Abundant microbial taxa are more sensitive to land-use intensification than their rare counterparts

Soil microbial communities are critical for sustaining agricultural ecosystem functioning. However, our understanding remains limited regarding how abundant and rare taxa diverge in their responses to land-use intensification in terms of community structure and underlying ecological mechanisms. Here, we used 16S rRNA and ITS amplicon sequencing to characterise the community structure, assembly mechanisms and functional diversity of abundant and rare soil microbial communities across an agricultural transect in Australia. Null-model analyses revealed contrasting assembly patterns: abundant taxa and rare fungi were mainly associated with stochastic processes (68.7%–98.6%), while rare bacterial taxa were more strongly shaped by deterministic selection (82.2%). Across the transect, rare communities exhibited higher functional diversity. Notably, abundant taxa responded more strongly to land-use types in terms of diversity and assembly patterns compared to their rare counterparts. Soil pH was a key driver of the diversity and stability of both abundant and rare taxa, whereas soil texture exerted a stronger influence on their assembly processes. These findings highlight distinct response mechanisms of abundant and rare microbial taxa and clarify how land-use changes differentially influence these sub-communities, thereby informing sustainable soil management and biodiversity conservation.