Identification ofatpDas an optimal reference gene to explore antibiotic resistance and stress tolerance inRahnella aquatilis

Disruption of the cell division protein ftsK gene changes elemental selenium generation, selenite tolerance, and cell morphology in Rahnella aquatilis HX2

AIMS

Some studies have indicated that the alterations in cellular morphology induced by selenite [Se(Ⅳ)] may be attributed to its inhibitory effects on cell division. However, whether the genes associated with cell division are implicated in Se(Ⅳ) metabolism remains unclear.

METHODS AND RESULTS

The ftsK gene in Rahnella aquatilis HX2 was mutated with an in-frame deletion strategy. The ftsK mutation strongly reduced the tolerance to selenite [Se(Ⅳ)] and the production of red elemental selenium [Se(0)] in R. aquatilis HX2, and this effect could not be attributed solely to the inhibition of cell growth. Deleting the ftsK gene also resulted in a significant decrease in bacterial growth of R. aquatilis HX2 during both exponential and stationary phases. The deletion of ftsK inhibited cell division, resulting in the development of elongated filamentous cells. Furthermore, the loss-of-function of FtsK significantly impacted the expression of seven genes linked to cell division and Se(Ⅳ) metabolism by at least 2-fold, as unveiled by real-time quantitative PCR (RT-qPCR) under Se(Ⅳ) treatment.

CONCLUSIONS

These findings suggest that FtsK is associated with Se(Ⅳ) tolerance and Se(0) generation and is a key player in coordinating bacterial growth and cell morphology in R. aquatilis HX2.

Nitrate reductase involves in selenite reduction in Rahnella aquatilis HX2 and the characterization and anticancer activity of the biogenic selenium nanoparticles

BACKGROUND

Biogenic selenium nanoparticles (SeNPs) show numerous advantages including their high stability, low toxicity, and high bioactivity. While metabolism of SeNPs remains not well studied and need more investigation to reveal the process.

PURPOSE

The objective of the study was to investigate the relationship between nitrate reductase and selenite reduction in Rahnella aquatilis HX2, characterize the properties of HX2 produced SeNPs, and explore their potential applications, particularly their anticancer activity.

PROCEDURES

Selenium species were measured by high-performance liquid chromatography coupled to inductively coupled plasma - Mass spectrometry (HPLC-ICP-MS). Transcription level of nitrate reductase was determined by Real-time quantitative PCR. Morphology, particle size, crystal structure and surface chemistry of SeNPs were determined by electron microscopy, dynamic light scattering method, Raman scattering, X-ray photoelectron spectroscopy, respectively. Anti cancer cell activity was measured by CCK-8 assay.

MAIN FINDINGS

SeNP production in R. aquatilis HX2 was correlated with the cell growth. The products of selenite reduction in HX2 detected by HPLC-ICP-MS included SeNPs, selenocysteine (SeCys), Se-Methylselenocysteine (MeSeCys), and 7 unknown compounds. Nitrate addition experiments suggested the involvement of nitrate reductase in selenite reduction in HX2. Both the cellular membrane and cytoplasm of HX2 exhibited selenite-reducing ability, indicating that membrane-associated nitrate reductase was not the sole selenite reductase in HX2. Characterization of the biogenic SeNPs revealed a spherical morphology and amorphous structure of them. Surface chemistry analysis implicated the binding of extracellular polymeric substances to the biogenic SeNPs, and the presence of Se0, Se2-, and electron-rich Se atoms on the surface of SeNPs. Finally, the IC50 values of the biogenic SeNPs were 36.49 μM for HepG2 and 3.70 μM for HeLa cells.

CONCLUSIONS

The study first revealed that the nitrate reductase is involving in selenite reduction in R. aquatilis HX2. The biogenic SeNPs coordinated with organic substances in the surface. And SeNPs produced by R. aquatilis HX2 showed excellent anticancer activities on HepG2 and HeLa cells.

Functional analysis and comparative genomics of Rahnella perminowiae S11P1 and Variovorax sp. S12S4, two plant growth-promoting rhizobacteria isolated from Crocus sativus L. (saffron) rhizosphere

BACKGROUND

Rahnella perminowiae S11P1 and Variovorax sp. S12S4 are two plant growth-promoting rhizobacteria that were previously isolated from the rhizosphere of Crocus sativus L. (saffron), and have demonstrated interesting PGP activities and promising results when used as inoculants in field trials. To further elucidate the molecular mechanisms underlying their beneficial effects on plant growth, comprehensive genome mining of S11P1 and S12S4 and comparative genomic analysis with closely related strains were conducted.

RESULTS

Functional annotation of the two strains predicted a large number of genes involved in auxin and siderophore production, nitrogen fixation, sulfur metabolism, organic acid biosynthesis, pyrroloquinoline quinone production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, volatile organic compounds production, and polyamine biosynthesis. In addition, numerous genes implicated in plant-bacteria interactions, such as those involved in chemotaxis and quorum sensing, were predicted. Moreover, the two strains carried genes involved in bacterial fitness under abiotic stress conditions. Comparative genomic analysis revealed an open pan-genomic structure for the two strains. COG annotation showed that higher fractions of core and accessory genes were involved in the metabolism and transport of carbohydrates and amino acids, suggesting the metabolic versatility of the two strains as effective rhizosphere colonizers. Furthermore, this study reports the first comparison of Multilocus sequence analysis (MLSA) and core-based phylogenies of the Rahnella and Variovorax genera.

CONCLUSIONS

The present study unveils the molecular mechanisms underlying plant growth promotion and biocontrol activity of S11P1 and S12S4, and provides a basis for their further biotechnological application in agriculture.

Isolation, Characterization, and Genomic Analysis of Multidrug-Resistant Rahnella aquatilis from Fruits in China

Many fruits are consumed raw and act as vehicles for spreading antibiotic-resistant bacteria to consumers; hence, preventing foodborne diseases and ensuring food safety of fresh fruits are challenging. In this study, we aimed to analyze contamination in fruits and characterize antibiotic resistance genes in pathogenic microorganisms isolated from fruits. Sixty fruit samples were collected and screened for pathogenic microorganisms. The strains were identified, and the minimum inhibitory concentration for various antibiotics was determined. Antibiotic-resistant strains were analyzed by whole-genome sequencing. We isolated strain L46 from lemon samples and identified it as Rahnella aquatilis using MALDI-TOF MS and 16S rRNA sequencing. The whole genome of R. aquatilis L46 was 4.94 Mb and contained 291 putative antibiotic resistance genes (6.53%), including the gene coding for β-lactamase RAHN-1 CTX-M-2 and conferring resistance to ampicillin, polymyxin B, nitrofurantoin, imipenem, aztreonam, and cefotaxime. Thus, fruits can pose a potential hazard to human health and require greater surveillance and attention, as they may contain pathogenic and multidrug-resistant bacteria.

Disruption of the sensor kinase phoQ gene decreases acid resistance in plant growth-promoting rhizobacterium Rahnella aquatilis HX2

AIMS

Rahnella aquatilis HX2, a promising plant growth-promoting rhizobacterium (PGPR) in the field, contains genes homologous to the PhoP/PhoQ two-component regulatory system. Although this system regulates stress response in numerous pathogens, PhoP/PhoQ characterization in a PGPR has not received in-depth exploration.

METHODS AND RESULTS

The phoQ gene was mutated in strain HX2 using an in-frame deletion strategy. Compared to the wild type, the phoQ mutant exhibited increased sensitivity to acidic conditions (pH 4.0) in a chemically defined medium and in mild acidic natural soil (pH 5.7). The phoQ mutant also exhibited increased swimming motility under acidic conditions. Acid resistance was restored in the mutant by introducing the phoQ gene on a plasmid. Three acid resistance genes, add, cfa, and fur were downregulated significantly, whereas the chaperone encoding gene, dnak, was upregulated when the phoQ mutant was exposed to acid stress.

CONCLUSIONS

This study suggested that the PhoP/PhoQ system positively regulates the acid resistance of R. aquatilis HX2.

Nitrogen-fixing, phosphate-potassium-mobilizing ability of Rahnella bacteria isolated from wheat roots

As the number of people on earth increases, so does the need for food. Providing the population with environmentally friendly agricultural food is one of the urgent problems of our time. Currently, the main direction of modern organic farming is the use of biofertilizers. Bacterial preparations are capable of influencing the physiological processes of plants in small quantities, leading to increase in plant productivity. The objective of this work was to study rhizobacteria associated with wheat roots. For this purpose, we took more than 100 isolates of rhizobacteria from the rhizosphere and root surface of wheat plants grown in irrigated fields of Tashkent, Syrdarya, Andijan, Kashkadarya regions. Rhizobacteria were grown on nutrient media of Döbereiner, Ashby, Pikovsky, and Zack, and 25 isolates of associative rhizobacteria were selected based on the characteristics of absorption of molecular nitrogen, mobilization of phosphorus and potassium. They actively dissolved Сa3(PO4)2 and KAlSiO4 for 3 days. They were found to produce organic acids. In organic farming, nitrogen-fixing, phosphorus- and potassium-mobilizing rhizobacteria are of great practical importance, while our experiments on obtaining biological products are considered as an environmentally friendly and cost-effective way to increase crop yields. From the surface of wheat roots grown in different zones of Uzbekistan, when screening for nitrogen fixation, we selected 3 isolates with acetylene reductase activity of 79–91 nmol C2H4/flacon/24h. We determined that bacteria completely mobilized phosphate, forming 100% acid when grown in a medium containing Ca3(PO4)2 for 5 days. The ability of the bacteria to mobilize potassium was studied on a nutrient KAlSiO4-containing medium. The bacteria were observed to mobilize potassium, forming 90–100% acid within 15 days. Based on the study of the 16S rRNA gene of bacteria, we identified rhizobacteria UT3, UT4, and UT9 as Rahnella aquatilis.

Comparative Genomics Assisted Functional Characterization of Rahnella aceris ZF458 as a Novel Plant Growth Promoting Rhizobacterium

Many Rahnella strains have been widely described as plant growth-promoting rhizobacteria with the potential to benefit plant growth and protect plants from pathogens. R. aceris ZF458 is a beneficial plant bacterium isolated from swamp soil with the potential for biocontrol. Strain ZF458 has shown broad-spectrum antagonistic activities against a variety of plant pathogens and exhibited a dramatic effect on controlling Agrobacterium tumefaciens in sunflowers. The R. aceris ZF458 genome sequence contained a 4,861,340-bp circular chromosome and two plasmids, with an average G + C content of 52.20%. Phylogenetic analysis demonstrated that R. aceris ZF458 was closely related to R. aceris SAP-19. Genome annotation and comparative genomics identified the conservation and specificity of large numbers of genes associated with nitrogen fixation, plant growth hormone production, organic acid biosynthesis and pyrroloquinoline quinone production that specific to benefiting plants in strain ZF458. In addition, numerous conserved genes associated with environmental adaption, including the bacterial secretion system, selenium metabolism, two-component system, flagella biosynthesis, chemotaxis, and acid resistance, were also identified in the ZF458 genome. Overall, this was the first study to systematically analyze the genes linked with plant growth promotion and environmental adaption in R. aceris. The aim of this study was to derive genomic information that would provide an in-depth insight of the mechanisms of plant growth-promoting rhizobacteria, and could be further exploited to improve the application of R. aceris ZF458 in the agriculture field.

Selection and evaluation of suitable reference genes for quantitative gene expression analysis during infection of Cucumis sativus with Pectobacterium brasiliense

AIMS

Bacterial soft rot caused by Pectobacterium brasiliense (Pbr) has resulted in severe economic losses of cucumber production in northern China. Quantitative reverse transcription PCR (RT-qPCR) is widely used to determine the fold change in the expression of genes of interest, and an appropriate reference gene played a critical role in the evaluation of genes expression. However, the suitable reference genes for transcript normalization during the interaction between cucumber and Pbr have not yet been systematically validated. In this study, we aimed to identify the suitable reference genes for accurate and reliable normalization of cucumber and Pbr RT-qPCR data.

METHODS AND RESULTS

We selected fourteen candidate reference genes for cucumber and ten candidate reference genes for Pbr were analyzed by using four algorithms (the deltaCt method, BestKeeper, NormFinder and geNorm). Furthermore, five genes in cucumber involved in plant resistance and five genes in Pbr related to the virulence were selected to confirm the reliability of the reference genes by RT-qPCR. CsARF (ADP-ribosylation factor 1) and pgi (glucose-6-phosphate isomerase) were suggested as the most suitable reference genes for cucumber and Pbr, respectively.

CONCLUSION

Our results suggested that CsARF (ADP-ribosylation factor 1) and pgi (glucose-6-phosphate isomerase) could be as the reference genes to normalize expression data for cucumber and Pbr during the process of pathogen-host interaction, respectively.

SIGNIFICANCE AND IMPACT OF THE STUDY

To our knowledge, this is the first systematic study of the optimal reference genes specific to cucumber and Pbr, which could help advance the molecular interactions research in Cucurbitaceae vegetables and Pectobacterium species pathosystems.

Two-component system in Rahnella aquatilis is impacted by the hyphosphere of the arbuscular mycorrhizal fungus Rhizophagus irregularis

Two-component systems (TCS) are ubiquitous among bacteria, playing key roles in signalling events. However, to what extent the TCS of Rahnella aquatilis (a Phosphate solubilizing bacteria) is influenced by the hyphosphere of the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis is totally unknown. Here, the expression of 16 genes encoding the TCS of R. aquatilis (i.e. involved in carbon-sensing and nutrient-sensing) and of eight genes regulated by the PhoR TCS (i.e. involved in inorganic and organic phosphorus mobilization) were analysed at regular intervals in presence of hyphae of R. irregularis. The study was conducted under in vitro culture conditions with phytate as the unique source of phosphorus. In presence of the AM fungus, the expression of TCS genes involved in carbon-sensing and nutrient-sensing were stimulated. Only, BaeS at 30 and 120 min, and BaeR at 60 min were inhibited. In addition, the PhoR TCS stimulated the expression of genes encoding phosphatase but inhibited the expression of genes involved in gluconic acid production. As the mechanism of coupling environmental changes with cellular physiological changes, TCS plays a pivotal role in regulating specific gene expression in R. aquatilis, recognizing environmental signals. More importantly, TCS genes may regulate bacteria response to hyphal carbon to mobilize phosphorus efficiently in the hyphosphere.

Salt Tolerance Mechanism of the Rhizosphere Bacterium JZ-GX1 and Its Effects on Tomato Seed Germination and Seedling Growth

Salinity is one of the strongest abiotic factors in nature and has harmful effects on plants and microorganisms. In recent years, the degree of soil salinization has become an increasingly serious problem, and the use of plant growth-promoting rhizobacteria has become an option to improve the stress resistance of plants. In the present study, the salt tolerance mechanism of the rhizosphere bacterium Rahnella aquatilis JZ-GX1 was investigated through scanning electron microscopy observations and analysis of growth characteristics, compatible solutes, ion distribution and gene expression. In addition, the effect of JZ-GX1 on plant germination and seedling growth was preliminarily assessed through germination experiments. R. aquatilis JZ-GX1 was tolerant to 0-9% NaCl and grew well at 3%. Strain JZ-GX1 promotes salt tolerance by stimulating the production of exopolysaccharides, and can secrete 60.6983 mg/L of exopolysaccharides under the high salt concentration of 9%. Furthermore, the accumulation of the compatible solute trehalose in cells as the NaCl concentration increased was shown to be the primary mechanism of resistance to high salt concentrations in JZ-GX1. Strain JZ-GX1 could still produce indole-3-acetic acid (IAA) and siderophores and dissolve inorganic phosphorus under salt stress, characteristics that promote the ability of plants to resist salt stress. When the salt concentration was 100 mmol/L, strain JZ-GX1 significantly improved the germination rate, germination potential, fresh weight, primary root length and stem length of tomato seeds by 10.52, 125.56, 50.00, 218.18, and 144.64%, respectively. Therefore, R. aquatilis JZ-GX1 is a moderately halophilic bacterium with good growth-promoting function that has potential for future development as a microbial agent and use in saline-alkali land resources.

Identification and validation of reference genes for reliable analysis of differential gene expression during antibiotic induced persister formation in Klebsiella pneumoniae using qPCR

The study of differential gene expression in persister cells is compounded by ceasure of conventional cellular metabolic pathways during persistence. There is, hence, a requirement to identify and validate suitable reference genes whose expression remains stable during persistence. We evaluated the suitability of five genes viz. dnaJ, groEL, rpoB, kp751, kp4432 as references to study gene expression using real-time polymerase chain reaction (qPCR) during persister cell formation in Klebsiella pneumoniae. Results obtained showed that while dnaJ and groEL suffered from unstable expression; rpoB, kp751 and kp4432 showed stable expression. Further, it was observed that data normalization using either of the stable genes viz. rpoB, kp751, kp4432 alone, resulted in either too low expression levels or too high variation among replicates. Our study indicates the concurrent use of kp4432 and rpoB as reference genes to be the most suitable for reliable analysis of differential gene expression during antibiotic induced persister formation in K. pneumoniae. kp4432 and rpoB encode NAD-dependant phenylacetaldehyde dehydrogenase and DNA-directed RNA polymerase beta subunit respectively. The outcome of this study will increase the utility of qPCR in studying the temporal changes in gene expression during persistence. The study will also aid in understanding mechanisms underlying persister cell formation particularly in K. pneumoniae.

The complete genome sequence of Rahnella aquatilis ZF7 reveals potential beneficial properties and stress tolerance capabilities

Rahnella aquatilis ZF7 is a plant beneficial strain isolated from Sakura tree soil with potential for biocontrol. Here, we present the complete genome sequence of R. aquatilis ZF7, which consists of one 4.49 Mb circular chromosome and a 54-kb plasmid named pRAZF7. Phylogenetic analyses revealed that R. aquatilis ZF7 is much similar to the strains Rahnella sp. Y9602 and R. aquatilis HX2 than others evaluated. In this study, multiple genes encoding functions that likely contribute to plant growth promotion, biocontrol and stress tolerance were identified by comparative genome analyses, including IAA production, phosphate solubilization, antibiotic resistance and formation of Se nanoparticles (SeNPs). In addition, these functions were also confirmed by in vitro experiments. Considering its ability to form SeNPs, strain R. aquatilis ZF7 will contribute to nano-agriculture. Overall, the features of R. aquatilis ZF7 make it a high potential and competitive strain in biocontrol, and the genome data will help further studies on the mechanisms of plant growth promotion and biocontrol.