Soil management shapes bacterial and archaeal communities in soybean rhizosphere: Comparison of no-tillage and integrated crop-livestock systems

Sustainable agricultural systems play a crucial role in improving soil properties and enhancing crop yields. Particularly for soybean, a vital agricultural commodity, no-tillage (NT) and integrated crop-livestock (ICL) systems have been employed in tropical regions. Despite the recognized benefits of using NT and ICL, there is a significant knowledge gap regarding their impact on the rhizosphere microbiome of soybean. Therefore, this field study aimed to explore and compare the responses of the bacterial and archaeal communities within the soybean rhizosphere in both NT and ICL systems. To address this objective, in addition to sampling the soybean rhizosphere, we collected samples from the bulk soil in the NT area and the rhizospheres of grass (Urochloa brizantha) and corn (Zea mays L.) in the ICL system, covering the typical land use in this region. The results revealed distinct bacterial and archaeal communities in the soybean rhizosphere under NT and ICL. Specifically, the ICL system enriched the soybean rhizosphere with KD4_96 (score 3), Vicinamibacteraceae (score 3), Candidatus Nitrocosmicus (score 2.5), and Methylobacterium (score 2.5). In contrast, NT led to an enrichment of Solirubrobacter (score 3), Amycolatopsis (score 2.8), Sphingomonas (score 2.8), and Nitrososphaeraceae (score 2.5). Microbial community interactions exhibited greater complexity in the soybean rhizosphere under NT (676 nodes and 7095 edges). Notably, both bacterial and archaeal communities in the soybean rhizosphere under NT and ICL demonstrated potential functionality in nitrogen fixation. Thus, this study showed that NT and ICL promoted different responses of bacterial and archaeal communities within the soybean rhizosphere which, can influence the plant's performance.