Environmental nucleic acids: a field-based comparison for monitoring freshwater habitats using eDNA and eRNA

Nucleic acids released by organisms and isolated from environmental
substrates are increasingly being used for molecular biomonitoring. While
environmental DNA (eDNA) has received attention recently, the potential of
environmental RNA as a biomonitoring tool remains less explored. Several
recent studies using paired DNA and RNA metabarcoding of bulk samples
suggest that RNA might better reflect “metabolically active” parts of the
community. However, such studies mainly capture organismal eDNA and eRNA.
For larger eukaryotes, isolation of extra-organismal RNA will be
important, but viability needs to be examined in a field-based setting. In
this study we evaluate (a) whether extra-organismal eRNA release from
macroeukaryotes can be detected given its supposedly rapid degradation,
and (b) if the same field collection methods for eDNA can be applied to
eRNA. We collected eDNA and eRNA from water in lakes where fish community
composition is well documented, enabling a comparison between the two
nucleic acids in two different seasons with monitoring using conventional
methods. We found that eRNA is released from macroeukaryotes and can be
filtered from water and metabarcoded in a similar manner as eDNA to
reliably provide species composition information. eRNA had a small but
significantly greater true positive rate than eDNA, indicating that it
correctly detects more species known to exist in the lakes. Given
relatively small differences between the two molecules in describing fish
community composition, we conclude that if eRNA provides significant
advantages in terms of lability, it is a strong candidate to add to the
suite of molecular monitoring tools.