Data Mining of ELFA Bioindicators to Assess Soil Threats Across European Biogeoclimatic Regions Using the LUCAS Dataset

Soil threats, such as pollution, salinity, soil organic carbon (SOC) loss and compaction, are often difficult to quantify or costly to analyze and bioindicator research represents an important approach for their efficient evaluation. Microbial bioindicators can reflect early biological responses to soil degradation processes, offering a sensitive and cost-efficient complement to conventional soil analyses. The identification of microbial clade–specific indicators can be achieved in detail through metabarcoding technologies, although these methods typically require extensive data processing and advanced bioinformatics expertise.

In contrast, ester-linked fatty acid (ELFA) analysis provides an inexpensive biological method capable of quantifying major microbial groups in soil, including bacteria, fungi, Gram-positive, Gram-negative and Actinobacteria. We hypothesize that ELFA analysis can serve as a complementary and alternative technique for soil threat bioindication.

Using LUCAS 2018 soil survey data, we assessed relationships between soil threat proxies (estimated metal and metalloid concentrations, electrical conductivity, SOCmeasured/SOCexpected ratio and bulk density) and ELFA-derived parameters (both raw and ratio-transformed) through random forest modeling and ANOVA. Significant bioindicators (α < 0.05 and β > 0.8) were confirmed using generalized additive model (GAM) regressions across European biogeoclimatic regions (Alpin, Continental, Pannonian, Mediterranean, Boreal and Atlantic).

Our results demonstrate that Actinobacteria/Gram− ratio, fungi-to-bacteria (F/B) ratio, Gram+ and Gram− groups can serve as potential bioindicators for soils enriched in metals (Zn and Cd) and for SOC loss (SOC_observed/SOC_expected) as significantly highlighted by Random Forest, ANOVA and GAM analyses. Some responses were found to be specific to continental, boreal and Mediterranean biogeoclimates.

These findings support the inclusion of ELFA-based microbial metrics in European soil monitoring schemes such as LUCAS or the Soil Monitoring Law. Future research should integrate ELFA data with molecular bioindicators to refine multi-parameter soil threat assessments.