Cropping diminished the prevalence and soil-driven variability of rare bacterial communities in surface soils of the lower Namoi Valley, Australia

Land use and soil properties have important impacts on soil microbial communities, which are critical to sustainable land management and ecosystem functioning. However, the specific responses of microbial abundant and rare sub-communities to land use changes in distinct soil types are still not well understood. To address this, we collected soil samples from the surface layers of 13 soil classes, each comprising long-term intensive agricultural lands (cropping and pasture lands) and natural lands (undisturbed national parks and state forests) in the lower Namoi Valley of New South Wales, Australia. Using cluster analysis, two distinct soil groups, discriminated mainly on texture and therefore named Coarse-textured and Fine-textured groups, were identified based on a suite of soil properties. High-throughput sequencing results revealed that land use changes had a more pronounced impact on the structure of rare sub-communities compared to abundant sub-communities. Abundant sub-communities exhibited a higher prevalence in cropping environments than in natural lands in fine-textured soils and showed higher diversity in both soil groups. Conversely, rare sub-communities displayed a reversed trend, consistently demonstrating lower abundance and diversity in cropping lands. This suggests narrower niches, reduced environmental adaptability, and biotic homogenisation resulting from cropping practices. Cropping led to a reduction of 53.7 % of bacterial richness (observed ASVs) and 5.16 % of the relative abundance of rare sub-communities in coarse-textured topsoils, while fine-textured topsoils experienced a decrease of 67.1 % of ASVs and 7.62 % in relative abundance. Taken together, our findings underscore the importance of considering soil heterogeneity when assessing land use impacts on the response of bacterial communities to environmental changes, as well as the need to protect rare sub-communities for sustainable agricultural practices.