Rice endophytic fungal community and its potential role on rice grains Cd accumulation

Rice is a cadmium (Cd) high-accumulator, therefore, the soils Cd contamination may cause food security problems. Endophytes played a crucial role on host plants' heavy metal accumulation. However, the endophytic fungal community of rice and its role on rice grains Cd accumulation is still unclear. In this study, the endophytic fungal community of rice at different growth stages from different Cd-contaminated sites (LC and HC, contains lower and higher concentration of Cd, respectively) were investigated by high-throughput sequencing method. In addition, the culturable fungal endophytes were isolated and Cd tolerance assessments were also conducted for some of the isolates. The results showed that the soils Cd concentration and rice tissue showed greater effect on the endophytic fungal community than that of the rice growth stage. The dominant endophytic fungi changed with the soils Cd concentration, and higher Cd concentration reduced the species diversity (Shannon index) and evenness (Evenness index) of endophytic fungi, especially in the roots. In addition, the correlation analysis of dominant endophytic fungi with environmental factors showed that Alternaria, Fusarium and Saccharomyces had a significant positive correlation with Cd concentration. While, the linear discriminant analysis effect size (LEfSe) analysis showed that Stellatospora, Westerdykella, Sarocladium, Spencerozyma and Penicillium were the biomarkers (the relative abundance significantly increased) in multiple tissues from higher Cd-contaminated site. The endophytic fungi from site HC possessed higher ration of Cd tolerant isolates, and the tolerant isolates belong to Sarocladium, Alternaria, Fusarium, etc. Notably, the co-occurrence networks showed that higher Cd concentration increased modularity and number of communities of rice endophytes, especially in the roots, while decreased the positive correlation among different endophytic groups (genus level) in different tissues. These results suggested that rice may respond to higher Cd stress through enriching Cd tolerant endophytic fungi. While, the endophytic fungal community affected rice Cd tolerance by improving its microbiome stability, diversifying microbial survival strategies and maintaining the ecological balance.