Effects of Fertilisation Practices on Nutrient Cycling Through the Regulation of Soil’s Physicochemical Properties and Microbial Communities

Continuous cultivation and fertiliser inputs restructure the spatial distribution of soil nutrient pools and drive the evolution of the underlying soil microenvironment. To elucidate the effects of long-term agricultural interventions on nutrient dynamics and crop productivity in farmland, this study systematically evaluated the long-term ecological effects of fertilisation strategies based on a 46-year long-term wheat–soybean rotation experiment. Twelve fertilisation treatments, including an unfertilised control, straw return, organic manure, and different chemical fertiliser rates alone or in combination with organic amendments, were established. The physicochemical properties of non-rhizosphere soil were systematically determined, and metagenomic sequencing was used to characterise the bacterial community’s diversity and structure. Long-term excessive dependence on chemical fertilisers severely disrupted the soil chemical balance, as indicated by the excessive accumulation of available phosphorus, different available potassium levels among treatments, and decline in pH, increasing the environmental risks associated with agricultural production. The manure-only and manure plus low-rate mineral treatments had more available potassium and showed soil surface features of unverified composition in SEM images. Redundancy analysis revealed that the soil pH, available phosphorus, and available potassium were the principal physicochemical environmental factors associated with differences in non-rhizosphere bacterial communities. Structural equation modelling indicated that although high-rate chemical fertilisation directly promoted wheat yields by increasing available phosphorus, it indirectly suppressed non-rhizosphere microbial diversity by decreasing the soil pH, potentially threatening the long-term sustainability of agricultural productivity. Overall, optimising the fertiliser composition and adopting combined organic and mineral fertilisation are important for balancing soil nutrients, maintaining microbial ecological stability, and achieving sustainable agricultural development.