Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon
Identifieur interne : 000035 ( Main/Merge ); précédent : 000034; suivant : 000036Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon
Auteurs : Riccardo Rosselli [Italie] ; Ottavia Romoli [Italie] ; Nicola Vitulo [Italie] ; Alessandro Vezzi [Italie] ; Stefano Campanaro [Italie] ; Fabio De Pascale [Italie] ; Riccardo Schiavon [Italie] ; Maurizio Tiarca [Italie] ; Fabio Poletto [Italie] ; Giuseppe Concheri [Italie] ; Giorgio Valle [Italie] ; Andrea Squartini [Italie]Source :
- Scientific Reports [ 2045-2322 ] ; 2016.
Abstract
The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies.
Url:
DOI: 10.1038/srep32165
PubMed: 27577787
PubMed Central: 5006002
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strict</wicri:regionArea></affiliation></author><author><name sortKey="Valle, Giorgio" sort="Valle, Giorgio" uniqKey="Valle G" first="Giorgio" last="Valle">Giorgio Valle</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Department of Biology, University of Padova</institution>, Padova,<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Squartini, Andrea" sort="Squartini, Andrea" uniqKey="Squartini A" first="Andrea" last="Squartini">Andrea Squartini</name><affiliation wicri:level="1"><nlm:aff id="a4"><institution>Department of Agronomy Animals, Food, Natural Resources and Environment, DAFNAE, University of Padova</institution>, Legnaro (Padova)<country>Italy</country></nlm:aff><country xml:lang="fr">Italie</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Woese, C" uniqKey="Woese C">C. Woese</name></author><author><name sortKey="Fox, G" uniqKey="Fox G">G. Fox</name></author><author><name sortKey="Zablen, L" uniqKey="Zablen L">L. Zablen</name></author><author><name sortKey="Uchida, T" uniqKey="Uchida T">T. Uchida</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Woese, C R" uniqKey="Woese C">C. R. Woese</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rzhetsky, A" uniqKey="Rzhetsky A">A. 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Fox</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brown, C T" uniqKey="Brown C">C. T. Brown</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Campagna, D" uniqKey="Campagna D">D. Campagna</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, W" uniqKey="Li W">W. Li</name></author><author><name sortKey="Godzik, A" uniqKey="Godzik A">A. Godzik</name></author></analytic></biblStruct></listBibl></div1></back></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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