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.

中文翻译：

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确定用于土壤质量评估的新微生物功能标准

土壤中微生物的活性对于土壤的健壮功能和相关的生态系统服务至关重要。因此，有必要确定土壤微生物组的组成，多样性和功能，以确定其自然特性，功能和操作范围，以及评估由于人为活动引起的生态毒理作用。文献中目前存在许多微生物学方法，并且继续开发新的，更先进的方法。然而，这些方法中只有少数是标准化的。因此，有必要确定评估土壤质量的最有前途的非标准化方法，并将其转化为标准。与“生态系统服务方法”相一致，新方法应更多地关注土壤微生物的功能，包括养分循环和温室气体排放，病虫害防治和植物生长促进，碳循环和固存，以及土壤结构发育和过滤功能。现有的几种针对土壤微生物组功能的标准化方法主要包括在实验室中定义明确的条件下进行的测量，例如基础呼吸，酶活性和有机物的生物降解。本文着手总结和扩展国际标准化组织（ISO）土壤质量-生物表征小组委员会（ISO TC 190 / SC 4）内的最新讨论，其中需要开发科学合理的方法，超越现有测试系统，可以最好地满足未来用户评估土壤质量的实际需求。特别值得注意的是微生物生态学中分子方法的最新进展，该方法使用定量实时PCR（qPCR）产生了大量新的功能终点，这些终点比“经典”方法更为敏感。定量PCR基于对驱动相关过程的标记基因序列的评估，评估了可催化氮和磷循环，温室气体排放，包括农药降解在内的化学转化以及植物生长促进途径等主要转化步骤的微生物数量。在评估土壤质量的方法中，发现大多数方法都集中在细菌和相关终点上。描述真菌群落及其功能性状的技术远没有得到很好的体现。因此，提出了分析真菌酶活性的技术。另外，讨论了确定微生物生长速率和效率的方法，包括使用gloomalin作为土壤聚集的生化标记。此外，现场方法提出了包括垃圾袋测试和茶袋测试的改进在内的指示碳转换的指标。但是，显而易见的是，随着高通量测序技术和包括宏基因组学分析在内的大数据分析的不断发展，有可能将这些技术应用于标准化过程中以评估土壤微生物组的功能。总的来说，建议终点应代表土壤微生物的潜在功能，而不是实际的活动水平，因为后者在很大程度上取决于短期可变的土壤特性，例如气候条件，养分的可获得性和人为的土壤耕作活动。