The Ecobiomics project : Advancing metagenomics assessment of soil health and freshwater quality in Canada

Edge, Thomas A. and Baird, Donald J. and Bilodeau, Guillaume and Gagné, Nellie and Greer, Charles and Konkin, David and Newton, Glen and Séguin, Armand and Beaudette, Lee and Bilkhu, Satpal and Bush, Alexander and Chen, Wen and Comte, Jérôme and Condie, Janet and Crevecoeur, Sophie and El-Kayssi, Nazir and Emilson, Erik J.S. and Fancy, Donna Lee and Kandalaft, Iyad and Khan, Izhar U.H. and King, Ian and Kreutzweiser, David and Lapen, David and Lawrence, John and Lowe, Christine and Lung, Oliver and Martineau, Christine and Meier, Matthew and Ogden, Nicholas and Paré, David and Phillips, Lori and Porter, Teresita M. and Sachs, Joel and Staley, Zachery and Steeves, Royce and Venier, Lisa and Veres, Teodor and Watson, Cynthia and Watson, Susan and Macklin, James (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

Abstract

Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.