Abstract
Harnessing information encoded in environmental DNA (eDNA) in marine waters has the potential to revolutionize marine biomonitoring. Whether using organism-specific quantitative PCR assays or metabarcoding in conjunction with amplicon sequencing, scientists have illustrated that realistic organism censuses can be inferred from eDNA. The next step is establishing ways to link information obtained from eDNA analyses to actual organism abundance. This is only possible by understanding the processes that control eDNA concentrations. The present study uses mesocosm experiments to study the persistence of eDNA in marine waters and explore the role of sunlight in modulating eDNA persistence. We seeded solute-permeable dialysis bags with water containing indigenous eDNA and suspended them in a large tank containing seawater. Bags were subjected to two treatments: half the bags were suspended near the water surface where they received high doses of sunlight, and half at depth where they received lower doses of sunlight. Bags were destructively sampled over the course of 87 hours. eDNA was extracted from water samples and used as template for a Scomber japonicus qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. S. japonicus eDNA, as measured by qPCR, exhibited first order decay with a rate constant ~0.01 hr -1 with no difference in decay rate constants between the two experimental treatments. eDNA metabarcoding identified 190 organizational taxonomic units (OTUs) assigned to varying taxonomic ranks. There was no difference in marine fish communities as measured by eDNA metabarcoding between the two experimental treatments, but there was an effect of time. Given the differences in UVA and UVB fluence received by the two experimental treatments, we conclude that sunlight is not the main driver of fish eDNA decay in the experiments. However, there are clearly temporal effects that need to be considered when interpreting information obtained using eDNA approaches.
Highlights
Marine biodiversity is threatened by stressors including climate change, rising sea surface temperature, ocean acidification, overfishing, habitat loss, and nutrient, plastic, and pollution [1,2,3,4,5,6,7,8,9]
Researchers are exploring the use of a less-invasive method of biomonitoring which entails collecting water samples to capture extra-organismal, environmental DNA that has been shed from organisms and remains suspended in the water column [16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38]. eDNA from macroorganisms is in the form of scales, tissue, mucus, blood, feces, gametes, or any other secretion [35,37]. eDNA can be free-floating or bound to particles, with preliminary studies demonstrating the poly-disperse nature of eDNA [39,40,41]
S. japonicus eDNA suspended at the surface of the tank had a decay rate constant of 0.039 +/- 0.0031 hr -1 and S. japonicus eDNA suspended at depth had a decay rate constant of 0.038 +/0.0029 hr -1 (Fig 2)
Summary
Marine biodiversity is threatened by stressors including climate change, rising sea surface temperature, ocean acidification, overfishing, habitat loss, and nutrient, plastic, and pollution [1,2,3,4,5,6,7,8,9]. Biomonitoring, monitoring of organism abundance and diversity, is traditionally conducted using visual counts by divers or remote operated vehicles (ROVs), trawl nets, fishing, or tagging of individuals [10,11] These traditional methods can disturb habitats and harm organisms [11,12,13,14] and resultant datasets are spatially and temporally sparse [15]. EDNA decay may depend on whether it is extra-cellular or cellular, or if it is particle-bound or free-floating It may depend on abiotic factors such as sunlight, water temperature, pH, and salinity [46], and biotic factors such as grazers or enzymes in the water column [46,47]. Results provide insight into the persistence of eDNA and the effect of sunlight on the decay of eDNA in marine waters
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