The masking effect of extracellular DNA and robustness of intracellular DNA in anaerobic digester NGS studies: A discriminatory study of the total DNA pool. Issue 2 (3rd December 2020)

• Record Type: Journal Article
• Authors: Nagler, Magdalena; Podmirseg, Sabine Marie; Mayr, Markus; Ascher‐Jenull, Judith; Insam, Heribert
• Is Part Of: Molecular ecology. Volume 30:Issue 2(2021)
• Page Start: 438
• Page End: 450
• Publication Date: 2020-12-03
• Subjects: 16S rRNA sequencing -- anaerobic digestion -- exDNA -- iDNA -- methanogenic archaea; Molecular ecology -- Periodicals; Molecular population biology -- Periodicals; 576
• DOI: 10.1111/mec.15740
• Languages: English
• ISSNs: 0962-1083

Abstract

Abstract: Most commonly, next generation sequencing‐based microbiome studies are performed on the total DNA (totDNA) pool; however, this consists of extracellular‐ (exDNA) and intracellular (iDNA) DNA fractions. By investigating the microbiomes of different anaerobic digesters over time, we found that totDNA suggested lower species richness considering all and/or only common species and yielded fewer unique reads as compared to iDNA. Additionally, exDNA‐derived sequences were more similar to those from totDNA than from iDNA and, finally, iDNA showed the best performance in tracking temporal changes in microbial communities. We postulate that abundant sequences present within the exDNA fraction mask the overall results of totDNA and provide evidence that exDNA has the potential to qualitatively bias microbiome studies at least in the anaerobic digester environment as it contains information about cells that were lysed hours or days ago. iDNA, however, was found to be more appropriate in providing reliable genetic information about potentially alive as well as rare microbes within the target habitat.