Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Abstract

Coastal lagoons are an important habitat for endemic and threatened species in California that have suffered impacts from urbanization and increased drought. Environmental DNA has been promoted as a way to aid in the monitoring of biological communities, but much remains to be understood on the biases introduced by different protocols meant to overcome challenges presented by unique systems under study. Turbid water is one methodologic challenge to eDNA recovery in these systems as it quickly clogs filters, preventing timely processing of samples. We investigated biases in community composition produced by two solutions to overcome slow filtration due to turbidity: freezing of water prior to filtration (for storage purposes and long-term processing), and use of sediment (as opposed to water samples). Bias assessments of community composition in downstream eDNA analysis was conducted for two sets of primers, 12S (fish) and 16S (bacteria and archaea). Our results show that freezing water prior to filtration had no effects on community composition for either primer, even when using a filter of larger pore size (3 μm), and therefore it is a viable approach in this system for comparison of water borne fish, bacteria and archaea. However, the 16S primer showed significantly different community composition in sediments compared to water samples, although still recovering eDNA of organisms from the water column. Sediment sample replicates were heterogeneous, and therefore increasing the number of replicates would be recommended for similar habitats.

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

“…For the 12S and 16S primers, we were able to reach our threshold of 25 000 reads/sample in most cases, while that was not the case for all except one sample of the CO1 primer. Because of this limitation on the number of reads/sample, the CO1 metabarcode will not be discussed further in the main paper (but check the supplemental material for more details, (Turba et al, 2023b).…”

“…Scripts, code and data are available online: https://doi.org/doi:10.5068/D1BQ25 (Turba et al, 2023a). Supplementary information is available online: https://doi.org/10.5281/zenodo.7762005 (Turba et al, 2023b)…”