SFS Annual Meeting

5/22/2018  |   09:00 - 09:15   |  420 B

BIOMONITORING 2.0: FROM POTENTIAL TO PRACTICE Traditional morphology-based identification is a slow, often inaccurate process, focused on restricted groups of organisms, which can lead to incomplete and highly-limited observations of local biodiversity. The advent of high-throughput sequencing approaches such as DNA metabarcoding provide an opportunity to overcome such bottlenecks and develop more universal, complete, diagnostic assessment frameworks. In 2016, Environment and Climate Change Canada, in collaboration with other federal departments, initiated the GRDI project to accelerate the incorporation of DNA metabarcoding methods for ecosystem monitoring. We present the initial results from three studies, including a comparison of metabarcoding with traditional biomonitoring surveys in Atlantic Canada, an ongoing experimental study of agricultural land-use change in an eastern Ontario watershed, and a long-term study on oil sand extraction impacts on wetlands in northern Alberta. We demonstrate how the sensitivity of DNA improves our power to detect change; as well as where caution should be exercised. Based on recent research, and our experience implementing large-scale DNA monitoring programs, we comment on the challenges, opportunities, and pitfalls associated with a transition towards a new model for ecosystem assessment; “Biomonitoring 2.0”.

Alex Bush (Primary Presenter/Author), Environment and Climate Change Canada, abush@unb.ca;


Terri Porter (Co-Presenter/Co-Author), Department of Natural Resources Canada, mailto:terrimporter@gmail.com;


Royce Steeves (Co-Presenter/Co-Author), Department of Fisheries and Oceans Canada, Royce.Steeves@dfo-mpo.gc.ca;


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


Nellie Gagné (Co-Presenter/Co-Author), Department of Fisheries and Oceans Canada, Nellie.Gagne@dfo-mpo.gc.ca;


Erik Emilson (Co-Presenter/Co-Author), Great Lakes Forestry Centre, Canadian Forest Service, erik.emilson@canada.ca;


David Lapen (Co-Presenter/Co-Author), Agriculture and Agri-Foods Canada, david.lapen@agr.gc.ca;


Nick Ogden (Co-Presenter/Co-Author), Public Health Agency of Canada, nicholas.ogden@canada.ca;


Oliver Lung (Co-Presenter/Co-Author), Canadian Food Inspection Agency, Oliver.Lung@inspection.gc.ca;


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;


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5/22/2018  |   09:15 - 09:30   |  420 B

COMPARISON OF QUANTITATIVE PCR WITH DIGITAL DROPLET PCR FOR DETECTION AND QUANTIFICATION OF ENVIRONMENTAL DNA FROM INVASIVE ASIAN CARP Invasive Asian Carp include four species: Silver Carp, Bighead Carp, Grass Carp, and Black Carp. All four species have invaded the Mississippi River system and currently threaten to invade the Great Lakes. Environmental DNA (eDNA) is being used for early detection and monitoring of Asian Carp populations. Quantitative PCR (qPCR) assays are currently used for targeted analysis of Asian Carp eDNA because they provide both detection and an estimate of the concentration of eDNA of the target species. We tested digital droplet PCR to evaluate its potential as a replacement or complement to qPCR analysis. Potential advantages of ddPCR are less variation at low concentrations of the target sequence, absolute quantification independent of a standard curve, and resistance to PCR inhibitors in water samples. We compared the limit of detection (LOD) and limit of quantification (LOQ) of both techniques for known concentrations of synthetic DNA containing an Asian Carp target sequence. We further compared the performance of ddPCR and qPCR with environmental samples from areas invaded by Asian Carp, and finally compared their performance with environmental samples spiked with varying levels of algae, a common source of PCR inhibitors.

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


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5/22/2018  |   09:30 - 09:45   |  420 B

DNA METABARCODING BASED STREAM ASSESSMENTS – WE’RE READY! Accurate assessment of macrozoobenthic community composition is essential for stream health monitoring. In order to improve the accuracy of monitoring efforts we developed novel DNA metabarcoding methods and validated them using 18 monitoring samples of the Finnish government that were initially determined using larval morphology. Our metabarcoding pipeline showed improved species resolution compared to morphological identifications and on average detected 57% more taxa across samples. All four primer sets, that were specifically developed for freshwater macrozoobenthos, performed equally good. Furthermore, the stream assessment results of both approaches were very similar, despite the lack of precise abundance data for the DNA-based method. In addition to delivering highly reproducible data, we also developed bioinformatic methods to extract information on intraspecific diversity of the entire community. With laboratory costs of ~$250 per sample, metabarcoding has become a feasible method. Consequently, we scaled up our metabarcoding protocols to allow processing and sequencing of hundreds of samples within weeks. While DNA based assessment methods should be further refined (e.g. improved primers, PCR free mitogenomics), we argue that current metabarcoding protocols are already mature enough to be used for routine monitoring and water quality assessment.

Vasco Elbrecht (Primary Presenter/Author), Centre for Biodiversity Genomics (University of Guelph), elbrecht@uoguelph.ca;


Edith Vamos (Co-Presenter/Co-Author), University Duisburg Essen, edith.vamos@uni-due.de ;


Bianca Peinert (Co-Presenter/Co-Author), University Duisburg Essen, bianca.peinert@uni-due.de;


Jukka Aroviita (Co-Presenter/Co-Author), Finnish Environment Institute (Syke), jukka.aroviita@ymparisto.fi;


Kristian Meissner (Co-Presenter/Co-Author), Finnish Environmental Institute (SYKE), kristian.meissner@ymparisto.fi;


Florian Leese (Co-Presenter/Co-Author), University of Duisburg-Essen, florian.leese@uni-due.de;


Dirk Steinke (Co-Presenter/Co-Author), Centre for Biodiversity Genomics (University of Guelph), dsteinke@uoguelph.ca;


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5/22/2018  |   09:45 - 10:00   |  420 B

EFFECTS OF FIELD SAMPLING DESIGN ON ENVIRONMENTAL DNA PERFORMANCE FOR FISH, ZOOPLANKTON, AND ZOOBENTHOS IN TEMPERATE LAKES We evaluate how depth and location of environmental DNA (eDNA) water samples differentially affects performance of meta-barcoding for diverse freshwater taxa including fish, zooplankton, and zoobenthos in temperate lakes. We took eDNA water samples in 12 Michigan lakes, stratified as three nearshore and three offshore random locations. At each of these six locations per lake, we took a 250 ml surface water sample, and a 250 ml sample from just above the lake bed using a Van Dorn sampler. We filtered eDNA from water samples and Illumina-sequenced gene fragments to characterize fish, zooplankton, and zoobenthos communities. eDNA-estimated species richness was greater for zooplankton than zoobenthos regardless of sample location or depth across lakes. For fish, eDNA results differed considerably between lakes, but location and depth of water samples within lakes had little effect on characterizing communities. Alternatively, for zooplankton, eDNA results were relatively similar between our lakes, but deep water and offshore samples were consistently different from nearshore and shallow eDNA samples within lakes. We demonstrate that sampling design for eDNA meta-barcoding should account for the target taxonomic group in temperate lakes.

Eric Larson (Primary Presenter/Author), University of Illinois, erlarson@illinois.edu;


Jennifer Drummond (Co-Presenter/Co-Author), Rice University, jenn@rice.edu;


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


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


Crysta Gantz (Co-Presenter/Co-Author), Portland State University, cgantz@pdx.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;


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


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5/22/2018  |   10:00 - 10:15   |  420 B

ENHANCING PREDICTABILITY OF PRIMER SPECIFICITY FOR EDNA DETECTION OF AQUATIC SPECIES Environmental DNA (eDNA) techniques have increased in popularity for single-species detection during the past decade owing to their high sensitivity relative to conventional survey methods. Using primers with high specificity can selectively magnify DNA signals collected from the environment, allowing the detection of rare or newly invasive species. However, the absence of guidelines for specific primer design may compromise the benefits of eDNA detection by incurring high costs and wasted effort during primer development. In this study, we investigated the relative importance of different primer properties (i.e. 3’ stability, guanine-cytosine content, dimer stability) and primer-template mismatch properties (i.e. total number, the type, and position of mismatches) in predicting primer specificity, using seven wetland fish species. Specificity was significantly increased if the 3’ end of the primers (the last five nucleotides) had fewer guanine/cytosine (i.e. was less stable) and more mismatches. Generally, all purine-purine and one of the pyrimidine-pyrimidine mismatches (cytosine-cytosine) have greater effects (except at the 3’ terminal) on primer specificity than other types of mismatches. Our study identifies primer properties that are critical for designing species-specific primers and should enable cost-effective and routine implementation of eDNA in species detection.

Ying Kin Ken So (Primary Presenter/Author), School of Biological Sciences, the University of Hong Kong, Hong Kong, u3500795@hku.hk;


Billy Hau (Co-Presenter/Co-Author), The University of Hong Kong, chhau@hku.hk;


David Dudgeon (Co-Presenter/Co-Author), School of Biological Sciences, the University of Hong Kong, Hong Kong, ddudgeon@hku.hk;


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5/22/2018  |   10:15 - 10:30   |  420 B

ENVIRONMENTAL FACTORS AFFECTING BACTERIAL COMMUNITY COMPOSITION IN THE HYPEREUTROPHIC MACATAWA WATERSHED Project Clarity works to mitigate the impact of urbanization and agricultural activity in the Macatawa Watershed, including high sediment, nutrient and fecal coliform loading. We are assessing project impact on water quality in order to aid decisions about public access to recreational waters and mitigation strategies. Weekly samples over the course of a 1 year period from 12 representative sites were analyzed for biological (e.g., community 16S rRNA sequencing, fecal indicator bacteria, Escherichia coli genome sequencing), chemical (e.g., DO/BOD, nutrients), and physical parameters (e.g., temperature, pH). Results indicate continued high phosphorous, total suspended solids, and E. coli levels, exceeding total maximum daily load targets for the watershed. Patterns in microbial communities show variation influenced by season and geographical location (e.g., stream or lake location). Rain events impact the communities to a lesser degree. Diversity of microbial communities increases in late fall and winter. Identification of microbial taxa acting as signatures of environmental conditions could lead to new methods of monitoring water quality. These data provide a baseline for monitoring remediation efforts in the Macatawa Watershed and may serve as a comparison for hypereutrophic watersheds around the nation.

Aaron Best (Co-Presenter/Co-Author), Hope College, best@hope.edu;


Thomas Garcia (Co-Presenter/Co-Author), Hope College, thomas.garcia@hope.edu;


Cassandra Harders (Co-Presenter/Co-Author), Hope College, cassandra.harders@hope.edu;


Abagail Jeavons (Co-Presenter/Co-Author), Hope College, abagail.jeavons@hope.edu;


Mallory Luke (Co-Presenter/Co-Author), Hope College, mallory.luke@hope.edu;


Andrew Klein (Co-Presenter/Co-Author), Hope College, andrew.klein@hope.edu;


Abbygale Parshall (Co-Presenter/Co-Author), Hope College, abbygale.parshall@hope.edu;


Leslie Perez (Co-Presenter/Co-Author), Hope College, leslie.perez@hope.edu;


Eleda Plouch (Co-Presenter/Co-Author), Hope College, eleda.plouch@hope.edu;


Adam Slater (Co-Presenter/Co-Author), Hope College, adam.slater@hope.edu;


Daniel Wade (Co-Presenter/Co-Author), Hope College, daniel.wade@hope.edu;


Francesco Moen (Co-Presenter/Co-Author), Hope College, moen@hope.edu;


Chelsea Payne (Co-Presenter/Co-Author), Hope College, cepayne7@gmail.com;


Randall Wade (Co-Presenter/Co-Author), Hope College, wade@hope.edu;


Brent Krueger (Co-Presenter/Co-Author), Hope College, kruegerb@hope.edu;


Michael Pikaart (Co-Presenter/Co-Author), Hope College, pikaart@hope.edu;


Sarah Brokus (Primary Presenter/Author), Hope College, brokus@hope.edu;


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