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SFS Annual Meeting

Thursday, June 6, 2024
13:30 - 15:00

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S10 Environmental DNA as a Tool for Understanding Connections

13:30 - 13:45 | Salon 5/6 | HARMFUL BENTHIC CYANOBACTERIA PROLIFERATIONS IN STREAMS AND RIVERS: USEPA RESEARCH TO INFORM SAMPLING AND ANALYTICAL PROCEDURES FOR RISK ASSESSMENT

6/06/2024  |   13:30 - 13:45   |  Salon 5/6

HARMFUL BENTHIC CYANOBACTERIA PROLIFERATIONS IN STREAMS AND RIVERS: USEPA RESEARCH TO INFORM SAMPLING AND ANALYTICAL PROCEDURES FOR RISK ASSESSMENT Benthic harmful cyanobacteria blooms pose a significant threat to domestic animals, wildlife, and humans. U.S. states, tribes, and local agencies need consistent approaches to characterize relative risk and inform mitigation practices. USEPA is addressing this need with multi-year, multi-site field research and controlled experiments. In 2023, research focused on evaluating in-stream sampling methods that quantify spatial extent at the reach scale and assess the toxin exposure risk from disturbing benthic mats. A stream mesocosm study designed to control the relative dominance of specific strains of benthic cyanobacteria was conducted in parallel with the field effort. Field measurements and 2200 samples were scheduled among seven field crews, making multiple visits to seven pilot test sites across six states (CA/KS/OH/UT/VA/WA) and was accomplished with 98% completeness. Laboratory analyses are ongoing and include general water quality variables, pigments, microscope counts, and DNA metabarcoding of periphyton samples, qPCR analyses for toxin biosynthesis genes, and several cyanotoxin-specific analyses. All periphyton samples were collected such that measures were normalized to stream bed area and biomass. The same analyses were run on samples from the mesocosm study, but in addition, effects on macroinvertebrates and fish were tested. Preliminary results are providing a) rationale for streamlining field sampling techniques so that more sites can be surveyed in 2024 and b) insight into the variation in benthic cyanobacteria growth forms, community structures, toxins, and their potential effects on stream biota that can help guide recommendations for risk assessment in the future.

Christopher Nietch (Primary Presenter/Author), U.S. Environmental Protection Agency, nietch.christopher@epa.gov;

Katrina Laidlaw (Co-Presenter/Co-Author), U.S. EPA/ Region 8, laidlaw.tina@epa.gov;

Avery Tatters (Co-Presenter/Co-Author), U.S. EPA/ Office of Research and Development, tatters.avery@epa.gov;

Heath Mash (Co-Presenter/Co-Author), U.S. EPA/ Office of Research and Development, mash.heath@epa.gov;

Jingrang Lu (Co-Presenter/Co-Author), U.S. EPA/ Office of Research and Development, lu.jingrang@epa.gov;

Jim Lazorchak (Co-Presenter/Co-Author), United States Environmental Protection Agency, Office of Research and Development, Center for Environmental Measurement and Modeling, Cincinnati, OH 45268, lazorchak.jim@epa.gov;

Toby Sanan (Co-Presenter/Co-Author), U.S. EPA/ Office of Research and Development, sanan.toby@epa.gov;

Erik Pilgrim (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, pilgrim.erik@epa.gov;

Paul Weaver (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, weaver.paul@epa.gov;

Laura Webb (Co-Presenter/Co-Author), U.S. EPA/ Region 7, webb.laura@epa.gov;

Rochelle Labiosa (Co-Presenter/Co-Author), US Environmental Protection Agency, labiosa.rochelle@epa.gov;

Marcie Tidd (Co-Presenter/Co-Author), U.S. EPA/ Region 8, tidd.marcie@epa.gov;

Hilary Snook (Co-Presenter/Co-Author), U.S. EPA/ Region 1, snook.hilary@epa.gov;

Nathan Smucker (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, smucker.nathan@epa.gov;

13:45 - 14:00 | Salon 5/6 | SPATIAL DISTRIBUTION OF MICROBIOMES IN HEADWATERS: CONTINUUM OR DISCONTINUUM?

6/06/2024  |   13:45 - 14:00   |  Salon 5/6

Spatial distribution of microbiomes in headwaters: continuum or discontinuum? With the advances of genomic-based approaches, patterns and controls of microbiome structure and function are starting to emerge for streams and rivers. Here we provide an overview of our major findings on headwater microbiomes. The diversity in substrate characteristics appears to reflect on microbial structure as we found that rock biofilms contained more cyanobacteria and algae while sediments contain greater abundance of Acidobacteria and Deltaproteobacteria. Significant differences in biofilm composition were observed when microbial colonization started in summer vs. winter seasons. Algae were important in the early development of biofilm communities during winter, while heterotrophic bacteria played a more critical role during summer colonization and development of biofilms. Despite distinct early community succession in different seasons, biofilm community structures converged after 70 days. During storm events, significant successional changes of microbial community structure and function were observed, with Cyanobacteria/photosynthesis as one of the primary recovering processes. Large storm events inoculated microbes from terrestrial and streambeds to headwaters, resetting the community assembly and reconnecting the continuum of headwater microbiomes. Regarding spatial drivers, longitudinal gradients showed that 68% of the variation in total microbial biomass was explained by sediment atomic carbon-to-nitrogen ratio (C:N ratio), percent carbon, sediment surface area, and percent water content. Localized hydraulic and thermal conditions also showed to affect microbial diversity. Altogether, results suggest that local environments (reaches and stream orders) likely dominate the discontinuity of microbiomes (“hotspots” and “hot moments”), while catchment scale dictate the continuity of microbiome assembly geographically and globally.

Jinjun Kan (Primary Presenter/Author), Stroud Water Research Center, jkan@stroudcenter.org;

Raven Bier (Co-Presenter/Co-Author), University of Georgia, rbier@srel.uga.edu;

Marc Peipoch (Co-Presenter/Co-Author), Stroud Water Research Center, mpeipoch@stroudcenter.org;

Melinda Daniels (Co-Presenter/Co-Author), Stroud Water Research Center, mdaniels@stroudcenter.org;

Diana Oviedo-Vargas (Co-Presenter/Co-Author), Stroud Water Research Center, doviedo@stroudcenter.org;

14:00 - 14:15 | Salon 5/6 | THE DIVERSITY OF FRESHWATER ALGAL ASSEMBLAGES ACROSS THE UNITED STATES AS REVEALED BY DNA METABARCODING

6/06/2024  |   14:00 - 14:15   |  Salon 5/6

The diversity of freshwater algal assemblages across the United States as revealed by DNA metabarcoding As freshwater algae respond strongly to environmental conditions, algal communities are routinely used as indicators of aquatic health. Algal bioassessments have historically relied upon microscopy-based identifications that are typically slow, expensive, taxonomically restricted, and inconsistent across analysts and time. Metabarcoding of water column DNA (environmental DNA, or eDNA) can characterize assemblages more quickly, at lower cost, and with higher taxonomic precision than microscopy. As such, eDNA metabarcoding has the potential to improve bioassessments, but relationships between environmental conditions and eDNA-derived algal assemblage composition need to be determined first. We performed metabarcoding of algal 23S rRNA for 1,230 freshwater eDNA samples collected from 51 lakes and 617 streams across the conterminous United States. This effort constitutes the largest published water column eDNA survey yet of algal diversity across freshwaters in the U.S. Despite strong spatial structuring of algal eDNA assemblages nationwide, we found that select taxa and algal divisions were responsive to human-influenced gradients of catchment integrity and, possibly, eutrophication. Nevertheless, we also identified the need for additional sampling and metadata collection before algal eDNA can be used for large-scale biomonitoring in the U.S. We also found that only 2% of algal ESVs could be assigned to U.S. morphospecies, highlighting the importance of building a more comprehensive reference sequence database to integrate existing morphospecies autecology with eDNA-based bioassessments.

Nicholas Schulte (Primary Presenter/Author), Jonah Ventures, nicholas.o.schulte@gmail.com;

Joseph Craine (Co-Presenter/Co-Author), Jonah Ventures, josephmcraine@gmail.com;

Devin Leopold (Co-Presenter/Co-Author), Jonah Ventures, devin.leopold@gmail.com;

Jessica Devitt (Co-Presenter/Co-Author), Jonah Ventures, jessicadevitt10@gmail.com;

Noah Fierer (Co-Presenter/Co-Author), University of Colorado Boulder, noahfierer@gmail.com;

14:15 - 14:30 | Salon 5/6 | ECOLOGICAL CONNECTIVITY OF AQUATIC INVERTEBRATE COMMUNITIES ACROSS THE LOWER COLORADO RIVER BASIN REVEALED USING ENVIRONMENTAL DNA

6/06/2024  |   14:15 - 14:30   |  Salon 5/6

Ecological connectivity of aquatic invertebrate communities across the Lower Colorado River Basin revealed using environmental DNA River networks are among the most biodiverse habitats on the planet, despite their geographic scarcity compared to other habitat types. River networks exist in complex geographical arrangements that lead to environmental and spatial heterogeneity that promotes biodiversity of all aquatic taxa, and is particularly influential for aquatic invertebrate communities that possess a variety of environmental tolerances and dispersal abilities . Aquatic invertebrates can disperse between habitats through either the river network or across terrestrial pathways, making them good indicators of ecological connectivity in complex landscapes. In the Lower Colorado River Basin, aquatic habitats are set within an arid landscape containing areas of high human impact, as well as protected natural ecosystems. The wide range of environmental conditions and landscape configurations in this system support diverse aquatic invertebrate communities in many types of habitats, but natural and anthropogenic barriers might reduce this connectivity by limiting viable habitat and impeding dispersal. To assess ecological connectivity in the Lower Colorado Basin, we utilized eDNA metabarcoding to capture aquatic invertebrate community composition at sites with high geographic and environmental diversity. Patterns of beta-diversity will be compared to landscape and environmental distances to infer patterns of ecological connectivity across multiple pathways for dispersal. Investigating how aquatic invertebrate communities are influenced by ecological connectivity in the Lower Colorado Basin will provide insight into how aquatic communities are influenced by landscape heterogeneity and will identify where poorly-connected communities might pose a risk for biodiversity in the Basin.

Jared Freedman (Primary Presenter/Author), Oregon State University, freedmaj@oregonstate.edu;

Ted Kennedy (Co-Presenter/Co-Author), USGS Southwest Biological Science Center, Grand Canyon Monitoring and Research Center, tkennedy@usgs.gov;

Molly Burke (Co-Presenter/Co-Author), Oregon State University, Molly.Burke@oregonstate.edu;

Dave Lytle (Co-Presenter/Co-Author), Oregon State University, lytleda@oregonstate.edu;

14:30 - 14:45 | Salon 5/6 | FISH EDNA ILLUMINATES BIOTIC CONNECTIVITY IN LENTIC HABITATS

6/06/2024  |   14:30 - 14:45   |  Salon 5/6

FISH eDNA ILLUMINATES BIOTIC CONNECTIVITY IN LENTIC HABITATS Fish community assessment is an important component of evaluating ecosystem health. Environmental DNA (eDNA) may supplement conventional methods by enhancing rare species detection and reducing field effort required for spatial and habitat specific coverage. However, eDNA is not typically paired with physical catch surveys because molecular methods remain under-studied in management contexts and may not fit well with existing protocols. We aim to develop efficient, scalable methods for eDNA fish community surveys in freshwater lentic systems with varying habitat complexity and species diversity to illuminate fish biodiversity over different habitats and spatial scales. We conducted eDNA fish surveys of 9 lakes in the northern Minnesota to determine the number and allocation of samples required to detect maximal species richness using different lake zone (littoral vs. open-water) and gear type (eDNA vs. physical catch) approaches. Our 2021 survey (1093 samples from 318 sites) indicate certain species were missed with either conventional or eDNA methods, although there was considerable overlap. In small (26-40 ha) and medium (92-124 ha) lakes, eDNA methods detected as many or more species than conventional methods, with eDNA detecting 88-100% of species from historical observations and physical methods from one year’s field effort detecting 50-100% of species from historical observations. We expect results to provide insight on the within-lake connectivity of fish communities and their eDNA and how to efficiently incorporate eDNA sampling into existing broad scale surveys to increase the probability of detecting new invaders and native fish species that may be missed by conventional methods.

Courtney Larson (Primary Presenter/Author), U.S. Environmental Protection Agency, larson.courtney@epa.gov;

Chelsea Hatzenbuhler (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, hatzenbuhler.chelsea@epa.gov ;

Aubree Szczepanski (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, szczepanski.aubree@epa.gov;

Greg Peterson (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, Peterson.Greg@epa.gov;

Erik Pilgrim (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, pilgrim.erik@epa.gov;

Joel Hoffman (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, hoffman.joel@epa.gov;

Anett Trebitz (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, Trebitz.Anett@epa.gov;

14:45 - 15:00 | Salon 5/6 | COMPARATIVE PHYLOGEOGRAPHY OF LAKE TANGANYIKA CICHLID FISHES BASED ON ENVIRONMENTAL DNA

6/06/2024  |   14:45 - 15:00   |  Salon 5/6

COMPARATIVE PHYLOGEOGRAPHY OF LAKE TANGANYIKA CICHLID FISHES BASED ON ENVIRONMENTAL DNA Environmental DNA (eDNA) offers a powerful tool for assessing the distribution of aquatic species. Surveys in large lakes suggest that eDNA metabarcoding yields species inventories that are broadly comparable to traditional survey methods, but inferences about intraspecific genetic variation may also be possible. Here we present results from eDNA sampling along the eastern shore of Lake Tanganyika to evaluate biogeographic patterns of cichlid fishes, including testing whether Mahale Mountains National Park represents an important refuge. We find 689 distinct haplotypes at the ND2 locus, with 612 haplotypes matching to reference sequences from 83 cichlid species encompassing all major lineages. An additional 214 distinct haplotypes could be identified to the genus level. Species richness varied among sites, but was not clearly elevated within the protected area. Haplotypes diversity within species enabled us to evaluate the phylogeography of 63 species. Most species showed either panmixia across the study area or strong north-south differentiation. The regionalization of phylogeographic patterns suggests persistent barriers to dispersal for many lineages, while panmixia was often observed in large-bodied species that do not maintain feeding or breeding territories. Fine-scale isolation by distance was rare in our dataset, likely reflecting the limited sequence length available from eDNA. Taken together, these findings indicate that eDNA metabarcoding can offer parallel insights into the distribution and phylogeography of many species simultaneously, creating new opportunities to use metaphylogeography to resolve the influence of historical environmental change, species traits, and conservation reserves on genetic connectivity between animal populations.

Kristy Deiner (Co-Presenter/Co-Author), University of Notre Dame, alpinedna@gmail.com;

Kara Andres (Co-Presenter/Co-Author), Cornell University, kja68@cornell.edu;

Colin Apse (Co-Presenter/Co-Author), The Nature Conservancy, capse@tnc.org;

Ismael Kimirei (Co-Presenter/Co-Author), Tanzania Fisheries Research Institute, ismaelkimirei@tafiri.go.tz;

Yiyuan Li (Co-Presenter/Co-Author), University of Notre Dame, yli19@nd.edu ;

David Lodge (Co-Presenter/Co-Author), Cornell University, dml356@cornell.edu;

Jacqueline Lopez (Co-Presenter/Co-Author), University of Notre Dame, jlopez11@nd.edu;

Michael Pfrender (Co-Presenter/Co-Author), University of Notre Dame, Michael.Pfrender.1@nd.edu ;

Mark Renshaw (Co-Presenter/Co-Author), Hawai'i Pacific University, mrenshaw@hpu.edu;

Rashid Tamatamah (Co-Presenter/Co-Author), Tanzania Fisheries Research Institute, rashid.tamatamah@uvuvi.go.tz;

Katie Wagner (Co-Presenter/Co-Author), University of Wyoming, Catherine.Wagner@uwyo.edu;

Pete McIntyre (Primary Presenter/Author), Cornell University, pbm3@cornell.edu ;