Integrating DNA-based microbial profiling and organic matter chemistry into soil monitoring: Insights from archived Swedish soils

Soil provides critical ecosystem services, yet anthropogenic pressures have accelerated degradation, prompting the implementation of an EU-wide soil monitoring law aiming to improve all soils by 2050. Despite recent methodological advances that make high-throughput data collection feasible, biological indicators remain underrepresented in most national soil monitoring programmes. Data from DNA-based metabarcoding of soil microorganisms is increasingly highlighted as important to include. Here, we evaluated the potential of integrating DNA-based microbial community data and spectroscopic analyses into soil monitoring using 75 archived samples representing agricultural soils from southern Sweden with a wide range of organic matter contents. Fungal and prokaryotic communities were strongly correlated, and their compositions were also related to the spectroscopy data. Contrary to common assumptions, indices of fungal and prokaryotic diversity were not positively related to soil organic carbon content. Instead, links were detected only when the chemical composition of organic matter was taken into consideration. Specifically, fungal diversity was positively correlated with the abundance of alkyl-C, which is indicative of more decomposed organic matter. We highlight data on microbial community and data from mid-IR spectroscopy as particularly interesting candidates for inclusion in soil monitoring programmes. However, it may be more informative to focus on analysing community composition and potential functioning rather than species richness.