Bio2 Team co-hosts major biomonitoring science forum

The Environment Canada Canadian Aquatic Biomonitoring Network (CABIN) Team and the Biodiversity Institute of Ontario, University of Guelph, co-hosted the 3nd biennial CABIN Science Forum on December 2-3, 2014 in Guelph, Ontario. Previous science forums were held in Vancouver, BC in 2010 and Fredericton, NB in 2012. The 2-day forum (agenda) included themed sessions with short presentations by CABIN partners, followed by discussion periods. The forum also included tours of the facilities of the University of Guelph’s Biodiversity Institute and Centre for Biodiversity Genomics. One of the main themes was “Biomonitoring 2.0: Genomics and its application in Biomonitoring”. In total, over 70 attendees from industry, government, and academia were in attendance with nearly 100 more participating via web conference.

Plenary speakers from Canada, USA, and China came to present some of their recent genomic biomonitoring research and participate in the discussion, including:

  • Xiaowei Zhang; Nanjing University; “Environmental Genomics Reveal Environmental Threshold of Ammonia for the Protection of Zooplankton in Freshwater Ecosystem”
  • Eric Stein; Southern California Coastal Water Research Project; “Application of eDNA and Metabarcoding to Routine Stream and Wetland Biomonitoring Programs in California”
  • Erik Pilgrim; US EPA; “Expanding Bioassessment into Understudied or Novel Communities through DNA Metabarcoding”
  • Joel Gibson; University of Guelph; “Assessing Boreal Aquatic Ecosystems using DNA Metasystematics and Next-generation Sequencing”
  • Shadi Shokralla; University of Guelph; “Biomonitoring 2.0: a New Implementation of Next-generation Sequencing Technologies for Environmental DNA Research and Ecosystem Assessment”


The discussion of genomics and biomonitoring gets lively.


Bio2 team member, Shadi Shokralla, leads forum attendees through a tour of the University of Guelph lab facilities.

Biomonitoring 2.0 hosts major molecular workshops at the Joint Aquatic Sciences Meeting

May, 2014 saw the first ever Joint Aquatic Sciences Meeting iunnamedn Portland, Oregon. Over 3,500 members of the Society for Freshwater Science, Association for the Sciences of Limnology and Oceanography, Phycological Society of America, and Society of Freshwater Scientists gathered for a five-day meeting. Members of the Biomonitoring 2.0 team were present in full force with presentations and posters given by students, postdocs, and collaborators in the project. Team members were also instrumental in organizing collaborative workshops focusing on the use of genomic data in the bioassessment of wetlands. These workshops brought together international researchers to discuss results and future plans. Stay posted for future developments in this network of wetlands scientists.







Biomonitoring 2.0 team publishes NGS biodiversity results in PNAS

Web-Malaise-GibsonPNASstory-SmallThe Biomonitoring 2.0 team published their latest findings in the Proceedings of the National Academy of Science, USA. The Gibson et al. study continues the teams’ research into timely, cost-effective approaches to identifying the contents of species-rich mixed environmental samples. Using next-generation sequencing (NGS) of the cytochrome c oxidase subunit I (COI), 16S ribosomal, and 18S ribosomal gene regions, the authors were able to accurately detect 91% of the 1,066 individuals morphologically identified from a single Malaise trap from Costa Rica’s Area de Conservación Guanacaste. For the first time bacteria and protozoa were detected in the passively collected mixed arthropod sample, including insect-associated microbes. This latest publication advances the team’s efforts to integrate a metasystematic approach into biodiversity research and monitoring.

To download the Open Access article, please visit:

Student and PostDoc presentations at the OE3C

The Hajibabaei Lab was well represented at the Ontario Ecology Evolution and Ethology Colloquium (OE3C) held May 8-10th, 2014 at the University of Guelph. Students, post docs, and faculty from universities all over the province (as well as a few out of province) were in attendance, presenting research from a diverse range of topics. Joel Gibson, post-doctoral fellow and Biomonitoring 2.0 project manager, captured the audience’s attention with his compelling talk on the merits of DNA metabarcoding approaches. Graduate students Lisa Ledger, Nicole Fahner (also part of Biomonitoring 2.0), and Gina Capretta followed this up with poster presentations on their respective research projects and fielded questions from excited researchers. Of note, Lisa was awarded first place for her poster on environmental metabarcoding for beta diversity assessment of Costa Rican tropical dry forest!




2013 field sampling with the local community

August 2013 was an exciting month for the Biomonitoring 2.0 project. Team members once again traveled to Fort Smith, Northwest Territories and Fort Chipewyan, Alberta. In addition to sampling within Wood Buffalo National Park, new field sampling sites were selected. These new sites were selected as part of a project focus on integrating new genomic techniques with the needs of local stakeholders.

The Dog River and the Salt River are two major tributaries of the Slave River. Members of the Salt River First Nations helped to select sites along the Salt River which winds along the northeast corner of Wood Buffalo National Park. A crew of field technicians and summer students from the Smith’s Landing First Nations assisted with sampling on the Dog River which empties into the North side of the Slave River. Team members from Smith’s Landing were able to provide an oral account of the present and historical
use of the Dog River for fishing and trapping.

Water, soil, benthic, and terrestrial arthropod samples were gathered from key sites along both rivers. These samples were then brought back to Guelph for genomic analysis. The results will be brought back to Fort Smith in 2014 and presented to First Nations team members. Together, all team members will determine the best interpretation and future use of genomic data for biomonitoring activities.