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

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Published
  • Thomas A. Edge
  • Donald J. Baird
  • Guillaume Bilodeau
  • Nellie Gagné
  • Charles Greer
  • David Konkin
  • Glen Newton
  • Armand Séguin
  • Lee Beaudette
  • Satpal Bilkhu
  • Wen Chen
  • Jérôme Comte
  • Janet Condie
  • Sophie Crevecoeur
  • Nazir El-Kayssi
  • Erik J.S. Emilson
  • Donna Lee Fancy
  • Iyad Kandalaft
  • Izhar U.H. Khan
  • Ian King
  • David Kreutzweiser
  • David Lapen
  • John Lawrence
  • Christine Lowe
  • Oliver Lung
  • Christine Martineau
  • Matthew Meier
  • Nicholas Ogden
  • David Paré
  • Lori Phillips
  • Teresita M. Porter
  • Joel Sachs
  • Zachery Staley
  • Royce Steeves
  • Lisa Venier
  • Teodor Veres
  • Cynthia Watson
  • Susan Watson
  • James Macklin
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Article number135906
<mark>Journal publication date</mark>25/03/2020
<mark>Journal</mark>Science of the Total Environment
Volume710
Number of pages11
<mark>State</mark>Published
Early online date5/12/19
<mark>Original language</mark>English

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.