SFS Annual Meeting

5/22/2018  |   14:00 - 14:15   |  420 B

QIIME: A GOOD BIOINFORMATICS PIPELINE FOR ILLUMINA NEXTSEQ AMPLICION SEQUENCING DATA PROCESSING? Quantitative Insights Into Microbial Ecology (QIIME) is one of the most commonly used bioinformatics pipelines for processing data generated from amplicon sequencing, regardless of which next-generation sequencing (NGS) platform is used. Most researchers use NGS and QIIME to characterize microbial communities in different environments; from guts of organisms to soil samples. Although it has been about four years since the Illumina NextSeq was released, there have been fewer publications regarding the use of the NextSeq, especially for downstream bioinformatics processing in comparison to that of other NGS platforms. We constructed a pipeline for downstream bioinformatics processing of data generated from the NextSeq using publically available QIIME scripts. However, instead of looking at microbial communities, we are characterizing fish and invertebrate communities in aquatic ecosystems. In doing so, we are focusing in on using NGS as a tool for early detection and monitoring for Asian Carp. Although the pipeline has been completed, we hope to make this pipeline completely automated with the help of HTCondor.

Yer Lor (Primary Presenter/Author), USGS, ylor@usgs.gov;


Katie Bockrath (Co-Presenter/Co-Author), USFWS, katherine_bockrath@fws.gov;


S.Grace McCalla (Co-Presenter/Co-Author), USGS, smccalla@usgs.gov;


Jon Amberg (Co-Presenter/Co-Author), USGS, jamberg@usgs.gov;


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5/22/2018  |   14:15 - 14:30   |  420 B

MONITORING AQUATIC INVASIVE SPECIES THROUGH MULTI-MARKER METABARCODING: HOW DOES ENVIRONMENTAL DNA COMPARE TO ICHTHYOPLANKTON TOW SAMPLING? Ichthyoplankton tows provide one of the earliest possible detections of aquatic invasive species by collecting larval fish and eggs. However, ichthyoplankton tows can be costly, time consuming, and taxonomic identification of the larvae and eggs is challenging. Individual genetic identification of a larvae or egg can confirm visual identification when there is uncertainty, but the process is slow and tissue destructive. We developed a multi-marker sequencing (metabarcoding) method that can identify species of a fish community without destructive sampling or visually identifying each larvae or egg. By using an eDNA approach, non-destructive genetic identification of the entire tow is possible, allowing for specimen recovery if an invasive species is positively identified in a tow. We compared how accurately species identification can be determined by collecting DNA from ethanol used to preserve tow samples and using multiple genetic markers to identify the species composition of the tow. We also determined if environmental DNA in water collected simultaneously with the ichthyoplankton tow provides similar fish community data as the tow itself.

Maren Tuttle-Lau (Co-Presenter/Co-Author), USFWS, maren_tuttle-lau@fws.gov;


S.Grace McCalla (Co-Presenter/Co-Author), USGS, smccalla@usgs.gov;


Yer Lor (Co-Presenter/Co-Author), USGS, ylor@usgs.gov;


Katie Bockrath (Primary Presenter/Author), USFWS, katherine_bockrath@fws.gov;


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5/22/2018  |   14:30 - 14:45   |  420 B

HOW GENE MARKER AND PCR PRIMER CHOICE INFLUENCE DNA METABARCODING OF AQUATIC COMMUNITIES Molecular genetic tools like DNA barcoding/metabarcoding hold promise for improving our ability to characterize biotic composition, with relevance to detecting invasive species, monitoring species of concern, or describing diversity for bioassessments. To be most effective, these genetic techniques must work across various levels of biodiversity and while DNA barcoding is touted as ‘universally’ applicable, in practice, this is rarely the case. Using data from ballast water, larval fish, lake zooplankton, and stream periphyton communities, we will discuss how decisions about choice of genetic marker and PCR primers influence analyses of aquatic biodiversity, including taxonomic resolution, species composition, and measures of dominance or rarity of component taxa. We will also discuss the challenge of combining data across multiple genetic markers in an effort to provide guidance for future aquatic DNA barcoding research.

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

Aabir Banerji (Co-Presenter/Co-Author), U.S. EPA, banerji.aabir@epa.gov;


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


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


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


Aaron P. Maloy (Co-Presenter/Co-Author), United States Fish and Wildlife Service, Northeast Fishery Center, aaron_maloy@fws.gov;


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


Richard Mitchell (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, mitchell.richard@epa.gov;
Richard Mitchell is a biologist with EPA’s Office of Wetland Oceans and Watersheds. He is a team member of the National Aquatic Resource Surveys (NARS) and has led the National Rivers and Stream Assessment (NRSA) for over seven years. In additional to leading NRSA, he has been involved in various effort to develop biological indicators for use in NARS, and more general for the bioassessment community.

Christy Meredith (Co-Presenter/Co-Author), NRC Fellow, USEPA, MED,Duluth MN, Meredith.Christy@epa.gov;


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


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


Lester Yuan (Co-Presenter/Co-Author), U.S. Environmental Protection Agency, yuan.lester@epa.gov;


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5/22/2018  |   14:45 - 15:00   |  420 B

COMPARISON OF ELECTROFISHING AND ENVIRONMENTAL DNA DETECTION METHODOLOGIES IN SMALL COLD WATER STREAMS Use of eDNA can provide insight into fish biodiversity surveys when electrofishing may not be feasible. However, studies that directly compare the data obtained from traditional techniques to those using eDNA are needed. The two primary eDNA detection techniques are quantitative PCR (qPCR) and metabarcoding. qPCR is used for the targeted detection of a specific species, while metabarcoding is used for assessment of the broader species community. Here we evaluated the effectiveness of qPCR and metabarcoding for species detection relative to electrofishing. For five small (<25 cfs) coldwater streams, no differences were found in the relative abundance measures obtained using qPCR, metabarcoding, and electrofishing. In all cases, species data recovered using the various techniques were highly correlated (Pearson r > 0.88). These data suggest that similar measures of presence/absence and relative abundance can be obtained using eDNA detection techniques in small, relatively non-complex stream habitats as compared to that of electrofishing. Additional studies are necessary to evaluate the repeatability of this work and whether similar results can be obtained from a wider diversity of habitat types with increasing species complexity.

Aaron P. Maloy (Primary Presenter/Author), United States Fish and Wildlife Service, Northeast Fishery Center, aaron_maloy@fws.gov;


Christopher B. Rees (Co-Presenter/Co-Author), United States Fish and Wildlife Service, Northeast Fishery Center, Christopher_Rees@fws.gov;


Henry R. Quinlan (Co-Presenter/Co-Author), United States Fish and Wildlife Service, Ashland Fish and Wildlife Conservation Office, Henry_Quinlan@fws.gov;


Mark J. Brouder (Co-Presenter/Co-Author), United States Fish and Wildlife Service, Ashland Fish and Wildlife Conservation Office, mark_brouder@fws.gov;


Meredith L. Bartron (Co-Presenter/Co-Author), United States Fish and Wildlife Service, Northeast Fishery Center, meredith_bartron@fws.gov;


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

FRESHWATER QUALITY ASSESSMENT USING DIATOM DNA METABARCODING: PROGRESS AND PROSPECTS IN THE FRAME OF FRENCH RIVERS MONITORING NETWORKS DNA-metabarcoding of benthic diatoms has shown its potential for water quality assessment. Several optimizations have been proposed now for major steps of the workflow: taxonomic resolution of DNA barcodes, efficiency of DNA extraction methods, completion of barcode reference database, and use of correction factor to obtain taxa quantification equivalent to microscopy. Placed end-to-end, those improvements make the DNA-metabarcoding approach a viable alternative to the morphological approach (microscopy) for quality assessment of rivers in monitoring networks. We set up this bioassessment innovative approach, using the diatom rbcL barcode, at the scale of river monitoring networks in Mayotte Island and France. The DNA-metabarcoding approach proved to be faster and cheaper than the classical one. Molecular-based quality index values were highly correlated to morphological ones and congruent with the river quality status. Correlation between molecular and morphological based indices were increased by the completion of the reference database and the use of correction factors. Those results confirm the potential of DNA-metabarcoding for bioassessment, but also raised questions about the need of standardization and harmonization prior its implementation into biomonitoring campaigns.

Sinziana Rivera (Co-Presenter/Co-Author), INRA CARRTEL, sinziana.rivera@inra.fr;


Isabelle Domaizon (Co-Presenter/Co-Author), INRA CARRTEL, isabelle.domaizon@inra.fr;


Frédéric Rimet (Co-Presenter/Co-Author), INRA CARRTEL, frederic.rimet@inra.fr;


Agnès Bouchez (Co-Presenter/Co-Author), INRA (French National Institute for Agricultural Research), agnes.bouchez@inra.fr;


Valentin Vasselon (Primary Presenter/Author), INRA CARRTEL, Valentin.Vasselon@inra.fr;


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

MORPHOLOGICAL AND DNA METHODOLOGIES IN ASSESSING BENTHIC MACROINVERTEBRATE COMMUNITIES In 2015, we collected aquatic macroinvertebrates from 13 national parks in the National Capital Region Network. Historically, the National Park Service has sampled 11 of these sites and analyzed these data by subsampling 100 individuals. The first objective of this study was to determine the efficacy of only examining subsamples. Thus, we identified all organisms in the sample and compared this to 50 permutations of randomly selecting 100, 200 and 300 organism subsamples. The Brillouin diversity index of the entire sample was higher than that calculated on the computer-generated subsamples 75% of the time, illustrating that biodiversity is masked using traditional morphological protocols. Therefore, we explored the use of eDNA to evaluate samples and improve macroinvertebrate bioassessments. The second objective of this study was to examine the use of COI and 16S as markers for metabarcoding of aquatic macroinvertebrates. Ultimately, we made a large contribution to the effort of building a robust 16S rDNA barcode database for aquatic macroinvertebrate metabarcoding through the generation and curation of 74 unique sequences.

Aaron Aunins (Co-Presenter/Co-Author), U.S. Geological Survey, aaunins@usgs.gov;


Jay Stauffer (Co-Presenter/Co-Author), The Pennsylvania State University, vc5@psu.edu;


Sara Mueller (Primary Presenter/Author), The Pennsylvania State University, sjm5467@psu.edu;


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