Bacterial community structure in different niches under threejhum fallow cycle lengths
A total of 14,52,455 sequences were obtained from 60 samples (18 samples each of LARS, SARS, RI, and 6 samples of BS) (Table S2). The total OTUs from all the samples belonged to 43 bacterial phyla. The majority of the OTUs belonged to the Proteobacteria (49.8 %), followed byAcidobacteria (12.1 %), Bacteroidetes (11.1 %),Actinobacteria (8.25%), Verrucomicrobia (4.40 %),Planctomycetes (2.55 %), Chloroflexi (2.34 %),Cyanobacteria (2.32 %), Firmicutes (1.40 %) andGemmatimonadetes (1.35 %). The results were complex, but the main results among the ten most abundant phyla (main effects only, all p < 0.001) are as follows: Proteobacteria proportional abundance increased from the BS to the RI whereas Acidobacteria ,Verrucomicrobia , Planctomycetes Chloroflexi, andGemmatimonadetes abundance declined across this sequence of niches; Cyanobacteria and Firmicutes abundance were greatest in the RI, but the other niches did not differ from one another (Fig 2 b, d). In terms of fallow age, the abundance ofProteobacteria and Bacteroidetes increased, whereas that of Acidobacteria and Cyanobacteria declined from the younger to older fallow ages; whilst the 5-year fallow was often distinct, the 8-year and 20-year fallows were more similar to one another (Fig 2a, c). The abundance of Acidobacteria ,Actinobacteria , Verrucomicrobia , Cyanobacteria, andGemmatimonadetes was greatest in rice, whereasProteobacteria was least abundant in rice. The genusPseudomonas made up 19.3 % of all sequences; it was found at the greatest abundance in the RI followed by the SARS but was at low abundance in the LARS and BS (Fig 3 b); it was also greater abundance in 20-year than in 5-year or 8-year fallow cycles (Fig 3 a).
Spearman’s rank correlation among the top 20 bacterial genera in 5-year fallow cycle fields showed a general negative correlation between the genus Psuedomonas and other bacterial genera (r ≤ -0.86, p < 0.05) except with Streptophyta with which it was positively correlated (r ≥ 0.86, p < 0.05) (Fig 4a). On the other hand, among the top 20 bacterial genera in 8-year and 20-yearjhum fallow cycles, Pseudomonas was positively correlated with Enterobacteriacae_ (r ≥ 0.6, p < 0.05),Pedobacter (r ≥ 0.55, p < 0.05), Flavobacterium(r ≥ 0.45, p < 0.05) , Stenotrophomonas (r ≥ 0.75, p < 0.05), Arthrobacter (r ≥ 0.65, p < 0.05),Variovorax (r ≥ 0.61, p < 0.05) (Fig 4b, c).
Weighted Principal Coordinate Analysis (PCoA) results based on the Unifrac distance method, which measures the dissimilarity coefficient between the samples, showed that niches clustered distinctly and were reflective of their distinctive bacterial composition (test statistic = 4.68767, p-value = 0.005; Fig 5a). The clustering was less distinct on the basis of bacterial community composition of jhum fallow cycle length (Fig. 5b).