Soil fumigation effectively mitigates replanting obstacles induced by intensive cultivation, yet its non-targeted biocidal effects can suppress beneficial microbial activity, potentially compromising agricultural sustainability. Microbial inoculation, as a strategy to supplement beneficial microorganisms, is often employed to restore soil microbial communities. However, in practice, commonly used exogenous microbial consortia exhibit poor adaptability in non-native environments, frequently resulting in limited efficacy. To address this limitation, we propose an ecological intervention based on the reintroduction of indigenous cultivable microorganisms: cultivable microbial communities were isolated from healthy adjacent soils and inoculated into fumigated soils affected by replanting obstacles. The experimental soil consisted of black soil under continuous cropping, collected from Northeast China. The three treatments were continuous cropping soil (control), fumigated continuous cropping soil and fumigated continuous cropping soil after inoculation of indigenous cultivable microorganisms. Using high-throughput sequencing and agronomic–chemical analyses, combined with cross-domain networks and procrustes analysis, we systematically assessed the ecological effects of this approach on microbial restoration and the alleviation of replanting obstacles. The results showed that indigenous cultivable microorganism inoculation significantly increased the richness of bacterial and fungal communities in fumigated soils within 21 days, extending microbial richness and diversity. Furthermore, inoculation accelerated the reconstruction of dominant microbial community structures, with the relative abundance of dominant species reaching up to 80%. Positive synergistic interactions between bacteria and fungi increased by approximately 10%, enhancing network stability. Key bacterial taxa, such as Paenibacillus and Mycobacterium, were significantly correlated with available potassium and phosphorus content, while Micromonospora, Massilia, and Flavisolibacter influenced plant fresh weight, total nitrogen, and potassium accumulation. Key fungal taxa, such as Cryptococcus and Phialemonium, were significantly associated with soil organic matter stability, maize photosynthetic efficiency, plant dry weight, and total phosphorus content. This study confirms the ecological adaptability and functionality of indigenous cultivable microorganisms in soil ecosystem restoration, offering a low-risk, highly effective localized intervention strategy for sustainable agriculture.

Microbial inoculation represents an environmentally friendly biocontrol strategy that can enhance soil quality, improve crop growth efficiency, and promote sustainable agriculture. However, the long-term effects and ecological safety of non-native microbial inoculants in soil remain uncertain. Here, we explore and evaluate a safer and potentially more effective inoculation strategy—the reintroduction of native microbiota—to maintain agricultural ecosystem health. Native microbiota were extracted from black soil in northeastern China and reintroduced into the indigenous soil. Two treatments were established: original soil (control) and original soil with a mixture of native microbiota, each with nine replicates. Soil samples were collected at 0, 21, and 90 days post-inoculation. Using high-throughput sequencing and agronomic chemical analyses, we dynamically monitored soil nitrogen, phosphorus, and potassium contents, as well as microbial community composition. Crops were harvested at day 90 to measure dry weight, fresh weight, and SPAD values. The results revealed that the number of colonizing species was lower than the number of inoculated species, yet crop agronomic traits and chemical composition were significantly improved, particularly SPAD values and total phosphorus content. Soil abiotic factors exhibited limited resistance but retained partial recovery capacity, showing a notable increase in readily available potassium at days 0 and 21. Native microbiota inoculation promoted positive synergistic interactions within the microbial community. Furthermore, this study underscores the practical significance of cultivable microorganisms in agricultural applications. Collectively, our findings demonstrate the feasibility of native microbiota reintroduction, highlighting its potential to optimize soil microbial communities, enhance soil properties, and improve crop performance, thereby providing a scientific basis for soil remediation and sustainable agriculture.

Long-term intensive farming has degraded the structural stability of black soil in Northeast China. This study evaluated the effects of fermentation-derived materials and fungal-derived chitin on water-stable aggregates and microbial functional potential in this soil. Four treatments were established: sterile water control (CK), uninoculated fermentation broth substrate (W), live Trichoderma asperellum fermentation broth (P), and cell-free fermentation filtrate (F). Aggregate stability was monitored during a 60-day incubation, and metagenomic sequencing was performed on the most responsive 0.5–0.25 mm dry-sieved fraction. An exogenous chitin addition experiment was also conducted to evaluate the potential contribution of fungal cell-wall-derived chitin to aggregate stabilisation. The W, P, and F treatments increased the proportion of water-stable aggregates >0.25 mm, mean weight diameter, and geometric mean diameter, while decreasing fractal dimension. Among the treatments, the uninoculated fermentation broth substrate showed the strongest effect, particularly in the 0.5–0.25 mm dry-sieved fraction. Metagenomic analysis showed that the uninoculated fermentation broth substrate altered microbial community composition, changed the relative abundances of taxa such as Sphingomonas sediminicola, Priestia megaterium, and Trichoderma asperellum, and increased the relative abundance of carbohydrate-active enzyme-related genes, including those encoding glycosyltransferases, carbohydrate esterases, and glycoside hydrolases. Chitin addition also improved aggregate stability and altered microbial community structure. These findings suggest that the uninoculated fermentation broth substrate and fungal-derived chitin improved black soil aggregate stability, potentially through shifts in microbial community composition and carbohydrate-related functional potential. This study provides a scientific basis for using fermentation-derived materials to improve the structure of degraded black soil.