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Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host-associated and free-living Aquimarina (Bacteroidetes, Flavobacteriaceae) species

2019-11Journal article Open access
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dc.contributor.authorSilva, Sandra G.
dc.contributor.authorBlom, Jochen
dc.contributor.authorKeller-Costa, Tina
dc.contributor.authorCosta, Rodrigo
dc.date.accessioned2020-07-24T10:51:48Z
dc.date.available2020-07-24T10:51:48Z
dc.date.issued2019-11
dc.description.abstractThis study determines the natural product biosynthesis and full coding potential within the bacterial genus Aquimarina. Using comprehensive phylogenomics and functional genomics, we reveal that phylogeny instead of isolation source [host-associated (HA) vs. free-living (FL) habitats] primarily shape the inferred metabolism of Aquimarina species. These can be coherently organized into three major functional clusters, each presenting distinct natural product biosynthesis profiles suggesting that evolutionary trajectories strongly underpin their secondary metabolite repertoire and presumed bioactivities. Aquimarina spp. are highly versatile bacteria equipped to colonize HA and FL microniches, eventually displaying opportunistic behaviour, owing to their shared ability to produce multiple glycoside hydrolases from diverse families. We furthermore uncover previously underestimated, and highly complex secondary metabolism for the genus by detecting 928 biosynthetic gene clusters (BGCs) across all genomes, grouped in 439 BGC families, with polyketide synthases (PKSs), terpene synthases and non-ribosomal peptide synthetases (NRPSs) ranking as the most frequent BGCs encoding drug-like candidates. We demonstrate that the recently described cuniculene (trans-AT PKS) BGC is conserved among, and specific to, the here delineated A. megaterium-macrocephali-atlantica phylogenomic clade. Our findings provide a timely and in-depth perspective of an under-explored yet emerging keystone taxon in the cycling of organic matter and secondary metabolite production in marine ecosystems.
dc.description.sponsorshipPortuguese Science and Technology Foundation (FCT)Portuguese Foundation for Science and Technology [PTDC/MAR-BIO/1547/2014, UID/BIO/04565/2013]
dc.description.sponsorshipInstitute for Bioengineering and Biosciences, Programa Operacional Regional de Lisboa 2020 [007317]
dc.description.sponsorshipFCTPortuguese Foundation for Science and Technology [PD/BD/143029/2018]
dc.identifier.doi10.1111/1462-2920.14747
dc.identifier.issn1462-2912
dc.identifier.urihttp://hdl.handle.net/10400.1/14272
dc.language.isoeng
dc.peerreviewedyes
dc.publisherWiley
dc.subjectLatercula Lewin 1969
dc.subjectSp Nov.
dc.subjectEmended description
dc.subjectBacterial symbiont
dc.subjectGene-cluster
dc.subjectSp. Nov.
dc.subjectDisease
dc.subjectReclassification
dc.subjectDiversity
dc.subjectSoftware
dc.titleComparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host-associated and free-living Aquimarina (Bacteroidetes, Flavobacteriaceae) species
dc.typejournal article
dspace.entity.typePublication
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/5876/UID%2FBIO%2F04565%2F2013/PT
oaire.citation.endPage4019
oaire.citation.issue11
oaire.citation.startPage4002
oaire.citation.titleEnvironmental Microbiology
oaire.citation.volume21
oaire.fundingStream5876
person.familyNameda Silva Costa
person.givenNameRodrigo
person.identifier115920
person.identifier.ciencia-id5917-D500-D251
person.identifier.orcid0000-0002-5932-4101
person.identifier.ridN-7274-2013
person.identifier.scopus-author-id7203063627
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccess
rcaap.typearticle
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relation.isAuthorOfPublication.latestForDiscovery4495127c-16f2-4231-9fc1-b471c661036b
relation.isProjectOfPublicationfd301fb7-cd44-4ebc-9a8f-3406cf796e3a
relation.isProjectOfPublication.latestForDiscoveryfd301fb7-cd44-4ebc-9a8f-3406cf796e3a

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