Whole Genome Sequencing and Analysis of Plant Growth Promoting Bacteria Isolated from the Rhizosphere of Plantation Crops Coconut, Cocoa and Arecanut

Abstract

Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization's report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H2S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified.

Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions

“…Various species of bacteria have been reported to promote plant growth by providing phytohormones or enzymes [55,67,68]. The current study revealed that CS51 promoted plant growth through the production of GAs and IAA ( Figure 1A,B).…”

“…Furthermore, we identified genes related to auxin biosynthesis, which included tryptophan synthase beta chain (TSb) (CCZ28_16130), tryptophan synthase alpha chain (TSa) (CCZ28_16125), phosphoribosylanthranilate isomerase (PRAI), and anthranilate phosphoribosyltransferase (APRT) ( Table 2). Previously, a study reported [67] the presence of tryptophan-related genes may be associated with IAA production in the bacteria. Similarly, genes related to phosphorus (P), sulfur (S), and nitrogen (N) in CS51 were analyzed ( Table 2).…”

Microbial diversity in leaves, trunk and rhizosphere of coconut palms (Cocos nucifera L.) associated with the coconut lethal yellowing phytoplasma in Grand-Lahou, Cte dIvoire

“…In all cases these genera were present in both symptomless and symptomatic palms. Enterobacter has been isolated from the rhizosphere of coconut palms in India and proposed as a candidate for further biofertilizer development (Gupta et al, 2014); while Penicillium and Trichoderma have been combined and used as biocontrol against Ganoderma wilt of coconut (Srinivasulu et al, 2001). Since these genera have been tested in coconut palms, further investigation may help clarifying their possible role as potential bioinoculant or biofertilizer to mitigate CILY.…”

Comprehensive Genome Analysis on the Novel Species Sphingomonas panacis DCY99T Reveals Insights into Iron Tolerance of Ginseng

“…However, the presence of tryptophan biosynthesis gene cluster (trpA, trpB, and trpD), phosphoribosylanthranilate isomerase (trpF; locus AWL63_13430), indole pyruvate ferredoxin oxidoreductase (locus AWL63_18305), and indole-3-glycerol phosphate synthase (locus AWL63_21155) which involve in branchpoint of indole acetic acid biosynthesis pathway shows the potential for indole acetic acid production [58]. Previous studies have indicated that the presence of tryptophan-related genes in rhizobacteria is associated with the production of indole acetic acid [59,60]. Thus, the comparative analysis of the tryptophan biosynthesis gene cluster of strain LK11 and DCY99 T was carried out.…”