Novel trends of genome evolution in highly complex tropical sponge microbiomes

Lade...
Vorschaubild
Datum
2022
Autor:innen
Carlson, David E.
Low, Jun Siong
Thacker, Robert W.
Herausgeber:innen
Kontakt
ISSN der Zeitschrift
eISSN
item.preview.dc.identifier.isbn
Bibliografische Daten
Verlag
Schriftenreihe
URI (zitierfähiger Link)
DOI (zitierfähiger Link)
ArXiv-ID
Internationale Patentnummer
Link zur Lizenz
EU-Projektnummer
Projekt
Open Access-Veröffentlichung
Sammlungen
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published
Erschienen in
Microbiome ; 10 (2022), 1. - 164. - BioMed Central. - eISSN 2049-2618
Zusammenfassung
Background
Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes—the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism.

Results
A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts’ molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes.

Conclusions
These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes.
Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
570 Biowissenschaften, Biologie
Schlagwörter
Sterols, Metagenomics, Microbiome, Sponge, Ircinia, Marine, Tropical
Konferenz
Rezension
undefined / . - undefined, undefined. - (undefined; undefined)
Zitieren
ISO 690KELLY, Joseph B., David E. CARLSON, Jun Siong LOW, Robert W. THACKER, 2022. Novel trends of genome evolution in highly complex tropical sponge microbiomes. In: Microbiome. BioMed Central. 10(1), 164. eISSN 2049-2618. Available under: doi: 10.1186/s40168-022-01359-z
BibTex
@article{Kelly2022-10-24Novel-59081,
  year={2022},
  doi={10.1186/s40168-022-01359-z},
  title={Novel trends of genome evolution in highly complex tropical sponge microbiomes},
  number={1},
  volume={10},
  journal={Microbiome},
  author={Kelly, Joseph B. and Carlson, David E. and Low, Jun Siong and Thacker, Robert W.},
  note={Article Number: 164}
}
RDF
<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/59081">
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/59081/1/Kelly_2-bcafeqrkbnj23.pdf"/>
    <dcterms:abstract xml:lang="eng">Background&lt;br /&gt;Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes—the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism.&lt;br /&gt;&lt;br /&gt;Results&lt;br /&gt;A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts’ molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes.&lt;br /&gt;&lt;br /&gt;Conclusions&lt;br /&gt;These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes.</dcterms:abstract>
    <dc:language>eng</dc:language>
    <dcterms:title>Novel trends of genome evolution in highly complex tropical sponge microbiomes</dcterms:title>
    <dc:contributor>Low, Jun Siong</dc:contributor>
    <dc:creator>Low, Jun Siong</dc:creator>
    <dcterms:rights rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:creator>Carlson, David E.</dc:creator>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dcterms:issued>2022-10-24</dcterms:issued>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-11-09T07:55:10Z</dc:date>
    <dc:creator>Thacker, Robert W.</dc:creator>
    <dc:contributor>Kelly, Joseph B.</dc:contributor>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/59081"/>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/59081/1/Kelly_2-bcafeqrkbnj23.pdf"/>
    <dc:rights>Attribution 4.0 International</dc:rights>
    <dc:creator>Kelly, Joseph B.</dc:creator>
    <dc:contributor>Thacker, Robert W.</dc:contributor>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-11-09T07:55:10Z</dcterms:available>
    <dc:contributor>Carlson, David E.</dc:contributor>
  </rdf:Description>
</rdf:RDF>
Interner Vermerk
xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter
Kontakt
URL der Originalveröffentl.
Prüfdatum der URL
Prüfungsdatum der Dissertation
Finanzierungsart
Kommentar zur Publikation
Allianzlizenz
Corresponding Authors der Uni Konstanz vorhanden
Internationale Co-Autor:innen
Universitätsbibliographie
Ja
Begutachtet
Ja