SFS Annual Meeting

5/22/2018  |   11:00 - 11:15   |  420 B

METABARCODING AND BIODIVERSITY IN STREAMS: USING MULTIPLE TOOLS TO ASSESS AQUATIC ECOSYSTEMS Stream ecosystems are a complex assemblage of macro and microorganisms which respond to external stressors, including temperature, land use, nutrients, and contaminants. The composition, diversity and function of these organisms may be an important indicator of stream health and function, and species assemblages, such as invertebrates, periphyton and fish are used to evaluate stream ecosystem health and biodiversity. eDNA metabarcoding potentially allows resource managers to identify a wider range of species at substantially lower cost. We used standard barcodes (16S, 18S and CO1) to identify bacteria, algae, and vertebrate species in water samples collected from 40 NH streams. Data on water chemistry, land use and invertebrates is also available at each site. We are applying multivariate and phylogenic network analyses to identify correlations between biodiversity metrics within and across taxonomic groups and water quality stressors. Initial analysis shows decreasing biodiversity associated with temperature and nutrients, and we will discuss these results, along with some of the challenges we have encountered.

Kelley Thomas (Co-Presenter/Co-Author), University of New Hampshire, kelley.thomas@unh.edu;


Devin Thomas (Co-Presenter/Co-Author), University of New Hampshire, devin.thomas@unh.edu;


Alison Watts (Primary Presenter/Author), University of New Hampshire, alison.watts@unh.edu;


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5/22/2018  |   11:15 - 11:30   |  420 B

MONITORING OF MICROBIAL COMMUNITIES AT A HIGH ELEVATION STREAM IMPAIRED BY CHRONIC METALS CONTAMINATION The Arkansas River has been impaired by metal pollution due to historical mining in nearby Leadville, Colorado. By the late 1990s, implementation of water treatment facilities resulted in significant improvements in water quality. Despite improved water quality, macroinvertebrate community structure remains different between upstream reference sites and sites downstream of California Gulch, the inlet that contributes metal contamination. Our hypothesis for this discrepancy is that metal concentrations are low enough to not be directly toxic to macroinvertebrate communities, but high enough to alter the stream microbial communities. This change in the base of the stream food web would indirectly structure macroinvertebrate communities through altered microbial biomass (e.g. food quality). To address this, we sampled benthic sediments at multiple sites upstream and downstream of California Gulch, across multiple seasons (spring and fall), and years (2015 – 2017). Microbial community composition was measured using 16S rRNA gene amplicon sequencing. Our results show: (1) microbial communities were indeed different between sites upstream and downstream of California Gulch, (2) downstream sediments were elevated in metals concentrations relative to upstream communities, and (3) dietary metals exposure is likely an important driver of macroinvertebrate community structure.

Brian Wolff (Primary Presenter/Author), Colorado State University, wolffba@gmail.com;


William Clements (Co-Presenter/Co-Author), Colorado State University, William.Clements@colostate.edu ;


Ed Hall (Co-Presenter/Co-Author), Colorado State University, ed.hall@colostate.edu;


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5/22/2018  |   11:30 - 11:45   |  420 B

USE OF METABARCODING OF ENVIRONMENTAL DNA SAMPLES TO ASSESS FRESHWATER MUSSEL POPULATION RESTORATION EFFORTS IN THE CLINCH RIVER The Clinch River (Virginia and Tennessee) is one of the most biologically diverse freshwater systems in the country. Known for its high species richness of freshwater mussels, the system contains 46 extant species, including 20 federally listed species. Declines in these diverse mussel communities are linked to anthropogenic alteration of habitat and water quality. In 1998, a large chemical spill killed more than 7,000 mussels, necessitating habitat restoration as well as captive breeding and release of mussels in the early 2000’s. Monitoring of this system is ongoing to better understand effects of these disturbances and subsequent restoration efforts. Non-invasive environmental DNA (eDNA) sampling may become a useful tool for such monitoring efforts. To investigate the utility of eDNA metabarcoding to detect and describe local mussel communities, we collected water samples near well characterized freshwater mussel beds in the Clinch River. We present results from our 2017 water samples and relate community structure obtained from eDNA sampling to known species composition at each site. Finally, we also address ways to improve the use of eDNA metabarcoding for monitoring of freshwater taxa.

Katy Klymus (Primary Presenter/Author), U.S.Geological Survey, kklymus@usgs.gov;


Catherine Richter (Co-Presenter/Co-Author), Columbia Environmental Research Center, USGS, CRichter@usgs.gov;


Nathan Thompson (Co-Presenter/Co-Author), U.S. Geological Survey, nthompson@usgs.gov;


Jess Jones (Co-Presenter/Co-Author), U.S. Fish and Wildlife Service, Jess_Jones@fws.gov;


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5/22/2018  |   11:45 - 12:00   |  420 B

USING OCCUPANCY MODELING TO COMPARE TRADITIONAL VERSUS DNA METABARCODING METHODS FOR CHARACTERIZING ZOOPLANKTON BIODIVERSITY IN LAKE SUPERIOR DNA metabarcoding tools could increase our ability to monitor changes in zooplankton biodiversity, as well as to detect newly-introduced invasive zooplankton taxa while still rare. Nonetheless, the use of DNA-metabarcoding for characterizing zooplankton biodiversity in the Great Lakes has not been fully explored. In summer 2016, we collected multiple zooplankton samples within the same locations extending from nearshore areas of Western Lake Superior to the open lake. Individual zooplankton taxa were sequenced and this genetic information will be added to online databases. We used occupancy modeling methods to explore whether DNA meta-barcoding increased the likelihood that individual zooplankton taxa would be detected when present. Zooplankton community composition showed high spatial variability. At least 16 of the 39 taxa we observed were rare, being typically detected in only 1/3 replicates at a site using traditional identification, which involves identifying subsamples. Occupancy modeling results that at least twice as many replicates would be needed to detect these taxa reliably using traditional ID (e.g., total replicates > 6). However, preliminary findings indicate that DNA metabarcoding could increase detectability of some zooplankton taxa, thus complementing traditional taxonomy in characterizing spatial patterns of zooplankton biodiversity.

Christy Meredith (Primary Presenter/Author), NRC Fellow, USEPA, MED,Duluth MN, Meredith.Christy@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;


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

John Martinson (Co-Presenter/Co-Author), U.S Environmental Protection Agency, martinson.john@epa.gov;


Sara Okum (Co-Presenter/Co-Author), USEPA/NERL/SED,ORISE, Cincinnati, OH, okum.sara@epa.gov;


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5/22/2018  |   12:00 - 12:15   |  420 B

USING EDNA TO ELUCIDATE DISTRIBUTION OF FISH SPECIES IN A COMPLEX RIVER SYSTEM Environmental DNA (eDNA) analysis is a noninvasive genetic tool that can improve efficiency and reduce costs associated with species detection in aquatic systems. eDNA methods are widely used to assess presence/absence of target species and have recently demonstrated potential for estimating biodiversity in controlled environments. We applied eDNA methods to estimate distribution of fish species in a large and complex system. The St. Louis River Estuary provides a suitable study area because fish diversity and species distribution is well documented, thanks to past and ongoing fishery assessments and invasive species early detection monitoring. We collected water samples from 240 randomly selected sites extending over 30 river km in June and October. At 30 sites, an additional water sample was collected for an inter-lab comparison. Composition and spatial distribution patterns derived from eDNA data are being compared to traditional adult and larval fish survey data to understand the different perspectives they give. Results from our study provide insight into the efficacy of eDNA methods for estimating fish distribution in large, complex aquatic systems and begin to inform us about how these methods can be operationalized for use by management agencies.

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


W. Lindsay Chadderton (Co-Presenter/Co-Author), The Nature Conservancy, lchadderton@tnc.org;


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


Sara Okum (Co-Presenter/Co-Author), USEPA/NERL/SED,ORISE, Cincinnati, OH, okum.sara@epa.gov;


Brett Olds (Co-Presenter/Co-Author), Oceanic Institute of Hawaii Pacific University, bolds@hpu.edu;


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

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


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


Andrew Tucker (Co-Presenter/Co-Author), The Nature Conservancy, atucker@tnc.org;


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5/22/2018  |   12:15 - 12:30   |  420 B

UNDERSTANDING VARIATION ASSOCIATED WITH BIOINFORMATICS PROCESSING OF ENVIRONMENTAL GENOMIC DATA Metabarcoding is increasingly used in biomonitoring worldwide. The lack of standardized bioinformatics approaches for environmental metabarcoding data compromises data quality. Understanding the sources of variability in the bioinformatics process will help practitioners make informed decisions about where standardization is important and account for uncertainty associated with the bioinformatics process. This study examined variation among a diverse group of bioinformatics workflows through intercalibration. By quantifying the relative contribution of variance at each step of the bioinformatics process, we documented how bioinformatics pipelines influence the ecological interpretation of environmental metabarcoding assessments. Five participating labs each received the same 18S rRNA sequence dataset to analyze through their pipelines. We compared output between labs at sequence counts, OTUs or sequence-types, community composition, taxonomic ID and ecological relationships. Initial analyses resulted in substantial interlaboratory variability in sequence numbers, OTUs and number of families. We reduced variability among labs by reconciling several key steps in the bioinformatic process. The intercalibration process allowed us to develop recommendations that will reduce the overall uncertainty associated with application of metabarcoding for environmental assessment while still allowing flexibility in the bioinformatic process.

Eric Stein (Primary Presenter/Author), Southern California Coastal Water Research Project, erics@sccwrp.org;


Joshua Steele (Co-Presenter/Co-Author), Southern California Coastal Water Research Project, joshuas@sccwrp.org;


Anthony Chariton (Co-Presenter/Co-Author), Macquarie University, Anthony.Chariton@mq.edu.au;


Paul Greenfield (Co-Presenter/Co-Author), Macquarie University, Paul.Greenfield@csiro.au;


Luke Thompson (Co-Presenter/Co-Author), NOAA Southwest Fisheries Science Center, luke.thompson@noaa.gov;


John Martinson (Co-Presenter/Co-Author), U.S Environmental Protection Agency, martinson.john@epa.gov;


Donald Baird (Co-Presenter/Co-Author), Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, NB, Canada, djbaird@unb.ca;


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

Mehrdad Hajibabaei (Co-Presenter/Co-Author), Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, ON, Canada, mhajibab@uoguelph.ca;


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