Dataset Information

Genomic Diversity of Two Hydrocarbon-Degrading and Plant Growth-Promoting Pseudomonas Species Isolated from the Oil Field of Bobrka (Poland).

ABSTRACT: Hydrocarbon-degrading bacteria are important resources for use in phytoremediation applications. Yet, for many hydrocarbonoclastic strains the genetic information regarding pollutant degradation and detoxification has not been thoroughly revealed. In this study, hydrocarbon-degrading bacteria were isolated from a long-term oil-polluted soil in Bóbrka, Poland. Pseudomonas spp. was the most dominant species. Of all 69 isolated strains tested in the laboratory using qualitative biochemical assays, 61% showed the capability to use diesel as sole carbon source, 33% could produce indole, 19% produced siderophores, 36% produced organic acids, and 54% were capable of producing 1-aminocyclopropane-1-carboxylate (ACC)-deaminase. From all morphologically and genetically different strains, two representative Pseudomonas spp., strain VI4.1 and VI4T1, were selected for genome sequencing. Genomic analyses indicated the presence of the full naphthalene dioxygenase operon (plasmid and chromosomal), of genes involved in the degradation of BTEX compounds (Benzene, Toluene, Ethylbenzene, Xylene) and alkanes (alkB gene) as well as the anthranilate degradation pathway (strain VI4T1) and terephthalate dioxygenase protein (strain VI4.1). Proton transfer reaction time-of-flight mass spectrometry (PTR-TOF-MS) analyses confirmed naphthalene and BTEX degradation within seven days. Motility, resistance to abiotic stresses, high and low temperatures, low pH, and salinity were confirmed at the genetic level and experimentally verified. The presence of multiple degradative and plant growth promotion genes, together with the in vitro experimental evidence, indicates the high value of these two strains and their potential use for sustainable site clean-up.

SUBMITTER: Imperato V

PROVIDER: S-EPMC6628094 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Bacterial endophytes with the capacity to degrade petroleum hydrocarbons and promote plant growth may facilitate phytoremediation for the removal of petroleum hydrocarbons from contaminated soils. A hydrocarbon-degrading, biosurfactant-producing, and plant-growth-promoting endophytic bacterium, Pseudomonas aeruginosa L10, was isolated from the roots of a reed, Phragmites australis, in the Yellow River Delta, Shandong, China. P. aeruginosa L10 efficiently degraded C10-C26n-alkanes from diesel oil, as well as common polycyclic aromatic hydrocarbons (PAHs) such as naphthalene, phenanthrene, and pyrene. In addition, P. aeruginosa L10 could produce biosurfactant, which was confirmed by the oil spreading method, and surface tension determination of inocula. Moreover, P. aeruginosa L10 had plant growth-stimulating attributes, including siderophore and indole-3-acetic acid (IAA) release, along with 1-aminocyclopropane-1-carboxylic (ACC) deaminase activity. To explore the mechanisms underlying the phenotypic traits of endophytic P. aeruginosa L10, we sequenced its complete genome. From the genome, we identified genes related to petroleum hydrocarbon degradation, such as putative genes encoding monooxygenase, dioxygenase, alcohol dehydrogenase, and aldehyde dehydrogenase. Genome annotation revealed that P. aeruginosa L10 contained a gene cluster involved in the biosynthesis of rhamnolipids, rhlABRI, which should be responsible for the observed biosurfactant activity. We also identified two clusters of genes involved in the biosynthesis of siderophore (pvcABCD and pchABCDREFG). The genome also harbored tryptophan biosynthetic genes (trpAB, trpDC, trpE, trpF, and trpG) that are responsible for IAA synthesis. Moreover, the genome contained the ACC deaminase gene essential for ACC deaminase activity. This study will facilitate applications of endophytic P. aeruginosa L10 to phytoremediation by advancing the understanding of hydrocarbon degradation, biosurfactant synthesis, and mutualistic interactions between endophytes and host plants.

Project description:The study was designed to isolate and characterize Pseudomonas spp. from sugarcane rhizosphere, and to evaluate their plant- growth- promoting (PGP) traits and nitrogenase activity. A biological nitrogen-fixing microbe has great potential to replace chemical fertilizers and be used as a targeted biofertilizer in a plant. A total of 100 isolates from sugarcane rhizosphere, belonging to different species, were isolated; from these, 30 isolates were selected on the basis of preliminary screening, for in vitro antagonistic activities against sugarcane pathogens and for various PGP traits, as well as nitrogenase activity. The production of IAA varied from 312.07 to 13.12 μg mL-1 in tryptophan supplemented medium, with higher production in AN15 and lower in CN20 strain. The estimation of ACC deaminase activity, strains CY4 and BA2 produced maximum and minimum activity of 77.0 and 15.13 μmoL mg-1 h-1. For nitrogenase activity among the studied strains, CoA6 fixed higher and AY1 fixed lower in amounts (108.30 and 6.16 μmoL C2H2 h-1 mL-1). All the strains were identified on the basis of 16S rRNA gene sequencing, and the phylogenetic diversity of the strains was analyzed. The results identified all strains as being similar to Pseudomonas spp. Polymerase chain reaction (PCR) amplification of nifH and antibiotic genes was suggestive that the amplified strains had the capability to fix nitrogen and possessed biocontrol activities. Genotypic comparisons of the strains were determined by BOX, ERIC, and REP PCR profile analysis. Out of all the screened isolates, CY4 (Pseudomonas koreensis) and CN11 (Pseudomonas entomophila) showed the most prominent PGP traits, as well as nitrogenase activity. Therefore, only these two strains were selected for further studies; Biolog profiling; colonization through green fluorescent protein (GFP)-tagged bacteria; and nifH gene expression using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The Biolog phenotypic profiling, which comprised utilization of C and N sources, and tolerance to osmolytes and pH, revealed the metabolic versatility of the selected strains. The colonization ability of the selected strains was evaluated by genetically tagging them with a constitutively expressing GFP-pPROBE-pTetr-OT plasmid. qRT-PCR results showed that both strains had the ability to express the nifH gene at 90 and 120 days, as compared to a control, in both sugarcane varieties GT11 and GXB9. Therefore, our isolated strains, P. koreensis and P. entomophila may be used as inoculums or in biofertilizer production for enhancing growth and nutrients, as well as for improving nitrogen levels, in sugarcane and other crops. The present study, to the best of our knowledge, is the first report on the diversity of Pseudomonas spp. associated with sugarcane in Guangxi, China.

Dataset Information

Genomic Diversity of Two Hydrocarbon-Degrading and Plant Growth-Promoting Pseudomonas Species Isolated from the Oil Field of Bobrka (Poland).

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