Metagenomic Analysis of Bacterial Community Associated with Rhizosphere and Phyllosphere of Basmati Rice

Rice is one of the most important crops for feeding about more than half of the worlds population. Yield of rice crop is significantly hampered by various biotic and abiotic factors. Application of cost-effective and environment-friendly bioinoculant is a common practice to combat the yield losses of rice in this era. The rhizosphere and phyllosphere of rice plants provide specific habitats for various micro-organisms. In the present study, the bacterial population dwelling the rhizosphere and phyllosphere of Basmati rice were explored using metagenomic approach from rice growing areas of Punjab, Pakistan. The bacterial communities associated with the rice rhizosphere of different rice growing areas as well as phyllosphere/rhizosphere were compared. Out of 20,069 16S rRNA gene sequences retreived from rhizosphere soil, 6485 were originated from Faisalabad, 5174 from Gujranwala and 8410 from Sheikhupura. Data analyses revelead that Proteobactria was dominant phylum at all three sites. Choloflexi was second abundant phylum at Sheikhupura, while Actinobacteria and Firmicutes at Gujranwala and Faisalabad. In addition to dominant culturable PGPB Bacillus genus at all three sites, Nitrosospira, Gaiella, Marmoricola, Clostridium sensu stricto. Maximum geners were detected from Faisalabad (159), followed by Sheikhupura (146) and Gujranwala (131). Comparison of the common sequences at the genus-level revealed that maximum number of shared genera (101) were observed in Sheikhupura and Gujranwala. 50 genera were specifically related to Faisalabad, while 27 and 21 genera were detected for Sheikhupura and Gujranwala. In the phyllosphere, Proteobacteria (79.6%) was detected as dominant phylum followed by Firmicutes (9.8%), Bacteroidetes (8.6%), Chloroflexi (4.3%) and Actinobacteria (0.9%). Comparison of phyllosphere and rhizosphere showed less bacterial diversity in the phyllosphere but Bradyrhizobium, Sphingomonas, GP6, Pseudomonas, Bacillus are abuundant. Fifteen genera were detected at both compartments. Furthermore, we may select these strains for development of compatible inocula for application in the rhizosphere and phyllosphere of rice.