Identification of new microbial functional standards for soil quality assessment
Authors: Thiele-Bruhn Sören , Schloter Michael , Wilke Berndt-Michael , Beaudette Lee A. , Martin-Laurent Fabrice , Cheviron Nathalie , Mougin Christian , Römbke Jörg 
Published: January 2020

Abstract. The activity of microorganisms in soil is important for a robust
functioning of soil and related ecosystem services. Hence, there is a
necessity to identify the composition, diversity, and function of the soil
microbiome in order to determine its natural properties, functioning, and
operating range as well as 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 these methods are standardised.
Consequently, there is a need to identify the most promising
non-standardised methods for assessing soil quality and to transform them
into standards. In agreement with the “Ecosystem Service Approach”, new
methods should focus more on soil microbial functions, including nutrient
cycling and greenhouse gas emission, pest control and plant growth
promotion, carbon cycling and sequestration, as well as soil structure
development and filter function. The few existing standardised methods
available that focus on the function of the soil microbiome mostly include
measurements, like basal respiration, enzyme activities, and biodegradation
of organic matter, under well-defined conditions in the lab. This paper sets
out to summarise 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, going beyond the
existing test systems. Of particular note is the current evolution of
molecular methods in microbial ecology that use quantitative real-time PCR
(qPCR) to produce a large number of new functional endpoints which are more
sensitive as compared to “classical” methods. Quantitative PCR assesses the
abundance of microbes that catalyse major transformation steps in nitrogen
and phosphorus cycling, greenhouse gas emissions, chemical transformations
including pesticide degradation, and plant growth promotion pathways based
on the assessment of marker gene sequences that drive the related processes.
In the assessment of soil quality methods, it was found that most methods
focus on bacteria and related endpoints. Techniques to describe fungal
communities as well as their functional traits are far less represented. 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. However, it is obvious that with increasing
developments in high throughput sequencing technologies and big data
analyses, including metagenomics analysis, it will be possible to implement
these technologies into the standardisation process for assessing the
functions of the soil microbiome. Overall, 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.