2
|
Santamaría RI, Bustos P, Van Cauwenberghe J, González V. Hidden diversity of double-stranded DNA phages in symbiotic Rhizobium species. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200468. [PMID: 34839703 PMCID: PMC8628074 DOI: 10.1098/rstb.2020.0468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In this study, we addressed the extent of diversification of phages associated with nitrogen-fixing symbiotic Rhizobium species. Despite the ecological and economic importance of the Rhizobium genus, little is known about the diversity of the associated phages. A thorough assessment of viral diversity requires investigating both lytic phages and prophages harboured in diverse Rhizobium genomes. Protein-sharing networks identified 56 viral clusters (VCs) among a set of 425 isolated phages and predicted prophages. The VCs formed by phages had more proteins in common and a higher degree of synteny, and they group together in clades in the associated phylogenetic tree. By contrast, the VCs of prophages showed significant genetic variation and gene loss, with selective pressure on the remaining genes. Some VCs were found in various Rhizobium species and geographical locations, suggesting that they have wide host ranges. Our results indicate that the VCs represent distinct taxonomic units, probably representing taxa equivalent to genera or even species. The finding of previously undescribed phage taxa indicates the need for further exploration of the diversity of phages associated with Rhizobium species. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.
Collapse
Affiliation(s)
- Rosa I. Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
3
|
Ford S, Moeskjær S, Young P, Santamaría RI, Harrison E. Introducing a Novel, Broad Host Range Temperate Phage Family Infecting Rhizobium leguminosarum and Beyond. Front Microbiol 2021; 12:765271. [PMID: 34858375 PMCID: PMC8631192 DOI: 10.3389/fmicb.2021.765271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/13/2021] [Indexed: 02/01/2023] Open
Abstract
Temperate phages play important roles in bacterial communities but have been largely overlooked, particularly in non-pathogenic bacteria. In rhizobia the presence of temperate phages has the potential to have significant ecological impacts but few examples have been described. Here we characterize a novel group of 5 Rhizobium leguminosarum prophages, capable of sustaining infections across a broad host range within their host genus. Genome comparisons identified further putative prophages infecting multiple Rhizobium species isolated globally, revealing a wider family of 10 temperate phages including one previously described lytic phage, RHEph01, which appears to have lost the ability to form lysogens. Phylogenetic discordance between prophage and host phylogenies suggests a history of active mobilization between Rhizobium lineages. Genome comparisons revealed conservation of gene content and order, with the notable exception of an approximately 5 kb region of hypervariability, containing almost exclusively hypothetical genes. Additionally, several horizontally acquired genes are present across the group, including a putative antirepressor present only in the RHEph01 genome, which may explain its apparent inability to form lysogens. In summary, both phenotypic and genomic comparisons between members of this group of phages reveals a clade of viruses with a long history of mobilization within and between Rhizobium species.
Collapse
Affiliation(s)
- Sam Ford
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Sara Moeskjær
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Peter Young
- Department of Biology, University of York, York, United Kingdom
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, México City, Mexico
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| |
Collapse
|
5
|
Gunathilake KMD, Halmillawewa AP, MacKenzie KD, Perry BJ, Yost CK, Hynes MF. A bacteriophage infecting Mesorhizobium species has a prolate capsid and shows similarities to a family of Caulobacter crescentus phages. Can J Microbiol 2020; 67:147-160. [PMID: 32905709 DOI: 10.1139/cjm-2020-0281] [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] [Indexed: 11/22/2022]
Abstract
Mesorhizobium phage vB_MloS_Cp1R7A-A1 was isolated from soil planted with chickpea in Saskatchewan. It is dissimilar in sequence and morphology to previously described rhizobiophages. It is a B3 morphotype virus with a distinct prolate capsid and belongs to the tailed phage family Siphoviridae. Its genome has a GC content of 60.3% and 238 predicted genes. Putative functions were predicted for 57 genes, which include 27 tRNA genes with anticodons corresponding to 18 amino acids. This represents the highest number of tRNA genes reported yet in a rhizobiophage. The gene arrangement shows a partially modular organization. Most of the structural genes are found in one module, whereas tRNA genes are in another. Genes for replication, recombination, and nucleotide metabolism form the third module. The arrangement of the replication module resembles the replication module of Enterobacteria phage T5, raising the possibility that it uses a recombination-based replication mechanism, but there is also a suggestion that a T7-like replication mechanism could be used. Phage termini appear to be long direct repeats of just over 12 kb in length. Phylogenetic analysis revealed that Cp1R7A-A1 is more closely related to PhiCbK-like Caulobacter phages and other B3 morphotype phages than to other rhizobiophages sequenced thus far.
Collapse
Affiliation(s)
| | - Anupama P Halmillawewa
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.,Department of Microbiology, University of Kelaniya, Sri Lanka
| | - Keith D MacKenzie
- Biology Department, University of Regina, Regina Saskatchewan, Canada
| | - Benjamin J Perry
- Biology Department, University of Regina, Regina Saskatchewan, Canada.,Department of Microbiology, University of Otago, Dunedin, New Zealand
| | | | - Michael F Hynes
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
9
|
Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaqué D, Bork P, Acinas SG, Wincker P, Sullivan MB. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 2016; 537:689-693. [PMID: 27654921 DOI: 10.1038/nature19366] [Citation(s) in RCA: 461] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 08/12/2016] [Indexed: 12/26/2022]
Abstract
Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.
Collapse
Affiliation(s)
- Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Department of Marine Biology, Federal University of Rio de Janeiro, Rio de Janeiro, CEP 21941-902, Brazil
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, A-1090 Vienna, Austria
- Austrian Polar Research Institute, A-1090 Vienna, Austria
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elena Lara
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
- Institute of Marine Sciences (CNR-ISMAR), National Research Council, 30122 Venezia, Italy
| | - Julie Poulain
- CEA - Institut de Génomique, GENOSCOPE, 91057 Evry, France
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, 28359 Bremen, Germany
- MARUM, Bremen University, 28359 Bremen, Germany
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Directors' Research, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Céline Dimier
- CNRS, UMR 7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, 29680 Roscoff, France
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR 8197, INSERM U1024, F-75005 Paris, France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'océanographie de Villefranche, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7093, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'océanographie de Villefranche, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7093, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
| | - Corinne Cruaud
- CEA - Institut de Génomique, GENOSCOPE, 91057 Evry, France
| | | | - Carlos M Duarte
- Mediterranean Institute of Advanced Studies, CSIC-UiB, 21-07190 Esporles, Mallorca, Spain
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, 91057 Evry, France
- CNRS, UMR 8030, 91057 Evry, France
- Université d'Evry, UMR 8030, 91057 Evry, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| |
Collapse
|