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

Research output: Contribution to Journal/Magazine › Comment/debate › peer-review

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The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. / Edge, Thomas A.; Baird, Donald J.; Bilodeau, Guillaume et al.
In: Science of the Total Environment, Vol. 710, 135906, 25.03.2020.

Research output: Contribution to Journal/Magazine › Comment/debate › peer-review

Harvard

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, DL, 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, vol. 710, 135906. https://doi.org/10.1016/j.scitotenv.2019.135906

APA

Edge, T. A., Baird, D. J., 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, E. J. S., Fancy, D. L., Kandalaft, I., ... Macklin, J. (2020). The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. Science of the Total Environment, 710, Article 135906. https://doi.org/10.1016/j.scitotenv.2019.135906

Vancouver

Edge TA, Baird DJ, Bilodeau G, Gagné N, Greer C, Konkin D et al. The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. Science of the Total Environment. 2020 Mar 25;710:135906. Epub 2019 Dec 5. doi: 10.1016/j.scitotenv.2019.135906

Author

Edge, Thomas A. ; Baird, Donald J. ; Bilodeau, Guillaume et al. / The Ecobiomics project : Advancing metagenomics assessment of soil health and freshwater quality in Canada. In: Science of the Total Environment. 2020 ; Vol. 710.

Bibtex

@article{508c388f7aae4076ad95318cf3f349b1,
title = "The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada",
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.",
keywords = "Invertebrate biodiversity, Metagenomics, Microbiomes, Soil health, Water quality",
author = "Edge, {Thomas A.} and Baird, {Donald J.} and Guillaume Bilodeau and Nellie Gagn{\'e} and Charles Greer and David Konkin and Glen Newton and Armand S{\'e}guin and Lee Beaudette and Satpal Bilkhu and Alexander Bush and Wen Chen and J{\'e}r{\^o}me Comte and Janet Condie and Sophie Crevecoeur and Nazir El-Kayssi and Emilson, {Erik J.S.} and Fancy, {Donna Lee} and Iyad Kandalaft and Khan, {Izhar U.H.} and Ian King and David Kreutzweiser and David Lapen and John Lawrence and Christine Lowe and Oliver Lung and Christine Martineau and Matthew Meier and Nicholas Ogden and David Par{\'e} and Lori Phillips and Porter, {Teresita M.} and Joel Sachs and Zachery Staley and Royce Steeves and Lisa Venier and Teodor Veres and Cynthia Watson and Susan Watson and James Macklin",
year = "2020",
month = mar,
day = "25",
doi = "10.1016/j.scitotenv.2019.135906",
language = "English",
volume = "710",
journal = "Science of the Total Environment",
issn = "0048-9697",
publisher = "Elsevier Science B.V.",

}

RIS

TY - JOUR

T1 - The Ecobiomics project

T2 - Advancing metagenomics assessment of soil health and freshwater quality in Canada

AU - Edge, Thomas A.

AU - Baird, Donald J.

AU - Bilodeau, Guillaume

AU - Gagné, Nellie

AU - Greer, Charles

AU - Konkin, David

AU - Newton, Glen

AU - Séguin, Armand

AU - Beaudette, Lee

AU - Bilkhu, Satpal

AU - Bush, Alexander

AU - Chen, Wen

AU - Comte, Jérôme

AU - Condie, Janet

AU - Crevecoeur, Sophie

AU - El-Kayssi, Nazir

AU - Emilson, Erik J.S.

AU - Fancy, Donna Lee

AU - Kandalaft, Iyad

AU - Khan, Izhar U.H.

AU - King, Ian

AU - Kreutzweiser, David

AU - Lapen, David

AU - Lawrence, John

AU - Lowe, Christine

AU - Lung, Oliver

AU - Martineau, Christine

AU - Meier, Matthew

AU - Ogden, Nicholas

AU - Paré, David

AU - Phillips, Lori

AU - Porter, Teresita M.

AU - Sachs, Joel

AU - Staley, Zachery

AU - Steeves, Royce

AU - Venier, Lisa

AU - Veres, Teodor

AU - Watson, Cynthia

AU - Watson, Susan

AU - Macklin, James

PY - 2020/3/25

Y1 - 2020/3/25

N2 - 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.

AB - 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.

KW - Invertebrate biodiversity

KW - Metagenomics

KW - Microbiomes

KW - Soil health

KW - Water quality

U2 - 10.1016/j.scitotenv.2019.135906

DO - 10.1016/j.scitotenv.2019.135906

M3 - Comment/debate

C2 - 31926407

AN - SCOPUS:85077650216

VL - 710

JO - Science of the Total Environment

JF - Science of the Total Environment

SN - 0048-9697

M1 - 135906

ER -