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

Abstract

Introduction: The study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes.

Methods: Genes 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.

Results: Abundance 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.

Discussion: These 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.

Keywords: ARG; CAZyme; HGT; KEGG; antibiotics; cell membrane.

Figure 1

Abundance of viral non-redundant genes in soil, e.g., bulk (S) and rhizosphere (R), microbiomes of Moringa oleifera. For more taxonomic details, see Supplementary Table S2.

Figure 2

List of phages at family/genus/species levels in soil microbiomes of Moringa oleifera.

Figure 3

Query number of viral genes encoding CAZymes of CAZy glycoside hydrolase (GH) class along with their groups in soil microbiomes of Moringa oleifera across soil types. Group 1 = GH43, Group 2 = GH43/GH51/GH54/GH62/GH2/GH3, Group 3 = GH43/GH30/GH39/GH51/GH52/ GH54/GH1/GH116/GH120, and Group 4 = GH23. For more details, see Supplementary Table S7.

Figure 4

Abundance of viral genes encoding GH CAZyme groups in soil, e.g., bulk (S) and rhizosphere (R), microbiomes of Moringa oleifera. Orange box = CAZyme group 1, green box = CAZyme group 2, pink box = CAZyme group 3, blue box = CAZyme group 4. EC 3.2.1.99 = arabinanase, EC 3.2.1.145 = galactan 1,3-beta-galactosidase, EC 3.2.1.8 = endo-beta-1,4-xylanase, EC 3.2.1.55 = alpha-L- arabinofuranosidase, EC 3.2.1.37 = beta-xylosidase, EC 3.2.1.17 = lysozyme type G, and EC 3.2.1.14 = chitinase. For more details, see Supplementary Table S9.

Figure 5

Query number of viral genes encoding enzymes generated from KEGG analysis in soil, e.g., bulk (S) and rhizosphere (R), microbiomes of Moringa oleifera. EC 1.1.1.26 = glyoxylate reductase, EC 5.3.3.2 = isopentenyl-diphosphate delta isomerase, EC 3.4.23.36 = signal peptidase II, EC 1.17.4.2 = ribonucleoside-triphosphate reductase (thioredoxin), EC 2.1.1.72 = DNA adenine methylase, EC 3.6.1.23 = dUTP pyrophosphatase, and EC 1.17.4.1 = ribonucleoside- diphosphate reductase alpha/beta chain. For more details, see Supplementary Table S13.

Figure 6

Abundance of viral genes encoding enzymes generated from KEGG analysis in soil, e.g., bulk (S) and rhizosphere (R), microbiomes of Moringa oleifera. EC 1.1.1.26 = glyoxylate reductase, EC 5.3.3.2 = isopentenyl-diphosphate delta isomerase, EC 3.4.23.36 = signal peptidase II, EC 1.17.4.2 = ribonucleoside-triphosphate reductase (thioredoxin), EC 2.1.1.72 = DNA adenine methylase, EC 3.6.1.23 = dUTP pyrophosphatase, and EC 1.17.4.1 = ribonucleoside- diphosphate reductase alpha/beta chain. For more details, see Supplementary Table S15.

Figure 7

Abundance of genes in bacteria that host phages of soil, e.g., bulk (S) and rhizosphere (R), microbiomes of Moringa oleifera. For more details, see Supplementary Table S17.

Figure 8

Query numbers of antibiotic resistance genes (ARGs) in the phageome of soil, e.g., bulk (S) and rhizosphere (R), microbiomes of Moringa oleifera. Columns in red refer to highly abundant ARGs to be utilized further. For more details, see Supplementary Table S20.

Figure 9

Abundance of the selected antibiotic resistance genes (ARGs) in the phageome of soil, e.g., bulk (S) and rhizosphere (R), microbiomes of Moringa oleifera. For more details, see Supplementary Table S22.

Figure 10

Influence of viral parY and arr-1 genes in contributing antibiotic resistance in genus Streptomyces in the rhizospheric microbiome of M. oleifera via the two resistance mechanisms namely “antibiotic target alteration” and “antibiotic inactivation.” parY mutated gene acts against aminocoumarin, while arr-1 gene acts against rifampicin.