Soil biological properties are increasingly considered key indicators of soil health because soil biota regulate essential ecosystem functions such as nutrient cycling, organic matter turnover and plant productivity. However, their use in monitoring programmes remains challenging due to potentially high temporal and spatial variability. This raises an important question: are soil biological properties too sensitive for long-term and large-scale soil monitoring?
To address this, we evaluated the temporal dynamics of total and active soil microbial communities in an experimental grassland managed by NEIKER, where rotational grazing has been applied since 2013 and compared with a free-grazing system. Soil samples were collected every three weeks from April to November 2024 at two depths (0-20 cm and 20-50 cm). Environmental DNA (eDNA) and environmental RNA (eRNA) metabarcoding of 16S rRNA and ITS markers were used to characterize total and active prokaryotic and fungal communities.
DNA- and RNA-derived profiles showed clear differences. DNA-based community composition and alpha diversity remained relatively stable over time, indicating that the resident microbial community may provide robust indicators for long-term monitoring. In contrast, RNA-based profiles varied substantially between samplings, suggesting that active microbial communities respond rapidly to short-term changes in climate and pasture conditions.
These results highlight that the suitability of biological indicators depends on monitoring objectives and temporal scale. DNA-based metrics may be more suitable for detecting long-term trends, while RNA-based analyses can better capture short-term ecosystem responses. Our findings underline the importance of understanding seasonal variability and defining ecosystem-specific normal operating ranges to identify appropriate sampling periods and improve the integration of biological indicators into soil health monitoring programmes.