Complete genome analysis of sugarcane root associated endophytic diazotroph Pseudomonas aeruginosa DJ06 revealing versatile molecular mechanism involved in sugarcane development

Abstract

Sugarcane is an important sugar and bioenergy source and a significant component of the economy in various countries in arid and semiarid. It requires more synthetic fertilizers and fungicides during growth and development. However, the excess use of synthetic fertilizers and fungicides causes environmental pollution and affects cane quality and productivity. Plant growth-promoting bacteria (PGPB) indirectly or directly promote plant growth in various ways. In this study, 22 PGPB strains were isolated from the roots of the sugarcane variety GT42. After screening of plant growth-promoting (PGP) traits, it was found that the DJ06 strain had the most potent PGP activity, which was identified as Pseudomonas aeruginosa by 16S rRNA gene sequencing. Scanning electron microscopy (SEM) and green fluorescent protein (GFP) labeling technology confirmed that the DJ06 strain successfully colonized sugarcane tissues. The complete genome sequencing of the DJ06 strain was performed using Nanopore and Illumina sequencing platforms. The results showed that the DJ06 strain genome size was 64,90,034 bp with a G+C content of 66.34%, including 5,912 protein-coding genes (CDSs) and 12 rRNA genes. A series of genes related to plant growth promotion was observed, such as nitrogen fixation, ammonia assimilation, siderophore, 1-aminocyclopropane-1-carboxylic acid (ACC), deaminase, indole-3-acetic acid (IAA) production, auxin biosynthesis, phosphate metabolism, hydrolase, biocontrol, and tolerance to abiotic stresses. In addition, the effect of the DJ06 strain was also evaluated by inoculation in two sugarcane varieties GT11 and B8. The length of the plant was increased significantly by 32.43 and 12.66% and fresh weight by 89.87 and 135.71% in sugarcane GT11 and B8 at 60 days after inoculation. The photosynthetic leaf gas exchange also increased significantly compared with the control plants. The content of indole-3-acetic acid (IAA) was enhanced and gibberellins (GA) and abscisic acid (ABA) were reduced in response to inoculation of the DJ06 strain as compared with control in two sugarcane varieties. The enzymatic activities of oxidative, nitrogen metabolism, and hydrolases were also changed dramatically in both sugarcane varieties with inoculation of the DJ06 strain. These findings provide better insights into the interactive action mechanisms of the P. aeruginosa DJ06 strain and sugarcane plant development.

Evaluation of phyllosphere bacterial biocontrol agents for the suppression of rice foliar diseases

“…In the present study, seed bacterization with the different bacterial isolates, namely P. aeruginosa isolate Pf1 and B. subtilis isolate 1, increased the vigour index of rice seedlings. The mechanisms of plant growth promotion by phyllosphere bacteria are the production of phytohormones, enhanced availability of nutrients, reduction of ethylene levels, production of antibiotics, induced systemic resistance and competition for space and nutrients (Diniz et al, 2022;Guo et al, 2023;Singh et al, 2021) and they are the same as reported in the rhizobacteria (Duijff et al, 1994;Santiago et al, 2017;Van Loon, 1997).…”

“…Its genome contains genes responsible for nitrogen fixation, ammonia metabolism, siderophore and indole acetic acid (IAA) production, phosphate metabolism and biocontrol activity. It increased sugarcane growth and photosynthetic leaf gas exchange (Guo et al, 2023;Singh et al, 2021).…”

“…Mixture of two or more biocontrol agents is effective since they have different mechanisms of inhibitory actions(Ramamoorthy et al, 2001).Unfortunately, strains of P. aeruginosa are considered human opportunistic pathogens because they are isolated from the clinical samples. However, several P. aeruginosa strains were isolated from agricultural ecosystems and used as biocontrol agents and plant growth-promoting agents(Anjaiah et al, 2003;Guo et al, 2023;F I G U R E 5 (a) HCN production by by phyllosphere bacteria. (b) Siderophore production by phyllosphere bacteria.…”