Institute of Biochemistry and Physiology of Plants and Microorganisms

Traditional methods for quantitative identification of bacteria require long time, which substantially limits their operational efficiency. This paper proposes a rapid and simple method for counting S. aureus 209p and E. coli K12 bacterial cells on the basis of indirect surface-enhanced Raman scattering (SERS) using gold nanostar and nanorod tags conjugated with 4-nitrothiophenol. An increase in the SERS signal has been shown to depend on the number of nanoparticle-labeled bacterial cells. The developed procedure has appeared to be efficient both for the direct measurement of the signal from the freshly prepared complex and for measuring the signal from the cellular precipitate after centrifugation. The most statistically reliable results have been obtained using gold nanostars under the conditions of the direct precipitate-free measurement of the SERS signal from the bacteria complex.

The aim of this study was to test a hypothesis regarding the influence of the chromosomally located HSHK-RR gene, encoding a hybrid multisensory histidine kinase, on the morphology of bacteria of the Azospirillum genus. The strains used in this study were A. baldaniorum Sp245, the Laf – mutant Sp245.1062 (Sp245-HSHKΔRR-Km), and A. brasilense Sp7 and Sp7.10030 (Sp7-HSHKΔRR-Km). Bacterial morphology and motility were characterized using electron microscopy. Relative gene transcription levels were determined using real-time PCR. The hybrid sensor histidine kinase (HSHK-RR) genes in strains Sp245 (AZOBR_150176) and Sp7 (AMK58_10030) are 95% homologous. To obtain a mutant of the Sp7 strain, we replaced the AMK58_10030 gene with the HSHKΔRR-Km construct, created on the basis of AZOBR_150176. Replacement of the internal fragment of the HSHK-RR gene with the kanamycin resistance gene resulted in changes in the morphology and motility of cells in semisolid agar in the Sp245-HSHKΔRR-Km and Sp7-HSHKΔRR-Km mutants. The mutant cells were shorter than the cells of the parental strains Sp245 and Sp7 and moved more slowly in semisolid agar, forming colonies of a significantly smaller diameter. Both mutants retained the synthesis of a functional polar flagellum (Fla). However, in the case of Sp7-HSHKΔRR-Km, up to 45% of cells synthesized sparse or isolated lateral flagella (Laf) on agar media, whereas in Sp245-HSHKΔRR-Km, such bacteria accounted for no more than 15%. It was established that Laf biogenesis is under multistage control, including a two-component signaling system involving HSHK-RR, encoded in Sp245 and Sp7 strains by chromosomal genes AZOBR_150176 and AMK58_10030, respectively. Phenotypic analysis of mutants for the AZOBR_150176 and AMK58_10030 genes revealed that the studied HSHK-RR modulates the motility of Sp245 and Sp7 under mechanical stress, participating in the transcriptional control of the flagellin genes laf1 and components of the lateral flagellar assembly export system.

Ligninolytic fungi are promising organisms in developing bioremediation technologies due to their ability to degrade various pollutants. Fungi and their extracellular enzymes in soil inevitably collide with metabolites produced by other organisms. Here, we investigated the effect of some natural metabolites on the degradation of a model mixture of polycyclic aromatic hydrocarbons (PAHs) by the fungus Pleurotus ostreatus var. Florida. Fungus was grown in the liquid medium containing PAHs with or without the addition of natural metabolites. The degraded PAHs and the identification of metabolites were checked using high-performance liquid chromatography (HPLC). Enzymatic activities were measured spectrophotometrically using test substrates. The metabolite effects on the pure laccase and versatile peroxidase were also checked. All experimental treatments were analyzed using Excel 2019 (Microsoft Office 2019, USA). Indole-3-acetic acid (IAA) and salicylic acid increased PAH degradation by 25-70%. However, tryptophan, a precursor to IAA biosynthesis, slightly increased the degradation of only three-ring PAHs. The tested flavonoids reduced the PAH degradations, which may have resulted from the inhibition of mycelial growth by these compounds. Ferulic and cinnamic acids, precursors to lignin biosynthesis, also inhibited PAH degradation. Of the tested fungal metabolites, only veratryl alcohol promoted PAH degradation: the four-ring PAHs became more accessible to fungal degradation (43.5 and 38.1% for fluoranthene and pyrene, respectively). Oxalic and malonic acids, the most actively produced fungal organic acids, reduced the degradation of all PAHs but fluoranthene. HPLC led us to identify 9,10-phenanthrenequinone, 9,10-anthraquinone, and 9-fluorenone as the main metabolites of PAH degradation. P. ostreatus is a strong producer of extracellular laccases and peroxidases, whose involvement in PAH degradation is also well known. In our study, the most vigorous laccase inducers were tryptophan and ferulic acid (40 and 60%, respectively), whereas IAA and salicylic acid were weaker inducers (about 20%). Ferulic and salicylic acids increased versatile peroxidase activity by 1.5-2 times, whereas other effectors reduced it to varying degrees. These results are important for developing environmental biotechnologies that combine phyto- and mycoremediation.

From a structural point of view, plasmonic nanoparticles are always at least two-layer structures with a dielectric layer of stabilizing, targeting, fluorescent, Raman, or other functional molecules, often embedded in a matrix such as porous silica. To optimize the optical properties of such bioconjugates, one needs efficient analytical models based on simple physical ideas and with reasonable accuracy comparable to rigorous numerical methods requiring significant computer resources. Recently, we suggested an analytical approach ( J. Phys. Chem. C 2024, 128, 15029–15040) based on a combination of the modal expansion method (MEM) and the dipole equivalence method (DEM). The MEM+DEM method was exemplified by coated gold nanorods excited along the symmetry axis. Here, we extend the MEM+DEM approach for particles of various shapes and orientations, including random ones. To illustrate the possibilities of our method, we calculate extinction and scattering spectra of gold and silver nanorods, nanodiscs, triangle nanoprisms, bicones, and bipyramids with a dielectric coating thickness from 0 to 30 nm. For the main plasmonic peaks, we found excellent agreement between our analytical method and numerical simulations performed with COMSOL, except for some disagreement between MEM and COMSOL solutions for bicones with small rounding radii. This drawback of MEM for coated particles is explained by the unusual local field distribution with strong localization near the particle tips. To fix the point, we propose a factorized version of MEM that brings analytical spectra of coated bicones and bipyramids in good agreement with numerical counterparts. To illustrate the application of our method to real experimental colloids, we prepared 12 AuNR samples using a chemical etching with fine-tuning of the LPR over the 1020–630 nm range. By including the CTAB shell in the simulation model, we achieved excellent agreement between the calculated and measured dependence of the LPR peak position on the AuNR aspect ratio. In summary, our method makes it possible to use the MEM parameters of the original metal particles. It does not require additional numerical calculations to build analytical models for bilayered or multilayered conjugates. The presented analytical solutions depend on the particle shape, the shell thickness, and the shell refractive index, regardless of the particle size and the metal’s nature. Due to the simplicity and reasonable accuracy of the MEM+DEM analytical models, they can help apply machine learning to predict various plasmonic responses such as light absorption, scattering, surface enhanced Raman scattering (SERS), and metal-enhanced fluorescence (MEF).

Climate changes cause various types of abiotic stress in plants, thus affecting plant growth and causing decline in yield. An urgent need exists to develop an environmentally friendly attitude based on principles of sustainable agriculture. Nanomaterials may improve plant growth and enhance crop productivity by handling the conditions considered stressful for plants in a sustainable and ecofriendly manner. Selenium (Se) has been put into the category of beneficial elements in plants. Se-enriched crops present a successful choice of dietary resource for Se-supplemented food and feed owing to their high bioavailability and accessibility. Researchers from distinct areas, including both nanoscience and plant science, should encourage emerging innovations that are linked with abiotic stress in crop production. The implementation of Se nanoparticles (SeNPs) is considered one of the predominating mechanisms by plants to ameliorate stressful conditions. Increasing evidence of earlier research revealed that SeNPs could enhance plant growth and development, nutrient bioavailability, soil fertility, and stress response while maintaining environmental safety. Meanwhile, some earlier studies reported that SeNPs might have a multilateral influence on plants dependent on diverse Se nanomaterial traits, doses, and plant species. More efforts are required to enhance the knowledge of how SeNPs impact crops exposed to different abiotic detrimental factors. In light of contemporary research challenges linked to SeNPs and the prolonged application of Se nanomaterials to plants, the aim of this review is elucidating the principal fruitful areas of SeNP exploration, comparisons with bulk Se, insights into mechanisms of abiotic stress alleviation in plants, existing research uncertainties, and practical challenges for SeNP applications under varying environments.

Since infections associated with microbial communities threaten human health, research is increasingly focusing on the development of biofilms and strategies to combat them. Bacterial communities may include bacteria of one or several species. Therefore, examining all the microbes and identifying individual community bacteria responsible for the infectious process is important. Rapid and accurate detection of bacterial pathogens is paramount in healthcare, food safety, and environmental monitoring. Here, we analyze biofilm composition and describe the main groups of pathogens whose presence in a microbial community leads to infection (Staphylococcus aureus, Enterococcus spp., Cutibacterium spp., bacteria of the HACEK, etc.). Particular attention is paid to bacterial communities that can lead to the development of device-associated infections, damage, and disruption of the normal functioning of medical devices, such as cardiovascular implants, biliary stents, neurological, orthopedic, urological and penile implants, etc. Special consideration is given to tissue-located bacterial biofilms in the oral cavity, lungs and lower respiratory tract, upper respiratory tract, middle ear, cardiovascular system, skeletal system, wound surface, and urogenital system. We also describe methods used to analyze the bacterial composition in biofilms, such as microbiologically testing, staining, microcolony formation, cellular and extracellular biofilm components, and other methods. Finally, we present ways to reduce the incidence of biofilm-caused infections.

The gene polymorphism analysis for the genes presumably associated with the parthenogenetic development of the maize embryo and endosperm is presented. By sequencing and subsequent multiple alignment of transcripts of target genes (Zm_Hdt104, Zm_Chr106, Zm_Fie1 and Zm_Fie2) of the parthenogenetic (AT-1, AT-3 and AT-4) and the reference (B73) maize lines it was carried out. The presence of single nucleotide substitutions, deletions and insertions were determined, phylogenetic trees for the studied genes were constructed.

The great interest in SERS tags as bioanalysis platforms is due to their combination of strong optical signals, photostability, and narrow spectral lines. Despite significant progress in the synthesis of new types of SERS tags based on gold nanoparticles, obtaining microparticles possessing a Raman scattering intensity sufficient for detecting a single tag using a conventional Raman microscope is not a trivial task. In this work, hybrid colloidal nanocomposites based on silica microparticles and gold nanostars (AuNST) with the SiO2/AuNSTs/SiO2 composition have been synthesized and characterized. Two types of AuNSTs, one with a plasmon resonance at 700 nm and the other with two maxima at 650 and 900 nm, have been pre-synthesized and adsorbed on the surface of monodisperse colloidal silica particles 1.5 μm in diameter. Three types of thiolated aromatic molecules have been used as Raman reporters: 4-nitrothiophenol, naphthalenethiol, and 1,4-benzenedithiol. The possibility of measuring the SERS signal from a single microparticle with an intensity variation of no more than 20% has been demonstrated, as well as the possibility of multiplex determination of various microparticles in one Raman image. The stability, including photostability, of the measured SERS signal in time has been comprehensively assessed upon changes in the physicochemical parameters of a microenvironment.