Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture

Abstract

The rhizosphere of plants contains a wide range of microorganisms that can be cultivated and used for the benefit of agricultural practices. From garden soil near the rhizosphere region, Strain ES10-3-2-2 was isolated, and the cells were Gram-negative, aerobic, non-spore-forming rods that were 0.3-0.8 µm in diameter and 1.5-2.5 µm in length. The neighbor-joining method on 16S rDNA similarity revealed that the strain exhibited the highest sequence similarities with "Fibrivirga algicola JA-25" (99.2%) and Fibrella forsythia HMF5405^T (97.3%). To further explore its biotechnological potentialities, we sequenced the complete genome of this strain employing the PacBio RSII sequencing platform. The genome of Strain ES10-3-2-2 comprises a 6,408,035 bp circular chromosome with a 52.8% GC content, including 5038 protein-coding genes and 52 RNA genes. The sequencing also identified three plasmids measuring 212,574 bp, 175,683 bp, and 81,564 bp. Intriguingly, annotations derived from the NCBI-PGAP, eggnog, and KEGG databases indicated the presence of genes affiliated with radiation-resistance pathway genes and plant-growth promotor key/biofertilization-related genes regarding Fe acquisition, K and P assimilation, CO₂ fixation, and Fe solubilization, with essential roles in agroecosystems, as well as genes related to siderophore regulation. Additionally, T1SS, T6SS, and T9SS secretion systems are present in this species, like plant-associated bacteria. The inoculation of Strain ES10-3-2-2 to Arabidopsis significantly increases the fresh shoot and root biomass, thereby maintaining the plant quality compared to uninoculated controls. This work represents a link between radiation tolerance and the plant-growth mechanism of Strain ES10-3-2-2 based on in vitro experiments and bioinformatic approaches. Overall, the radiation-tolerant bacteria might enable the development of microbiological preparations that are extremely effective at increasing plant biomass and soil fertility, both of which are crucial for sustainable agriculture.

Keywords: Arabidopsis; PGPRs; biofertilizer; genome; siderophore.

Figure 1

The genome-based phylogenetic tree of ES10-3-2-2 and its related type strains determined using data from the Type Strain Genome Server. The phylogenetic tree was constructed using the calculated intergenomic distances to infer a balanced minimum evolution tree. This analysis utilized the FASTME v.2.1.6.1 software, incorporating Subtree Pruning and Regrafting (SPR) post-processing [17] to refine the tree topology. Branch support was determined through 100 pseudo-bootstrap replicates. The resulting trees were midpoint-rooted [18] and visualized using MEGA (v.8.2) software.

Figure 2

Circular map of the Strain ES10-3-2-2’s chromosome and plasmids. The outer circle shows the scale in metabases (Mb). The representations, from the outer to the inner circle, are forward- and reverse-strand CDSs.

Figure 3

Predicted components of T9SS and the gliding motility genes used in the genome of ES10-3-2-2. The representative image illustrates the gene components associated with the Type IX secretion system (T9SS) and gliding motility, as predicted by T9GPred [26].

Figure 4

Effect of Strain ES10-3-2-2 on plant-growth parameters. (A) The surface of leaves detached from 20-day-old (20 DAT) grown plants. Control (no bacterial suspension), Fe-EDTA-treated plant and 2 × 10⁶ cfu/mL bacterial suspension. (B) Graphical representation of the fresh weights of shoots and roots at 20 DAT. The median and SE were calculated with eight plants per treatment. Significant differences between the treated plants were *, p < 0.02 and **, p < 0.05.