Unraveling the genomic secrets of Tritonibacter mobilis AK171: a plant growth-promoting bacterium isolated from Avicennia marina

Abstract

The scarcity of freshwater resources resulting in a significant yield loss presents a pressing challenge in agriculture. To address this issue, utilizing abundantly available saline water could offer a smart solution. In this study, we demonstrate that the genome sequence rhizosphere bacterium Tritonibacter mobilis AK171, a halophilic marine bacterium recognized for its ability to thrive in saline and waterlogged environments, isolated from mangroves, has the remarkable ability to enable plant growth using saline irrigation. AK171 is characterized as rod-shaped cells, displays agile movement in free-living conditions, and adopts a rosette arrangement in static media. Moreover, The qualitative evaluation of PGP traits showed that AK171 could produce siderophores and IAA but could not solubilize phosphate nor produce hydrolytic enzymes it exhibits a remarkable tolerance to high temperatures and salinity. In this study, we conducted a comprehensive genome sequence analysis of T. mobilis AK171 to unravel the genetic mechanisms underlying its plant growth-promoting abilities in such challenging conditions. Our analysis revealed diverse genes and pathways involved in the bacterium's adaptation to salinity and waterlogging stress. Notably, T. mobilis AK171 exhibited a high level of tolerance to salinity and waterlogging through the activation of stress-responsive genes and the production of specific enzymes and metabolites. Additionally, we identified genes associated with biofilm formation, indicating its potential role in establishing symbiotic relationships with host plants. Furthermore, our analysis unveiled the presence of genes responsible for synthesizing antimicrobial compounds, including tropodithietic acid (TDA), which can effectively control phytopathogens. This genomic insight into T. mobilis AK171 provides valuable information for understanding the molecular basis of plant-microbial interactions in saline and waterlogged environments. It offers potential applications for sustainable agriculture in challenging conditions.

Keywords: Arabidopsis thaliana; Metabolites; Biocontrol; Mangrove; Red sea; Salinity.

Fig. 1

AK171 Morphology. (A) Colony morphology of Tritonibacter mobilis AK171 on ZM agar. (B) Scanning electron micrograph of T. mobilis AK171 growing in shaking (120 rpm) ZM broth for 3 h at 30 °C, showing rod shaped morphology (width 0.2 m and length 2.3 m). The cells aggregated in diplo-, star shape rosette, and few cells were elongated with different lengths ranging 3–5  m, Bar, 1 m

Fig. 2

AK171 enhances salt stress tolerance of Arabidopsis. Fresh weight enhancement of Arabidobsis thaliana seedlings germinated with AK171 in 1/2MS and stress conditions 100mM NaCl compared to non-colonized plants (MOCK). It shows both the significance and the growth of 20-day-old seedlings. The seedlings were stressed in (A) a solid (aerated) phase and (B) in a submerged root environment. Bar, 2 cm

Fig. 3

Genome features of AK171 genome. Circos map of AK171 genome. From the outer to the inner circle, representation is as follows: a. Whole genome sequences size split in Mbs (grey); b. genes (gold); c. forward strand coding sequences (pink); d. Reverse strand coding sequences (navy); e. Tandem repeats (brown); f. Noncoding rRNA (magenta); g. trna (yellow); h. Interspersed repeats (red); i. Transposons (orange); j. m6A (moccasin); k. m4A (cyan); l. GC content (grey)

Fig. 4

Phylogenomic classification of AK171 based on 16S. Tree based on 16S Basic Local Alignment Search Tool (BLAST) distance phylogenies (GBDP) using Type Strain Genome Server (TYGS) platform

Fig. 5

Phylogenomic classification of AK171 strain based on Whole Genome Sequence. Phylogenomic tree based on Genome Basic Local Alignment Search Tool (BLAST) distance phylogenies (GBDP) using Type Strain Genome Server (TYGS) platform

Fig. 6

Phylogenomic classification of AK171 strain based on Average Nucleotide Identity Tool software (https://www.ezbiocloud.net/tools/orthoani). Heatmap presents OrthoANI values of AK171 strain and five closely related species. The color gradient represent its percentage identity

Fig. 7

Phylogenomic classification of AK171 strain based on Average Amino Acid Identity (AAI). The top five highly identical bacterial species were analyzed for AAI