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.
Monochloramine (MCA) is a widely
used secondary disinfectant to
suppress microbial growth in drinking water distribution systems.
In monochloraminated drinking water, a significant amount of extracellular
DNA (eDNA) has been reported, which has many implications ranging
from obscuring DNA-based drinking water microbiome analyses to posing
potential health concerns. To address this, it is imperative for us
to know the origin of the eDNA in drinking water. Using Pseudomonas aeruginosa as a model organism, we report
for the first time that MCA induces the release of nucleic acids from
both biofilms and planktonic cells. Upon exposure to 2 mg/L MCA, massive
release of DNA from suspended cells in both MilliQ water and 0.9%
NaCl was directly visualized using live cell imaging in a CellASIC
ONIX2 microfluidic system. Exposing established biofilms to MCA also
resulted in DNA release from the biofilms, which was confirmed by
increased detection of eDNA in the effluent. Intriguingly, massive
release of RNA was also observed, and the extracellular RNA (eRNA)
was also found to persist in water for days. Sequencing analyses of
the eDNA revealed that it could be used to assemble the whole genome
of the model organism, while in the water, certain fragments of the
genome were more persistent than others. RNA sequencing showed that
the eRNA contains non-coding RNA and mRNA, implying its role as a
possible signaling molecule in environmental systems and a snapshot
of the past metabolic state of the bacterial cells.
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