Monday, May 23, 2016
15:30 - 17:00

<< Back to Schedule

15:30 - 15:45: / 304-305 BIOMONITORING, BUT NOT AS WE KNOW IT. MEETING THE CHALLENGE OF DNA-BASED OBSERVATION IN BIOASSESSMENT.

5/23/2016  |   15:30 - 15:45   |  304-305

BIOMONITORING, BUT NOT AS WE KNOW IT. MEETING THE CHALLENGE OF DNA-BASED OBSERVATION IN BIOASSESSMENT. The emergence of DNA as a detectable and quantifiable unit of observation in biodiversity science is arguably the single most important technical advance in ecology in our lifetimes. Biomonitoring, which relies on assessment of the composition of biological samples, has been an early adopter, using sample-extracted DNA to generate taxon lists as an alternative to laborious sorting and identification. Yet while this new technique allows us to observe systems at an unprecedented level of detail, it yields information which has critically different properties from traditional methods. First, the unit of observation shifts from individuals towards the detection of short DNA sequences. The bioinformatics challenge of detecting and enumerating these gene sequences has now largely been solved, although library development is lagging. However, a greater challenge remains to be addressed: how do we relate the occurrence of gene fragments in environmental samples to traditional observational data, and its associated body of ecological indices and ecological interpretation tools which support standard biomonitoring practice? By deconstructing some accepted truths of biomonitoring, I will demonstrate the transformative nature of this new observation method.

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


Presentation:
This presentation has not yet been uploaded.

15:45 - 16:00: / 304-305 GROUND TRUTHING DNA METABARCODING: PRIMERS, BIOMASS AND SPECIMEN SORTING

5/23/2016  |   15:45 - 16:00   |  304-305

GROUND TRUTHING DNA METABARCODING: PRIMERS, BIOMASS AND SPECIMEN SORTING DNA based identification of macrozoobenthos with DNA metabarcoding has the potential to fundamentally revolutionize the assessment of stream ecosystem health. In comparison to classical morphology-based assessments, high throughput sequencing approaches claim to provide a higher taxonomic resolution and comparable results while being cheaper and quicker at the same time. Currently, a wide range of laboratory protocols and bioinformatics approaches are used in case studies, but further rigorous method validation is needed to unveil also short comings and limitations of current strategies. Under this premise, we here used mock communities and complete kick samples to validate a single step PCR approach, which uses freshwater specific COI fusion primers, omitting the need for complicated library preparation. We used the Illumina MiSeq, NextSeq and HiSeq systems to explore primer bias, biomass / sequence abundance relationships, replication, alternative markers (16S), and effectiveness of sample presorting by biomass. Additionally, complete kick samples were identified morphologically and against our DNA metabarcoding approach. While few technical and conceptual issues need to be solved, our metabarcoding approach has unique strengths and can be applied for routine application.

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


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


Presentation:
This presentation has not yet been uploaded.

16:00 - 16:15: / 304-305 TOWARDS STANDARDIZATION OF DNA EXTRACTION FOR NEXT-GENERATION BIOMONITORING WITH DIATOMS

5/23/2016  |   16:00 - 16:15   |  304-305

TOWARDS STANDARDIZATION OF DNA EXTRACTION FOR NEXT-GENERATION BIOMONITORING WITH DIATOMS Current freshwater biomonitoring with diatoms is based on morphological analysis of their silica frustule, using microscope. This standardized approach is however time consuming and requires a high degree of taxonomic expertize. Nowadays, metabarcoding combined to high-throughput sequencing (HTS) is foreseen for next-generation biomonitoring, but still requires standardization. The first step to be standardized is DNA extraction from environmental samples. Five methods, combining various types of cell lysis and of DNA purification, were compared on 8 diatom pure cultures and 8 freshwater samples from sites with contrasted quality status and geographical origin. Methods were compared based on 1/ extracted-DNA quality and purity, 2/ community inventories from HTS (rbcL barcode), 3/ correlation with microscopy inventories and 4/ inferred quality indices. Even if the community composition remained stable whatever the DNA-extraction method, variations in the relative abundance of some abundant taxa were observed. IPS quality index values based on HTS and microscopy were well correlated for all methods. However, despite lower DNA purity, one of the methods showed higher DNA quantity together with higher fidelity to microscopy and seems promising for standardization.

Valentin Vasselon (Primary Presenter/Author), INRA, UMR CARRTEL, Thonon, France, valentin.vasselon@thonon.inra.fr;


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


Maria Kahlert ( Co-Presenter/Co-Author), Department of Aquatic Sciences and Assessment, SLU, Uppsala, Sweden, Maria.Kahlert@slu.se;


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


Agnès Bouchez ( Co-Presenter/Co-Author), INRA, UMR CARRTEL, Thonon, France, agnes.bouchez@thonon.inra.fr;


Presentation:
This presentation has not yet been uploaded.

16:15 - 16:30: / 304-305 METABARCODING AND HIGH-THROUGHPUT SEQUENCING FOR ASSESSING RIVER ECOLOGICAL QUALITY WITH DIATOM INDICES AT THE SCALE OF A REGULAR MONITORING NETWORK.

5/23/2016  |   16:15 - 16:30   |  304-305

METABARCODING AND HIGH-THROUGHPUT SEQUENCING FOR ASSESSING RIVER ECOLOGICAL QUALITY WITH DIATOM INDICES AT THE SCALE OF A REGULAR MONITORING NETWORK. Diatoms are excellent indicators of freshwater pollution and are currently used to monitor ecological quality in rivers. Standardized methodologies are based on microscopic determinations which are time consuming and prone to identification uncertainties. Use of metabarcoding is a way to avoid these shortcomings. High-throughput sequencing (HTS) now offers the opportunity to implement this approach at the scale of regular biomonitoring networks. Following proof-of-concept studies, we applied the metabarcoding approach to the monitoring of the river network of Mayotte (French oversea territory) in the context of the European Water Framework Directive (WFD). We sequenced 88 diatom samples collected in Mayotte Rivers over 2 years using HTS Ion-Torrent technology. Taxonomic identification was done using the curated reference database, called R-Syst::diatom, that we recently released in open-access. Diatom quality indices obtained from HTS inventories were compared to those obtained from microscopic inventories based on morphology. HTS and microscopy inventories of diatom species were significantly correlated. Derived quality indices were also significantly correlated between the 2 approaches opening interesting perspectives for high-throughput biomonitoring in regular networks. Bioassessment can now learned lessons from these studies.

Agnès Bouchez (Primary Presenter/Author), INRA, UMR CARRTEL, Thonon, France, agnes.bouchez@thonon.inra.fr;


Cecile Chardon ( Co-Presenter/Co-Author), INRA, UMR CARRTEL, Thonon, France, cecile.chardon@thonon.inra.fr;


François Keck ( Co-Presenter/Co-Author), INRA, UMR CARRTEL, Thonon, France, francois.keck@thonon.inra.fr;


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


Kalman Tapolczai ( Co-Presenter/Co-Author), INRA, UMR CARRTEL, Thonon, France, kalman.tapolczai@thonon.inra.fr;


Valentin Vasselon ( Co-Presenter/Co-Author), INRA, UMR CARRTEL, Thonon, France, valentin.vasselon@thonon.inra.fr;


Presentation:
This presentation has not yet been uploaded.

16:30 - 16:45: / 304-305 COMPARING METAGENOMIC AND MORPHOLOGICAL PERIPHYTON ASSEMBLAGE DATA TO MAJOR ENVIRONMENTAL GRADIENTS

5/23/2016  |   16:30 - 16:45   |  304-305

COMPARING METAGENOMIC AND MORPHOLOGICAL PERIPHYTON ASSEMBLAGE DATA TO MAJOR ENVIRONMENTAL GRADIENTS Biomonitoring has historically utilized morphological identifications to assess biological assemblages, but in recent years, new methods have been developed that allow for faster and more complete identification of biological assemblages by DNA metabarcoding. Unlike morphological data, metabarcoding allows for a broader identification of taxonomic groups such as Fungi that are infrequently identified in morphological studies. In the current study we use side-by-side samples collected during the summer of 2014 as part of US EPA’s National Rivers and Streams Assessment to compare and contrast relationships between DNA identification and morphological periphyton assemblage data and major environmental gradients. This study allowed for a direct comparisons of the two taxonomic identification techniques over a large spatial scale to assess their efficacy at identifying important environmental gradients that may be driving periphyton assemblages. Initial findings show primary producers from the genetic and morphological data share similar relationships to certain environmental gradients (e.g. conductivity and total nitrogen), but genetic results suggest additional periphyton groups not typically assessed also show strong relationships that may provide additional insights.

Richard Mitchell (Primary Presenter/Author), U.S. Environmental Protection Agency, mitchell.richard@epa.gov;


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


Amina Pollard ( Co-Presenter/Co-Author), U.S. Environmental Protection Agency, pollard.amina@epa.gov;


Erik Pilgrim ( Co-Presenter/Co-Author), USEPA/NERL/SED, Cincinnati, OH, pilgrim.erik@epa.gov;


Presentation:
This presentation has not yet been uploaded.

16:45 - 17:00: / 304-305 A COI LIBRARY FOR NORTH AMERICAN FRESHWATER INVERTEBRATE GENERA: PROGRESS, PITFALLS AND PROSPECTS

5/23/2016  |   16:45 - 17:00   |  304-305

A COI LIBRARY FOR NORTH AMERICAN FRESHWATER INVERTEBRATE GENERA: PROGRESS, PITFALLS AND PROSPECTS Identification of taxa from bulk samples of environmental DNA is currently limited by the availability of reference barcode sequences. We assessed genus-level COI sequence availability for North American freshwater invertebrate genera in public databases (GenBank, BOLD), to explore the relative representation of key taxonomic groups. For those groups with sufficient sequence data, we assessed sequence metadata including geographic coverage. A list of >2500 genera was compiled from literature and online searches. Overall, 55.2% of genera were represented. Molluscs showed the greatest coverage (73%), while nematodes were poorest (15%). Nearly two-thirds of insect genera were represented. However, more detailed investigations revealed additional issues: restricted geographic distribution of sequences, skewed distributions among genera and species within groups, multiple sequences from the same individual and erroneous sequences (e.g. Wolbachia). To support the adoption of genomic tools in biomonitoring, effort is needed to expand reference libraries, particularly for poorly studied taxa and genera with biased sequence coverage. Genus-level identification represents substantial improvement in taxonomic resolution for biomonitoring and can support the development of diagnostic metrics linked to trait and trophic interaction data.

Colin Curry (Primary Presenter/Author), Environment Canada @ Canadian Rivers Institute, colin.curry@unb.ca;


Joel Gibson ( Co-Presenter/Co-Author), Royal British Columbia Museum, jfgibson@uoguelph.ca;


Shadi Shokralla ( Co-Presenter/Co-Author), University of Guelph, shadi.shokralla@gmail.com;


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


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


Presentation:
This presentation has not yet been uploaded.