The northeast region of China is an important grain‐growing area. However, severe soil salinization in the region impairs plant production. In the present study, organic fertilizer application (composted poultry manure) was evaluated as a potential strategy for remediating saline–alkali soil and promoting rice growth. Following continuous organic fertilizer application for 4 years, the contents of basic cations, including sodium (Na+) and chlorine cations (Cl−), decreased significantly (p < .05) (soil Na + decreased from 24.3 mg kg−1 to 21.8 mg kg−1 and soil Cl‐ decreased from 570.4 mg kg−1 to 38.5 mg kg−1), while soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), available nitrogen (AN) and available potassium (AK) were markedly increased (especially for soil AK, which increased from 85.8 mg kg−1 to 141.7 mg kg−1) compared to the treatment without organic fertilizer application. In addition, the relative abundance of plant growth‐promoting bacteria such as Thiobacillius, Methylobacter, Rhodoferax, Lysobacter and Flavobacterium increased significantly, whereas halophilic genera (Nitriliruptor, Mongoliicoccus, Litoribacter, Halomonas and Aliidiomarina) decreased markedly. Bacterial diversity also increased significantly, with data analysis suggesting that such shifts translated into more abundant plant‐growth‐related gene functions. According to structural equation modelling results, soil bacterial diversity was a key factor driving the maintenance of healthy plant growth in saline–alkali soil. These results suggested that organic fertilizers could improve the physicochemical properties of saline–alkali soil by altering interactions between rice plants and bacteria, for example, via the recruitment of specific beneficial microbial communities to increase their salinity–alkali stress tolerance, and, in turn, promote their growth.

Understanding the processes that regulate communities of microorganisms is a key issue and focus in microbial ecology. Although fungi play a critical role in soil biogeochemical cycling, their community assembly processes remain largely unknown, especially in agricultural soils. In this study, we investigated the relative importance of five community assembly processes (variable selection, homogeneous selection, homogeneous dispersal, dispersal limitation and an undominated process) in soil fungal communities under long‐term (28 years, 1990–2018) fertilization management consisting of 12 different treatments in triplicate field plots. Using Illumina MiSeq sequencing of the 18S rRNA eukaryotic gene, we observed that fungal communities in manure treatments were all structured primarily by homogeneous dispersal, whereas the communities in chemical fertilizer treatments were structured primarily by homogeneous dispersal and an undominated process. Soil calcium played an important role in shaping the soil fungal community, whereas soil organic matter concentrations had a considerable impact on the soil fungal phylogenetic community composition. Overall, our results suggest that fertilization management should be considered as a key factor driving microbial community assembly processes in farmed soils.Highlights Soil Ca played a key role in shaping eukaryotic microbial community Chemical fertilization resulted in homogenous selection and undominated processes. A combination of chemical and manure fostered homogenous selection processes.

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