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SFS Annual Meeting

Wednesday, June 5, 2024
13:30 - 15:00

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S09 Challenges and Opportunities in eDNA

13:30 - 13:45 | Salon 5/6 | TEMPERATURE INCREASES ENVIRONMENTAL DNA (EDNA) REMOVAL RATES IN FLOWING WATERS.

6/05/2024  |   13:30 - 13:45   |  Salon 5/6

TEMPERATURE INCREASES ENVIRONMENTAL DNA (EDNA) REMOVAL RATES IN FLOWING WATERS. Climate change is expected to increase temperatures in freshwater ecosystems of North America. While the positive relationship between increasing water temperature and the degradation of environmental DNA (eDNA) has been well-documented, no studies have directly measured the impact of temperature on eDNA fate and transport in streams. To investigate how elevated temperature may impact eDNA detection and removal in flowing waters, we conducted experimental additions of Common Carp (Cyprinus carpio) and Steelhead Trout (Oncorhynchus mykiss) eDNA in recirculating mesocosms (N=12) lined with cobble substrate to compare eDNA removal under varying water temperatures (20-26°C), which we hypothesized would influence biofilm colonization and microbial activity. To estimate eDNA removal from the water column, we collected water samples from each mesocosm six times over 24 hrs, and used sequential filtration to isolate eDNA particle sizes. Total eDNA removal rates were 64% higher for the mesocosms maintained at 26°C compared to 20°C and 23°C. Smaller eDNA particles (0.2 µm) were removed faster (k=0.36 h-1) than larger particles (>1.0 µm; k=0.23 h-1), and this difference was greatest at 26°C compared to lower temperatures. These results contrast our previous findings where, under cooler temperatures (14-17°C), larger eDNA particles were removed more rapidly than small particles. These results suggest that eDNA removal in streams and rivers may be dominated by physical trapping at lower temperatures and microbial degradation at higher temperatures. Models will need to account for temperature to accurately predict eDNA removal in warmer locations and/or seasons, as well as for future climate scenarios.

Elise Snyder (Primary Presenter/Author), The University of Notre Dame, esnyder4@nd.edu;

Jennifer L. Tank (Co-Presenter/Co-Author), University of Notre Dame, jtank@nd.edu;

Abagael Pruitt (Co-Presenter/Co-Author), University of Notre Dame, apruitt2@nd.edu;

Brett Peters (Co-Presenter/Co-Author), University of Notre Dame, Brett.W.Peters.48@nd.edu;

Pedro Brandao-Dias (Co-Presenter/Co-Author), Rice University, pb21@rice.edu;

Kyle Bibby (Co-Presenter/Co-Author), University of Notre Dame, kbibby@nd.edu;

Arial Shogren (Co-Presenter/Co-Author), University of Alabama, ashogren@ua.edu;

Diogo Bolster (Co-Presenter/Co-Author), University of Notre Dame, diogo.bolster.5@nd.edu;

Scott Egan (Co-Presenter/Co-Author), scott.p.egan@rice.edu , Rice University;

Gary Lamberti (Co-Presenter/Co-Author), University of Notre Dame, glambert@nd.edu;

13:45 - 14:00 | Salon 5/6 | LEAF LITTER INPUTS AND THEIR BIOFILMS INFLUENCE SIZE-SPECIFIC EDNA REMOVAL RATES IN STREAMS

6/05/2024  |   13:45 - 14:00   |  Salon 5/6

LEAF LITTER INPUTS AND THEIR BIOFILMS INFLUENCE SIZE-SPECIFIC EDNA REMOVAL RATES IN STREAMS Seasonal dynamics in streams, such as allochthonous organic matter inputs during autumn leaf fall, result in physical and biological changes that may influence eDNA removal from the water column. We explored the impact of the experimental addition of leaf litter using short-term releases of Common Carp (Cyprinus carpio) and Steelhead Trout (Oncorhynchus mykiss) eDNA using recirculating mesocosms and outdoor experimental streams to quantify eDNA removal rates. We conducted replicate releases over time and quantified eDNA removal for different particle sizes using sequential filtration. For both mesocosms and streams, Carp and Steelhead eDNA were removed at similar rates (TukeyHSD, ANOVA; p>0.05). Using experimental streams, larger (>1.2µm) eDNA particles were removed 10x faster than smaller (0.4µm; ANOVA; p<0.001), which often persisted over the 50m experimental reaches. For larger particles, we observed faster eDNA removal in streams with added leaves on Day 4 (Two-way ANOVA; p=0.048), but not on Day 16, perhaps due to colder temperatures. In mesocosms, 0.4µm particles were removed from the water column 21% faster than larger particles (>1.2 µm; TukeyHSD; p<0.001), and this effect was more pronounced in treatments when leaves had biofilms. In the experimental streams, physical removal via benthic substrate preferentially trapped larger eDNA particles, whereas in mesocosms, which lacked benthic substrate, longer water column residence times achieved via recirculation increased the relative contribution of leaf biofilms to eDNA removal. These contrasting results demonstrate that environmental context (substrate composition, temperature, and microbial activity) can mediate the effect of leaf litter on size-specific eDNA removal in streams.

Erik Curtis (Primary Presenter/Author), University of Notre Dame, ecurtis@nd.edu;

Jennifer L. Tank (Co-Presenter/Co-Author), University of Notre Dame, jtank@nd.edu;

Elise Snyder (Co-Presenter/Co-Author), University of Notre Dame, esnyder4@nd.edu;

Pedro Brandao-Dias (Co-Presenter/Co-Author), Rice University, pb21@rice.edu;

Abagael Pruitt (Co-Presenter/Co-Author), University of Notre Dame, apruitt2@nd.edu;

Arial Shogren (Co-Presenter/Co-Author), University of Alabama, ashogren@ua.edu;

Diogo Bolster (Co-Presenter/Co-Author), University of Notre Dame, diogo.bolster.5@nd.edu;

Scott Egan (Co-Presenter/Co-Author), scott.p.egan@rice.edu , Rice University;

Kyle Bibby (Co-Presenter/Co-Author), University of Notre Dame, kbibby@nd.edu;

Gary Lamberti (Co-Presenter/Co-Author), University of Notre Dame, glambert@nd.edu;

14:00 - 14:15 | Salon 5/6 | MONITORING BIODIVERSITY AND ENVIRONMENTAL ASSESSMENT OF FRESHWATER MACROINVERTEBRATES IN ANTHROPOGENICALLY POLLUTED RIVERS USING EDNA

6/05/2024  |   14:00 - 14:15   |  Salon 5/6

Monitoring biodiversity and environmental assessment of freshwater macroinvertebrates in anthropogenically polluted rivers using eDNA Understanding the impact on the ecosystems by environmental changes caused by such as anthropogenic activities and climate change is increasingly important. Environmental DNA is a suitable tool for long-term monitoring due to its low sampling effort and promising approach to river management. Freshwater macroinvertebrates are popular as environmental impact indicators because their response to environmental changes is immediate. In this talk, the response of macroinvertebrate communities toward heavy metal pollution from an abandoned mine, comparing two methods: insect collection and eDNA will be shown. A total of five sites were surveyed along approximately 1.2 km section of a river downstream of a closed mine in Iwate Prefecture: a site with/without metal effects, a confluence of these sites, and two sites after the confluence. At each site, aquatic insect sampling, environmental DNA sampling, and metal concentration analysis were conducted. Environmental DNA samples were subjected to metabarcoding analysis targeting 142 bp and 313 bp of the COI region of mitochondrial DNA. The results showed that taxonomic diversity was lowest at the metal-impacted site (Cu=99.5ug/L, Cd=4.86 ug/L), and that the family Chironomidae was dominant, as indicated by both the capture-based sampling and environmental DNA. At the two sites after the confluence, taxonomic richness and abundance recovered more downstream in the sampling survey, but no clear recovery was observed in the environmental DNA. Although the discrepancies, environmental DNA clearly showed differences in community structure even at an only 500 m interval in lotic environments, indicating that quite localized communities can be investigated.

Noriko Uchida (Primary Presenter/Author), Tohoku University, noriko.uchida.d1@tohoku.ac.jp;

Yuichi Iwasaki (Co-Presenter/Co-Author), National Institute of Advanced Industrial Science and Technology, Japan, yuichiwsk@gmail.com;

Ryoichi Kuranishi (Co-Presenter/Co-Author), Kanagawa Institute of Technology, cji0820@kmd.biglobe.ne.jp;

Natsuko Kondoh (Co-Presenter/Co-Author), National Institute of Environmental Studies, kondo.natsuko@nies.go.jp;

14:15 - 14:30 | Salon 5/6 | IMPACTS OF LAND USE ON STREAM MULTITROPHIC DIVERSITY ASSESSED WITH MORPHOLOGICAL AND MOLECULAR METHODS

6/05/2024  |   14:15 - 14:30   |  Salon 5/6

Impacts of land use on stream multitrophic diversity assessed with morphological and molecular methods Watershed land use is a key threat to stream biodiversity, yet most studies that have documented impacts of land use on streams have focused on ‘horizontal communities’ (e.g. only fishes, or only benthic macroinverterbates). While sampling entire food webs and quantifying diversity across trophic levels is both time and resource-intensive, assessing ‘multitrophic diversity’ is important for conservation prioritisation and to understand community-mediated impacts on ecosystem functioning. The amplification and sequencing of multiple marker genes from environmental DNA (eDNA) samples could provide a faster, higher-throughput method to assess multitrophic diversity, as a single water sample contains eDNA from diverse groups. Working in an area of intensive agriculture in Southern Québec, Canada, we used a multi-marker eDNA metabarcoding approach to assess impacts of land use on stream diatoms, benthic macroinvertebrates, and fishes. For each group, we compared community composition obtained via molecular and traditional (morphological) methods and we identified the factors that drive composition and diversity. We found that: 1) the correspondence between eDNA and morphology was high for fishes but low for the other two groups; 2) irrespective of the specific taxa identified by eDNA and morphology, both methods were equally good at detecting impacts of land use on streams; and 3) each group responded differently to land use and had distinct physico-chemical drivers of community composition. Together, these results confirm the relevance of multitrophic approaches in stream ecology and suggest that eDNA metabarcoding is an efficient tool to complement resource-intensive morphological assessments.

Vincent Fugere (Primary Presenter/Author), Universite du Quebec a Trois-Rivieres, vincent.fugere@uqtr.ca;

14:30 - 14:45 | Salon 5/6 | AQUATIC BIOMONITORING WITH EDNA AND ERNA: A MESOCOSM STUDY ASSESSING TEMPORAL-SCALE DYNAMICS OF BIODIVERSITY ESTIMATES

6/05/2024  |   14:30 - 14:45   |  Salon 5/6

Aquatic biomonitoring with eDNA and eRNA: a mesocosm study assessing temporal-scale dynamics of biodiversity estimates Loss of river connectivity is a contributing factor to aquatic biodiversity loss. Although fish passage structures may be implemented to mitigate this, biomonitoring is needed to assess passage efficacy. As conventional methods may be costly, time-consuming, and biased, using environmental DNA (eDNA) as a biomarker for assessing biodiversity has received much attention. More recently, environmental RNA (eRNA) has also shown promise as a biomarker, as eRNA may provide additional information on how recently a species was present due to its rapid degradation rate. To assess the use of eDNA and eRNA (in combination, eNA) for estimating fish passage use, we conducted a series of mesocosm tank experiments to pair with field collected eNA water samples from inside fish passages. We set up 39 mesocosms containing unique numbers and combinations of steelhead trout (Oncorhynchus mykiss), channel catfish (Ictalurus punctatus), and largemouth bass (Micropterus salmoides), and sampled water for eNA quantity and presence at multiple time points across the 72-hour experiment. This data was then used to determine degradation rates of residual eNA and generate calibration curves for estimating eRNA /eDNA temporal dynamics. We analyzed samples with both qPCR species-specific primers and 12s metabarcoding sequencing. We will use these results to support our understanding of fish passage use from our field study that included six dams in Michigan. Taken together, this work will serve as foundational information to support the use of eNA with conventional monitoring approaches to provide more accurate estimates of fish passage use than conventional biomonitoring alone.

Steven Gardner (Primary Presenter/Author), Oak RIdge National Lab, gardnerst@ornl.gov;

Andrew Furtak (Co-Presenter/Co-Author), Oak RIdge National Lab, furtakaj@ornl.gov;

Xiu Marks (Co-Presenter/Co-Author), Oak RIdge National Lab, marksxj@ornl.gov;

Ed Pearce (Co-Presenter/Co-Author), Michigan Department of Natural Resources, PEARCEJ@michigan.gov;

Brenda Pracheil (Co-Presenter/Co-Author), Pacific Northwest National Laboratory, brenda.pracheil@pnnl.gov;

Kristine Moody (Co-Presenter/Co-Author), Oak RIdge National Lab, moodykn@ornl.gov;