Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera

Abstract

IntroductionThe study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes.MethodsGenes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil.ResultsAbundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include “antibiotic efflux pump” for ARGs soxR, OleC, and MuxB, “antibiotic target alteration” for parY mutant, and “antibiotic inactivation” for arr-1.DiscussionThese ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome.

Impacts of sulfamethoxazole stress on vegetable growth and rhizosphere bacteria and the corresponding mitigation mechanism

“…This finding revealed that Pseudomonas tend to host more functional genes than Hydrogenphaga . Correspondent to our discovery, Ashy et al also concluded that Pseudomonas was a key host for viral genes and antibiotic resistance genes in the rhizosphere of moringa ( Moringa oleifera ) ( Ashy et al, 2023 ). In the soil sample of spinach treated with water, Stenotrophomonas and Agrobacterium were not abundant genera, but hosted relatively large amounts of functional genes.…”

Moringa oleifera (Moringaceae) an in-depth review of its nutritional classification and therapeutic application

“…From the stem of M. oleifera, compounds such as vanillin, β-sitosterol, β-sitostenone, 4-hydroxymellin, and octacosanoic acid have been identified. It has been discovered that Moringa oleifera contains L-arabinose, galactose, glucuronic acid, L-rhamnose, mannose, and xylose (Ashy et al, 2023).…”

Warming alters life-history traits and competition in a phage community

“…Bacteria and phages are the most abundant host-parasite system on Earth (36,37). Phages play key roles in animal microbiomes and plant rhizospheres by maintaining microbiome diversity and providing protection from invasive pathogens (38)(39)(40)(41). They are also increasingly viewed as potential therapeutic alternatives to antibiotics given growing levels of antimicrobial resistance (42)(43)(44)(45).…”