RESULTS Basic Composition and Structure of the Phyllosphere Bacteria of Rubber Trees with Powdery Mildew
Four samples from each site region (BS, DZ, WZS, and WN), for a total of 16 tree-level leaf samples, were subjected to MiSeq high-throughput sequencing of the phyllosphere microbial DNA of hosts with powdery mildew. A total of 567,903 high-quality sequence fragments were read after processing the raw data, with the number of sequences in a single sample ranging from 30,261 to 44,775, with an average of 35,494. A total of 520 OTUs were detected in the four regions after implementing the quality control protocol. Across all regions, there were 36 overlapping OTUs, constituting 6.92% of the total. This indicated that, although all the samples were collected from a rubber powdery mildew phyllosphere environment, there were significant differences in OTU levels among the four regions (Figure 1).
The rarefication curves showed differences in the diversity of the different sample phyla. The flattening of the rarefication curves for each sample indicated that the amount of sequenced data was reasonably sufficient, with a robust sequencing depth encompassing nearly all phyla in the samples (Figure S1).
The community composition of each sample was tallied at various taxonomic levels, and a total of 24 phyla, 49 classes, 100 orders, 172 families, and 256 genera of bacteria were identified. Apart from WZS_3, the other samples were dominated at the phylum level byCyanobacteria , Poteobacteria , and Actinobacteria . The dominant phyla in individual regions also included Firmicutesand Bacteroidetes , which had different relative abundances across regions (Figure 2-1, 2-2). Excluding WZS_3, in the 15 samples the relative abundance of Cyanobacteria ranged from 71.24% to 98.29%, that of Proteobacteria from 1.55% to 23.13%, and that of Actinobacteria from 0.82% to 1.23%. The relative abundances of Cyanobacteria , Proteobacteria , andActinobacteria in WZS_3 were 0.04%, 28.92%, and 10.59%, respectively.
The dominant genera in BS were Cyanobacteria_norank (“norank” is used when there is no scientific name for this level in the taxonomic genealogy), Mitochondria_norank, and Rhodococcus ; in DZ, Cyanobacteria_norank, Mitochondria_norank, and Curtobacteriumdominated; in WN, Cyanobacteria_norank, Pseudomonas , andPantoea dominated; and in WZS, Cyanobacteria_norank,Rhodococcus , and Pantoea dominated (Figure 2-1, 2-2). In these regions, the most dominant communities in healthy rubber tree leaves (Level 0) consisted of Cyanobacteria_norank, and likewise for the dominant communities of infected leaves (Level 3). The relative abundances (mean values) are shown in Table S2. Among subdominant genera, the subdominant genera of both uninfected and Level 3-infected leaves in BS were Mitochondria_norank and Rhodococcus ; the subdominant genera in DZ were Mitochondria_norank (uninfected leaves) and Curtobacterium (Level 3-infected leaves); the subdominant genera in WN were Mitochondria_norank, Bacillus (uninfected leaves), Pseudomonas , and Pantoea (Level 3-infected leaves); and the subdominant genera in WZS were Rhodococcus(uninfected leaves) and Acidobacteria_norank (Level 3-infected leaves). The relative abundances of subdominant genera in healthy leaves and Level 3 leaves from the four regions are listed in Table S2.
In summary, the composition of the dominant genera varied little between healthy leaves and Level 3-infected leaves. Although other dominant genera were different among regions, their relative abundances were not high. Therefore, the composition of genus-level communities of the three levels of infected and healthy leaves of rubber trees at the same growing site was similar, except for some differences in members’ relative abundances, while community composition at the genus level differed markedly among regions.