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Messer LF, Bourne DG, Robbins SJ, Clay M, Bell SC, McIlroy SJ, Tyson GW. A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience. Nat Commun 2024; 15:2902. [PMID: 38575584 PMCID: PMC10995205 DOI: 10.1038/s41467-024-46905-5] [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: 08/29/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.
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Affiliation(s)
- Lauren F Messer
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia.
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Megan Clay
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia
| | - Sara C Bell
- College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
- Australian Institute of Marine Science, Townsville, QLD, 4810, Australia
| | - Simon J McIlroy
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, 4102, Australia.
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2
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Rosani U. Tracing RNA viruses associated with Nudibranchia gastropods. PeerJ 2022; 10:e13410. [PMID: 35586129 PMCID: PMC9109684 DOI: 10.7717/peerj.13410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/19/2022] [Indexed: 01/14/2023] Open
Abstract
Background Nudibranchia is an under-studied taxonomic group of gastropods, including more than 3,000 species with colourful and extravagant body shapes and peculiar predatory and defensive strategies. Although symbiosis with bacteria has been reported, no data are available for the nudibranch microbiome nor regarding viruses possibly associated with these geographically widespread species. Methods Based on 47 available RNA sequencing datasets including more than two billion reads of 35 nudibranch species, a meta-transcriptome assembly was constructed. Taxonomic searches with DIAMOND, RNA-dependent-RNA-polymerase identification with palmscan and viral hallmark genes identification by VirSorter2 in combination with CheckV were applied to identify genuine viral genomes, which were then annotated using CAT. Results A total of 20 viral genomes were identified as bona fide viruses, among 552 putative viral contigs resembling both RNA viruses of the Negarnaviricota, Pisuviricota, Kitrinoviricota phyla and actively transcribing DNA viruses of the Cossaviricota and Nucleocytoviricota phyla. The 20 commonly identified viruses showed similarity with RNA viruses identified in other RNA-seq experiments and can be putatively associated with bacteria, plant and arthropod hosts by co-occurence analysis. The RNA samples having the highest viral abundances showed a heterogenous and mostly sample-specific distribution of the identified viruses, suggesting that nudibranchs possess diversified and mostly unknown viral communities.
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3
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Mehta P, Yadav M, Ahmed V, Goyal K, Pandey R, Chauhan NS. Culture-Independent Exploration of the Hypersaline Ecosystem Indicates the Environment-Specific Microbiome Evolution. Front Microbiol 2021; 12:686549. [PMID: 34777269 PMCID: PMC8581802 DOI: 10.3389/fmicb.2021.686549] [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: 03/27/2021] [Accepted: 09/30/2021] [Indexed: 01/08/2023] Open
Abstract
Sambhar Salt Lake, situated in the state of Rajasthan, India is a unique temperate hypersaline ecosystem. Exploration of the salt lake microbiome will enable us to understand microbiome functioning in nutrient-deprived extreme conditions, as well as enrich our understanding of the environment-specific microbiome evolution. The current study has been designed to explore the Sambhar Salt Lake microbiome with a culture-independent multi-omics approach to define its metagenomic features and prevalent metabolic functionaries. The rRNA feature and protein feature-based phylogenetic reconstruction synchronously (R = 0.908) indicated the dominance of the archaea (Euryarchaeota) and bacteria (Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria). Metabolic reconstruction identified selective enrichment of the protein features associated with energy harvesting and stress tolerance (osmotic, oxidative, metal/metalloid, heat/cold, antibiotic, and desiccation). Metabolites identified with metabolome analysis confirmed physiological adaptation of the lake microbiome within a hypersaline and nutrient-deprived environment. Comparative metagenomics of the 212 metagenomes representing freshwater, alkaline, and saline ecosystem microbiome indicated the selective enrichment of the microbial groups and genetic features. The current study elucidates microbiome functioning within the nutrient-deprived harsh ecosystems. In summary, the current study harnessing the strength of multi-omics and comparative metagenomics indicates the environment-specific microbiome evolution.
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Affiliation(s)
- Priyanka Mehta
- Genomics and Molecular Medicine, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Monika Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Vasim Ahmed
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Khushboo Goyal
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Rajesh Pandey
- Genomics and Molecular Medicine, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
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Renoz F, Foray V, Ambroise J, Baa-Puyoulet P, Bearzatto B, Mendez GL, Grigorescu AS, Mahillon J, Mardulyn P, Gala JL, Calevro F, Hance T. At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica. Front Cell Infect Microbiol 2021; 11:660007. [PMID: 34268133 PMCID: PMC8275996 DOI: 10.3389/fcimb.2021.660007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/14/2021] [Indexed: 01/10/2023] Open
Abstract
Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial associates of insects that are at the gateway to a host-dependent lifestyle.
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Affiliation(s)
- François Renoz
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Vincent Foray
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
- Institut de Recherche sur la Biologie de l’insecte, UMR 7261, CNRS, Université de Tours, Tours, France
| | - Jérôme Ambroise
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | | | - Bertrand Bearzatto
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Gipsi Lima Mendez
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Luc Gala
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2i, UMR203, F-69621, Villeurbanne, France
| | - Thierry Hance
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
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Silveira CB, Cavalcanti GS, Walter JM, Silva-Lima AW, Dinsdale EA, Bourne DG, Thompson CC, Thompson FL. Microbial processes driving coral reef organic carbon flow. FEMS Microbiol Rev 2017; 41:575-595. [PMID: 28486655 DOI: 10.1093/femsre/fux018] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 04/10/2017] [Indexed: 01/13/2023] Open
Abstract
Coral reefs are one of the most productive ecosystems on the planet, with primary production rates compared to that of rain forests. Benthic organisms release 10-50% of their gross organic production as mucus that stimulates heterotrophic microbial metabolism in the water column. As a result, coral reef microbes grow up to 50 times faster than open ocean communities. Anthropogenic disturbances cause once coral-dominated reefs to become dominated by fleshy organisms, with several outcomes for trophic relationships. Here we review microbial processes implicated in organic carbon flux in coral reefs displaying species phase shifts. The first section presents microbial players and interactions within the coral holobiont that contribute to reef carbon flow. In the second section, we identify four ecosystem-level microbial features that directly respond to benthic species phase shifts: community composition, biomass, metabolism and viral predation. The third section discusses the significance of microbial consumption of benthic organic matter to reef trophic relationships. In the fourth section, we propose that the 'microbial phase shifts' discussed here are conducive to lower resilience, facilitating the transition to new degradation states in coral reefs.
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Affiliation(s)
- Cynthia B Silveira
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil.,Biology Department, San Diego State University, 5500 Campanille Dr, San Diego, CA 92182, USA
| | - Giselle S Cavalcanti
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil.,Biology Department, San Diego State University, 5500 Campanille Dr, San Diego, CA 92182, USA
| | - Juline M Walter
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil
| | - Arthur W Silva-Lima
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil
| | - Elizabeth A Dinsdale
- Biology Department, San Diego State University, 5500 Campanille Dr, San Diego, CA 92182, USA
| | - David G Bourne
- College of Science and Engineering, James Cook University and Australian Institute of Marine Science, Townsville, Queensland 4810, Australia
| | - Cristiane C Thompson
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil
| | - Fabiano L Thompson
- Institute of Biology and COPPE/SAGE, Federal University of Rio de Janeiro. Av. Carlos Chagas Filho, 373, Cidade Universitária, RJ 21941-599, Brazil
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Hesse U, van Heusden P, Kirby BM, Olonade I, van Zyl LJ, Trindade M. Virome Assembly and Annotation: A Surprise in the Namib Desert. Front Microbiol 2017; 8:13. [PMID: 28167933 PMCID: PMC5253355 DOI: 10.3389/fmicb.2017.00013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/03/2017] [Indexed: 11/13/2022] Open
Abstract
Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further complicated by the mosaic nature of viral genomes. In this paper, we focus on biocomputational aspects of virome analysis, emphasizing latent pitfalls in sequence annotation. Using simulated viromes that mimic environmental data challenges we assessed the performance of five assemblers (CLC-Workbench, IDBA-UD, SPAdes, RayMeta, ABySS). Individual analyses of relevant scaffold length fractions revealed shortcomings of some programs in reconstruction of viral genomes with excessive read coverage (IDBA-UD, RayMeta), and in accurate assembly of scaffolds ≥50 kb (SPAdes, RayMeta, ABySS). The CLC-Workbench assembler performed best in terms of genome recovery (including highly covered genomes) and correct reconstruction of large scaffolds; and was used to assemble a virome from a copper rich site in the Namib Desert. We found that scaffold network analysis and cluster-specific read reassembly improved reconstruction of sequences with excessive read coverage, and that strict data filtering for non-viral sequences prior to downstream analyses was essential. In this study we describe novel viral genomes identified in the Namib Desert copper site virome. Taxonomic affiliations of diverse proteins in the dataset and phylogenetic analyses of circovirus-like proteins indicated links to the marine habitat. Considering additional evidence from this dataset we hypothesize that viruses may have been carried from the Atlantic Ocean into the Namib Desert by fog and wind, highlighting the impact of the extended environment on an investigated niche in metagenome studies.
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Affiliation(s)
- Uljana Hesse
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
- South African National Bioinformatics Institute, University of the Western CapeBellville, South Africa
| | - Peter van Heusden
- South African National Bioinformatics Institute, University of the Western CapeBellville, South Africa
| | - Bronwyn M. Kirby
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
| | - Israel Olonade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
| | - Leonardo J. van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western CapeBellville, South Africa
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7
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Carlos C, Pereira LB, Ottoboni LMM. Comparative genomics of Paracoccus sp. SM22M-07 isolated from coral mucus: insights into bacteria-host interactions. Curr Genet 2016; 63:509-518. [PMID: 27796486 DOI: 10.1007/s00294-016-0658-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
One of the main goals of coral microbiology is to understand the ways in which coral-bacteria associations are established and maintained. This work describes the sequencing of the genome of Paracoccus sp. SM22M-07 isolated from the mucus of the endemic Brazilian coral species Mussismilia hispida. Comparative analysis was used to identify unique genomic features of SM22M-07 that might be involved in its adaptation to the marine ecosystem and the nutrient-rich environment provided by coral mucus, as well as in the establishment and strengthening of the interaction with the host. These features included genes related to the type IV protein secretion system, erythritol catabolism, and succinoglycan biosynthesis. We experimentally confirmed the production of succinoglycan by Paracoccus sp. SM22M-07 and we hypothesize that it may be involved in the association of the bacterium with coral surfaces.
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Affiliation(s)
- Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53703, USA.
| | - Letícia Bianca Pereira
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (UNICAMP), C. P. 6010, Campinas, SP, 13083-875, Brazil
| | - Laura Maria Mariscal Ottoboni
- Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (UNICAMP), C. P. 6010, Campinas, SP, 13083-875, Brazil
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Tangherlini M, Dell'Anno A, Zeigler Allen L, Riccioni G, Corinaldesi C. Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses. Sci Rep 2016; 6:28428. [PMID: 27329207 PMCID: PMC4916513 DOI: 10.1038/srep28428] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022] Open
Abstract
In benthic deep-sea ecosystems, which represent the largest biome on Earth, viruses have a recognised key ecological role, but their diversity is still largely unknown. Identifying the taxonomic composition of viruses is crucial for understanding virus-host interactions, their role in food web functioning and evolutionary processes. Here, we compared the performance of various bioinformatic tools (BLAST, MG-RAST, NBC, VMGAP, MetaVir, VIROME) for analysing the viral taxonomic composition in simulated viromes and viral metagenomes from different benthic deep-sea ecosystems. The analyses of simulated viromes indicate that all the BLAST tools, followed by MetaVir and VMGAP, are more reliable in the affiliation of viral sequences and strains. When analysing the environmental viromes, tBLASTx, MetaVir, VMGAP and VIROME showed a similar efficiency of sequence annotation; however, MetaVir and tBLASTx identified a higher number of viral strains. These latter tools also identified a wider range of viral families than the others, providing a wider view of viral taxonomic diversity in benthic deep-sea ecosystems. Our findings highlight strengths and weaknesses of available bioinformatic tools for investigating the taxonomic diversity of viruses in benthic ecosystems in order to improve our comprehension of viral diversity in the oceans and its relationships with host diversity and ecosystem functioning.
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Affiliation(s)
- M Tangherlini
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - A Dell'Anno
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - L Zeigler Allen
- Microbial and Environmental Genomics, J Craig Venter Institute, San Diego, CA, USA
| | - G Riccioni
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - C Corinaldesi
- Department of Environmental and Life Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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Alex A, Antunes A. Whole Genome Sequencing of the Symbiont Pseudovibrio sp. from the Intertidal Marine Sponge Polymastia penicillus Revealed a Gene Repertoire for Host-Switching Permissive Lifestyle. Genome Biol Evol 2015; 7:3022-32. [PMID: 26519859 PMCID: PMC5635592 DOI: 10.1093/gbe/evv199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Sponges harbor a complex consortium of microbial communities living in symbiotic relationship benefiting each other through the integration of metabolites. The mechanisms influencing a successful microbial association with a sponge partner are yet to be fully understood. Here, we sequenced the genome of Pseudovibrio sp. POLY-S9 strain isolated from the intertidal marine sponge Polymastia penicillus sampled from the Atlantic coast of Portugal to identify the genomic features favoring the symbiotic relationship. The draft genome revealed an exceptionally large genome size of 6.6 Mbp compared with the previously reported genomes of the genus Pseudovibrio isolated from a coral and a sponge larva. Our genomic study detected the presence of several biosynthetic gene clusters—polyketide synthase, nonribosomal peptide synthetase and siderophore—affirming the potential ability of the genus Pseudovibrio to produce a wide variety of metabolic compounds. Moreover, we identified a repertoire of genes encoding adaptive symbioses factors (eukaryotic-like proteins), such as the ankyrin repeats, tetratrico peptide repeats, and Sel1 repeats that improve the attachment to the eukaryotic hosts and the avoidance of the host’s immune response. The genome also harbored a large number of mobile elements (∼5%) and gene transfer agents, which explains the massive genome expansion and suggests a possible mechanism of horizontal gene transfer. In conclusion, the genome of POLY-S9 exhibited an increase in size, number of mobile DNA, multiple metabolite gene clusters, and secretion systems, likely to influence the genome diversification and the evolvability.
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Affiliation(s)
- Anoop Alex
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIMAR/CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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