A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples

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dc.contributor.authorPérez, V.
dc.contributor.authorLiu, Y.
dc.contributor.authorHengst, M.B.
dc.contributor.authorWeyrich, L.S.
dc.date.issued2022
dc.description.abstractHigh Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol–chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.
dc.description.statementofresponsibilityVilma Pérez, Yichen Liu, Martha B. Hengst, and Laura S. Weyrich
dc.identifier.citationMicroorganisms, 2022; 10(8):1623-1-1623-29
dc.identifier.doi10.3390/microorganisms10081623
dc.identifier.issn2076-2607
dc.identifier.issn2076-2607
dc.identifier.urihttps://hdl.handle.net/2440/136505
dc.language.isoen
dc.publisherMDPI
dc.relation.granthttp://purl.org/au-research/grants/arc/FT180100407
dc.rights© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).
dc.source.urihttps://doi.org/10.3390/microorganisms10081623
dc.subjectenvironmental genomics
dc.subjectancient DNA
dc.subjectsedaDNA
dc.subjectsoil
dc.subjectpaleomicrobiome
dc.titleA Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples
dc.typeJournal article
pubs.publication-statusPublished

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