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Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges

2014Journal article Open access
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dc.contributor.authorHardoim, Cristiane
dc.contributor.authorCardinale, Massimiliano
dc.contributor.authorCucio, Ana C. B.
dc.contributor.authorEsteves, Ana
dc.contributor.authorBerg, Gabriele
dc.contributor.authorXavier, Joana R.
dc.contributor.authorCox, C. J.
dc.contributor.authorCosta, Rodrigo
dc.date.accessioned2018-12-07T14:53:08Z
dc.date.available2018-12-07T14:53:08Z
dc.date.issued2014
dc.description.abstractComplex and distinct bacterial communities inhabit marine sponges and are believed to be essential to host survival, but our present-day inability to domesticate sponge symbionts in the laboratory hinders our access to the full metabolic breadth of these microbial consortia. We address bacterial cultivation bias in marine sponges using a procedure that enables direct comparison between cultivated and uncultivated symbiont community structures. Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and lrcinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. Whereas cultivation-independent methods revealed species-specific bacterial community structures in these hosts, cultivation-dependent methods resulted in equivalent community assemblages from both species. Between 15 and 18 bacterial phyla were found in S. spinosulus and I. variabilis using cultivation-independent methods. However, Alphaproteobacteria and Gammaproteobacteria dominated the cultivation-dependent bacterial community. While cultivation-independent methods revealed about 200 and 220 operational taxonomic units (OTUs, 97% gene similarity) in S. spinosulus and I. variabilis, respectively, only 33 and 39 OTUs were found in these species via culturing. Nevertheless, around 50% of all cultured OTUs escaped detection by cultivation-independent methods, indicating that standard cultivation makes otherwise host-specific bacterial communities similar by selectively enriching for rarer and generalist symbionts. This study sheds new light on the diversity spectrum encompassed by cultivated and uncultivated sponge-associated bacteria. Moreover, it highlights the need to develop alternative culturing technologies to capture the dominant sponge symbiont fraction that currently remains recalcitrant to laboratory manipulation.
dc.description.sponsorshipPortuguese Foundation for Science and Technology (FCT) [PTDC/MAR/101431/2008]; FCT [SFRH/BD/60873/2009]; FCT postdoctoral fellowship [SFRII/BPD/62946/2009]; European Regional Development Fund (ERDF) through the COMPETE (Operational Competitiveness) Programme; FCT under the project [PEst-C/MAR/LA0015/2011]; FCT-funded research project [PTDC/BIA-MIC/3865/2012]
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.3389/fmicb.2014.00611
dc.identifier.issn1664-302X
dc.identifier.urihttp://hdl.handle.net/10400.1/11365
dc.language.isoeng
dc.peerreviewedyes
dc.publisherFrontiers Research Foundation
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectTargeted Oligonucleotide Probes
dc.subjectCandidate Phylum Poribacteria
dc.subjectCell genomics reveals
dc.subject16S Ribosomal-Rna
dc.subjectIn-Situ detection
dc.subjectMicrobial community
dc.subjectCoastal waters
dc.subjectAplysina-Fulva
dc.subjectDiversity
dc.subjectMicroorganisms
dc.titleEffects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges
dc.typejournal article
dspace.entity.typePublication
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FMAR%2F101431%2F2008/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/SFRH/SFRH%2FBD%2F60873%2F2009/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBIA-MIC%2F3865%2F2012/PT
oaire.citation.startPage611
oaire.citation.titleFrontiers in Microbiology
oaire.citation.volume5
oaire.fundingStream3599-PPCDT
oaire.fundingStreamSFRH
oaire.fundingStream3599-PPCDT
person.familyNameHardoim
person.familyNameEsteves
person.familyNameCox
person.familyNameda Silva Costa
person.givenNameCristiane
person.givenNameAna
person.givenNameCymon
person.givenNameRodrigo
person.identifier293165
person.identifier115920
person.identifier.ciencia-id6B15-9771-1D04
person.identifier.ciencia-id5917-D500-D251
person.identifier.orcid0000-0003-4650-0177
person.identifier.orcid0000-0002-9614-0635
person.identifier.orcid0000-0002-4927-979X
person.identifier.orcid0000-0002-5932-4101
person.identifier.ridD-4544-2015
person.identifier.ridD-1303-2012
person.identifier.ridN-7274-2013
person.identifier.scopus-author-id22950697100
person.identifier.scopus-author-id7402112716
person.identifier.scopus-author-id7203063627
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccess
rcaap.typearticle
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