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

Abstract

17 Rice is one of the most important crops for feeding about more than half of the world's 18 population. Yield of rice crop is significantly hampered by various biotic and abiotic 19 factors. Application of cost-effective and environment-friendly bioinoculant is a 20 common practice to combat the yield losses of rice in this era. The rhizosphere and 21 phyllosphere of rice plants provide specific habitats for various micro-organisms. In the 22 present study, the bacterial population dwelling the rhizosphere and phyllosphere of 23 Basmati rice were explored using metagenomic approach from rice growing areas of 24 Punjab, Pakistan. The bacterial communities associated with the rice rhizosphere of 25 different rice growing areas as well as phyllosphere/rhizosphere were compared. Out 26 of 20,069 16S rRNA gene sequences retreived from rhizosphere soil, 6485 were 27 originated from Faisalabad, 5174 from Gujranwala and 8410 from Sheikhupura. Data 28 analyses revelead that Proteobactria was dominant phylum at all three sites. Choloflexi 29 was second abundant phylum at Sheikhupura, while Actinobacteria and Firmicutes at 30 Gujranwala and Faisalabad. In addition to dominant culturable PGPB Bacillus genus at 31 all three sites, Nitrosospira, Gaiella, Marmoricola, Clostridium sensu stricto.32 Maximum geners were detected from Faisalabad (159), followed by Sheikhupura (146) 33 and Gujranwala (131). Comparison of the common sequences at the genus-level 34 revealed that maximum number of shared genera (101) were observed in Sheikhupura 35 and Gujranwala. 50 genera were specifically related to Faisalabad, while 27 and 21 36 genera were detected for Sheikhupura and Gujranwala. 37 In the phyllosphere, Proteobacteria (79.6%) was detected as dominant phylum 38 followed by Firmicutes (9.8%), Bacteroidetes (8.6%), Chloroflexi (4.3%) and39 Actinobacteria (0.9%). Comparison of phyllosphere and rhizosphere showed less 40 bacterial diversity in the phyllosphere but Bradyrhizobium, Sphingomonas, GP6, 41 Pseudomonas, Bacillus are abuundant. Fifteen genera were detected at both 42 compartments. Furthermore, we may select these strains for development of compatible 43 inocula for application in the rhizosphere and phyllosphere of rice. 44

Plant Growth-Promoting Bacteria as an Emerging Tool to Manage Bacterial Rice Pathogens

“…Interestingly, the population of bacteria in rice rhizosphere was explored metagenomically. In 2020, the population of bacteria in the rhizosphere and phyllosphere of Basmati rice was reported [ 197 ]. Bacterial population associated with the rice rhizosphere from three different rice growing areas (Faisalabad, Gujranwala, and Sheikhupura) of Punjab, Pakistan, were compared.…”

Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression

“…The NGS metabarcoding-based microbiome profiling revealed the predominance of phylum Proteobacteria on the rice phyllosphere. The predominance of Proteobacteria consisting of bacterial communities belonging to Enterobacteriaceae and Pseudomonadaceae is reported on the phyllosphere by many workers ( Knief et al, 2012 ; Ren et al, 2014 ; Roman-Reyna et al, 2019 ; Yasmin et al, 2020 ). At the lower taxonomic genus hierarchy, Pantoea followed by Pseudomonas and Enterobacter were overrepresented on both the rice genotypes.…”

Deciphering Core-Phyllomicrobiome of Rice Genotypes Grown in Contrasting Mountain and Island Agroclimatic Zones: Implications for Microbiome Engineering Against Blast Disease

“…mNGS-survey coupled with culturing-based validation revealed diverse bacterial ora on the phyllosphere of rice. Members belong to phyla such as Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were found consistently on phyllosphere of both the resistant and susceptible genotypes grown Mountain and Island zones; dominance phylum -Proteobacteria on phyllosphere is reported by many workers [64][65][66]. Recently, Roman-Reyna et al [67] found region-speci c microbial hubs belonging to diverse bacterial families in rice after studying 3024 accessions.…”