Exotic groundcover in an endangered grassy woodland associates with soil microbial functions that may contribute to the persistence of poor vegetation condition

Ecosystem degradation often drives shifts in soil and vegetation condition creating persistent self-reinforcing legacy effects that act as barriers to restoration. However, how soil microbial functional potential and taxonomic composition associate with vegetation condition is poorly understood. Here, we investigated this relationship using the grey box grassy woodland as our model system – a nationally Endangered ecosystem in Australia that is challenging to restore. Using shotgun metagenomics, we characterised the soil microbiome at 10 spatially paired intact and poor vegetation condition sites (100 to 1000 m between pairs) within a 70 km² patch of the Mt. Lofty Ranges, South Australia, with vegetation condition quantified as the proportion of exotic groundcover and midstory. We show that vegetation condition associated with the composition of nitrogen cycling (R² = 0.130) and phosphorus cycling (R² = 0.219) genes. In addition, compositions of specific functional genes such as denitrification, nitrate/nitrite ammonification and alkylphosphonate utilisation also associated with vegetation condition. The relative abundance of several carbon cycling genes (e.g., xylose utilisation) increased along the exotic groundcover gradient. However, vegetation condition had no effect on bacterial community composition. Our results indicate that vegetation condition is linked to shifts in microbial functional potential, specifically functions involved in nitrogen, phosphorus and carbon cycling. Such associations may contribute to the persistence of weedy alternative stable states in this Endangered ecosystem and represent a potential biotic barrier to restoration.