAM34_DSMZ with infection of the laboratory derived strain ACAM34_UNSW allowed us to identify host responses to virus infection that were only activated in ACAM34_UNSW upon the loss of virus defense mechanisms. We identify one of two S-layer proteins as primary receptor for HRTV-DL1 and conclude that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. Additionally, we identify archaeal homologs to eukaryotic proteins potentially being involved in the defense against virus infection.
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Affiliation(s)
- Coraline Mercier
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
| | - Daniela Thies
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW, Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW, Australia
| | - Susanne Erdmann
- Max Planck Institute for Marine Microbiology, Archaeal Virology, Bremen, Germany
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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8
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Trubl G, Stedman KM, Bywaters KF, Matula EE, Sommers P, Roux S, Merino N, Yin J, Kaelber JT, Avila-Herrera A, Johnson PA, Johnson JC, Borges S, Weber PK, Pett-Ridge J, Boston PJ. Astrovirology: how viruses enhance our understanding of life in the Universe. INTERNATIONAL JOURNAL OF ASTROBIOLOGY 2023; 22:247-271. [PMID: 38046673 PMCID: PMC10691837 DOI: 10.1017/s1473550423000058] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus-host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.
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Affiliation(s)
- Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kenneth M. Stedman
- Center for Life in Extreme Environments, Department of Biology, Portland State University, Portland, OR, USA
| | | | | | | | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Nancy Merino
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Aram Avila-Herrera
- Computing Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter Anto Johnson
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | | | - Peter K. Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, USA
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9
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Gebhard LJ, Vershinin Z, Alarcón-Schumacher T, Eichler J, Erdmann S. Influence of N-Glycosylation on Virus-Host Interactions in Halorubrum lacusprofundi. Viruses 2023; 15:1469. [PMID: 37515157 PMCID: PMC10384203 DOI: 10.3390/v15071469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
N-glycosylation is a post-translational modification of proteins that occurs across all three domains of life. In Archaea, N-glycosylation is crucial for cell stability and motility, but importantly also has significant implications for virus-host interactions. While some archaeal viruses present glycosylated proteins or interact with glycosylated host proteins, the direct influence of N-glycosylation on archaeal virus-host interactions remains to be elucidated. In this study, we generated an N-glycosylation-deficient mutant of Halorubrum lacusprofundi, a halophilic archaeon commonly used to study cold adaptation, and examined the impact of compromised N-glycosylation on the infection dynamics of two very diverse viruses. While compromised N-glycosylation had no influence on the life cycle of the head-tailed virus HRTV-DL1, we observed a significant effect on membrane-containing virus HFPV-1. Both intracellular genome numbers and extracellular virus particle numbers of HFPV-1 were increased in the mutant strain, which we attribute to instability of the surface-layer which builds the protein envelope of the cell. When testing the impact of compromised N-glycosylation on the life cycle of plasmid vesicles, specialized membrane vesicles that transfer a plasmid between host cells, we determined that plasmid vesicle stability is strongly dependent on the host glycosylation machinery. Our study thus provides important insight into the role of N-glycosylation in virus-host interactions in Archaea, while pointing to how this influence strongly differs amongst various viruses and virus-like elements.
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Affiliation(s)
- L Johanna Gebhard
- Max Planck Institute for Marine Microbiology, Archaeal Virology, 28359 Bremen, Germany
| | - Zlata Vershinin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva 84105, Israel
| | | | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva 84105, Israel
| | - Susanne Erdmann
- Max Planck Institute for Marine Microbiology, Archaeal Virology, 28359 Bremen, Germany
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10
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Gebhard LJ, Duggin IG, Erdmann S. Improving the genetic system for Halorubrum lacusprofundi to allow in-frame deletions. Front Microbiol 2023; 14:1095621. [PMID: 37065119 PMCID: PMC10102395 DOI: 10.3389/fmicb.2023.1095621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Halorubrum lacusprofundi is a cold-adapted halophilic archaeon isolated from Deep Lake, Antarctica. Hrr. lacusprofundi is commonly used to study adaptation to cold environments and thereby a potential source for biotechnological products. Additionally, in contrast to other haloarchaeal model organisms, Hrr. lacusprofundi is also susceptible to a range of different viruses and virus-like elements, making it a great model to study virus-host interactions in a cold-adapted organism. A genetic system has previously been reported for Hrr. lacusprofundi; however, it does not allow in-frame deletions and multiple gene knockouts. Here, we report the successful generation of uracil auxotrophic (pyrE2) mutants of two strains of Hrr. lacusprofundi. Subsequently, we attempted to generate knockout mutants using the auxotrophic marker for selection. However, surprisingly, only the combination of the auxotrophic marker and antibiotic selection allowed the timely and clean in-frame deletion of a target gene. Finally, we show that vectors established for the model organism Haloferax volcanii are deployable for genetic manipulation of Hrr. lacusprofundi, allowing the use of the portfolio of genetic tools available for H. volcanii in Hrr. lacusprofundi.
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Affiliation(s)
- L. Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Iain G. Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW, Australia
| | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen, Germany
- *Correspondence: Susanne Erdmann,
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11
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Abstract
Viruses are highly abundant and the main predator of microorganisms. Microorganisms of each domain of life are infected by dedicated viruses. Viruses infecting archaea are genomically and structurally highly diverse. Archaea are undersampled for viruses in comparison with bacteria and eukaryotes. Consequently, the infection mechanisms of archaeal viruses are largely unknown, and most available knowledge stems from viruses infecting a select group of archaea, such as crenarchaea. We employed Haloferax tailed virus 1 (HFTV1) and its host, Haloferax gibbonsii LR2-5, to study viral infection in euryarchaea. We found that HFTV1, which has a siphovirus morphology, is virulent, and interestingly, viral particles adsorb to their host several orders of magnitude faster than most studied haloarchaeal viruses. As the binding site for infection, HFTV1 uses the cell wall component surface (S)-layer protein. Electron microscopy of infected cells revealed that viral particles often made direct contact with their heads to the cell surface, whereby the virion tails were perpendicular to the surface. This seemingly unfavorable orientation for genome delivery might represent a first reversible contact between virus and cell and could enhance viral adsorption rates. In a next irreversible step, the virion tail is orientated toward the cell surface for genome delivery. With these findings, we uncover parallels between entry mechanisms of archaeal viruses and those of bacterial jumbo phages and bacterial gene transfer agents. IMPORTANCE Archaeal viruses are the most enigmatic members of the virosphere. These viruses infect ubiquitous archaea and display an unusually high structural and genetic diversity. Unraveling their mechanisms of infection will shed light on the question if entry and egress mechanisms are highly conserved between viruses infecting a single domain of life or if these mechanisms are dependent on the morphology of the virus and the growth conditions of the host. We studied the entry mechanism of the tailed archaeal virus HFTV1. This showed that despite "typical" siphovirus morphology, the infection mechanism is different from standard laboratory models of tailed phages. We observed that particles bound first with their head to the host cell envelope, and, as such, we discovered parallels between archaeal viruses and nonmodel bacteriophages. This work contributes to a better understanding of entry mechanisms of archaeal viruses and a more complete view of microbial viruses in general.
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12
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Staying below the Radar: Unraveling a New Family of Ubiquitous "Cryptic" Non-Tailed Temperate Vibriophages and Implications for Their Bacterial Hosts. Int J Mol Sci 2023; 24:ijms24043937. [PMID: 36835353 PMCID: PMC9966536 DOI: 10.3390/ijms24043937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023] Open
Abstract
Bacteriophages are the most abundant biological entities in the oceans and play key roles in bacterial activity, diversity and evolution. While extensive research has been conducted on the role of tailed viruses (Class: Caudoviricetes), very little is known about the distribution and functions of the non-tailed viruses (Class: Tectiliviricetes). The recent discovery of the lytic Autolykiviridae family demonstrated the potential importance of this structural lineage, emphasizing the need for further exploration of the role of this group of marine viruses. Here, we report the novel family of temperate phages under the class of Tectiliviricetes, which we propose to name "Asemoviridae" with phage NO16 as a main representative. These phages are widely distributed across geographical regions and isolation sources and found inside the genomes of at least 30 species of Vibrio, in addition to the original V. anguillarum isolation host. Genomic analysis identified dif-like sites, suggesting that NO16 prophages recombine with the bacterial genome based on the XerCD site-specific recombination mechanism. The interactions between the NO16 phage and its V. anguillarum host were linked to cell density and phage-host ratio. High cell density and low phage predation levels were shown to favor the temperate over the lytic lifestyle for NO16 viruses, and their spontaneous induction rate was highly variable between different V. anguillarum lysogenic strains. NO16 prophages coexist with the V. anguillarum host in a mutualistic interaction by rendering fitness properties to the host, such as increased virulence and biofilm formation through lysogenic conversion, likely contributing to their global distribution.
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13
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Yi H, Fu C, Diao K, Li Z, Cui X, Xiao W. Characterization and genomic analysis of a novel halovirus infecting Chromohalobacter beijerinckii. Front Microbiol 2022; 13:1041471. [PMID: 36569053 PMCID: PMC9769972 DOI: 10.3389/fmicb.2022.1041471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Bacteriophages function as a regulator of host communities and metabolism. Many phages have been isolated and sequenced in environments such as the ocean, but very little is known about hypersaline environments. Phages infecting members of the genus Chromohalobacter remain poorly understood, and no Chromohalobacter phage genome has been reported. In this study, a halovirus infecting Chromohalobacter sp. F3, YPCBV-1, was isolated from Yipinglang salt mine. YPCBV-1 could only infect host strain F3 with burst size of 6.3 PFU/cell. It could produce progeny in 5%-20% (w/v) NaCl with an optimal concentration of 10% (w/v), but the optimal adsorption NaCl concentration was 5%-8% (w/v). YPCBV-1 is sensitive to pure water and depends on NaCl or KCl solutions to survive. YPCBV-1 stability increased with increasing salinity but decreased in NaCl saturated solutions, and it has a broader salinity adaptation than the host. YPCBV-1 has a double-stranded DNA of 36,002 bp with a G + C content of 67.09% and contains a total of 55 predicted ORFs and no tRNA genes. Phylogenetic analysis and genomic network analysis suggested that YPCBV-1 is a novel Mu-like phage under the class Caudoviricetes. Auxiliary metabolic gene, SUMF1/EgtB/PvdO family non-heme iron enzyme, with possible roles in antioxidant was found in YPCBV-1. Moreover, DGR-associated genes were predicted in YPCBV-1 genome, which potentially produce hypervariable phage tail fiber. These findings shed light on the halovirus-host interaction in hypersaline environments.
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Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus. Proc Natl Acad Sci U S A 2022; 119:e2205037119. [PMID: 35994644 PMCID: PMC9436352 DOI: 10.1073/pnas.2205037119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses are important ecological, biogeochemical, and evolutionary drivers in every environment. Upon infection, they often cause the lysis of the host cell. However, some viruses exhibit alternative life cycles, such as chronic infections without cell lysis. The nature and the impact of chronic infections in prokaryotic host organisms remains largely unknown. Here, we characterize a novel haloarchaeal virus, Haloferax volcanii pleomorphic virus 1 (HFPV-1), which is currently the only virus infecting the model haloarchaeon Haloferax volcanii DS2, and demonstrate that HFPV-1 and H. volcanii are a great model system to study virus-host interactions in archaea. HFPV-1 is a pleomorphic virus that causes a chronic infection with continuous release of virus particles, but host and virus coexist without cell lysis or the appearance of resistant cells. Despite an only minor impact of the infection on host growth, we uncovered an extensive remodeling of the transcriptional program of the host (up to 1,049 differentially expressed genes). These changes are highlighted by a down-regulation of two endogenous provirus regions in the host genome, and we show that HFPV-1 infection is strongly influenced by a cross-talk between HFPV-1 and one of the proviruses mediated by a superinfection-like exclusion mechanism. Furthermore, HFPV-1 has a surprisingly wide host range among haloarchaea, and purified virus DNA can cause an infection after transformation into the host, making HFPV-1 a candidate for being developed into a genetic tool for a range of so far inaccessible haloarchaea.
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15
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Chen S, Tu D, Hong T, Luo Y, Shen L, Ren P, Lu P, Chen X. Genomic features of a new head-tail halovirus VOLN27B infecting a Halorubrum strain. Gene 2022; 841:146766. [PMID: 35908623 DOI: 10.1016/j.gene.2022.146766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/26/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
Relatively few viruses infecting haloarchaea (haloviruses) have been reported. In this study, the genome sequence of VOLN27B, a recently described archaeal tailed virus (arTV) with a myovirus morphotype was described, along with the sequence of its host, Halorubrum spp. LN27. Halovirus VOLN27B contains a linear, dsDNA genome of 76,891 bp which is predicted to encode 109 proteins and four tRNAs (tRNAThr, tRNAArg, tRNAGly and tRNAAsn). The DNA G+C content of VOLN27B genome is 56.1 mol%, nearly 10% lower than that of its host strain. A 315 bp LTR (long terminal repeat) was detected in the genome. The genome of its host strain LN27 was 3,301,211 bp (chromosome and 1 plasmid) with a DNA G+C content of 68.3 mol% and 3,142 annotated protein coding genes. At least two hypothetical proviruses were detected in the genome. It lacked a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) locus. Sequence similarity and phylogenetic tree reconstructions placed it within the genus Halorubrum as a potential new species. VOLN27B exhibits a distinct difference in the frequency of codon usage against its host strain Halorubrum sp. LN27. The organization of VOLN27B genome shows remarkable synteny and amino acid sequence similarity to the genomes and predicted proteins of HF1-like haloviruses (genus Haloferacalesvirus) and a provirus in the genome of Halorubrum depositum Y78. VOLN27B and its host Halorubrum sp. LN27 comprise a new virus-host system from a hypersaline ecosystem and can be used to further understand the novel biology at extreme salt concentration.
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Affiliation(s)
- Shaoxing Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
| | - Demei Tu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tao Hong
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuqing Luo
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Peng Lu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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16
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The Viral Susceptibility of the Haloferax Species. Viruses 2022; 14:v14061344. [PMID: 35746816 PMCID: PMC9229481 DOI: 10.3390/v14061344] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus–host model systems. Euryarchaea belonging to the genus Haloferax are interesting models, as a reliable genetic system and versatile microscopy methods are available. However, only one virus infecting the Haloferax species is currently available. In this study, we tested ~100 haloarchaeal virus isolates for their infectivity on 14 Haloferax strains. From this, we identified 10 virus isolates in total capable of infecting Haloferax strains, which represented myovirus or siphovirus morphotypes. Surprisingly, the only susceptible strain of all 14 tested was Haloferax gibbonsii LR2-5, which serves as an auspicious host for all of these 10 viruses. By applying comparative genomics, we shed light on factors determining the host range of haloarchaeal viruses on Haloferax. We anticipate our study to be a starting point in the study of haloarchaeal virus–host interactions.
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17
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Martínez GM, Pire C, Martínez-Espinosa RM. Hypersaline environments as natural sources of microbes with potential applications in biotechnology: the case of solar evaporation systems to produce salt in Alicante County (Spain). CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100136. [PMID: 35909606 PMCID: PMC9325878 DOI: 10.1016/j.crmicr.2022.100136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/14/2022] [Accepted: 04/24/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guillermo Martínez Martínez
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Corresponding author.
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18
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Shu WS, Huang LN. Microbial diversity in extreme environments. Nat Rev Microbiol 2022; 20:219-235. [PMID: 34754082 DOI: 10.1038/s41579-021-00648-y] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 01/02/2023]
Abstract
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa, survive and thrive in extreme environments. These unique and reduced-complexity ecosystems offer a tremendous opportunity for studying the structure, function and evolution of natural microbial communities. Marker gene surveys have resolved patterns and ecological drivers of these extremophile assemblages, revealing a vast uncultured microbial diversity and the often predominance of archaea in the most extreme conditions. New omics studies have uncovered linkages between community function and environmental variables, and have enabled discovery and genomic characterization of major new lineages that substantially expand microbial diversity and change the structure of the tree of life. These efforts have significantly advanced our understanding of the diversity, ecology and evolution of microorganisms populating Earth's extreme environments, and have facilitated the exploration of microbiota and processes in more complex ecosystems.
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Affiliation(s)
- Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, People's Republic of China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, People's Republic of China.
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19
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Li R, Zhu L, Cui L, Zhu YG. Viral diversity and potential environmental risk in microplastic at watershed scale: Evidence from metagenomic analysis of plastisphere. ENVIRONMENT INTERNATIONAL 2022; 161:107146. [PMID: 35183943 DOI: 10.1016/j.envint.2022.107146] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Microplastics (MPs) have been considered as a new vector for the long-distance transport of pathogens in aquatic ecosystems. However, the composition of viral communities attached on MPs and their environmental risk are largely unknown. Here, we profiled the viral diversity and potential risk in five different MPs collected from the Beilun River based on metagenomic analysis. Nearly 2863 million raw reads were produced and assembled, and annotation resulted in the identification of 1719 different species of viruses in MPs. Viruses in polypropylene (PP) displayed the highest diversity, with about 250 specific viruses detected. Source tracking of viruses in MPs by the fast expectation-maximization microbial source tracking method (FEAST) demonstrated that viruses in upstream and downstream MPs are two major sources of viruses in estuary. Furthermore, the MP-type-dependent potential environmental risk of viruses was significant based on both antibiotic resistance genes (ARGs) and virulence factors (VFs) detected in viral metagenomes, and PP was confirmed with the highest potential environmental risk. This study reveals the high diversity and potential environmental risk of viruses in different MPs, and provides an important guidance for future environmental monitoring and understanding the potential risks associated with both viral transmission and MPs pollution.
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Affiliation(s)
- Ruilong Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Marine Sciences, Guangxi University, Nanning 530004, China
| | - Longji Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Li Cui
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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20
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Saccò M, White NE, Harrod C, Salazar G, Aguilar P, Cubillos CF, Meredith K, Baxter BK, Oren A, Anufriieva E, Shadrin N, Marambio-Alfaro Y, Bravo-Naranjo V, Allentoft ME. Salt to conserve: a review on the ecology and preservation of hypersaline ecosystems. Biol Rev Camb Philos Soc 2021; 96:2828-2850. [PMID: 34747117 DOI: 10.1111/brv.12780] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 02/01/2023]
Abstract
When it comes to the investigation of key ecosystems in the world, we often omit salt from the ecological recipe. In fact, despite occupying almost half of the volume of inland waters and providing crucial services to humanity and nature, inland saline ecosystems are often overlooked in discussions regarding the preservation of global aquatic resources of our planet. As a result, our knowledge of the biological and geochemical dynamics shaping these environments remains incomplete and we are hesitant in framing effective protective strategies against the increasing natural and anthropogenic threats faced by such habitats. Hypersaline lakes, water bodies where the concentration of salt exceeds 35 g/l, occur mainly in arid and semiarid areas resulting from hydrological imbalances triggering the accumulation of salts over time. Often considered the 'exotic siblings' within the family of inland waters, these ecosystems host some of the most extremophile communities worldwide and provide essential habitats for waterbirds and many other organisms in already water-stressed regions. These systems are often highlighted as natural laboratories, ideal for addressing central ecological questions due to their relatively low complexity and simple food web structures. However, recent studies on the biogeochemical mechanisms framing hypersaline communities have challenged this archetype, arguing that newly discovered highly diverse communities are characterised by specific trophic interactions shaped by high levels of specialisation. The main goal of this review is to explore our current understanding of the ecological dynamics of hypersaline ecosystems by addressing four main research questions: (i) why are hypersaline lakes unique from a biological and geochemical perspective; (ii) which biota inhabit these ecosystems and how have they adapted to the high salt conditions; (iii) how do we protect biodiversity from increasing natural and anthropogenic threats; and (iv) which scientific tools will help us preserve hypersaline ecosystems in the future? First, we focus on the ecological characterisation of hypersaline ecosystems, illustrate hydrogeochemical dynamics regulating such environments, and outline key ecoregions supporting hypersaline systems across the globe. Second, we depict the diversity and functional aspects of key taxa found in hypersaline lakes, from microorganisms to plants, invertebrates, waterbirds and upper trophic levels. Next, we describe ecosystem services and discuss possible conservation guidelines. Finally, we outline how cutting-edge technologies can provide new insights into the study of hypersaline ecology. Overall, this review sheds further light onto these understudied ecosystems, largely unrecognised as important sources of unique biological and functional diversity. We provide perspectives for key future research avenues, and advocate that the conservation of hypersaline lakes should not be taken with 'a grain of salt'.
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Affiliation(s)
- Mattia Saccò
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Nicole E White
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, 3349001, Chile
| | - Gonzalo Salazar
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile.,Núcleo Milenio INVASAL, Concepción, 3349001, Chile
| | - Pablo Aguilar
- Núcleo Milenio INVASAL, Concepción, 3349001, Chile.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Carolina F Cubillos
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Karina Meredith
- Australian Nuclear Science and Technology Organisation (ANSTO), Locked Bag 2001, Kirrawee DC, NSW, 2232, Australia
| | - Bonnie K Baxter
- Great Salt Lake Institute, Westminster College, Salt Lake City, UT, 84105, U.S.A
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, the Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Elena Anufriieva
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, 2 Nakhimov Avenue 2, Sevastopol, 299011, Russia
| | - Nickolai Shadrin
- A.O. Kovalevsky Institute of Biology of the Southern Seas, Russian Academy of Sciences, 2 Nakhimov Avenue 2, Sevastopol, 299011, Russia
| | - Yeri Marambio-Alfaro
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Chile
| | - Víctor Bravo-Naranjo
- Facultad de Ciencias, Universidad de La Serena, Benavente 980, La Serena, Coquimbo, Chile
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Kent St, Bentley, WA, 6102, Australia.,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
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21
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Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes. PLoS Biol 2021; 19:e3001442. [PMID: 34752450 PMCID: PMC8651126 DOI: 10.1371/journal.pbio.3001442] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/07/2021] [Accepted: 10/17/2021] [Indexed: 11/19/2022] Open
Abstract
The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.
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Affiliation(s)
- Ying Liu
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
| | - Tatiana A. Demina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pakorn Aiewsakun
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David Prangishvili
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
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22
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Badel C, Da Cunha V, Oberto J. Archaeal tyrosine recombinases. FEMS Microbiol Rev 2021; 45:fuab004. [PMID: 33524101 PMCID: PMC8371274 DOI: 10.1093/femsre/fuab004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 01/13/2021] [Indexed: 12/16/2022] Open
Abstract
The integration of mobile genetic elements into their host chromosome influences the immediate fate of cellular organisms and gradually shapes their evolution. Site-specific recombinases catalyzing this integration have been extensively characterized both in bacteria and eukarya. More recently, a number of reports provided the in-depth characterization of archaeal tyrosine recombinases and highlighted new particular features not observed in the other two domains. In addition to being active in extreme environments, archaeal integrases catalyze reactions beyond site-specific recombination. Some of these integrases can catalyze low-sequence specificity recombination reactions with the same outcome as homologous recombination events generating deep rearrangements of their host genome. A large proportion of archaeal integrases are termed suicidal due to the presence of a specific recombination target within their own gene. The paradoxical maintenance of integrases that disrupt their gene upon integration implies novel mechanisms for their evolution. In this review, we assess the diversity of the archaeal tyrosine recombinases using a phylogenomic analysis based on an exhaustive similarity network. We outline the biochemical, ecological and evolutionary properties of these enzymes in the context of the families we identified and emphasize similarities and differences between archaeal recombinases and their bacterial and eukaryal counterparts.
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Affiliation(s)
- Catherine Badel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Violette Da Cunha
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Jacques Oberto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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23
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Li X, Cheng Z, Dang C, Zhang M, Zheng Y. Metagenomic and viromic data mining reveals viral threats in biologically treated domestic wastewater. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2021; 7:100105. [PMID: 36160698 PMCID: PMC9488056 DOI: 10.1016/j.ese.2021.100105] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/02/2021] [Accepted: 06/02/2021] [Indexed: 05/07/2023]
Abstract
Activated sludge (AS), a common biological secondary treatment process in wastewater treatment plants (WWTPs), is known to remove a large spectrum of microorganisms. Yet little is known about its effect on the entire viral community. After compiling 3 Tbp of next-generation sequencing (NGS) metagenomic/viromic datasets consisted of 119 sub-datasets of influent, effluent, and AS samples from 27 WWTPs, viral removal efficacy is evaluated through data mining. The normalized abundance of viruses suggests effluents exhibit the highest viral prevalence (3.21 ± 3.26%, n = 13) followed by the AS (0.48 ± 0.25%, n = 57) and influents (0.23 ± 0.17%, n = 17). In contrast, plasmids, representing genetic element of bacteria, show higher average prevalence (0.73 ± 0.82%, n = 17) in influents than those of the AS (0.63 ± 0.26%, n = 57) and effluents (0.35 ± 0.42%, n = 13). Furthermore, the abundance-occupancy analysis identifies 142 core phage viruses and 17 non-phages core viruses, including several pathogenic viruses in the AS virome. The persistent occurrence of pathogenic viruses, coupled with non-favorable virus removal by the AS treatment, reveals the hidden virus threats in biologically treated domestic wastewater. The mechanisms for why viruses persist and the possibility that WWTPs are potential hotspots for viral survival deserve attention.
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Affiliation(s)
- Xiang Li
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhanwen Cheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chenyuan Dang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Miao Zhang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yan Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Corresponding author. School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055 China.
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24
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Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico. Microorganisms 2021; 9:microorganisms9051096. [PMID: 34065163 PMCID: PMC8160830 DOI: 10.3390/microorganisms9051096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 12/25/2022] Open
Abstract
The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3′-sn-glycerol-1′-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea.
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Halolysin R4 of Haloferax mediterranei confers its host antagonistic and defensive activities. Appl Environ Microbiol 2021; 87:AEM.02889-20. [PMID: 33579684 PMCID: PMC8091122 DOI: 10.1128/aem.02889-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halolysins, which are subtilisin-like serine proteases of haloarchaea, are usually secreted into the extracellular matrix via the twin-arginine translocation pathway. A small number of activated molecules can greatly affect cell growth owing to their proteolytic activity. It is, however, unclear as to whether this proteolysis-based growth inhibition by halolysins conveys antagonistic or defensive effects against other resident abd potentially competitive microorganisms. Here, we report that halolysin R4 (HlyR4), encoded by the hlyR4 gene, is the key enzyme in the initial steps of extracellular protein utilization in Haloferax mediterranei HlyR4 shows significant antagonistic activity against other haloarchaeal strains. Deletion of hlyR4 completely halts the inhibition activity of Hfx. mediterranei towards other haloarchaea, while correspondingly, complementation of hlyR4 almost completely restores the inhibition activity. Furthermore, Hfx. mediterranei strains containing hlyR4 showed a certain amount of resistance to halocins and halolysins in milieu, and this function of hlyR4 is reproducible in Haloarcula hispanica The versatility of HlyR4 enables its host to outcompete other haloarchaea living in the same hypersaline environment. Intriguingly, unlike the growth phase-dependent halolysins SptA and Nep, it is likely that HlyR4 may be secreted independent of growth phase. This study provides a new peptide antibiotics candidate in haloarchaea, as well as new insight towards a better understanding of the ecological roles of halolysins.Importance: This study shows that halolysin R4 from Haloferax mediterranei provides its host antagonistic and defensive activities against other haloarchaea, which expands our knowledge on the traditional function of haloarchaeal extracellular proteases. Haloarchaeal extracellular serine proteases have been previously discussed as growth-phase-dependent proteins, whereas our study reports constitutive expression of halolysin R4. This work also clearly reveals a hidden diversity of extracellular proteases from haloarchaea. Studies on multifunctional halolysins reveal that they play an important ecological role in shaping microbial community composition and provide a new perspective towards understanding the intricate interactions between haloarchaeal cells in hypersaline environments. HlyR4 can lyse competing cells living in the same environment, and the cell debris may probably be utilized as nutrients, which may constitute an important part of nutrient cycling in extremely hypersaline environments.
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Tittes C, Schwarzer S, Pfeiffer F, Dyall-Smith M, Rodriguez-Franco M, Oksanen HM, Quax TEF. Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1. Front Microbiol 2021; 12:625599. [PMID: 33664716 PMCID: PMC7921747 DOI: 10.3389/fmicb.2021.625599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/28/2021] [Indexed: 01/14/2023] Open
Abstract
Hypersaline environments are the source of many viruses infecting different species of halophilic euryarchaea. Information on infection mechanisms of archaeal viruses is scarce, due to the lack of genetically accessible virus–host models. Recently, a new archaeal siphovirus, Haloferax tailed virus 1 (HFTV1), was isolated together with its host belonging to the genus Haloferax, but it is not infectious on the widely used model euryarcheon Haloferax volcanii. To gain more insight into the biology of HFTV1 host strain LR2-5, we studied characteristics that might play a role in its virus susceptibility: growth-dependent motility, surface layer, filamentous surface structures, and cell shape. Its genome sequence showed that LR2-5 is a new strain of Haloferax gibbonsii. LR2-5 lacks obvious viral defense systems, such as CRISPR-Cas, and the composition of its cell surface is different from Hfx. volcanii, which might explain the different viral host range. This work provides first deep insights into the relationship between the host of halovirus HFTV1 and other members of the genus Haloferax. Given the close relationship to the genetically accessible Hfx. volcanii, LR2-5 has high potential as a new model for virus–host studies in euryarchaea.
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Affiliation(s)
- Colin Tittes
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sabine Schwarzer
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mike Dyall-Smith
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tessa E F Quax
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Freiburg, Germany
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Schwarzer S, Rodriguez-Franco M, Oksanen HM, Quax TEF. Growth Phase Dependent Cell Shape of Haloarcula. Microorganisms 2021; 9:231. [PMID: 33499340 PMCID: PMC7911496 DOI: 10.3390/microorganisms9020231] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 01/08/2023] Open
Abstract
Several haloarchaea are reported to be pleomorphic, while others exhibit remarkable shapes, such as squares. Recently, Haloferax volcanii was found to alter its morphology during growth. Cells are motile rods in early exponential phase, and immotile plates in stationary phase. It is unknown if this growth phase dependent cell shape alteration is a specific feature of Hfx. volcanii, or conserved amongst haloarchaea. Here, we studied the cell shape and motility of two haloarchaea species Haloarcula hispanica and Haloarcula californiae. With a combination of light and electron microscopy, we observed that both strains undergo a growth phase dependent morphological development, albeit in a slightly different fashion as Hfx. volcanii. For both Haloarcula strains, the cell size is changing throughout growth. Cell shape seems to be related with motility, as highly motile cells on semi-solid agar plates are predominantly rod-shaped. We conclude that the growth phase dependent cell morphology alteration might be a common feature amongst haloarchaea, and that cell shape is generally linked with a motile life style. The conservation of this phenomenon underscores the importance of studies of the molecular mechanisms regulating cell shape in archaea.
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Affiliation(s)
- Sabine Schwarzer
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany;
| | - Marta Rodriguez-Franco
- Cell Biology, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany;
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland;
| | - Tessa E. F. Quax
- Archaeal Virus-Host Interactions, Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany;
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Viruses in Extreme Environments, Current Overview, and Biotechnological Potential. Viruses 2021; 13:v13010081. [PMID: 33430116 PMCID: PMC7826561 DOI: 10.3390/v13010081] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 12/27/2022] Open
Abstract
Virus research has advanced significantly since the discovery of the tobacco mosaic virus (TMV), the characterization of its infection mechanisms and the factors that determine their pathogenicity. However, most viral research has focused on pathogenic viruses to humans, animals and plants, which represent only a small fraction in the virosphere. As a result, the role of most viral genes, and the mechanisms of coevolution between mutualistic viruses, their host and their environment, beyond pathogenicity, remain poorly understood. This review focuses on general aspects of viruses that interact with extremophile organisms, characteristics and examples of mechanisms of adaptation. Finally, this review provides an overview on how knowledge of extremophile viruses sheds light on the application of new tools of relevant use in modern molecular biology, discussing their value in a biotechnological context.
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29
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Kasirajan L, Maupin-Furlow JA. Halophilic archaea and their potential to generate renewable fuels and chemicals. Biotechnol Bioeng 2020; 118:1066-1090. [PMID: 33241850 DOI: 10.1002/bit.27639] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/27/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
Lignocellulosic biofuels and chemicals have great potential to reduce our dependence on fossil fuels and mitigate air pollution by cutting down on greenhouse gas emissions. Chemical, thermal, and enzymatic processes are used to release the sugars from the lignocellulosic biomass for conversion to biofuels. These processes often operate at extreme pH conditions, high salt concentrations, and/or high temperature. These harsh treatments add to the cost of the biofuels, as most known biocatalysts do not operate under these conditions. To increase the economic feasibility of biofuel production, microorganisms that thrive in extreme conditions are considered as ideal resources to generate biofuels and value-added products. Halophilic archaea (haloarchaea) are isolated from hypersaline ecosystems with high salt concentrations approaching saturation (1.5-5 M salt concentration) including environments with extremes in pH and/or temperature. The unique traits of haloarchaea and their enzymes that enable them to sustain catalytic activity in these environments make them attractive resources for use in bioconversion processes that must occur across a wide range of industrial conditions. Biocatalysts (enzymes) derived from haloarchaea occupy a unique niche in organic solvent, salt-based, and detergent industries. This review focuses on the use of haloarchaea and their enzymes to develop and improve biofuel production. The review also highlights how haloarchaea produce value-added products, such as antibiotics, carotenoids, and bioplastic precursors, and can do so using feedstocks considered "too salty" for most microbial processes including wastes from the olive-mill, shell fish, and biodiesel industries.
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Affiliation(s)
- Lakshmi Kasirajan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Coimbatore, India
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA.,Genetics Institute, University of Florida, Gainesville, Florida, USA
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30
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Jalasvuori M. Silent rain: does the atmosphere-mediated connectivity between microbiomes influence bacterial evolutionary rates? FEMS Microbiol Ecol 2020; 96:5841522. [PMID: 32436564 DOI: 10.1093/femsec/fiaa096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/20/2020] [Indexed: 01/21/2023] Open
Abstract
Air carries a vast number of bacteria and viruses over great distances all the time. This leads to continuous introduction of foreign genetic material to local, established microbial communities. In this perspective, I ask whether this silent rain may have a slowing effect on the overall evolutionary rates in the microbial biosphere. Arguably, the greater the genetic divergence between gene 'donors' and 'recipients', the greater the chance that the gene product has a deleterious epistatic interaction with other gene products in its genetic environment. This is due to the long-term absence of check for mutual compatibility. As such, if an organism is extensively different from other bacteria, genetic innovations are less probable to fit to the genome. Here, genetic innovation would be anything that elevates the fitness of the gene vehicle (e.g. bacterium) over its contemporaries. Adopted innovations increase the fitness of the compatible genome over incompatible ones, thus possibly tempering the pace at which mutations accumulate in existing genomes over generations. I further discuss the transfer of bacteriophages through atmosphere and potential effects that this may have on local dynamics and perhaps phage survival.
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Affiliation(s)
- Matti Jalasvuori
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, FI-40014, Finland
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31
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Naureen Z, Dautaj A, Anpilogov K, Camilleri G, Dhuli K, Tanzi B, Maltese PE, Cristofoli F, De Antoni L, Beccari T, Dundar M, Bertelli M. Bacteriophages presence in nature and their role in the natural selection of bacterial populations. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:e2020024. [PMID: 33170167 PMCID: PMC8023132 DOI: 10.23750/abm.v91i13-s.10819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/23/2020] [Indexed: 01/21/2023]
Abstract
Phages are the obligate parasite of bacteria and have complex interactions with their hosts. Phages can live in, modify, and shape bacterial communities by bringing about changes in their abundance, diversity, physiology, and virulence. In addition, phages mediate lateral gene transfer, modify host metabolism and reallocate bacterially-derived biochemical compounds through cell lysis, thus playing an important role in ecosystem. Phages coexist and coevolve with bacteria and have developed several antidefense mechanisms in response to bacterial defense strategies against them. Phages owe their existence to their bacterial hosts, therefore they bring about alterations in their host genomes by transferring resistance genes and genes encoding toxins in order to improve the fitness of the hosts. Application of phages in biotechnology, environment, agriculture and medicines demands a deep insight into the myriad of phage-bacteria interactions. However, to understand their complex interactions, we need to know how unique phages are to their bacterial hosts and how they exert a selective pressure on the microbial communities in nature. Consequently, the present review focuses on phage biology with respect to natural selection of bacterial populations.
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Affiliation(s)
- Zakira Naureen
- Department of Biological Sciences and Chemistry, College of Arts and Sciences, University of Nizwa, Nizwa, Oman.
| | | | | | | | | | | | | | | | | | - Tommaso Beccari
- Department of Pharmaceutical Science, University of Perugia, Perugia, Italy.
| | - Munis Dundar
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey.
| | - Matteo Bertelli
- EBTNA-LAB, Rovereto (TN), Italy; MAGI EUREGIO, Bolzano, Italy; MAGI'S LAB, Rovereto (TN), Italy.
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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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33
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Abstract
Viruses are extremely diverse and modulate important biological and ecological processes globally. However, much of viral diversity remains uncultured and yet to be discovered. Several powerful culture-independent tools, in particular metagenomics, have substantially advanced virus discovery. Among those tools is single-virus genomics, which yields sequenced reference genomes from individual sorted virus particles without the need for cultivation. This new method complements virus culturing and metagenomic approaches and its advantages include targeted investigation of specific virus groups and investigation of genomic microdiversity within viral populations. In this Review, we provide a brief history of single-virus genomics, outline how this emergent method has facilitated advances in virus ecology and discuss its current limitations and future potential. Finally, we address how this method may synergistically intersect with other single-virus and single-cell approaches.
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New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities. ISME JOURNAL 2020; 14:1821-1833. [PMID: 32322010 DOI: 10.1038/s41396-020-0653-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 12/22/2022]
Abstract
Viruses of hyperthermophilic archaea represent one of the least understood parts of the virosphere, showing little genomic and morphological similarity to viruses of bacteria or eukaryotes. Here, we investigated virus diversity in the active sulfurous fields of the Campi Flegrei volcano in Pozzuoli, Italy. Virus-like particles displaying eight different morphotypes, including lemon-shaped, droplet-shaped and bottle-shaped virions, were observed and five new archaeal viruses proposed to belong to families Rudiviridae, Globuloviridae and Tristromaviridae were isolated and characterized. Two of these viruses infect neutrophilic hyperthermophiles of the genus Pyrobaculum, whereas the remaining three have rod-shaped virions typical of the family Rudiviridae and infect acidophilic hyperthermophiles belonging to three different genera of the order Sulfolobales, namely, Saccharolobus, Acidianus, and Metallosphaera. Notably, Metallosphaera rod-shaped virus 1 is the first rudivirus isolated on Metallosphaera species. Phylogenomic analysis of the newly isolated and previously sequenced rudiviruses revealed a clear biogeographic pattern, with all Italian rudiviruses forming a monophyletic clade, suggesting geographical structuring of virus communities in extreme geothermal environments. Analysis of the CRISPR spacers suggests that isolated rudiviruses have experienced recent host switching across the genus boundary, potentially to escape the targeting by CRISPR-Cas immunity systems. Finally, we propose a revised classification of the Rudiviridae family, with the establishment of six new genera. Collectively, our results further show that high-temperature continental hydrothermal systems harbor a highly diverse virome and shed light on the evolution of archaeal viruses.
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35
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Comparative Genomics of Two New HF1-like Haloviruses. Genes (Basel) 2020; 11:genes11040405. [PMID: 32276506 PMCID: PMC7230728 DOI: 10.3390/genes11040405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022] Open
Abstract
Few genomes of the HF1-group of viruses are currently available, and further examples would enhance the understanding of their evolution, improve their gene annotation, and assist in understanding gene function and regulation. Two novel HF1-group haloviruses, Serpecor1 and Hardycor2, were recovered from widely separated hypersaline lakes in Australia. Both are myoviruses with linear dsDNA genomes and infect the haloarchaeon Halorubrum coriense. Both genomes possess long, terminal direct repeat (TDR) sequences (320 bp for Serpecor1 and 306 bp for Hardycor2). The Serpecor1 genome is 74,196 bp in length, 57.0% G+C, and has 126 annotated coding sequences (CDS). Hardycor2 has a genome of 77,342 bp, 55.6% G+C, and 125 annotated CDS. They show high nucleotide sequence similarity to each other (78%) and with HF1 (>75%), and carry similar intergenic repeat (IR) sequences to those originally described in HF1 and HF2. Hardycor2 carries a DNA methyltransferase gene in the same genomic neighborhood as the methyltransferase genes of HF1, HF2 and HRTV-5, but is in the opposite orientation, and the inferred proteins are only distantly related. Comparative genomics allowed us to identify the candidate genes mediating cell attachment. The genomes of Serpecor1 and Hardycor2 encode numerous small proteins carrying one or more CxxC motifs, a signature feature of zinc-finger domain proteins that are known to participate in diverse biomolecular interactions.
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Rodela ML, Sabet S, Peterson A, Dillon JG. Broad Environmental Tolerance for a Salicola Host-Phage Pair Isolated from the Cargill Solar Saltworks, Newark, CA, USA. Microorganisms 2019; 7:E106. [PMID: 31010175 PMCID: PMC6518143 DOI: 10.3390/microorganisms7040106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/13/2019] [Accepted: 04/17/2019] [Indexed: 11/29/2022] Open
Abstract
Phages greatly influence the ecology and evolution of their bacterial hosts; however, compared to hosts, a relatively low number of phages, especially halophilic phages, have been studied. This study describes a comparative investigation of physicochemical tolerance between a strain of the halophilic bacterium, Salicola, isolated from the Cargill Saltworks (Newark, CA, USA) and its associated phage. The host grew in media between pH 6-8.5, had a salinity growth optimum of 20% total salts (ranging from 10%-30%) and an upper temperature growth limit of 48 °C. The host utilized 61 of 190 substrates tested using BIOLOG Phenotype MicroArrays. The CGφ29 phage, one of only four reported Salicola phages, is a DNA virus of the Siphoviridae family. Overall, the phage tolerated a broader range of environmental conditions than its host (salinity 0-30% total salts; pH 3-9; upper thermal limit 80 °C) and is the most thermotolerant halophilic phage ever reported. This study is the most comprehensive investigation to date of a Salicola host-phage pair and provides novel insights into extreme environmental tolerances among bacteriophages.
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Affiliation(s)
- Meghan L Rodela
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA.
| | - Shereen Sabet
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA.
| | - Allison Peterson
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA.
| | - Jesse G Dillon
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA.
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Mizuno CM, Prajapati B, Lucas‐Staat S, Sime‐Ngando T, Forterre P, Bamford DH, Prangishvili D, Krupovic M, Oksanen HM. Novel haloarchaeal viruses from Lake Retba infecting
Haloferax
and
Halorubrum
species. Environ Microbiol 2019; 21:2129-2147. [DOI: 10.1111/1462-2920.14604] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Carolina M. Mizuno
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Bina Prajapati
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - Soizick Lucas‐Staat
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Telesphore Sime‐Ngando
- CNRS UMR 6023, Université Clermont‐AuvergneLaboratoire "Microorganismes: Génome et Environnement" (LMGE) F‐63000, Clermont‐Ferrand France
| | - Patrick Forterre
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Dennis H. Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
| | - David Prangishvili
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Mart Krupovic
- Unité Biologie Moléculaire du Gène chez les ExtrêmophilesInstitut Pasteur, 25 rue du Docteur Roux 75015, Paris France
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of Helsinki Finland
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38
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El Omari K, Li S, Kotecha A, Walter TS, Bignon EA, Harlos K, Somerharju P, De Haas F, Clare DK, Molin M, Hurtado F, Li M, Grimes JM, Bamford DH, Tischler ND, Huiskonen JT, Stuart DI, Roine E. The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins. Nat Commun 2019; 10:846. [PMID: 30783086 PMCID: PMC6381117 DOI: 10.1038/s41467-019-08728-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 01/22/2019] [Indexed: 11/09/2022] Open
Abstract
Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, whereas very little is known about membrane fusion in prokaryotes. Haloarchaeal pleomorphic viruses (HRPVs) have a membrane envelope decorated with spikes that are presumed to be responsible for host attachment and membrane fusion. Here we determine atomic structures of the ectodomains of the 57-kDa spike protein VP5 from two related HRPVs revealing a previously unreported V-shaped fold. By Volta phase plate cryo-electron tomography we show that VP5 is monomeric on the viral surface, and we establish the orientation of the molecules with respect to the viral membrane. We also show that the viral membrane fuses with the host cytoplasmic membrane in a process mediated by VP5. This sheds light on protein structures involved in prokaryotic membrane fusion.
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Affiliation(s)
- Kamel El Omari
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Sai Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Thomas S Walter
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Eduardo A Bignon
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Pentti Somerharju
- Department of Biochemistry and Developmental Biology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Felix De Haas
- Thermo Fisher Scientific, Achtseweg Noorg 5, 5651 GG, Eindhoven, The Netherlands
| | - Daniel K Clare
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Mika Molin
- Helsinki Institute of Life Science HiLIFE, Institute of Biotechnology, University of Helsinki, Viikinkaari 5, 00014, Helsinki, Finland
| | - Felipe Hurtado
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | - Mengqiu Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| | - Nicole D Tischler
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile.
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Helsinki Institute of Life Science HiLIFE and Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
| | - David I Stuart
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Elina Roine
- Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
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39
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The Biogeography of Great Salt Lake Halophilic Archaea: Testing the Hypothesis of Avian Mechanical Carriers. DIVERSITY 2018. [DOI: 10.3390/d10040124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Halophilic archaea inhabit hypersaline ecosystems globally, and genetically similar strains have been found in locales that are geographically isolated from one another. We sought to test the hypothesis that small salt crystals harboring halophilic archaea could be carried on bird feathers and that bird migration is a driving force of these distributions. In this study, we discovered that the American White Pelicans (AWPE) at Great Salt Lake soak in the hypersaline brine and accumulate salt crystals (halite) on their feathers. We cultured halophilic archaea from AWPE feathers and halite crystals. The microorganisms isolated from the lakeshore crystals were restricted to two genera: Halorubrum and Haloarcula, however, archaea from the feathers were strictly Haloarcula. We compared partial DNA sequence of the 16S rRNA gene from our cultivars with that of similar strains in the GenBank database. To understand the biogeography of genetically similar halophilic archaea, we studied the geographical locations of the sampling sites of the closest-matched species. An analysis of the environmental factors of each site pointed to salinity as the most important factor for selection. The geography of the sites was consistent with the location of the sub-tropical jet stream where birds typically migrate, supporting the avian dispersal hypothesis.
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40
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Wu YT, Yang CY, Chiang PW, Tseng CH, Chiu HH, Saeed I, Baatar B, Rogozin D, Halgamuge S, Degermendzhi A, Tang SL. Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia. Front Microbiol 2018; 9:1763. [PMID: 30177915 PMCID: PMC6109700 DOI: 10.3389/fmicb.2018.01763] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022] Open
Abstract
Microorganisms are critical to maintaining stratified biogeochemical characteristics in meromictic lakes; however, their community composition and potential roles in nutrient cycling are not thoroughly described. Both metagenomics and metaviromics were used to determine the composition and capacity of archaea, bacteria, and viruses along the water column in the landlocked meromictic Lake Shunet in Siberia. Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial bins (0.2–5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). The bacterial and archaeal communities were dominated by Thiocapsa and Methanococcoides, respectively, whereas the viral community was dominated by Siphoviridae. The archaeal and bacterial assemblages and the associated energy metabolism were significantly related to the various depths, in accordance with the stratification of physicochemical parameters. Reconstructed elemental nutrient cycles of the three layers were interconnected, including co-occurrence of denitrification and nitrogen fixation in each layer and involved unique processes due to specific biogeochemical properties at the respective depths. According to the gene annotation, several pre-dominant yet unknown and uncultured bacteria also play potentially important roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific to the host archaea and bacteria in the mixolimnion. This study provides insights into the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was determined to harbor specific and diverse viral, bacterial, and archaeal communities that intimately interacted, revealing patterns shaped by indigenous physicochemical parameters.
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Affiliation(s)
- Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Neipu, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yu Yang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ching-Hung Tseng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Germark Biotechnology Co., Ltd., Taichung, Taiwan
| | - Hsiu-Hui Chiu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Isaam Saeed
- Optimisation and Pattern Recognition Group, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Bayanmunkh Baatar
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Sciences, Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Denis Rogozin
- Institute of Biophysics, Siberian Division of Russian Academy of Sciences, Krasnoyarsk, Russia.,Siberian Federal University, Krasnoyarsk, Russia
| | - Saman Halgamuge
- Optimisation and Pattern Recognition Group, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrei Degermendzhi
- Institute of Biophysics, Siberian Division of Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.,Department of Life Sciences, Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
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41
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Atanasova NS, Demina TA, Krishnam Rajan Shanthi SNV, Oksanen HM, Bamford DH. Extremely halophilic pleomorphic archaeal virus HRPV9 extends the diversity of pleolipoviruses with integrases. Res Microbiol 2018; 169:500-504. [PMID: 29772256 DOI: 10.1016/j.resmic.2018.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 10/16/2022]
Abstract
Certain pleomorphic archaeal viruses are highly infectious even at saturated salt. These viruses belong to the genus Betapleolipovirus of the recently described archaeal virus family Pleolipoviridae. Pleolipoviruses comprise single-stranded or double-stranded, circular or linear DNA genomes that share countless homologues among various archaeal genetic elements. Here we describe a new extremely halophilic betapleolipovirus, Halorubrum pleomorphic virus 9 (HRPV9), which has an integrase gene. We also identified new genes encoding minor pleolipoviral structural proteins. The studies on HRPV9 enhance our knowledge on pleolipoviruses, especially their reciprocal relatedness and relation to certain archaeal plasmids, proviruses and membrane vesicles.
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Affiliation(s)
- Nina S Atanasova
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014, Helsinki, Finland; Finnish Meteorological Institute, Erik Palménin aukio 1, FI-00560, Helsinki, Finland.
| | - Tatiana A Demina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014, Helsinki, Finland.
| | - Sudar N V Krishnam Rajan Shanthi
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014, Helsinki, Finland.
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014, Helsinki, Finland.
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9B, FI-00014, Helsinki, Finland.
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42
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Wang CX, Li X. JMT-1: a novel, spherical lytic halotolerant phage isolated from Yuncheng saline lake. Braz J Microbiol 2018; 49 Suppl 1:262-268. [PMID: 29699780 PMCID: PMC6328844 DOI: 10.1016/j.bjm.2018.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/07/2018] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
This work described a novel halotolerant phage, JMT-1, with a spherical morphology. JMT-1, which was isolated from a hypersaline lake, could produce clear plaques on Chromohalobacter sp. LY7-3. The purified virions are spherical, have no visible tail, and are about 30–50 nm in diameter. JMT-1 has a wide host range, and this study showed that the phage can infect at least five halophilic bacteria. The proteins of JMT-1 were analyzed using sodium dodecyl sulfate polyacrylamide gel electrophoresis, and six proteins were detected. Results show that JMT-1 is a bacteriophage with a linear double-stranded DNA. Meanwhile, the genome is approximately 23 kb in length and is sensitive to the restriction endonucleases Bam I, EcoR I, Hind III and Kpa I. JMT-1 has a high titer, approaching 1.5 × 109 pfu/mL after dilution to 10−6 pfu/mL. The phage is also sensitive to chloroform but not to temperature, pH, and lowered salt concentration. JMT-1 is a spherical lytic halotolerant phage with a wide host range and has the tolerance to specific extreme environments. These data could provide references for studying phage resources in extreme environments and would also provide the useful methods for isolation and identification of other valuable phage in the salt lake environment.
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Affiliation(s)
- Chuan-Xu Wang
- Yuncheng University, Life Science College, Yuncheng, Shanxi, China
| | - Xin Li
- Yuncheng University, Life Science College, Yuncheng, Shanxi, China.
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43
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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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44
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Archaeal Viruses from High-Temperature Environments. Genes (Basel) 2018; 9:genes9030128. [PMID: 29495485 PMCID: PMC5867849 DOI: 10.3390/genes9030128] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 12/21/2022] Open
Abstract
Archaeal viruses are some of the most enigmatic viruses known, due to the small number that have been characterized to date. The number of known archaeal viruses lags behind known bacteriophages by over an order of magnitude. Despite this, the high levels of genetic and morphological diversity that archaeal viruses display has attracted researchers for over 45 years. Extreme natural environments, such as acidic hot springs, are almost exclusively populated by Archaea and their viruses, making these attractive environments for the discovery and characterization of new viruses. The archaeal viruses from these environments have provided insights into archaeal biology, gene function, and viral evolution. This review focuses on advances from over four decades of archaeal virology, with a particular focus on archaeal viruses from high temperature environments, the existing challenges in understanding archaeal virus gene function, and approaches being taken to overcome these limitations.
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45
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Berliner AJ, Mochizuki T, Stedman KM. Astrovirology: Viruses at Large in the Universe. ASTROBIOLOGY 2018; 18:207-223. [PMID: 29319335 DOI: 10.1089/ast.2017.1649] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viruses are the most abundant biological entities on modern Earth. They are highly diverse both in structure and genomic sequence, play critical roles in evolution, strongly influence terran biogeochemistry, and are believed to have played important roles in the origin and evolution of life. However, there is yet very little focus on viruses in astrobiology. Viruses arguably have coexisted with cellular life-forms since the earliest stages of life, may have been directly involved therein, and have profoundly influenced cellular evolution. Viruses are the only entities on modern Earth to use either RNA or DNA in both single- and double-stranded forms for their genetic material and thus may provide a model for the putative RNA-protein world. With this review, we hope to inspire integration of virus research into astrobiology and also point out pressing unanswered questions in astrovirology, particularly regarding the detection of virus biosignatures and whether viruses could be spread extraterrestrially. We present basic virology principles, an inclusive definition of viruses, review current virology research pertinent to astrobiology, and propose ideas for future astrovirology research foci. Key Words: Astrobiology-Virology-Biosignatures-Origin of life-Roadmap. Astrobiology 18, 207-223.
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Affiliation(s)
| | | | - Kenneth M Stedman
- 3 Center for Life in Extreme Environments and Biology Department, Portland State University , Oregon, USA
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46
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Krupovic M, Cvirkaite-Krupovic V, Iranzo J, Prangishvili D, Koonin EV. Viruses of archaea: Structural, functional, environmental and evolutionary genomics. Virus Res 2017; 244:181-193. [PMID: 29175107 DOI: 10.1016/j.virusres.2017.11.025] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022]
Abstract
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, Paris, France.
| | | | - Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - David Prangishvili
- Department of Microbiology, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, Paris, France
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
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47
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Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes. ISME JOURNAL 2017; 12:424-437. [PMID: 29099492 PMCID: PMC5776456 DOI: 10.1038/ismej.2017.175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/16/2017] [Accepted: 08/23/2017] [Indexed: 12/12/2022]
Abstract
Hypersaline environments close to saturation harbor the highest density of virus-like particles reported for aquatic systems as well as low microbial diversity. Thus, they offer unique settings for studying virus–host interactions in nature. However, no viruses have been isolated so far infecting the two most abundant inhabitants of these systems (that is, the euryarchaeon Haloquadratum walsbyi and the bacteroidetes Salinibacter ruber). Here, using three different co-occurring strains, we have isolated eight viruses infecting the ubiquitous S. ruber that constitute three new different genera (named as ‘Holosalinivirus’, ‘Kryptosalinivirus’ and ‘Kairosalinivirus’) according to their genomic traits, different host range, virus–host interaction capabilities and abundances in natural systems worldwide. Furthermore, to get a more complete and comprehensive view of S. ruber virus assemblages in nature, a microcosm experiment was set with a mixture of S. ruber strains challenged with a brine virus concentrate, and changes of viral populations were monitored by viral metagenomics. Only viruses closely related to kairosalinivirus (strictly lytic and wide host range) were enriched, despite their low initial abundance in the natural sample. Metagenomic analyses of the mesocosms allowed the complete recovery of kairosalinivirus genomes using an ad hoc assembly strategy as common viral metagenomic assembly tools failed despite their abundance, which underlines the limitations of current approaches. The increase of this type of viruses was accompanied by an increase in the diversity of the group, as shown by contig recruitment. These results are consistent with a scenario in which host range, not only virus and host abundances, is a key factor in determining virus fate in nature.
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48
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Eskelin K, Lampi M, Meier F, Moldenhauer E, Bamford DH, Oksanen HM. Halophilic viruses with varying biochemical and biophysical properties are amenable to purification with asymmetrical flow field-flow fractionation. Extremophiles 2017; 21:1119-1132. [PMID: 29019077 DOI: 10.1007/s00792-017-0963-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/14/2017] [Indexed: 01/21/2023]
Abstract
Viruses come in various shapes and sizes, and a number of viruses originate from extremities, e.g. high salinity or elevated temperature. One challenge for studying extreme viruses is to find efficient purification conditions where viruses maintain their infectivity. Asymmetrical flow field-flow fractionation (AF4) is a gentle native chromatography-like technique for size-based separation. It does not have solid stationary phase and the mobile phase composition is readily adjustable according to the sample needs. Due to the high separation power of specimens up to 50 µm, AF4 is suitable for virus purification. Here, we applied AF4 for extremophilic viruses representing four morphotypes: lemon-shaped, tailed and tailless icosahedral, as well as pleomorphic enveloped. AF4 was applied to input samples of different purity: crude supernatants of infected cultures, polyethylene glycol-precipitated viruses and viruses purified by ultracentrifugation. All four virus morphotypes were successfully purified by AF4. AF4 purification of culture supernatants or polyethylene glycol-precipitated viruses yielded high recoveries, and the purities were comparable to those obtained by the multistep ultracentrifugation purification methods. In addition, we also demonstrate that AF4 is a rapid monitoring tool for virus production in slowly growing host cells living in extreme conditions.
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Affiliation(s)
- Katri Eskelin
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Mirka Lampi
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Florian Meier
- Postnova Analytics, Max-Planck-Str. 14, 86899, Landsberg, Germany
| | | | - Dennis H Bamford
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Hanna M Oksanen
- Department of Biosciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland.
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49
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Philosof A, Yutin N, Flores-Uribe J, Sharon I, Koonin EV, Béjà O. Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota. Curr Biol 2017; 27:1362-1368. [PMID: 28457865 PMCID: PMC5434244 DOI: 10.1016/j.cub.2017.03.052] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 03/09/2017] [Accepted: 03/21/2017] [Indexed: 12/16/2022]
Abstract
Marine group II Euryarchaeota (MG-II) are among the most abundant microbes in oceanic surface waters [1, 2, 3, 4]. So far, however, representatives of MG-II have not been cultivated, and no viruses infecting these organisms have been described. Here, we present complete genomes for three distinct groups of viruses assembled from metagenomic sequence datasets highly enriched for MG-II. These novel viruses, which we denote magroviruses, possess double-stranded DNA genomes of 65 to 100 kilobases in size that encode a structural module characteristic of head-tailed viruses and, unusually for archaeal and bacterial viruses, a nearly complete replication apparatus of apparent archaeal origin. The newly identified magroviruses are widespread and abundant and therefore are likely to be major ecological agents. A novel viral group, magroviruses, likely infects marine group II archaea Magroviruses are highly abundant in oceanic surface waters worldwide Magroviruses have linear, double-stranded DNA genomes of about 100 kilobases Magroviruses encode a near complete replication apparatus of apparent archaeal origin
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Affiliation(s)
- Alon Philosof
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - José Flores-Uribe
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona 11016, Israel; Tel Hai College, Upper Galilee 12210, Israel
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
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50
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Demina TA, Pietilä MK, Svirskaitė J, Ravantti JJ, Atanasova NS, Bamford DH, Oksanen HM. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae. Viruses 2017; 9:v9020032. [PMID: 28218714 PMCID: PMC5332951 DOI: 10.3390/v9020032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 01/10/2017] [Accepted: 02/13/2017] [Indexed: 11/16/2022] Open
Abstract
Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016.
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Affiliation(s)
- Tatiana A Demina
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Maija K Pietilä
- Department of Food and Environmental Sciences, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Julija Svirskaitė
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Janne J Ravantti
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Nina S Atanasova
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
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