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Title: Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture

Abstract

Management of soil biological resources to optimise plant production, efficiency of nutrient inputs, and system sustainability is an emerging opportunity for pastoral agriculture. To attain these goals, suitable tools that can assess the functional state of the soil ecosystem must be developed and standardised approaches to their application adopted. Towards this end, we have undertaken comprehensive, high-density functional-gene microarray analysis (GeoChip5) of environmental DNA (eDNA) extracted from 50 pastoral soils. When combined with soil, environmental and management metadata, the information can be used to provide insights into soil biological processes spanning greenhouse gas emissions, through to natural suppression of plant root diseases. To give an example of a structured workflow of analysis in a pastoral system context, we analysed the GeoChip data using a combination of approaches spanning routine univariate methods through to more complex multivariate and network-based analysis. Analyses were restricted to comparing effects of land-use (dairy or ‘other’ farming systems), and exploring relationships of the GeoChip data with the soil properties from each sample. These exemplar analyses introduce a pathway for the application of eDNA approaches (GeoChip or others) to deliver outcomes for pastoral agricultural in New Zealand.

Authors:
 [1];  [1];  [2];  [1];  [3];  [4];  [5];  [6];  [1]
+ Show Author Affiliations
  1. AgResearch Ltd, Christchurch (New Zealand)
  2. AgResearch Ltd, Christchurch (New Zealand); Lincoln Univ., Canterbury (New Zealand)
  3. AgResearch Ltd, Christchurch (New Zealand); Univ. of Thessaly, Larisa (Greece)
  4. Lincoln Univ., Canterbury (New Zealand)
  5. Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tsinghua Univ., Beijing (China)
  6. Univ. of Oklahoma, Norman, OK (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1567065
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
New Zealand Journal of Agricultural Research (New Zealand)
Additional Journal Information:
Journal Name: New Zealand Journal of Agricultural Research (New Zealand); Journal Volume: 59; Journal Issue: 4; Journal ID: ISSN 0028-8233
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Data analysis; eDNA; environmental genomics; GeoChip; soil ecosystem function

Citation Formats

Wakelin, Steve A, Cave, VM, Dignam, BE, D’Ath, C., Tourna, M., Condron, LM, Zhou, J., Van Nostrand, JD, and O’Callaghan, M. Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture. United States: N. p., 2016. Web. doi:10.1080/00288233.2016.1209529.
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Wakelin, Steve A, Cave, VM, Dignam, BE, D’Ath, C., Tourna, M., Condron, LM, Zhou, J., Van Nostrand, JD, & O’Callaghan, M. Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture. United States. https://doi.org/10.1080/00288233.2016.1209529
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Wakelin, Steve A, Cave, VM, Dignam, BE, D’Ath, C., Tourna, M., Condron, LM, Zhou, J., Van Nostrand, JD, and O’Callaghan, M. Mon . "Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture". United States. https://doi.org/10.1080/00288233.2016.1209529. https://www.osti.gov/servlets/purl/1567065.
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@article{osti_1567065,
title = {Analysis of soil eDNA functional genes: potential to increase profitability and sustainability of pastoral agriculture},
author = {Wakelin, Steve A and Cave, VM and Dignam, BE and D’Ath, C. and Tourna, M. and Condron, LM and Zhou, J. and Van Nostrand, JD and O’Callaghan, M.},
abstractNote = {Management of soil biological resources to optimise plant production, efficiency of nutrient inputs, and system sustainability is an emerging opportunity for pastoral agriculture. To attain these goals, suitable tools that can assess the functional state of the soil ecosystem must be developed and standardised approaches to their application adopted. Towards this end, we have undertaken comprehensive, high-density functional-gene microarray analysis (GeoChip5) of environmental DNA (eDNA) extracted from 50 pastoral soils. When combined with soil, environmental and management metadata, the information can be used to provide insights into soil biological processes spanning greenhouse gas emissions, through to natural suppression of plant root diseases. To give an example of a structured workflow of analysis in a pastoral system context, we analysed the GeoChip data using a combination of approaches spanning routine univariate methods through to more complex multivariate and network-based analysis. Analyses were restricted to comparing effects of land-use (dairy or ‘other’ farming systems), and exploring relationships of the GeoChip data with the soil properties from each sample. These exemplar analyses introduce a pathway for the application of eDNA approaches (GeoChip or others) to deliver outcomes for pastoral agricultural in New Zealand.},
doi = {10.1080/00288233.2016.1209529},
journal = {New Zealand Journal of Agricultural Research (New Zealand)},
number = 4,
volume = 59,
place = {United States},
year = {Mon Jul 25 00:00:00 EDT 2016},
month = {Mon Jul 25 00:00:00 EDT 2016}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1080/00288233.2016.1209529
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Cited by: 9 works
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Figures / Tables:

Figure 1 Figure 1: Pipeline of analysis of environmental genomics for applied pastoral productive and environmental outcomes. Collection of soil for environmental genomics can (and should) be made alongside analysis of other soil properties (pH, C, N, P, S, etc). Standard field sampling (corer with numerous subsamples across the field) and homogenisationmore » of the soil sample allows for representative ‘DNA’ to be extracted. Extraction of eDNA from soils is now routine, with commercially available kits and service providers. Analysis of eDNA can be conducted using a range of different methods, most of which are accessible through service providers. Routine analysis, such as qPCR, can be conducted by most biologically focused research institutes. The approach for data will be highly dependent on the intended use for the researcher or farmer. For example, understanding how farm management pathways result in emergence of soil-borne disease suppression; this will require highly complex analysis based on ecosystem reconstruction. Many farmers, however, maybe interested in detection of key genes of interest for their farming system; e.g. are there sufficient rhizobia in the soil to enable clover nodulation, or what is the disease and pathogen load of a soil before pasture renovation (allowing for targeted pesticide use)? These analyses, therefore, enable ‘informed decision making’ that takes into consideration soil biological resources. The use of this approach builds, over time, an understanding of the normal operating range of farming systems, identifies new opportunities to alter the trajectory of emergence of functions, and provides a basis to benchmark performance and ideally build genetic gain.« less
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    Works referencing / citing this record:

    A review on the applications and recent advances in environmental DNA (eDNA) metagenomics
    journal, July 2019

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    • Reviews in Environmental Science and Bio/Technology, Vol. 18, Issue 3
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    Managing soil microbiology: realising opportunities for the productive land-based sectors
    journal, February 2018

    Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture
    journal, July 2019

    • Attwood, Graeme T.; Wakelin, Steve A.; Leahy, Sinead C.
    • Frontiers in Nutrition, Vol. 6
    • DOI: 10.3389/fnut.2019.00107

    Applications of the Soil, Plant and Rumen Microbiomes in Pastoral Agriculture
    journal, July 2019

    • Attwood, Graeme T.; Wakelin, Steve A.; Leahy, Sinead C.
    • Frontiers in Nutrition, Vol. 6
    • DOI: 10.3389/fnut.2019.00107
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