3.1 Bacterial and fungal richness and diversity
For the entire sampling set, a total of 1,353,140 bacterial sequences (raw tags) with an average length of 253 bp, and 1,150,116 fungal sequences with an average length of 240 bp, were identified. As a result of chimeral filtration and quality control, 1,279,641 bacterial and 1,101,677 fungal high-quality sequences (clean tags) were obtained (Appendix S1 & S2). In addition, the total number of 16S and ITS reads obtained from the 18 and 14 soil samples, respectively, with two and six samples not successfully sequenced of each. The phylogenetic relationship of more than 500 bacterial and 200 fungal genera that are identified in SPF-treated rhizosphere soil, respectively (Appendix Figure S1). Rarefaction curves of most samples tend to be flat, suggesting that reasonable sequencing depth has been attained, although extra rare bacterial taxa are likely present in the sample (Appendix Figure S2).
Shannon and Chao1, the community richness index, showed that the bacterial diversity of SPF-treated rhizosphere soil was significantly higher than that of SP-treated and bulk soil (SK) (p < 0.05, Figure 1a,b). α diversity in the SF group was found significantly increased compared to that in SP group (p < 0.05). In addition, α diversity of the excipient treatment (SA) was also investigated and compared with the others, which showed distinctive increased in diversity compared with that of SP and SK (p< 0.05). It is likely that the excipients added into SPF, SP, and SF did not decrease the diversity of the rhizosphere bacterial community of sugarcane. Shannon and Chao1 of the fungal diversity in the SPF were the highest (p < 0.05, Figure 1c,d), followed by SF and SP, and these indices were the lowest in the SA group, indicating that SPF has the best fungal community richness.
According to the principal coordinate analysis (PCoA) plots, the bacterial community structure of the PW treatment was separated from those of the other treated groups by PCo1 (49.88%) and PCo2 (19.15%) (Figure 2a). The PCoA analysis based on weighted UniFrac metrics placed the bacterial community of SPF-treated soil much closer to the SP- and SF- treated soils, while the SK treatment was distantly placed. Beta-diversity between five groups also demonstrated that there were significant differences on bacterial community structure between SPF and SP, between SP and SA, between SP and SK, separately (p< 0.05, Wilcox test, Appendix Figure S3a). In addition, Adonis (permutational MANOVA) showed that there were significant differences on bacterial communities between SP and SF (R2 = 6.87, p < 0.05). The fungal communities of each group were separated by PCo1 (78.44%) and PCo2 (5.52%) based on weighted UniFrac analysis (Figure 2b). The fungal community structure of SPF was much similar to that of SP, but significantly distinct from SF (p < 0.05, Appendix Figure S3b).