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