Microorganisms are pivotal for soil health. However, few studies have examined how microbial communities and networks respond to the combined factors of crop yield and nitrogen use efficiency (NUE), which are critical indicators for sustainable agriculture that balance productivity and environmental concerns. To analyze the microbial communities and networks in relation to healthy soil under sustainable agricultural practices, we collected soil samples from six typical pitaya orchards in Hainan Province, China. The composition of soil bacterial and fungal communities was analyzed using high-throughput sequencing targeting the 16S rRNA and ITS regions, respectively, and the co-occurrence networks were constructed to evaluate the complexity and stability. High NUE was positively correlated with yield and microbial diversity, but negatively correlated with soil organic carbon, total nitrogen, and available potassium. Soil bacterial networks displayed greater complexity in high-yield orchards, whereas fungal networks exhibited increased stability in low-yield orchards. Nutrient inputs varied among yield–NUE groups. The bacterial community exhibited higher diversity and complexity in the high yield–high NUE (HH) group and the low yield–high NUE group, whereas fungal diversity was similar in all groups. The relative abundance of specific bacterial phyla differed between the HH and the low yield–low NUE groups, whereas fungal abundance showed no significant variation. Soil bacterial networks showed significant differences in co-occurrence patterns among yield–NUE groups, with the HH group displaying higher complexity and cohesion. In contrast, fungal networks were consistent among all groups. The results highlight that HH agricultural practices, through the synergistic effect of high yield and high NUE, not only enhance pitaya productivity and nutrient uptake, but also improve the complexity of the soil microbial community and network. This enhancement has the potential to fortify soil–plant–microorganism interactions, thereby playing a crucial role in improving soil health and promoting sustainable agriculture.
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