Soils sentinels: A step towards harmonisation of microbial parameters in European initiatives

Abstract

Soil health is a critical component of agroecosystems, supporting plant growth, nutrient cycling, and ecosystem services. However, soil is a non-renewable resource on human timescales, and its degradation poses significant challenges for sustainable agriculture. Despite numerous European initiatives (e.g., LUCAS, EcoFINDERS, EXCALIBUR, SHARInG-MeD, among others), there remains a lack of consensus on standardized soil health indicators, particularly regarding microbiological parameters. This review examines current limitations of microbial indicators used in European soil monitoring and research initiatives across three complementary dimensions: (i) community structure and taxonomy; (ii) microbial abundance or biomass; and (iii) microbial functionality. For community structure and taxonomy, methodological variability in metabarcoding approaches is addressed, including sample design, primer selection, sequencing platforms, read length, bioinformatic pipelines, and taxonomic reference databases. Microbial abundance or biomass is assessed through a range of approaches, including phospholipid fatty acid (PLFA) analysis, substrate-induced respiration (SIR), ester-linked fatty acid methyl ester (EL-FAME) analysis, quantitative PCR (qPCR) and culture-based methods, highlighting differences in their application and limitations for cross-study comparison, as well as methodological inconsistencies, particularly in PLFA-based approaches. Functional indicators of microbial activity are also considered, highlighting challenges in enzyme activity assays, the standardisation of functional gene analyses and shotgun metagenomics, which can provide both taxonomic and functional information. Finally, it discusses the integration of these variables through emerging context-dependent predictive modelling approaches. Overall, the synthesis underscores that methodological heterogeneity remains a major barrier to cross-study comparability and calls for improving standardisation to enhance the robustness of microbial ecology research and its application in ecosystem function assessment. Harmonising these methods could enhance cross-project data integration, supporting policy development for sustainable soil management in Europe.