Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa

Abstract

In this study, one bacterial strain, ESM-1, was isolated from rhizosphere of Eruca sativa, growing in Al Hofouf, Saudia Arabia, after enrichment with methanol as a sole carbon and energy source in a batch culture. ESM-1 was characterized by a polyphasic approach. The strain was identified as Delftia acidovorans at similarity level of 99.9% of the 16S rRNA gene sequences. Results of the Biolog Gen III MicroPlate test system showed that strain ESM-1 reacted positively to 47 (50%) including the one-carbon compound formic acid, and partially positive to 6 (∼6.4%) out of the 94 different the traits examined. The total cellular fatty acids composition of the strain ESM-1 was (C16:1ω7c/C16:1ω6c) and C16:0) and matched that of Delftia acidovorans at a similarity index of 0.9, providing a robustness to the ESM-1 identification. Furthermore, ESM-1 displayed a complex polar lipid profile consisting of phosphatidylethanolamine, phosphatidylglycerol, glycolipid, aminolipid, in addition to uncharacterized lipids. The DNA G+C content of the strain was 66.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain ESM1-1 was clearly clustered within the Delftia clade and constructed a monophyletic subcluster with Delftia acidovorans NBRC14950. The results addressed that ESM-1 is a facultative methylotrophic bacterium indigenous to Al Hofouf region and opens the door for potential biotechnological applications (e.g., bioremediation) of this strain, in future. Additionally, these findings assure that the total cellular fatty acid analysis and 16S rRNA gene are reliable tool for bacterial characterization and identification.

Isolation and characterization of bacteria from tomato and assessment of its plant growth-promoting traits in three economically important crops in Al-Ahsa region, Saudi Arabia

“…sterilized distilled water five times. Inocula of strain SLK10 were prepared as outlined previously (Khalifa et al, 2019). Plant seeds 6 -1…”

“…Despite numerous studies having documented the potential benefits of rhizobacteria in the Kingdom, including in Al-Ahsa (Khalifa and Almalki 2015;Khalifa et al, 2016;Khalifa et al, 2019, Khalifa et al, 2020, few studies have focused on the role of rhizobacteria in alleviating salinity stress in plants. Recently, Khalifa et al (2019) been documented in the literature.…”

Isolation, identification and characterization of soil bacteria for the production of ferulic acid through co-culture fermentation using banana stem waste

“…Biolog Gen III Microplate system is beneficial to evaluate the characteristics of bacteria to react with different type of substrate within a short time. Positive results have been shown by many studies in estimating metabolic activities of microbe using the system [52][53][54][55][56]. Substrate utilization test using the system interprets the potential of bacteria to ferment and hydrolyze various substrates simultaneously at the same plate.…”

Técnicas aplicadas en la investigación agrícola para cuantificar la fijación de nitrógeno: una revisión sistemática

“…Otros genes identificados por PCR son 16S rRNA (Akemi et al, 2017;Jaiswal, Msimbira, & Dakora, 2017;Tahon & Willems, 2017), porque permite una clasificación filogenética más detallada a nivel de especie (Osei, Abaidoo, Ahiabor, & Boddey, 2018;Ribeiro et al, 2018), genes rec A, atpD, gln II y nod C con análisis de secuencia multilocus (MLSA) (Leite et al, 2017;Mwenda, Hara, De Meyer, Howieson, & Terpolilli, 2018;Rigonato et al, 2017). Con esta técnica, se ha logrado identificar el gen nifH en géneros Paenibacillus, Enterobacter, Klebsiella y Pantoea (Ndungu et al, 2018), que no son reconocidos por fijar nitrógeno, de modo que es posible que hayan obtenido la capacidad de fijación de nitrógeno a través de la transferencia lateral de genes; sin embargo, las fuerzas evolutivas de la transferencia lateral de genes no son bien conocidas (Khalifa & AlMalki, 2018).…”