Background: The soil microbiome drives soil ecosystem function, and soil microbial functionality is directly linked to interactions between microbes and the soil environment. However, the context-dependent interactions in the soil microbiome remain largely unknown. Results: Using latent variable models (LVMs), we disentangle the biotic and abiotic interactions of soil bacteria, fungi and environmental factors using the Qinghai-Tibetan Plateau soil ecosystem as a model. Our results show that soil bacteria and fungi not only interact with each other but also shift from competition to facilitation or vice versa depending on environmental variation; that is, the nature of their interactions is context-dependent. Conclusions: Overall, elevation is the environmental gradient that most promotes facilitative interactions among microbes but is not a major driver of soil microbial community composition, as evidenced by variance partitioning. The larger the tolerance of a microbe to a specific environmental gradient, the lesser likely it is to interact with other soil microbes, which suggests that facilitation does not necessarily lead to niche expansion.

Soil amendments may enhance crop yield and quality by increasing soil nutrient levels and improving nutrient absorption efficiency, potentially through beneficial microbial interactions. In this work, the effects of amending soil with straw-based carbon substrate (SCS), a novel biochar material, on soil nutrients, soil microbial communities, and maize yield were compared with those of soil amendment with conventional straw. The diversity and abundance of soil bacterial and fungal communities were significantly influenced by both the maize growth period and the treatment used. Regression analysis of microbial community variation indicated that Rhizobiales, Saccharimonadales, and Eurotiales were the bacterial and fungal taxa that exhibited a positive response to SCS amendment during the growth stages of maize. Members of these taxa break down organic matter to release nutrients that promote plant growth and yield. In the seedling and vegetative stages of maize growth, the abundance of Rhizobiales is positively correlated with the total nitrogen (TN) content in the soil. During the tasseling and physiological maturity stages of corn, the abundance of Saccharimonadales and Eurotiales is positively correlated with the content of total carbon (TC), total phosphorus (TP), and available phosphorus (AP) in the soil. The results suggest that specific beneficial microorganisms are recruited at different stages of maize growth to supply the nutrients required at each stage. This targeted recruitment strategy optimizes the availability of nutrients to plants and ultimately leads to higher yields. The identification of these key beneficial microorganisms may provide a theoretical basis for the targeted improvement of crop yield and soil quality. This study demonstrates that SCS amendment enhances soil nutrient content and crop yield compared with conventional straw incorporation and sheds light on the response of soil microorganisms to SCS amendment, providing valuable insights for the future implementation of this material.

The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice; male parent Oryza sativa cultivated rice; their F1 progeny; and the F2, F3 and F4 self-crossing generations. Our results showed that the bacterial and fungal α-diversities of the hybrid F1 and self-crossing generations (F2, F3, F4) were closer to one of the two parental lines, which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly. Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes. In the parental and self-crossing progenies, the reduction of community dissimilarity was higher for the fungal community than for the bacterial community.

SPX-domain proteins (small proteins with only the SPX domain) have been proven to be involved in phosphate-related signal transduction and regulation pathways. Except for OsSPX1 research showing that it plays a role in the process of rice adaptation to cold stress, the potential functions of other SPX genes in cold stress are unknown. Therefore, in this study, we identified six OsSPXs from the whole genome of DXWR. The phylogeny of OsSPXs has a strong correlation with its motif. Transcriptome data analysis showed that OsSPXs were highly sensitive to cold stress, and real-time PCR verified that the levels of OsSPX1, OsSPX2, OsSPX4, and OsSPX6 in cold-tolerant materials (DXWR) during cold treatment were higher than that of cold-sensitive rice (GZX49). The promoter region of DXWR OsSPXs contains a large number of cis-acting elements related to abiotic stress tolerance and plant hormone response. At the same time, these genes have expression patterns that are highly similar to cold-tolerance genes. This study provides useful information about OsSPXs, which is helpful for the gene-function research of DXWR and genetic improvements during breeding.

Soil microbial communities are vital for saline-alkaline ecosystem functioning; however, their succession during land degradation and their influence on phosphorus (P) transformation remain unclear. To address this gap, this study investigated the dynamics of soil microbial communities and P fractions along a degradation gradient from native grassland to Suaeda salsa vegetation and ultimately to bare land in the Songnen Plain, China. The results revealed that progressive saline-alkaline degradation significantly altered soil properties, increased the proportion of stable P fractions, and reduced microbial alpha diversity. Network analysis revealed that bacterial communities shifted from competition to cooperation along the salinity–alkalinity degradation gradient, indicating a cooperative strategy to cope with environmental stress. Fungal networks exhibit progressively reduced complexity and stability with increasing degradation. Partial least squares path modeling confirmed that soil pH and electrical conductivity directly and indirectly regulated P fractions by reshaping microbial communities, with bacteria exhibiting a stronger total effect than fungi. In conclusion, saline-alkaline degradation drives microbial community succession, which mediates the transformation of soil P into more stable forms and exacerbates P limitation. This study provides a scientific basis for targeted restoration and sustainable management of saline-alkaline ecosystems.