Can plant-beneficial bacteria be used as an indicator of soil health?

Soil health is the continued capacity of soil to function as a vital living ecosystem that sustains plants, animals and humans, with soil biodiversity playing a critical role. However, its complexity and the lack of harmonized data make it challenging to establish measurable links between soil biodiversity and soil health. In this study, we explored the use of plant-beneficial bacteria (PBB) as potential indicators of soil health. Plant-beneficial bacteria are known to support plant growth and development by providing multiple benefits, such as biocontrol, growth promotion (e.g., nitrogen fixation), and stress resistance (e.g., drought tolerance). For this study, we analyzed eDNA data from 7500 soil samples collected across various land uses and soil types in Denmark. Plant-beneficial bacteria identification was based on a global database, which links microbial taxonomy with plant-beneficial traits from existing literature based on experiments, recording 396 genera that contribute to biocontrol, stress resistance, and growth-promoting functions. Our findings show that PBB are highly variable across different land uses. For instance, agricultural areas exhibited the highest median number of different PBB genera, with values ranging from approximately 5 to 320 genera, and showed significant variation. In contrast, heathlands displayed a lower number of PBB (around 40 genera) with less variability. Additionally, the number of PBB was negatively correlated with the soil C/N ratio. The variability of PBB across and within different land uses and soil properties suggests its potential to serve as an indicator of soil health.