1
|
Lossouarn J, Nesbø CL, Bienvenu N, Geslin C. Plasmid pMO1 from Marinitoga okinawensis, first non-cryptic plasmid reported within Thermotogota. Res Microbiol 2023; 174:104044. [PMID: 36805054 DOI: 10.1016/j.resmic.2023.104044] [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: 12/10/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/19/2023]
Abstract
Mobile genetic elements (MGEs), such as viruses and plasmids, drive the evolution and adaptation of their cellular hosts from all three domains of life. This includes microorganisms thriving in the most extreme environments, like deep-sea hydrothermal vents. However, our knowledge about MGEs still remains relatively sparse in these abyssal ecosystems. Here we report the isolation, sequencing, assembly, and functional annotation of pMO1, a 28.2 kbp plasmid associated with the reference strain Marinitoga okinawensis. Carrying restriction/modification and chemotaxis protein-encoding genes, pMO1 likely affects its host's phenotype and represents the first non-cryptic plasmid described among the phylum Thermotogota.
Collapse
Affiliation(s)
- Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada; Biozone, Department of Chemical Engineering and Applied Chemistry and BioZone, University of Toronto, 200 College Street, Toronto, Ontario, Canada, M5S 3E5.
| | - Nadège Bienvenu
- Univ Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France.
| | - Claire Geslin
- Univ Brest, Ifremer, CNRS, Unité Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France. mailto:
| |
Collapse
|
2
|
Haverkamp THA, Lossouarn J, Zhaxybayeva O, Lyu J, Bienvenu N, Geslin C, Nesbø CL. Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing. Environ Microbiol 2021; 23:7105-7120. [PMID: 34398506 DOI: 10.1111/1462-2920.15723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/24/2021] [Accepted: 08/13/2021] [Indexed: 11/30/2022]
Abstract
Phylogenomic analyses of bacteria from the phylum Thermotogota have shown extensive lateral gene transfer with distantly related organisms, particularly with Firmicutes. One likely mechanism of such DNA transfer is viruses. However, to date, only three temperate viruses have been characterized in this phylum, all infecting bacteria from the Marinitoga genus. Here we report 17 proviruses integrated into genomes of bacteria belonging to eight Thermotogota genera and induce viral particle production from one of the proviruses. All except an incomplete provirus from Mesotoga fall into two groups based on sequence similarity, gene synteny and taxonomic classification. Proviruses of Group 1 are found in the genera Geotoga, Kosmotoga, Marinitoga, Thermosipho and Mesoaciditoga and are similar to the previously characterized Marinitoga viruses, while proviruses from Group 2 are distantly related to the Group 1 proviruses, have different genome organization and are found in Petrotoga and Defluviitoga. Genes carried by both groups are closely related to Firmicutes and Firmicutes (pro)viruses in phylogenetic analyses. Moreover, one of the groups show evidence of recent gene exchange and may be capable of infecting cells from both phyla. We hypothesize that viruses are responsible for a large portion of the observed gene flow between Firmicutes and Thermotogota.
Collapse
Affiliation(s)
- Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, 78350, France
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Jie Lyu
- Université Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, F-29280, France
| | - Nadège Bienvenu
- Université Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, F-29280, France
| | - Claire Geslin
- Université Brest, CNRS, IFREMER, Laboratoire de Microbiologie des Environnements Extrêmes, Plouzané, F-29280, France
| | - Camilla L Nesbø
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5S 3E5, Canada
| |
Collapse
|
3
|
Zeng X, Alain K, Shao Z. Microorganisms from deep-sea hydrothermal vents. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:204-230. [PMID: 37073341 PMCID: PMC10077256 DOI: 10.1007/s42995-020-00086-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/17/2020] [Indexed: 05/03/2023]
Abstract
With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00086-4.
Collapse
Affiliation(s)
- Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E UMR6197, Univ Brest, CNRS, IFREMER, F-29280 Plouzané, France
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| |
Collapse
|
4
|
Su HN, Zhang YZ. Lifestyle of bacteria in deep sea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:15-17. [PMID: 33006410 DOI: 10.1111/1758-2229.12891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| |
Collapse
|
5
|
Thiroux S, Dupont S, Nesbø CL, Bienvenu N, Krupovic M, L'Haridon S, Marie D, Forterre P, Godfroy A, Geslin C. The first head-tailed virus, MFTV1, infecting hyperthermophilic methanogenic deep-sea archaea. Environ Microbiol 2020; 23:3614-3626. [PMID: 33022088 DOI: 10.1111/1462-2920.15271] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/20/2020] [Accepted: 10/03/2020] [Indexed: 11/27/2022]
Abstract
Deep-sea hydrothermal vents are inhabited by complex communities of microbes and their viruses. Despite the importance of viruses in controlling the diversity, adaptation and evolution of their microbial hosts, to date, only eight bacterial and two archaeal viruses isolated from abyssal ecosystems have been described. Thus, our efforts focused on gaining new insights into viruses associated with deep-sea autotrophic archaea. Here, we provide the first evidence of an infection of hyperthermophilic methanogenic archaea by a head-tailed virus, Methanocaldococcus fervens tailed virus 1 (MFTV1). MFTV1 has an isometric head of 50 nm in diameter and a 150 nm-long non-contractile tail. Virions are released continuously without causing a sudden drop in host growth. MFTV1 infects Methanocaldococcus species and is the first hyperthermophilic head-tailed virus described thus far. The viral genome is a double-stranded linear DNA of 31 kb. Interestingly, our results suggest potential strategies adopted by the plasmid pMEFER01, carried by M. fervens, to spread horizontally in hyperthermophilic methanogens. The data presented here open a new window of understanding on how the abyssal mobilome interacts with hyperthermophilic marine archaea.
Collapse
Affiliation(s)
- Sarah Thiroux
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Samuel Dupont
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Camilla L Nesbø
- Biozone, University of Toronto, Toronto, Ontario, M5S 3E5, Canada.,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2R3, 12, Canada
| | - Nadège Bienvenu
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France
| | - Stéphane L'Haridon
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Dominique Marie
- UPMC Univ Paris 06, INSU-CNRS, UMR 7144, Station Biologique de Roscoff, Sorbonne University, Roscoff, 29680, France
| | - Patrick Forterre
- Archaeal Virology Unit, Institut Pasteur, Paris, 75015, France.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS., Gif-sur-Yvette, 91198, France
| | - Anne Godfroy
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| | - Claire Geslin
- Laboratoire de Microbiologie des Environnements Extrêmes, Univ Brest, CNRS, IFREMER, Plouzané, F-29280, France
| |
Collapse
|
6
|
Tuttle MJ, Buchan A. Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence. Environ Microbiol 2020; 22:4919-4933. [PMID: 32935433 DOI: 10.1111/1462-2920.15233] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 08/23/2020] [Indexed: 12/12/2022]
Abstract
In the oceans, viruses that infect bacteria (phages) influence a variety of microbially mediated processes that drive global biogeochemical cycles. The nature of their influence is dependent upon infection mode, be it lytic or lysogenic. Temperate phages are predicted to be prevalent in marine systems where they are expected to execute both types of infection modes. Understanding the range and outcomes of temperate phage-host interactions is fundamental for evaluating their ecological impact. Here, we (i) review phage-mediated rewiring of host metabolism, with a focus on marine systems, (ii) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cultivated model systems to examine the consequences of lysogeny among several dominant marine bacterial lineages. We also readdress the prevalence of lysogeny among marine bacteria by probing a collection of 1239 publicly available bacterial genomes, representing cultured and uncultivated strains, for evidence of complete prophages. Our conservative analysis, anticipated to underestimate true prevalence, predicts 18% of the genomes examined contain at least one prophage, the majority (97%) were found within genomes of cultured isolates. These results highlight the need for cultivation of additional model systems to better capture the diversity of temperate phage-host interactions in the oceans.
Collapse
Affiliation(s)
- Matthew J Tuttle
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| |
Collapse
|
7
|
Thermotogales origin scenario of eukaryogenesis. J Theor Biol 2020; 492:110192. [PMID: 32044287 DOI: 10.1016/j.jtbi.2020.110192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
How eukaryotes were generated is an enigma of evolutionary biology. Widely accepted archaeal-origin eukaryogenesis scenarios, based on similarities of genes and related characteristics between archaea and eukaryotes, cannot explain several eukaryote-specific features of the last eukaryotic common ancestor, such as glycerol-3-phosphate-type membrane lipids, large cells and genomes, and endomembrane formation. Thermotogales spheroids, having multicopy-integrated large nucleoids and producing progeny in periplasm, may explain all of these features as well as endoplasmic reticulum-type signal cleavage sites, although they cannot divide. We hypothesize that the progeny chromosome is formed by random joining small DNAs in immature progeny, followed by reorganization by mechanisms including homologous recombination enabled with multicopy-integrated large genome (MILG). We propose that Thermotogales ancestor spheroids came to divide owing to the archaeal cell division genes horizontally transferred via virus-related particles, forming the first eukaryotic common ancestor (FECA). Referring to the hypothesis, the archaeal information-processing system would have been established in FECA by random joining DNAs excised from the MILG, which contained horizontally transferred archaeal and bacterial DNAs, followed by reorganization by the MILG-enabled homologous recombination. Thus, the large genome may have been a prerequisite, but not a consequence, of eukaryogenesis. The random joining of DNAs likely provided the basic mechanisms for eukaryotic evolution: producing the diversity by the formations of supergroups, novel genes, and introns that are involved in exon shuffling.
Collapse
|
8
|
Marinitoga lauensis sp. nov., a novel deep-sea hydrothermal vent thermophilic anaerobic heterotroph with a prophage. Syst Appl Microbiol 2019; 42:343-347. [DOI: 10.1016/j.syapm.2019.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/17/2019] [Accepted: 02/26/2019] [Indexed: 11/22/2022]
|
9
|
Haverkamp THA, Geslin C, Lossouarn J, Podosokorskaya OA, Kublanov I, Nesbø CL. Thermosipho spp. Immune System Differences Affect Variation in Genome Size and Geographical Distributions. Genome Biol Evol 2018; 10:2853-2866. [PMID: 30239713 PMCID: PMC6211235 DOI: 10.1093/gbe/evy202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 01/24/2023] Open
Abstract
Thermosipho species inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs, and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents, and hotsprings. Comparative genomics of 15 Thermosipho genomes separated them into three distinct species with different habitat distributions: The widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. Moreover, the species can be differentiated on the basis of genome size (GS), genome content, and immune system composition. For instance, the T. africanus genomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. GS differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found in T. affectus that contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA.
Collapse
Affiliation(s)
- Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway.,Norwegian Veterinary Institute, Oslo, Norway
| | - Claire Geslin
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Université de Bretagne Occidentale (UBO), Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Plouzané, France.,Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, Plouzané, France
| | - Julien Lossouarn
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Université de Bretagne Occidentale (UBO), Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Plouzané, France.,Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, Plouzané, France
| | - Olga A Podosokorskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Camilla L Nesbø
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
10
|
Parikka KJ, Jacquet S, Colombet J, Guillaume D, Le Romancer M. Abundance and observations of thermophilic microbial and viral communities in submarine and terrestrial hot fluid systems of the French Southern and Antarctic Lands. Polar Biol 2018. [DOI: 10.1007/s00300-018-2288-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
11
|
Mercier C, Lossouarn J, Nesbø CL, Haverkamp THA, Baudoux AC, Jebbar M, Bienvenu N, Thiroux S, Dupont S, Geslin C. Two viruses, MCV1 and MCV2, which infect Marinitoga
bacteria isolated from deep-sea hydrothermal vents: functional and genomic analysis. Environ Microbiol 2017; 20:577-587. [DOI: 10.1111/1462-2920.13967] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/25/2017] [Accepted: 10/19/2017] [Indexed: 11/27/2022]
Affiliation(s)
- C. Mercier
- Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, rue Dumont d'Urville; F-29280 Plouzané France
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer, UMR 6197 Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle de la Pointe du diable; F-29280 Plouzané France
| | - J. Lossouarn
- Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, rue Dumont d'Urville; F-29280 Plouzané France
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer, UMR 6197 Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle de la Pointe du diable; F-29280 Plouzané France
| | - C. L. Nesbø
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology; University of Oslo; Oslo 0316 Norway
- Department of Biological Sciences; University of Alberta; Edmonton AB T6G2R3 Canada
| | - T. H. A. Haverkamp
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology; University of Oslo; Oslo 0316 Norway
| | - A. C. Baudoux
- Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Equipe DIPO, Station Biologique de Roscoff; F-29680 Roscoff France
- CNRS, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff; F-29680 Roscoff France
| | - M. Jebbar
- Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, rue Dumont d'Urville; F-29280 Plouzané France
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer, UMR 6197 Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle de la Pointe du diable; F-29280 Plouzané France
| | - N. Bienvenu
- Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, rue Dumont d'Urville; F-29280 Plouzané France
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer, UMR 6197 Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle de la Pointe du diable; F-29280 Plouzané France
| | - S. Thiroux
- Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, rue Dumont d'Urville; F-29280 Plouzané France
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer, UMR 6197 Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle de la Pointe du diable; F-29280 Plouzané France
| | - S. Dupont
- Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, rue Dumont d'Urville; F-29280 Plouzané France
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer, UMR 6197 Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle de la Pointe du diable; F-29280 Plouzané France
| | - C. Geslin
- Université de Bretagne Occidentale (UBO), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes, rue Dumont d'Urville; F-29280 Plouzané France
- CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), rue Dumont d'Urville; F-29280 Plouzané France
- Ifremer, UMR 6197 Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle de la Pointe du diable; F-29280 Plouzané France
| |
Collapse
|
12
|
Beyond the canonical strategies of horizontal gene transfer in prokaryotes. Curr Opin Microbiol 2017; 38:95-105. [PMID: 28600959 DOI: 10.1016/j.mib.2017.04.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023]
Abstract
Efforts to identify and characterize strategies for horizontal gene transfer (HGT) in prokaryotes could have overlooked some mechanisms that do not entirely fit in with the canonical ones most often described (conjugation of plasmids, phage transduction and transformation). The difficulty in distinguishing the different HGT strategies could have contributed to underestimate their real extent. Here we review non classical HGT strategies: some that require mobile genetic elements (MGEs) and others independent of MGE. Among those strategies that require MGEs, there is a range of newly reported, hybrid and intermediate MGEs mobilizing only their own DNA, others that mobilize preferentially bacterial DNA, or both. Considering HGT strategies independent of MGE, a few are even not restricted to DNA transfer, but can also mobilize other molecules. This review considers those HGT strategies that are less commonly dealt with in the literature. The real impact of these elements could, in some conditions, be more relevant than previously thought.
Collapse
|
13
|
Draft Genome Sequences of Two Marinitoga camini Isolates Producing Bacterioviruses. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01261-16. [PMID: 27834711 PMCID: PMC5105104 DOI: 10.1128/genomea.01261-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we present the draft genome sequences of two thermophilic Marinitoga strain members of the Thermotogales order, Marinitoga camini DV1155 and Marinitoga camini DV1197. These strains were isolated from deep-sea hydrothermal vents of the Mid-Atlantic Ridge.
Collapse
|
14
|
Lossouarn J, Dupont S, Gorlas A, Mercier C, Bienvenu N, Marguet E, Forterre P, Geslin C. An abyssal mobilome: viruses, plasmids and vesicles from deep-sea hydrothermal vents. Res Microbiol 2015; 166:742-52. [DOI: 10.1016/j.resmic.2015.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/08/2015] [Accepted: 04/09/2015] [Indexed: 01/11/2023]
|