Extracellular DNA in Environmental Samples: Occurrence, Extraction, Quantification, and Impact on Microbial Biodiversity Assessment

Abstract

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

“…Assessing classical and extant biodiversity is conventionally anticipated by morphological and behavioral data obtained utilizing direct surveys, microscopes, binoculars, traps, and, most recently, bioacoustics [ 1 ]. These methods are often biased, intrusive, and/or predisposed by plummeting pool of taxonomic specialists for recognizing specimens [ 2 ].…”

Monochloramine Induces Release of DNA and RNA from Bacterial Cells: Quantification, Sequencing Analyses, and Implications

“…56 eDNA is known to persist in the environment for various periods depending on the type of medium, e.g., for days in water and up to thousands of years in sediments. 57 The DWDS would provide ideal conditions for its persistence. The coverage calculated based on read alignment from NGS data is prone to errors due to higher coverage obtained for genomic regions with higher GC content.…”

“…Additionally, DNA is known to be stable in a hydrophilic environment, which helps it maintain a helix structure, while hydrophobic conditions are conducive to DNA unwinding . eDNA is known to persist in the environment for various periods depending on the type of medium, e.g., for days in water and up to thousands of years in sediments . The DWDS would provide ideal conditions for its persistence.…”

Distinguishing different surface interactions for nucleotides adsorbed onto hematite and goethite particle surfaces through ATR-FTIR spectroscopy and DFT calculations

“…Previous studies have observed the preferential adsorption of the phosphate group over the nitrogenous nucleobases to various surfaces for nucleotides, oligonucleotides, and DNA. 5,[30][31][32][33][34][35] This suggests that the nucleotides are directly bound to these iron surfaces via the phosphate group. Fig.…”