Different storage conditions can influence microbial community structure and metabolic functions, affecting rice grains’ quality. However, the microbiological mechanisms by which different storage conditions affect the quality of rice grains are not yet well understood. This study monitored the quality (the content of starch, protein, etc.) and microbial community structure of rice grains stored under different storage conditions with nitrogen gas atmosphere (RA: normal temperature, horizontal ventilation, RB: normal temperature, vertical ventilation, RC: quasi-low temperature, horizontal ventilation). The results revealed that the rice grains stored under condition RB exhibited significantly lower quality compared to condition RA and RC. In addition, under this condition, the highest relative abundance of Aspergillus (16.0%) and Penicillium (0.4%) and the highest levels of aflatoxin A (3.77 ± 0.07 μg/kg) and ochratoxin B1 (3.19 ± 0.05 μg/kg) were detected, which suggested a higher risk of fungal toxin contamination. Finally, co-occurrence network analysis was performed, and the results revealed that butyl 1,2-benzenedicarboxylate was negatively correlated (p < 0.05) with Moesziomyces and Alternaria. These findings will contribute to the knowledge base of rice storage management and guide the development of effective control measures against undesirable microbial activities.

Rice storage conditions include location, granary depth, storage time, temperature and atmosphere. The fungi community varies during storage, but how these communities change remains unexplored so far. This study collected rice samples from granaries in different horizontal and vertical directions and storage time over two years. High-throughput ITS (Internal Transcribed Spacer) sequencing analysis revealed that Ascomycota (73.81%), Basidiomycota (6.56%) and Mucoromycota (9.42%) were the main Eumycota present during rice storage. The main fungi communities were Aspergillus sp., Fusarium sp., Rhizopus sp., Gibberella sp., Tilletia sp. and Penicillium sp. The contribution of storage time, horizontal orientation and vertical depth effect on fungi community relative abundance were 17.18%, 5.98% and 0.11%, respectively. Aspergillus sp. was the predominant Eubacterium during this process. The horizontal A was mainly occupied by Paraconiothyrium sp. and the location S, had Clavispora sp. Both of these varied dramatically during storage. Furthermore, Aspergillus sp., as a main mycotoxin producer, was the dominant fungi at vertical L1. This study comprehensively analyzed fungi community variation in horizontal and vertical directions to elucidate fungi community variation on rice during storage and to find the detrimental fungi. Therefore, it is important to improve granary ventilation systems and to ensure a uniform atmosphere to control fungi growth.