Niche differentiation of microbes and their functional signatures in Assam type tea (Camellia sinensis var. assamica)

Abstract We employed an Illumina-based high throughput metagenomics sequencing approach to unveil the overall rhizospheric as well as endophytic microbial community associated with an organically grown Camellia population located at the Experimental Tea Garden, Assam Agricultural University, Assam (India). Quality control (i.e. adapter trimming and duplicate removal) followed by de novo assembly revealed the tea endophytic metagenome to contain 24,231 contigs (total 7,771,089 base pairs with an average length of 321 bps) while tea rhizospheric soil metagenome contained 261,965 sequences (total 230537174 base pairs, average length 846). The most prominent rhizobacteria belonged to the genus viz., Bacillus (10.34%), Candidatus Koribacter (8.0%), Candidatus Solibacter (6.35%), Burkholderia (5.18%), Acidobacterium (4.08%), Pseudomonas (3.9%), Streptomyces (3.52%), Bradyrhizobium (2.76%) and Enterobacter (2.56%); while the endosphere was dominated by bacterial genus viz., Serratia (42.3%), Methylobacterium (7.6%), Yersinia (5.4%), Burkholderia (2.2%) etc. The presence of few agronomically important bacterial genuses such as Bradyrhizobium (1.18%), Rhizobium (0.8%), Sinorhizobium (0.34%), Azorhizobium and Flavobacterium (0.17% each) were also detected in the endosphere. KEGG pathway mapping highlighted the presence of microbial metabolite pathway genes related to tyrosine metabolism, tryptophan metabolism, glyoxylate and dicarboxylate metabolism and amino sugar metabolism which play important roles in endophytic activities including survival, growth promotion and host adaptation.