Alice Lemoinne, Guillaume Dirberg, Myriam Georges, Tony RobinetPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"
<p style="text-align: justify;">Following the development of high-throughput sequencers, environmental prokaryotic communities are usually described by metabarcoding with genetic markers on the 16S domain. However, short-read sequencing encounters a limitation in phylogenetic coverage and taxonomic resolution, due to the primers choice and read length. On these critical points, nanopore sequencing, a rising technology, suitable for long-read metabarcoding, was much undervalued because of its relatively higher error rate per read. Here we compared the prokaryotic community structure in a mock community and 52 sediment samples from two contrasted mangrove sites, described by short-reads on 16SV4-V5 marker (ca. 0.4kpb) analyzed by Illumina sequencing (MiSeq, V3), with those described by long-reads on bacterial nearly complete 16S (ca. 1.5 kpb) analyzed by Oxford Nanopore (MinION, R9.2). Short- and long-reads retrieved all the bacterial genera from the mock, although both showing similar deviations from the awaited proportions. From the sediment samples, with a coverage-based rarefaction of reads and after singletons filtering, co-inertia and Procrustean tests showed that bacterial community structures inferred from short- and long-reads were significantly similar, showing both a comparable contrast between sites and a coherent sea-land orientation within sites. In our dataset, 84.7 and 98.8% of the short-reads were assigned strictly to the same species and genus, respectively, than those detected by long-reads. Primer specificities of long-16S allowed it to detect 92.2% of the 309 families and 87.7% of the 448 genera that were detected by the short 16SV4-V5. Long-reads recorded 973 additional taxa not detected by short-reads, among which 91.7% were identified to the genus rank, some belonging to 11 exclusive phyla, albeit accounting for only 0.2% of total long-reads.</p>
microbial metabarcoding, environmental DNA, methods, primers, diversity
Rasmus Kirkegaard, Petra Pjevac, Craig Herbold, Kate Howell, Sebastien Massart, Nika Pende, Willem Stock, Vojtech Tlaskal, Olivier Gros, Mina Bizic, Aymé Spor, Konstantinos (Kostas) Kormas, A. Murat Eren, Graeme Nicol, Nadine Praeg
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