3.2 Microbial assemblages and diversity
Separate bacterial and fungal community profiling was conducted for 24 bulk soil and 24 rhizosphere samples to assess the structural and functional differences of soil microbial communities between CCS and FS. Briefly, bacterial community profiling yielded a total of 1 353 973 sequences, ranging from 35 649 to 74 817. Fungal profiling resulted in 1 653 670 sequences, ranging from 38 903 and 74 939. After subsampling of each sample to 11 000 (bacterial) and 10 000 (fungi) sequences (Figure S1), 3 921 bacterial (Table S1) and 1 099 fungal (Table S2) OTUs were identified across all samples.
Although no significant differences were found between C_NS and F_NS (neither in bacterial community richness nor in fungal community richness), alpha-diversity indexes indicated that bacterial community richness of bulk soil was higher in F_NS than in F_S; however, the differences were not significant for rhizosphere samples (Figure S2). F_NS had more fungal OTUs than F_S both in bulk soil and rhizosphere. However, the differences of bacterial or fungal community richness between C_NS and C_S were not pronounced neither in the bulk soil nor in the rhizosphere.
The taxonomy of microbial diversity was assessed by Circos. With regard to the abundance of bacterial phyla (Figure 2a), the rhizosphere and the bulk soil of N. tabacum were dominated by Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Patescibateria, Firmicutes, Acidobacteria and Gemmatimonadetes. Proteobacteria, Actinobacteria, and Bacteroidetes always dominated both sample types, while Firmicutes was relatively more abundant in CCS than in FS. Moreover, soil sterilization treatment prior to sowing significantly decreased the abundances of Chloroflexi and Acidobacteria. Cyanobateria were only detected in rhizosphere samples (Figure 2b). With regard to the abundance of fungal classes (Figure S3), the rhizosphere of N. tabacum and bulk soil were mainly dominated by Sordariomycetes, Eurotiomycetes, Mortierellomycetes and Dothideomycetes. Moreover, Agaricomycetes and Microbotryomycetes were only found in rhizosphere samples. Sordariomycetes dominated both sample types. By examining between-sample variation (i.e., beta-diversity and Bray-Curtis distances), PCoA (Figure 3) indicated marked differences among microbial communities of bulk soil and rhizosphere. The one exception was that no significant difference was found between fungal communities in the rhizosphere.
3.3 Specific microbial clades in