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Title: Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection
Authors: Leontidou, Kleopatra; Abad-Recio, Ion L.; Rubel, Verena and Filker, Sabine; Daeumer, Martin; Thielen, Alexander; Lanzen, Anders; Stoeck, Thorsten
Citation: ENVIRONMENTAL MICROBIOLOGY, 2023, 25, 3484-3501
Abstract: Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one-fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)-PCR-based assay that amplifies seven out of the nine hypervariable regions of the 16S rRNA gene, to interrogate bacterial communities in sediment samples collected from different coastal marine sites with an impact gradient. In parallel, we employed a traditional one-fragment analysis of the hypervariable V3-V4 region to investigate whether the RC-PCR reveals more of the `unseen' diversity obtained by the one-fragment approach. As a benchmark for the full deck of diversity, we subjected the samples to PCR-free metagenomic sequencing. None of the two PCR-based approaches recorded the full taxonomic repertoire obtained from the metagenomics datasets. However, the RC-PCR approach detected 2.8 times more bacterial genera compared to the near-saturation sequenced V3-V4 samples. RC-PCR is an ideal compromise between the standard one-fragment approach and metagenomics sequencing and may guide future environmental sequencing studies, in which bacterial diversity is a central subject.
Issue Date: 2023
Publisher: WILEY
Type: Article; Early Access
DOI: 10.1111/1462-2920.16530
ISSN: 1462-2912
E-ISSN: 1462-2920
Funder: This study was supported by a grant of the Deutsche Forschungsgemeinschaft for a joined project between the RPTU Kaiserslautern-Landau, awarded to TS and SF (grants STO 414/19-1 and Fi 2089/3-1) and AZTI. Furthermore, we thank Thomas A. Wilding of SAMS (Sc [STO 414/19-1, Fi 2089/3-1]
Deutsche Forschungsgemeinschaft
Appears in Publication types:Artículos científicos

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