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Discussion papers
https://doi.org/10.5194/soil-2019-42
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/soil-2019-42
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.

Forum article 10 Jul 2019

Forum article | 10 Jul 2019

Review status
This discussion paper is a preprint. It is a manuscript under review for the journal SOIL (SOIL).

Identification of new microbial functional standards for soil quality assessment

Sören Thiele-Bruhn1, Michael Schloter2, Berndt-Michael Wilke3, Lee A. Beaudette4, Fabrice Martin-Laurent5, Nathalie Cheviron6, Christian Mougin6, and Jörg Römbke7 Sören Thiele-Bruhn et al.
  • 1Universität Trier, Bodenkunde, Behringstr. 21, 54286 Trier, Germany
  • 2Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Abteilung für vergleichende Mikrobiomanalysen, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
  • 3TU Berlin, FG Bodenkunde, Ernst-Reuter-Platz 1, 10587 Berlin, Germany
  • 4Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1A 0H3, Canada
  • 5AgroSup Dijon, INRA, Université Bourgogne, Université Bourgogne Franche-Comté, Agroécologie, 17 rue Sully, 21065 Dijon Cédex, France
  • 6UMR ECOSYS, Platform Biochem-Env, INRA, AgroParisTech, Université Paris-Saclay, 78026, Versailles, France
  • 7ECT Oekotoxikologie GmbH, Böttgerstr. 2-14, 65439 Flörsheim, Germany

Abstract. The activity of microorganisms in soil is important for a robust functioning soil and related ecosystem service. Hence, there is a necessity to identify the indigenous soil microbial community for its functional properties using soil microbiological methods in order to determine the natural properties, functioning and operating range of soil microbial communities, and to assess ecotoxicological effects due to anthropogenic activities. Numerous microbiological methods currently exist in the literature and new, more advanced methods continue to be developed; however, only a limited number of the methods are standardized. Consequently, there is a need to identify the most promising non-standardized methods for assessing soil quality and develop these into standards. In alignment with the "Ecosystem Service Approach", new methods should focus on soil microbial function, including nutrient cycling, pest control and plant growth promotion, carbon cycling and sequestration, greenhouse gas emission, and soil structure. The few existing, function-related standard methods available focus on the estimation of microbial biomass, basal respiration, enzyme activities related to nutrient cycling, and organic chemical biodegradation. This paper sets out to summarize and expand on recent discussions within the International Organization for Standardization (ISO), Soil Quality - Biological Characterization sub-committee (ISO TC 190/SC 4) where a need was identified to develop scientifically sound methods which would best fulfil the practical needs of future users for assessing soil quality. Of particular note was the current evolution of molecular methods in microbial ecology that uses quantitative real time PCR (qPCR) to produce a large number of new endpoints and is more sensitive as compared to "classical" methods. Quantitative PCR assesses the activity of microbial genes that code for enzymes that catalyse major transformation steps in nitrogen and phosphorus cycling, greenhouse gas emissions, chemical transformations including pesticide degradation, and plant growth promotion pathways. In the assessment of soil quality methods, it was found that fungal methods were significantly underrepresented. As such, techniques to analyse fungal enzyme activities are proposed. Additionally, methods for the determination of microbial growth rates and efficiencies, including the use of glomalin as a biochemical marker for soil aggregation, are discussed. Furthermore, field methods indicative of carbon turnover, including the litter bag test and a modification to the tea bag test, are presented. As a final note, it is suggested that endpoints should represent a potential function of soil microorganisms rather than actual activity levels, as the latter can largely be dependent on short-term variable soil properties such as pedoclimatic conditions, nutrient availability, and anthropogenic soil cultivation activities.

Sören Thiele-Bruhn et al.
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Short summary
Soil quality depends on the functioning of soil microbiota. Only few standardized methods are available to assess this as well as adverse effects of human activities. So, it is needed to identify promising additional methods that target soil microbial function. Discussed are (i) molecular methods using qPCR for new endpoints, e.g. in N and P cycling and greenhouse gas emissions, (ii) techniques for fungal enzyme activities, and (iii) field methods on carbon turnover such as the litter bag test.
Soil quality depends on the functioning of soil microbiota. Only few standardized methods are...
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