Environmental DNA (eDNA) Shedding and Decay Rates to Model Freshwater Mussel eDNA Transport in a River

Freshwater mussels are vital components of stream ecosystems, yet remain threatened. Thus, timely and accurate species counts are critical for proper conservation and management. Mussels live in stream sediments and can be challenging to survey given constraints related to water depth, flow, and time of year. The use of environmental DNA (eDNA) to monitor mussel distributions and diversity is a promising tool. Before it can be used as a monitoring tool, however, we need to know how much eDNA mussels shed into their environment and how long the eDNA persists. Here, we present a novel application of eDNA to estimate both the presence/absence and abundance of a freshwater mussel species, <i>Lampsilis siliquoidea</i>. The eDNA shedding and decay rates reported within are the first for freshwater mussels. We determined that eDNA shedding was statistically similar across mussel densities, but that first-order decay constants varied between experimental treatments. Finally, we effectively modeled downstream transport of eDNA and present a model that can be used as a complementary tool to estimate mussel density. Our results suggest that eDNA has the potential to be a complementary tool to survey mussels and enhance current efforts to monitor and protect freshwater mussel biodiversity

Data from: Persistence of marine fish environmental DNA and the influence of sunlight

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

metadata file

List of samples sequenced with library and tag combinations; to be paired to OTU tabl

Oceans in Peril: Grand Challenges in Applied Water Quality Research for the 21st Century

Oceans cover most of the planet and 60% of the world\u27s population lives near the coast. Anthropogenic activities along coastlines and in the open ocean have placed the oceans in peril. According to a Pew Oceans Commission Report, among the greatest threats to the ocean are land-based runoff from coastal development, nutrient pollution, overfishing, and invasive species. Here, we describe threats due to microbial, nutrient, chemical, and plastic pollution in addition to declining biodiversity and describe fundamental and applied research needed to mitigate the threats. While the research needs are diverse, we identify several research foci that transcend individual threats: monitoring, fate and transport studies, modeling, innovative natural and engineered treatment systems, and toxicity and health studies. Research within the environmental engineering and science community that addresses these needs will contribute to improving ocean health

Results of GEE model on presence of 8 genera over time.

<p>Results of GEE model on presence of 8 genera over time.</p

OTU table after bioinformatics pipeline

Table of OTUs (rows) by sample (columns) after bioinformatics pipeline. See "OTUs fasta file" for representative sequences of each OTU. See "metadata file" to match library and tag number of samples to sample names

Persistence of marine fish environmental DNA and the influence of sunlight

<div><p>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 <i>Scomber japonicus</i> qPCR assay and a marine fish-specific 12S rRNA PCR assay. The latter was subsequently sequenced using a metabarcoding approach. <i>S</i>. <i>japonicus</i> 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.</p></div

Library 2 fastq file read 1

Library 2 fastq file read