Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium

Detalhes bibliográficos
Autor(a) principal: Karimi, Elham
Data de Publicação: 2017
Outros Autores: Ramos, Miguel, Gonçalves, Jorge M.S., Xavier, Joana R., Reis, Margarida P. Reis, Costa, Rodrigo
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10400.5/14604
Resumo: Original Research
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spelling Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortiumhost-microbe interactionsmarine spongesmicrobiomenext-generation sequencingsymbiosisOriginal ResearchCurrent knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n D 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis “endosymbiome” as a distinct consortium of uncultured prokaryotes displaying a likely “sit-and-wait” strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe–microbe and host–microbe gene transfer amenabilityXavier Perret (ed.)Repositório da Universidade de LisboaKarimi, ElhamRamos, MiguelGonçalves, Jorge M.S.Xavier, Joana R.Reis, Margarida P. ReisCosta, Rodrigo2018-01-02T14:21:51Z20172017-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.5/14604engKarimi E, Ramos M, Gonçalves JMS, Xavier JR, Reis MP and Costa R (2017) Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium. Front. Microbiol. 8:249910.3389/fmicb.2017.02499info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-03-06T14:44:38Zoai:www.repository.utl.pt:10400.5/14604Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T17:00:26.089986Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium
title Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium
spellingShingle Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium
Karimi, Elham
host-microbe interactions
marine sponges
microbiome
next-generation sequencing
symbiosis
title_short Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium
title_full Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium
title_fullStr Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium
title_full_unstemmed Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium
title_sort Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortium
author Karimi, Elham
author_facet Karimi, Elham
Ramos, Miguel
Gonçalves, Jorge M.S.
Xavier, Joana R.
Reis, Margarida P. Reis
Costa, Rodrigo
author_role author
author2 Ramos, Miguel
Gonçalves, Jorge M.S.
Xavier, Joana R.
Reis, Margarida P. Reis
Costa, Rodrigo
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Karimi, Elham
Ramos, Miguel
Gonçalves, Jorge M.S.
Xavier, Joana R.
Reis, Margarida P. Reis
Costa, Rodrigo
dc.subject.por.fl_str_mv host-microbe interactions
marine sponges
microbiome
next-generation sequencing
symbiosis
topic host-microbe interactions
marine sponges
microbiome
next-generation sequencing
symbiosis
description Original Research
publishDate 2017
dc.date.none.fl_str_mv 2017
2017-01-01T00:00:00Z
2018-01-02T14:21:51Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10400.5/14604
url http://hdl.handle.net/10400.5/14604
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Karimi E, Ramos M, Gonçalves JMS, Xavier JR, Reis MP and Costa R (2017) Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium. Front. Microbiol. 8:2499
10.3389/fmicb.2017.02499
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Xavier Perret (ed.)
publisher.none.fl_str_mv Xavier Perret (ed.)
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
_version_ 1799131091794132992

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