Metagenomic-based ecosystem biomonitoring (the EcoBiomics project)


Funding period: 2016-2022
Participating Departments and Agencies: Agriculture and Agri-Food Canada, Canadian Food Inspection Agency, Environment and Climate Change Canada, Fisheries and Oceans Canada, National Research Council of Canada, Natural Resources Canada, Public Health Agency of Canada
Lead: Donald Baird, ECCC and James Macklin, AAFC
Total GRDI funding: $12,828,864

Biodiversity is paramount in water and soil to sustain diverse ecosystem services and economic activities across Canada. Genomics tools are the only tools available to characterize this complex biodiversity. The Ecobiomics project develops advanced genomics tools to assess freshwater ecosystem biodiversity and water quality in lakes and rivers; evaluate the health of soil essential to the productivity of agricultural and forestry systems across Canada; and investigate soil remediation for the oil and mining sectors.

The EcoBiomics Project (Transcript)

This project will enable a more comprehensive perspective of water and soil as living systems. The project involves scientists from 7 federal departments and agencies.


  • Agomoh IV, Drury CF, Yang X, Phillips LA, Reynolds WD. 2021. Crop rotation enhances soybean yields and soil health indicators. Soil Sci Soc Am J. 85(4): 1185–1195.
  • Bergsveinson J, Lawrence JR, Schebel A, Wasserscheid J, Roy J, Conly M, Sanschagrin S, Korber DR, Tremblay J, Greer C, Droppo I. 2021. Impact of sample collection on prokaryotic and eukaryotic diversity of niche environments of the oil-sand mining impacted Athabasca River. Can. J. Microbiol.
  • Bergsveinson J, Perry BJ, Simpson GL, Yost CKY, Schutzman RJ, Hall BD, Cameron ADS. 2019. Spatial analysis of a hydrocarbon waste-remediating landfarm demonstrates influence of management practices on bacterial and fungal community structure. Microbial Biotechnology. 12:1199–1209.
  • Bergsveinson J, Roy J, Maynard C, Sanschagrin S, Freeman C, Swerhone G, Dynes J, Tremblay J, Greer C, Korber D, Lawrence JR. 2020. Metatranscriptomic insights into the response of river biofilm communities to ionic and nano-zinc oxide exposures. Frontiers in Microbiology. 11:267.
  • Bush A, Compson ZG, Monk WA, Porter TM, Steeves R, Emilson E, Gagné N, Hajibabaei M, Roy M, Baird DJ. 2020. Studying ecosystems with DNA metabarcoding: Lessons from biomonitoring of aquatic invertebrates. Frontiers i Ecology and Evolution, 7: 434.
  • Bush A, Monk WA, Compson ZG, Peters DL, Porter TM, Shokralla S, Wright MTG, Hajibabaei M, Baird DJ. 2020. DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness. Proceedings of the National Academy of Sciences. 117: 8539-8545.
  • Chen W, Radford D, Hambleton S. 2021. Towards improved detection and identification of rust fungal pathogens in environmental samples using a metabarcoding approach. Phytopathology 2021, 112(3):535-548.
  • Compson ZG, Monk WA, Hayden B, Bush A, O'Malley Z, Hajibabaei M, Porter TM, Wright MTG, Baker CJO, Al Manir MS, Curry RA, Baird DJ. 2020. Network-based biomonitoring: exploring freshwater food webs with stable isotopes analysis and DNA metabarcoding. Frontiers in Ecology and Evolution. 7: 395.
  • Correa-García S, Rheault K, Tremblay K, Séguin A, Yergeau E. 2021. Soil characteristics constrain the response of microbial communities and associated hydrocarbon degradation genes during phytoremediation. Applied and Environmental Microbiology.
  • Drury CF, Reynolds WD, Yang XM, McLaughlin NB, Calder WC, Phillips LA. 2021. Diverse Rotations Impact Microbial Processes, Seasonality and Overall N2O Emissions from Soils. Revised manuscript under review Soil Science Society of America Journal S-2021-02-0048-CA.R1.
  • Edge TA, Baird DJ, Bilodeau G, Gagné N, Greer C, Konkin D, Newton G, Séguin A, Beaudette L, Bilkhu S, Bush A, Chen W, Comte J, Condie J, Crevecoeur S, El-Kayssi N, Emilson EJS, Fancy D-L, Kandalaft I, Khan IUH, King I, Kreutzweiser D, Lapen D, Lawrence J, Lowe C, Lung O, Martineau C, Meier M, Ogden N, Paré D, Phillips L, Porter TM, Sachs J, Staley Z, Steeves R, Venier L, Veres T, Watson C, Watson S, Macklin J. 2020. The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada, Science of The Total Environment. 710:135906. ISSN 0048-9697.
  • Hajibabaei M, Porter TM, Robinson CV, Baird DJ, Shokralla S, Wright MTG. 2019. Watered-down biodiversity? A comparison of metabarcoding results from DNA extracted from matched water and bulk Tissue biomonitoring samples. PLoS One, 14: e0225409.
  • Hitchcock A, Krüger P, Bittencourt C, Swerhone G, Lawrence JR. 2019. Spatially Resolved Soft X-ray Spectroscopy in Scanning X-ray Microscopes. Microscopy and Microanalysis. 25. 254-255.
  • Hussain SI, Phillips LA, Hu Y, Frey SK, Geuder DS, Edwards M, Lapen DR, Ptacek CJ, Blowes DW. 2021. Differences in phosphorus biogeochemistry and mediating microorganisms in the matrix and macropores of an agricultural clay loam soil, Soil Biol Biochem. 161:108365.
  • Joseph R, Diochon A, Morris D, et al. 2022. Limited effect of wood ash application on soil quality as indicated by a multisite assessment of soil organic matter attributes. Glob Change Biol Bioenergy 14:5, 500-521.
  • Laigle I, Moretti M, Rousseau L, Gravel D, Venier L, Handa IT, Messier C, Morris D, Hazlett PM Fleming R, Webster K, Shipley B, Aubin I. In Press. Direct and Indirect Effects of Forest Anthropogenic Disturbance on Above and Below Ground Communities and Litter Decomposition. Ecosystems.
  • Lawrence JR, Paule A, Swerhone G, Roy J, Grigoryan A, Dynes J, Chekabab SM, Korber DR. 2019. Microscale and molecular analyses of river biofilm communities treated with microgram levels of cerium oxide nanoparticles indicate limited but significant effects. Environmental Pollution. 256:113515.
  • Lawrence, JR, Waiser M, Swerhone G, Roy J, Paule A, Korber D. 2019. N,N,‐diethyl‐m‐toluamide (DEET) exposure at environmentally relevant concentration influences river microbial community development. Environ Toxicol Chem. 38(11):2414-2425.
  • Makiola A, Compson ZG, Baird DJ, et al. 2020. Key questions for next-generation biomonitoring. Frontiers in the Environment. 7:197.
  • Mechai S, Bilodeau GJ, Lung O, Roy M, Steeves R, Gagne N, Baird D, Lapen DR, Ludwig A, NH Ogden. 2021. Mosquito identification from bulk samples using DNA metabarcoding: a protocol to support mosquito-borne disease surveillance in Canada. Journal of Medical Entomology. 58(4):1686-1700.
  • Mekontchou CG, Houle D, Bergeron Y, Roy M, Gardes M, Séguin A,  Drobyshev I. 2022. Contrasting structure of root mycorrhizal communities of black spruce and trembling aspen in different layers of the soil profile in the boreal mixedwoods of eastern Canada. Plant and Soil.
  • Meier MJ, Dodge AE, Dias Samarajeewa A, Beaudette LA. 2020. Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles. Environmental Pollution 258:113816.
  • Payette G, Geoffroy V, Martineau C, Villemur R. 2019. Dynamics of a methanol-fed marine denitrifying biofilm: 1-Impact of environmental changes on the denitrification and the co-occurrence of Methylophaga nitratireducenticrescens and Hyphomicrobium nitrativorans. PeerJ 7:e7497.
  • Pérez-Carrascal OM, Terrat Y, Giani A, Fortin N, Greer CW, Tromas N, Shapiro J. 2019. Coherence of Microcystis species revealed through population genomics. ISME Journal, 13:2887–2900.
  • Pérez-Guzmán L, Phillips LA, Acosta-Martínez V. 2021. Comparing EL-FAME microbial markers and p-nitrophenol enzyme activities with taxonomic and functional gene qPCR for soil health assessments. Soil Sci Soc Am J. 85(3):636-653.
  • Pérez-Guzmán L, Phillips LA, Seuradge BJ, Agomoh I, Drury CF, Acosta-Martínez V. 2021. An evaluation of biological soil health indicators in four long-term continuous agroecosystems in Canada. Agrosystems, Geosciences & Environment. 4(2):e20164.
  • Porter TM, Hajibabaei M. 2021. Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets. BMC bioinformatics, 22(1):1-20.
  • Porter TM, Morris DM, Basiliko N, Hajibabaei M, Doucet D, Bowman S, Emilson EJS, Emilson CE, Chartrand D, Wainio-Keizer K, Séguin A, Venier L. 2019. Variations in terrestrial arthropod DNA metabarcoding methods recover robust beta diversity but variable richness and site indicators. Sci Rep 9:18218.
  • Rheault K, Lachance D, Morency M-J, Thiffault É, Guittonny M, Isabel N, Martineau C, Séguin A. 2020. Plant genotype influences physicochemical properties of substrate as well as bacterial and fungal assemblages in the rhizosphere of balsam poplar. Frontiers in Microbiology.
  • Samad A, Pelletier G, Séguin A, Degenhardt D, Muench DG, Martineau M. 2022. Understanding willow transcriptional response in the context of tailings reclamation of oil sands exploitation. Frontiers in Plant Science.
  • Savard MM, Martineau C, Laganière J, Bégin C, Marion J, Smirnoff A, Stefani F, Bergeron J, Rheault K, Paré D, Séguin A. 2021. Nitrogen isotopes in the soil-to-tree continuum – Tree-rings express the soil biogeochemistry of boreal forests exposed to moderate airborne emissions. Science of the Total Environment. 780:146581.
  • Smenderovac E, Emilson C, Porter T, et al. 2022. Forest soil biotic communities show few responses to wood ash applications at multiple sites across Canada. Sci Rep 12:4171.
  • Tremblay, J, Yergeau E. 2019. Systematic processing of ribosomal RNA gene amplicon sequencing data. GigaScience 8(12) giz146.
  • Venier LA, Walton R, Brandt JP. 2021. Scientific considerations and challenges for addressing cumulative effects in forest landscapes in Canada. Environmental Reviews.
  • Villemur R, Payette G, Geoffroy V, Mauffrey F, Martineau C. 2019. Dynamics of a methanol-fed marine denitrifying biofilm: 2-Impact of environmental changes on the microbial community. PeerJ 7:e7467.

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Genomics R&D Initiative