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The composition of microbial communities in rock samples, reservoir water, and enrichment cultures from subsurface horizons of an uranium deposit (Russia) was determined. The studied horizons were located in the zone of hindered water exchange at a depth of 513–544 m, characterized by moderate salinity (up to 15 g/L) of reservoir water and the presence of charry plant organic matter. The biodiversity of autochthonous subsurface prokaryotes was determined by high-throughput sequencing of the V4 region of the 16S rRNA gene. Bacterial phyla predominant in the rock samples were Firmicutes (24.2%), Fusobacteriota (23.0%), Proteobacteria (18.7%), Actinobacteriota (15.5%) and Bacteroidota (9.0%). The predominant bacterial phylum in the reservoir water was Proteobacteria (90.7%), including representatives of the genera Methylophaga, Porphyrobacter, Roseovarius, Pseudomonas, and Methylococcus. Sequencing of the internal transcribed spacer (ITS) revealed occurrence of lower fungi of the genera Mucor and Thamnidium (phylum Mucoromycota) and of the genus Penicillium (phylum Ascomycota) in the rock samples; members of these genera are known for their resistance to heavy metals and the ability to use complex organic substrates. The functional characteristics of bacterial communities of the rock and reservoir water samples, predicted by the iVicodak program and the KEGG database, showed that reservoir water bacteria had a higher potential ability to carry out the pathways of carbohydrate, nitrogen, and sulfur metabolism, degradation of xenobiotics, benzoate, polycyclic aromatic hydrocarbons and chlorinated organic compounds than the rock microbiota. Enrichment cultures of iron-reducing and sulfate-reducing bacteria and pure cultures of denitrifying bacteria of the genera Bacillus, Paenibacillus, and Acinetobacter were obtained. These results indicate the presence of a small but viable microbial community that can participate in the processes of transformations of carbon, nitrogen, sulfur, and metals in the subsurface horizon when water exchange is activated.

Interaction of the anionic copolymer of acrylic acid and acrylamide with a molar ratio of monomer units of 75 : 25 and poly(N,N′-diallyl-N,N′-dimethylammonium chloride) in aqueous solution is studied. The interaction is accompanied by the formation of a polycomplex stabilized by multiple salt bonds between oppositely charged groups of both polyelectrolytes. A nonstoichiometric polycomplex with a tenfold excess of anionic groups is present in solution in the form of particles with a diameter of about 300 nm; the particles retain their aggregate stability for 30 days. The application of aqueous solutions of individual polymers and the nonstoichiometric polycomplex on the surface of sand with a particle size of 0.15 ± 0.05 mm is associated with the formation of composite polymer-sand coatings. The highest mechanical strength is possessed by coatings with the participation of an anionic copolymer and a polycomplex. For sand and polycomplex coatings, the weight loss during water treatment is 10%, which is lower than that in the case of traditional polyacrylamide soil stabilizer. The polycomplex at a concentration of up to 0.33 wt % does not exhibit toxicity to microorganisms, thereby indicating that the use of a negatively charged polycomplex is promising for obtaining waterproof protective coatings on the surface of sandy soils.

While liquid biopreparations for water and soil bioremediation are convenient and economically attractive, microbial survival under standard environmental conditions is poor. Microbial immobilization is a common and efficient method to preserve high viable cell titers. We tested the effect of three new materials on the survival of various hydrocarbon oxidizers during long-term storage. The suspended (planktonic) cultures stored under the same conditions served as a control when assessing the viability of immobilized cultures after long-term storage. The cells of Acinetobacter seifertii, Pseudomonas extremaustralis, P. aeruginosa, Rhodococcus erythropolis, and Dietzia maris grown with microcapsules (MCs) of chitosan-modified polyurea (represented by crumpled spheres, 40–200 µm in diameter) attached abundantly to the MC surface. After several months of storage with MCs, CFU titers were two to five times higher than in the control. Cultivation of P. aeruginosa and R. erythropolis with polylactide (PLA) MCs (represented by slightly crumpled thin-walled spheres 25–100 µm in size) resulted in the formation of thick biofilms on MC surface. After 30-day storage with these MCs, CFU titers of R. erytropolis were up to one thousand times higher than in the control. In the presence of PLA MCs, the respiration rates of both cultures were five to eight times higher than in the control without MCs. The reasons of the better survival of immobilized cells are being discussed. After storage for up to 12 months, CFU titers of bacteria (R. erythropolis, A. seifertii, P. aeruginosa, P. extremaustralis) and yeasts (Yarrovia lipolytica) immobilized in the gel based on silanol derivatives of humic substances were ten to one hundred times higher than in the control. After 4-month storage, hydrocarbon degradation by the stabilized cultures began earlier and was faster and more complete than in the control. The tested materials may be used to extend the storage time for the preparations of biotechnologically important bacteria and for application for petroleum bioremediation.

Multi-crystal data collection using synchrotron radiation was successfully applied to determine the three-dimensional structure of a triclinic crystal form of Dps from Escherichia coli at 2.0 Å resolution. The final data set was obtained by combining 261 partial diffraction data sets measured from crystals with an average size of approximately 5 µm. The most important features of diffraction data measurement and processing for low-symmetry crystals are discussed.

A new approach is described to increasing the numbers of viable cells in long-term stored populations (cultures) of the hydrocarbon-oxidizing bacterium Acinetobacter junii, which involves application of humic substances (HSs). HSs are produced due to condensation and oxidation of phenolic compounds, including alkylresorcinols, factors of intercellular microbial communication with stress-potentiating and antioxidant activity. HS addition to the stationary-phase bacterial culture was shown to result in 10- to 15-fold increase in cell viability for bacterial preparations stored for 1 to 4 months under provocative conditions (free air supply, growth medium, and temperatures of 20–25°C). Analysis of death curves for experimental and control A. junii cultures revealed two phases, with the initial stage of rapid death (0.167 log CFU/mL day), usual for autolysis of the regular stationary cells, and the stage of slower death (log 0.015 CFU/mL day), typical of persister cells. This was previously shown to be the feature determining this type of phenotypic heterogeneity in the populations of opportunistic bacteria. The concentration dependence of HSs effect on persisters formation was determined. While treatment of A. junii stationary cultures with hydrogen peroxide (0.03–0.3%) as a stress factor also resulted in enhanced persisters formation (fourfold), unlike the HS-treated variants they survived for not more than 1.5 to 2 months. Plating of the control and experimental variants (with HSs or H2O2) after long-term storage (2–4 months) revealed their phase variation spectrum to change due to replacement of the dominant colony morphology phenotype by the minor ones (40% and more), which is one of the features of the dormant cystlike bacterial forms. The ratios of the variants in the control and experiments (with HSs) were different. Comparison of the chemical composition of HS preparations indicated that the most oxidized hydrophilic HSs affected formation of persister cells, while less oxidized humates with higher antioxidant activity were responsible for the viability prolongation. Thus, the effect of HSs on bacterial populations includes induction of persister cell formation (their increased number), prolongation of the colony-forming capacity in the cells surviving under provocative storage conditions, and alteration of the phase variant spectrum of the stored populations. Formation of stress-induced persister cells developing into mature dormant forms supporting survival of the population (species) was established for saprotrophic bacteria (in the case of A. junii). In practical terms, HS-induced formation of persister cells may be recommended for development of diverse bacterial preparations.

Addition of humic compounds (9 preparations) to the cultures of hydrocarbon-oxidizing bacteria was shown to result in up to 15-fold increase in the number of viable cells in the cultures stored in the growth media with access to air at 20‒25°C. The most oxidized humates exhibited the highest activity in induction of persister formation, which subsequently matured to dormant forms, while unoxidized humates with antioxidant activity supported viability persistence.

The universal response of Escherichia coli to stress is enhancing the synthesis of specific histone-like Dps proteins that bind bacterial DNA. As a result, two-dimensional and three-dimensional crystalline arrays can be observed in the cytoplasm of starving bacteria. Conditions for obtaining in vitro co-crystals of DNA-Dps were selected, and their elemental composition was studied using analytical electron microscopy. It was found that Dps in the co-crystal retains its ferritin-like activity; that is, it can stimulate the oxidation of Fe2+ ions to Fe3+ and facilitate the accumulation of iron in the form of Fe2O3 in the inner cavity of the oligomer.

One of the universal mechanisms for the response of Escherichia coli to stress is the increase of the synthesis of specific histone-like proteins that bind the DNA, Dps. As a result, two-and three-dimensional crystalline arrays may be observed in the cytoplasm of starving cells. Here, we determined the conditions to obtain very thin two-dimensional DNA-Dps co-crystals in vitro, and studied their projection structures, using electron microscopy. Analysis of the projection maps of the free Dps crystals revealed two lattice types: hexagonal and rectangular. We used the fluorescently labeled DNA to prove that the DNA is present within the co-crystals with Dps in vitro, and visualized its position using transmission electron microscopy. Molecular modeling confirmed the DNA position within the crystal. We have also suggested a structural model for the DNA-Dps co-crystal dissolving in the presence of Mg2+ ions.

The mechanisms of interaction of DPS protein molecules (DNA-binding protein from starved cells) with DNA, which are important for understanding the protection of the genetic material of bacteria under stress, were examined. The results of studies of molecular dynamics studies of the complexes of E. coli DPS proteins with DNA showed that the main role in the binding of DNA molecules to DPS molecules is played by the amino acid residues Lys8 and Lys10 located in the disordered part of N-termini of DPS, and Lys27 in its ordered part. The pair of Asp23–Ser24 residues exerts a coordinating effect. A strong redistribution of Na+ ions from the outer part of the computational cell into DPS molecules and their preferential binding to His63 and Glu82 amino acid residues coordinating the binding site of the ferroxidase center, which can reduce the efficiency of binding of iron ions by this center, were found. A study of the recently understood three-dimensional crystal structure of E. coli DPS protein crystals (PDB ID: 6GCM) shows the presence of three types of mutually orthogonal channels: a wide channel and two narrow ones. The presence of DNA in the wide channels, unlike narrow ones, does not destroy but stabilizes the crystal. Crystal stabilization occurs due to the formation of additional interactions between the N-terminal regions of one DPS molecule with DNA and with another DPS molecule.

One of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormantEscherichia colicells, namely:nanocrystalline, liquid crystalline, and thefolded nucleosome-like. We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that innanocrystallineformation the majority of Dps protein is tightly bound to nucleoid DNA. We demonstrated that the population of the dormant cell is structurally heterogeneous, which allows cells to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.

Ever decreasing efficiency of antibiotic treatment due to growing antibiotic resistance of pathogenic bacteria is a critical issue in clinical practice. The two generally accepted major approaches to this problem are the search for new antibiotics and the development of antibiotic adjuvants to enhance the antimicrobial activity of known compounds. It was therefore the aim of the present study to test whether alkylresorcinols, a class of phenolic lipids, can be used as adjuvants to potentiate the effect of various classes of antibiotics. Alkylresorcinols were combined with 12 clinically used antibiotics. Growth-inhibiting activity against a broad range of pro- and eukaryotic microorganisms was determined. Test organisms did comprise 10 bacterial and 2 fungal collection strains, including E. coli and S. aureus, and clinical isolates of K. pneumoniae. The highest adjuvant activity was observed in the case of 4-hexylresorcinol (4-HR), a natural compound found in plants with antimicrobial activity. 50% of the minimal inhibitory concentration (MIC) of 4-HR caused an up to 50-fold decrease in the MIC of antibiotics of various classes. Application of 4-HR as an adjuvant revealed its efficiency against germination of bacterial dormant forms (spores) and prevented formation of antibiotic-tolerant persister cells. Using an in vivo mouse model of K. pneumoniae-induced sepsis, we could demonstrate that the combination of 4-HR and polymyxin was highly effective. 75% of animals were free of infection after treatment as compared to none of the animals receiving the antibiotic alone. We conclude that alkylresorcinols such as 4-HR can be used as an adjuvant to increase the efficiency of several known antibiotics. We suggest that by this approach the risk for development of genetically determined antibiotic resistance can be minimized due to the multimodal mode of action of 4-HR.

One of the adaptive strategies for the constantly changing conditions of the environment utilized in bacterial cells involves the condensation of DNA in complex with the DNA-binding protein, Dps. With the use of electron microscopy and electron tomography, we observed several morphologically different types of DNA condensation in dormant Escherichia coli cells, namely: nanocrystalline, liquid crystalline, and the folded nucleosome-like. We confirmed the presence of both Dps and DNA in all of the ordered structures using EDX analysis. The comparison of EDX spectra obtained for the three different ordered structures revealed that in nanocrystalline formation the majority of the Dps protein is tightly bound to nucleoid DNA. The dps-null cells contained only one type of condensed DNA structure, liquid crystalline, thus, differing from those with Dps. The results obtained here shed some light on the phenomenon of DNA condensation in dormant prokaryotic cells and on the general problem of developing a response to stress. We demonstrated that the population of dormant cells is structurally heterogeneous, allowing them to respond flexibly to environmental changes. It increases the ability of the whole bacterial population to survive under extreme stress conditions.

A series of X-ray diffraction experiments were performed for the first time to study stress-induced biocrystallization (structural response to stress) in the bacteria E. coli, the spore-forming bacteria Bacillus cereus, and in cells and spores of the mycelial fungus Umbelopsis ramanniana. High-intensity areas with spacings of 90 and 44 A are indicative of a periodically ordered arrangement (most likely nanocrystalline) of the bacterial nucleoid. For the starved bacteria Bacillus cereus, a peak at a spacing of 45 A is also assigned to nanocrystalline complexes of DNA with the Dps protein. The spores of the fungus Umbelopsis ramanniana VKM F-582, as well as the spores of Bacillus cereus, form ordered arrays of DNA molecules with DNA-condensing acid-soluble proteins SASPs. Starved dehydrated mycelial cells of the fungus Umbelopsis ramanniana form ordered structures with spacings from 27 to 55 A. A series of peaks reflect the formation of a number of ordered protein arrays, apparently with DNA, with continuously varying characteristic interplanar spacings.

Compaction and biocrystallization of the nucleoid are presently considered as a necessary and important stage in the transformation of the cell ultrastructure during change of microbial cultures strategies from growth to survival. Nucleoid biocrystallization in the stationary phase cells is achieved due to structural regularity of the DNA complexes with the histone-like Dps protein. Our experiments with Escherichia coli mutants, overproducers of the Dps protein, confirmed nucleoid biocrystallization in the late stationary phase cells. Since nucleoid biocrystallization was revealed in E. сoli cells without Dps overproduction at late stages of starvation, it is constitutive in the cycle of development of microbial populations. The present work concentrated on detection of the nucleoid biocrystalline structure in (1) long-starved (21 day in the chemostat mode) bacterial cells (genera Arthrobacter and Pseudomonas), (2) dormant ametabolic (anabiotic) cells of such prokaryotes as archaea and non-spore-forming bacteria, (3) endospores of bacilli, (4) streptomycete exospores, and (5) in the cells surviving in permafrost for (2‒3 Ma). The topics discussed include nucleoid biocrystallization as a necessary stage of maturation of the dormant microbial cells providing for survival and preservation of the species, dynamics of nucleoid biocrystallization during maturation of the dormant cells, and its possible role for the preservation of genetic information in the case of autolysis of most of the cells in a developing culture.

Structural, biochemical, and genetic changes caused by stress factors are known to be largely similar for cells of all modern organisms, which inherited the basic strategies of adaptation to different types of stress from their ancient ancestors. In the present work, the adaptation process is considered for the simplest example of the bacterial E. coli nucleoid. Experimental studies performed recently on prokaryotic bacterial cells, the simplest living organisms, have demonstrated that, under unfavorable environmental conditions (for example, starvation), bacterial cells can use biocrystallization, a special mechanism of protection of the genetic apparatus (nucleoid), generally untypical of living organisms. This mechanism helps to protect the nucleoid from damage and resume the activity of the bacterial cells later, upon improvement of the external conditions. The results of studying the structure of the nucleoid of E. coli bacteria (BL21-Gold strain (DE3)) subjected to starvation stress by using synchrotron radiation at the ESRF beamline ID23-1 are reported.

Background: Living organisms survive in constantly changing environmental conditions due to universal strategies of adaptation to various stresses based on structural, biochemical, and genetic rearrangements. One of adaptive strategies utilized in bacterial cells involves the protection of the nucleoid from unfavorable factors via binding of DNA to specific histone-like proteins. This strategy leads to the condensation of DNA in complexes with Dps (DNA-binding protein from starved cells), which has been discovered in starved for up to 48 hrs cells of the E. coli bacterium Methods: Electron microscopy and X-ray diffraction of synchrotron radiation studies were used to reveal distinct forms of nucleoid condensation in dormant E. coli cells that were starving for longer period – up to 7 months. Results: We have found and described not only previously detected forms of nucleoid condensation: quasi-nanocrystalline, quasi-liquid crystalline and spore-like, but also observed a new type of nucleoid condensation in dormant cells - folded nucleosome-like. Conclusion: According to the recognized concept of a bacterial population as a multicellular organism, their heterogeneity allows to respond flexibly to the environmental changes and to survive in stressful situations. Heterogeneity is the reason why we observed several types of nucleoid condensation in dormant E. coli cells. Heterogeneity of dormant cells increases the ability of the whole population to survive under various stress conditions. Results, observed here, shed a new light both on the phenomenon of nucleoid condensation in prokaryotic cells and on the general problem of developing a response to the stress.

Effect of human inherent immunity factors of, a gene-encoded antibacterial peptide indolicidin (Ind) and a cytokine interleukin 1 (IL1) on formation of antibiotic-tolerant persister cells surviving in the presence of ciprofloxacin (Cpf, 100 μg/mL) and ampicillin (Amp, 100 μg/mL) in submerged bacterial cultures (Staphylococcus aureus FGA 209P, Escherichia coli K12, and Pseudomonas aeruginosa PAO1) was studied. While Ind in physiological concentrations (0.3 and 3.0 μg/mL) introduced to the lag- or exponential-phase cultures of test organisms exhibited no reliable effect on population growth, the number of persisters increased at 3.0 μg/mL. Bactericidal Ind concentrations (9 μg/mL) suppressed S. aureus growth (-0.1% of surviving cells) with subsequent recovery due to development of the more antibiotic-tolerant white variant. Treatment with Cpf after Ind addition resulted in mutual potentiation of their antimicrobial activity, with the number of S. aureus persisters 2 to 3 orders of magnitude lower than in the case of the antibiotic alone. IL1, another immunity factor, when introduced (0.1-1 ng/mL) to the exponentially growing S. aureus culture (but not to the lag phase culture) had a temporary growth-static effect, with the number of persisters surviving Cpf treatment (100 μg/mL) increasing by 1 to 2 orders of magnitude. Electron microscopy revealed significant alterations in the outer cell envelope layer of surviving S. aureus cells, which should be associated with their changed antigenic properties. Thus, the factors of human inherent immunity have a dose-dependent effect on the growth of bacterial populations. In combination with antibiotics, they exhibit synergism of antimicrobial action (indolicidin) and minimize (indolicidin) or increase (interleukin 1) the frequency of formation of persister cells responsible for survival of a population subjected to an antibiotic attack.

The paper represents the study of interaction between deoxyribonucleic acid (DNA) and deoxyribonucleic acid-binding protein from starved cells (DPS) cluster formation and crystal growing within a cell. This study is a part of the project that includes European Synchrotron Radiation Facility (ESRF) investigations of in vivo and in vitro nanocrystallization processes of Escherichia coli (E. coli) nucleoid under stress condition combined with theoretical molecular dynamics approaches. Nucleoid biocrystallization is an adaptive mechanism of bacterial cells under stress. It is poorly understood at the present time. Understanding crystal formation process is a very important for molecular biology, pharmacology and other areas. In the simulation part the coarse-grained modeling of various combinations of the following molecules was used: DPS proteins (from 1 to 108 DPS dodecamers in simulation box), short DNA fragments with a length of 24 base pairs (b.p., from 1 to 100 DNA fragments in simulation box) and a part of pBluescript SK(+) plasmide with a length of 161 b.p., in the presence of ions. We defined structural, energetic and dynamic properties of DPS-DPS and DPS-DNA complexes in clusters and crystals that allow us to predict crystal formation and the structure of these crystals in experimental systems. Communicated by Ramaswamy H. Sarma.

Background: One of the universal mechanisms for the response of E.coli to stress is the increase of the synthesis of specific histone-like proteins that bind the DNA: Dps. As a result, two-and three-dimensional crystalline arrays may be observed in the cytoplasm of starving cells. Methods: The Dps protein was expressed in E.coli. A fluorescently labeled DNA template with a sequence of s603 (165 b.p) was obtained using a PCR/ Confocal laser scanning fluorescent images were recorded with an inverted LSM710-Confocor3 microscope (Zeiss, Germany). The stained grids were studied on an analytical transmission electron microscope JEM-2100 (JEOL, Japan) equipped with a LaB6 filament, with an accelerating voltage of 200 kV and low-dose conditions. The three-dimensional models of Dps crystals, and DNA-Dps co-crystals were constructed in the UCSF Chimera program package. Results: Here, we determined the conditions to obtain very thin two-dimensional DNA-Dps co-crystals in vitro and studied their projection structures using electron microscopy. Analysis of the projection maps of the free Dps crystals revealed that they form two lattice types: hexagonal and rectangular. We used the fluorescently labeled 165 b.p. DNA fragment to prove that the DNA forms the co-crystals with Dps in vitro and to visualize the DNA’s position. When comparing the structures of the co-crystals to the 2D crystals of free Dps, we observed extra-densities between Dps molecules that were 2 nm in diameter. Molecular modeling confirmed that DNA molecules may be located in the crevices between Dps molecules where positive-charged N-termini are exposed, or, alternatively, interact with the sides of the Dps molecules. We have also suggested a model for the DNA-Dps co-crystal dissolving in the presence of Mg2+ ions. Conclusion: In conclusion, our findings indicate that both models of DNA interactions with Dps may exist in the course of the co-crystal formation: the model suggested by, apparently, describes the mature DNA-Dps co-crystal, while the model of alternating layers may represent the earlier stages of co-crystal dissolving and DNA release.

Effect of sublethal doses of physical and chemical stressors (heat shock for 2 h at 45 degrees C and addition of C12-alkylhydroxybenzene, a microbial alarmone) on development of resistance to the subsequent lethal antibiotic attack and the role of the time interval between these treatments were studied on a submerged batch culture of Escherichia coli 12. The interval sufficient for the development of stress response provides for development of temporary adaptive resistance to the antibiotic attack, resulting in increased number of surviving persister cells. The interval below the time required for the stress response potentiates cell death and results in a decreased number of persisters. Heterogeneity of the fractions (10(-4) to 10(-2)% of the intial CFU number) surviving lethal doses of an antibiotic (a mpicillin or ciprofloxacin) was found. Apart from a low number of antibiotic-resistant cells (up to 0.005% of surviving cells), the fractions contained antibiotic-tolerant forms, such as temporarily resistant metabolically adapted cells, long-term persisters, and the cells of slowly growing SCV variants with small colonies (d ≤ 1 mm). Persisters are hypothesized to act as precursors for cystlike dormant cells (CLC), in which the cell differentiation stage is completed and the processes of cell ametabolism (transition to the anabiotic state) are still incomplete.

Efficiency of MALDI mass spectrometry for differentiation between phenotypic phase variants (in colony morphology and virulence/avirulence) was investigated for saprotrophic and opportunistically pathogenic bacteria of five genera (Acinetobacter, Arthrobacter, Rhodococcus, Corynebacterium, and Escherichia). Analysis of MALDI spectra (on the SA and HCCA matrices) included (1) determination of similarity of the protein spectra as a percentage of the common protein peaks to the total amount of proteins, which reflects the phylogenetic relationships of the objects and has been recommended for identification of closely related species; (2) comparison of intensities of the common peaks; and (3) the presence of specific peaks as determinative characteristics of the variants. Under the standard analytical conditions, the similarity between the MALDI profiles was shown to increase in the row: genus–species–strain–variant. Assessment of intensities of the common peaks was most applicable for differentiation between phase variants, especially in the case of high similarity of their profiles. Phase variants (A. oxydans strain K14) with similar colony morphotypes (S, R, M, and Sm) grown on different media (LB agar, TSA, and TGYg) exhibited differences in their protein profiles reflecting the differences in their physiological characteristics. This finding is in agreement with our previous results on screening of the R. opacus with similar colony morphology and different substrate specificity in decomposition of chlorinated phenols. Analysis of MALDI spectra is probably the only efficient method for detection of such variants.

Effect of the antibiotics kanamycin and ampicillin on growth and phase variation of the populations of four strains of lactic acid bacteria (Lactobacillus sp. M67AT, L. casei MB, Enterococcus faecium M, and E. faecium M3185) was studied. The presence of antibiotics in the medium resulted in a dose-dependent decrease in viable cell numbers and in partial or complete substitution of the dominant S variant with the minor Sm and Sb variants. The variants differed in colony morphology, as well as in some physiological, biochemical, biotechnological, and probiotic characteristics. The Sm type variants of all strains exhibited the highest resistance to antibiotics. High production of exopolysaccharides was found in Sb variants of lactobacilli and in S variants of enterococci. The highest antibacterial activity was found in Sm variants of lactobacilli, especially in Lactobacillus sp. M76AT The latter is biotechnologically the most promising strain, since all variants fermented milk yielding the products with uniformly pronounced functional and organoleptic properties. These patterns are of importance for the understanding of the mechanisms of antibiotic resistance and for selection of the variants with desired properties, as well as for quality control of the lactic acid bacteria starter cultures.

The effect of the extracellular peptide reactivating factor (RF) synthesized by Luteococcus casei on stress response of Escherichia coli cells subjected to UV irradiation was studied. For these studies, we constructed a test strain carrying the umuD-lacZ operon. The expression rate of this operon reflects the rate of SOS response. Protective effect of RF, defined as the number of cells retaining the colony-forming activity (CFU) after UV irradiation (49–1166 J/m2), was dose-dependent, species-nonspecific, and increasing with increase of the stress load. RF was demonstrated to possess the properties of a direct adaptogen: 15 min of preincubation with RF caused a 1.5–6-fold decrease in expression of the umuD SOS response gene in UV-treated cells, concurrently with a 1.2–7.5 times increase in the number of viable cells (those having retained their colony-forming activity). The probable mechanisms of the protective effect of RF are being discussed.

A comparative study was conducted on the adaptive mechanisms of the strains Arthrobacter oxydans K14 and Acinetobacter lwoffii EK30A isolated from permafrost subsoil sediments and of those of the analogous collection strains (Ac-1114 Type and BSW-27, respectively). In each pair of the strains compared, the strains differed in terms of (i) growth-related, physiological, and biochemical properties; (ii) resistance to stress factors; (iii) capacity for generation of dormant forms (DFs) under growth arrest conditions, and (iv) intrapopulation production of phase variants. The strains isolated from permafrost displayed a lower growth rate but were more resistant to repeated freezing-thawing treatment than the collection strains. Under the same growth conditions, the permafrost strains formed larger numbers of cystlike anabiotic DFs, extraordinarily small cells, and forms that became nonculturable during long-term storage. Resuscitation of the nonculturable forms resulted in a 2- to-7-fold increase in the percentage of FISH-detectable metabolically active cells. The permafrost strains were also distinguished by increased genome lability. This facilitated their dissociation into intrapopulation variants with phenotypically distinct colonial and morphological properties and different antibiotic resistance. The phenotypic variability was more prominent in Arthrobacter (for which it was not reported previously) than in Acinetobacter. In the populations produced by plating the dormant bacterial forms, the qualitative and quantitative characteristics of the phase variant spectra varied depending on the formation conditions and the composition of the solid media used for the plating. Thus, the permafrost isolates of A. oxydans and Ac. lwoffii were distinguished from their collection analogs by a more manifest adaptive potential including stress resistance, the intensity of DF generation under growth arrest conditions, and increased intrapopulation variability.

Effect of sublethal doses of physical and chemical stressors (heat shock for 2 h at 45 degrees C and addition of C12-alkylhydroxybenzene, a microbial alarmone) on development of resistance to the subsequent lethal antibiotic attack and the role of the time interval between these treatments were studied on a submerged batch culture of Escherichia coli 12. The interval sufficient for the development of stress response provides for development of temporary adaptive resistance to the antibiotic attack, resulting in increased number of surviving persister cells. The interval below the time required for the stress response potentiates cell death and results in a decreased number of persisters. Heterogeneity of the fractions (10(-4) to 10(-2)% of the intial CFU number) surviving lethal doses of an antibiotic (a mpicillin or ciprofloxacin) was found. Apart from a low number of antibiotic-resistant cells (up to 0.005% of surviving cells), the fractions contained antibiotic-tolerant forms, such as temporarily resistant metabolically adapted cells, long-term persisters, and the cells of slowly growing SCV variants with small colonies (d ≤ 1 mm). Persisters are hypothesized to act as precursors for cystlike dormant cells (CLC), in which the cell differentiation stage is completed and the processes of cell ametabolism (transition to the anabiotic state) are still incomplete.

Effect of human inherent immunity factors of, a gene-encoded antibacterial peptide indolicidin (Ind) and a cytokine interleukin 1 (IL1) on formation of antibiotic-tolerant persister cells surviving in the presence of ciprofloxacin (Cpf, 100 μg/mL) and ampicillin (Amp, 100 μg/mL) in submerged bacterial cultures (Staphylococcus aureus FGA 209P, Escherichia coli K12, and Pseudomonas aeruginosa PAO1) was studied. While Ind in physiological concentrations (0.3 and 3.0 μg/mL) introduced to the lag- or exponential-phase cultures of test organisms exhibited no reliable effect on population growth, the number of persisters increased at 3.0 μg/mL. Bactericidal Ind concentrations (9 μg/mL) suppressed S. aureus growth (-0.1% of surviving cells) with subsequent recovery due to development of the more antibiotic-tolerant white variant. Treatment with Cpf after Ind addition resulted in mutual potentiation of their antimicrobial activity, with the number of S. aureus persisters 2 to 3 orders of magnitude lower than in the case of the antibiotic alone. IL1, another immunity factor, when introduced (0.1-1 ng/mL) to the exponentially growing S. aureus culture (but not to the lag phase culture) had a temporary growth-static effect, with the number of persisters surviving Cpf treatment (100 μg/mL) increasing by 1 to 2 orders of magnitude. Electron microscopy revealed significant alterations in the outer cell envelope layer of surviving S. aureus cells, which should be associated with their changed antigenic properties. Thus, the factors of human inherent immunity have a dose-dependent effect on the growth of bacterial populations. In combination with antibiotics, they exhibit synergism of antimicrobial action (indolicidin) and minimize (indolicidin) or increase (interleukin 1) the frequency of formation of persister cells responsible for survival of a population subjected to an antibiotic attack.

The influence of hexylresorcinol on the structure, equilibrium fluctuations, and functional activity of water-soluble enzyme lysozyme was studied over a wide range of hexylresorcinol concentrations. Hexylresorcinol was found to be not only a stabilizer of lysozyme. At low hexylresorcinol concentrations (2 to 10 molecules per lysozyme globule), the activity of lysozyme sharply increased; activity began to decrease as the concentration grew. The influence of hexylresorcinol on the structural, dynamic, and functional lysozyme characteristics is well described by models of preferential hydration and preferential protein interaction with hexylresorcinol. The hexylresorcinol molecule consists of hydrophobic (alkyl radical) and hydrophilic (aromatic nucleus) moieties, which has additional regulatory action on the functional activity of lysozyme. As the concentration of hexylresorcinol increases, the effect of regions with preferential hydration begins to noticeably predominate over the effect of preferential interaction with hexylresorcinol. At hexylresorcinol concentrations higher than 100 molecules per lysozyme globule, the activity of lysozyme is fully inhibited. This is caused by the preferential hydration of the protein with the displacement of hexylresorcinol from direct contacts with it. The displacement of hexylresorcinol causes the formation of high-density hexylresorcinol micelles. Dense micelles interfere with the approach of substrates to the protein and fully inhibit its functional activity. The complete inhibition of lysozyme activity occurs at hexylresorcinol concentrations lower by an order of magnitude than glycerol inhibiting concentrations.

The influence of three chemical chaperones: glycerol, 4-hexylresorcinol, and 5-methylresorcinol on the structure, equilibrium fluctuations, and functional activity of the hydrophilic enzyme lysozyme and the transmembrane reaction center (RC) protein from Rb. sphaeroides in a broad range of concentrations has been studied. The chosen chemical chaperones differ strongly in their structure and action on hydrophilic and membrane proteins. The influence of the chemical chaperones (except methylresorcinol) on the structure, dynamics, and functional properties of lysozyme and RC protein are well described in the framework of extended models of preferential hydration and preferential interaction of protein with a chemical chaperone. A molecule of hexylresorcinol consists of a hydrophobic (alkyl radical) and a hydrophilic (aromatic core) moieties; this provides for additional regulation of the functional activity of lysozyme and RC by hexylresorcinol. The influence of methylresorcinol on proteins differs from that of glycerol and hexylresorcinol. Methylresorcinol interacts with the surface of lysozyme directly, not via water hydrogen bonds. This leads to a decrease in the denaturation temperature and an increase in the amplitude of equilibrium fluctuations, allowing it to be a powerful activator. Methylresorcinol interacts with the membrane RC protein only by the condensation of hydration water, which is negligible in this case. Therefore, methylresorcinol does not affect the functional properties of the RC protein. It is concluded that different chaperones at the same concentration as well as one and the same chaperone at different concentrations produce protein 3D structures differing in dynamic and functional characteristics.

The adaptogenic effect of the chemical analogues of alkylhydroxybenzenes (AHBs), bacterial extracellular autoregulators (the individual compound C7-AHB and its technical preparation Sidovit), was demonstrated for two pseudomonad species, Pseudomonas aeruginosa and P. fluorescens. The protective effect of AHBs resulted in increased growth rate and biomass accumulation in bacteria grown under suboptimal conditions within the species tolerance range. The adaptogenic effect of AHBs (10–50 μmg/l) was more pronounced under more unfavorable growth conditions. In the case of P. fluorescens, the individual compound C7-AHB increased the biomass yield by 30% under alkaline conditions (pH 9.5), when the growth rate decreased by 80–90% compared to the optimum (pH 5.5–7.5). The Sidovit preparation, containing a mixture of natural AHBs with C7-AHB as the main component, increased the growth rate of P. aeruginosa by 40–60% at nonoptimal temperatures (45 and 10°C) or under enhanced salinity (1% NaCl). The action of AHBs as regulators of the rpoS and SOS response stress regulons was demonstrated to be among the mechanisms of their adaptogenic effect, as was demonstrated with the relevant reporter genes in the model strains E. coli C600 thi, thr, leuΔ(pro-lac) with the osmE-lacZ and umuD-lacZ hybrid operons, respectively. AHBs are technologically and economically acceptable as adaptogenic supplements for bacterial preparations used in soil bioremediation and oil spillage removal under conditions unfavorable for microbial growth, including increased salinity, extreme pH, and fluctuating sub- or supraoptimal temperatures.

The ability of alkylhydroxybenzenes to change the enzyme activity of hen egg white lysozyme and its efficiency in the catalyzed hydrolysis of nonspecific substrates (chitin and yeasts) was demonstrated. A homolog, C7-AHB, was used as a modifier; this substance increased the lysozyme enzymatic activity over the entire studied range of concentrations. The effect of C7-AHB concentration (0.125–4.0 mg/ml), species (initial or oxidized), and the time (1–24 h) of lysozyme incubation with C7-AHB at 25°C in 0.05 M phosphate buffer (pH 7.4) on the lysozyme activity were studied by differential scanning microcalorimetry, as well as the thermodynamic parameters of its denaturation. The kinetic parameters of chitin hydrolysis by the C7-AHB-modified lysozyme were determined.

Alkylhydroxybenzenes (AHB) were found to control the activation of protective functions of microorganisms by inducing stress gene expression and increasing the frequency of the intrapopulation phase transitions which are responsible for the phenotypic variability of bacteria. We established the dependence of the regulatory effects of AHB on their structure (alkyl radical length) and concentration. A reversion assay using the tryptophan auxotrophic strain Bacillus subtilis trpA5 B 1733 indicated a relationship between the reversion frequency that was 40–120 times higher than the background value and phase transition’s intensity (with R → S transition rates up to 87% in contrast to 2% in the control experiment) induced by specific doses (5–100 mg/ml) of long-chain AHB such as C12-AHB acting for a short time (1 h) on vegetative (dividing or stationary-phase) B. subtilis cells. Using four test strains constructed from Escherichia coli C600 thi, thr, leuΔ(pro-lac) with transcriptional or translational vectors containing the hybrid umuD-lacZ or osmE-lacZ operons, we demonstrated that AHB perform the regulatory functions involved in controlling the SOS response gene expression and the general rpoS -dependent stationary-phase regulon, respectively. The dose-dependent effect of long-chain AHB (within the 50–100 µg/ml range) resulting in a two- to threefold increase in the stress gene expression, similar to the effect of natural stress factors such as UV irradiation and starvation, provides evidence that AHB function as alarmones (danger signals). From the fact that the osm E gene is upregulated by 35–70 µg/ml C12-AHB (its regulation level is increased up to twofold), it follows that C12-AHB controls rpoS-dependent regulation and the transition to the stationary phase. The effect of the short-chain homologue C7-AHB substantially differs from that of C12-AHB. C7-AHB in concentrations of 10–100µg/ml causes a significant decrease in osmE and umuD expression. A 30-min preincubation of cells with 10–100µg/ml C7-AHB protected them from UV irradiation, as was observed as a 3.6-fold decrease in umuD expression. Comparative analysis of the marker gene’s expression values in the strains with the transcriptional and translational vectors demonstrates that AHB nonspecifically activate stress regulons at the transcription level.

In our study, we investigated the capacity of alkylhydroxybenzenes (AHB), which are microbial anabiosis autoinducers, for alteration of the enzymatic activity of the hen egg-white lysozyme, as well as the efficiency of hydrolysis of specific (peptidoglycan) and nonspecific (chitin) substrates catalyzed by lysozyme. AHB homologues (C7-AHB and C12-AHB), which differ in their hydrophobicity and effects in their interaction with lysozyme, were used as modifying agents. C7-AHB stimulated enzymatic activity within the whole range of concentrations used (10−7−10−3 M). More hydrophobic C12-AHB exhibited this ability only at low concentrations and inhibited fermentative activity at high concentrations, acting as a mixed-type inhibitor. Both AHB homologues caused changes in the hydrophobicity of lysozyme molecules. An increase in the affinity level between the C7-AHB-modified enzyme and the nonspecific substrate (colloidal chitin or cell wall polymers of Saccharomyces sp.) was observed, which manifested itself in the enhancement of the hydrolysis rate by 200–500% (as compared to the native enzyme). A significant effect on the efficiency of the lysozyme-catalyzed modifications of the substrate (peptidoglycan, colloidal chitin) structure as a result of its complexation with AHB was demonstrated. A stabilizing effect of C7-AHB and C12-AHB was revealed, which ensured a high level of activity of the AHB-modified enzyme (as compared to the control) after heat treatment (functional stability), as well as at nonoptimal temperatures of catalysis (operational stability). The biological significance of lysozyme modification with AHB and the practical aspects of its application are discussed.

The effect of hexylresorcinol (HR), a chemical analogue of microbial anabiosis autoinducers of the alkylhydroxybenzene (AHB) group, on the stability of biological membranes and monolamellar liposomes formed of egg phosphatidylcholine (ePC) was studied. According to spectrophotometry and electron microscopy studies of HR-loaded liposomes in the presence of a surfactant Tween 20, the critical ratio between HR and ePC for liposome preservation was found to be close to equimolar. The trends in HR influence on membrane structural organization and stability of liposomes were also confirmed in experiments on intact bacterial cells explaining non-species-specific effect of AHBs. The demonstrated high efficiency of AHB biocides may be used in material and equipment protection against biocorrosion.

Population growth, the ratio between dissociants, pH, and levels of reducing sugars in the medium were monitored during prolonged (375 h) batch cultivation of Pseudomonas aeruginosa S and M dissociants on mineral medium with glucose. During the stationary growth phase (100–375 h), two scenarios were possible. The first one included extensive cell autolysis coupled to alkalinization of the medium and an increased ratio of the M dissociant. In the second case, acidification of the medium was coupled to the oscillating secondary growth, mostly of the M dissociant; the dynamics of cell numbers of this dissociant correlated with the dynamics of the culture optical density. In this scenario, periodical appearance of reducing sugars in the medium was detected; it was in the opposite phase with the changes of the M dissociant cell numbers. The differences between scenarios of P. aeruginosa growth in the late stationary phase were probably due to the physiological and biochemical characteristics of the S and M dissociants, including different pathways of glucose utilization (respiration or fermentation), resistance to acidification, as well as synthetic (proteolytic) activity and productivity of autoinducers.

The haloalkaliphilic chemolithoautotrophic gram-negative bacteria Thioalkalivibrio versutus, strain AL2, and Thioalkalimicrobium aerophilum, strain AL3, were shown to possess the capacity to produce resting forms, namely cystlike refractile cells (CRC), whose production was controlled by the level of the d1 extracellular factors exhibiting the function of anabiosis autoinducers. The conditions were elucidated that promote the formation of CRC in the developmental cycles of the cultures studied, in condensed cell suspensions undergoing autolysis, and under the action of exogenously introduced chemical analogues of anabiosis autoinducers (alkylhydroxybenzenes). The peculiarities of the fine structure of the resting cells obtained were studied. Distinctions were revealed (with respect to viability and thermotolerance) between the CRC formed under different conditions. The relationship between the growth strategy and survival strategy of extremophilic bacteria is discussed taking into account the effect of the d1 autoregulatory factors. A new model of CRC formation is proposed: CRC production in the life cycle of bacteria developing under conditions of increased concentration of anabiosis autoinducers.

X-ray microanalysis showed that vegetative cells, viable resting forms, and nonviable forms (micromummies) of the bacteria Bacillus cereus and Micrococcus luteus and the yeast Saccharomyces cerevisiae differ in the content of elements S, P, Ca, and K and Ca/K and P/S ratios. Viable resting forms (cystlike refractive cells and bacillar endospores) had more calcium and less phosphorus and potassium than vegetative cells, the difference being higher for bacilli than for micrococci and yeasts. The distinctive feature of all viable resting microbial forms was their low P/S ratios and high Ca/K ratios. The differences revealed in the cellular content and ratios of elements probably reflect changes in ionic homeostasis accompanying the transition of vegetative microbial cells to the dormant state. Relevant potassium parameters indicate that the membranes of viable resting forms retain their barrier function. At the same time, the nonviable micromummies, even those morphologically intact, of B. cereus and S. cerevisiae exhibited an anomalously low content of potassium, while those of M. luteus had an anomalously high content of this element. This suggests that the cellular membranes of micromummies lose their barrier function, which results in a free diffusion of potassium ions across the membranes. The possibility of using the elemental composition parameters for the quick analysis of the physiological state of microorganisms in natural environments is discussed.

The haloalkaliphilic, lithoautotrophic, sulfur-oxidizing gram-negative bacteria Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum were found to possess a special system for the autoregulation of their growth. The system includes the extracellular autoinducers of anabiosis (the d1 factor) and autolysis (the d2 factor). The principal components of the d1 factor are alkylhydroxybenzenes, as evidenced by specific qualitative reactions. The principal components of the d2 factor are free unsaturated fatty acids dominated by oleic acid isomers. Like the respective autoregulators of neutrophilic bacteria, the d1 factor of haloalkaliphilic bacteria presumably controls their growth and transition to anabiotic state, while the d2 factor controls autolytic processes. Alkylhydroxybenzenes of both microbial and chemical origin were found to influence bacterial respiration. The low-molecular-weight osmoprotectant glycine betaine enhanced the thermostability of trypsin. This suggests that both glycine betaine and the d1 factor serve as chemical chaperones.

Under the influence of alkyl hydroxybenzene (C6-AHB) added to cell suspensions at concentrations of (1–5) × 10–3M, the cells of Saccharomyces cerevisiae, Micrococcus luteus, and Thioalkalivibrio versutusunderwent dramatic changes in the ultrastructural organization of cell membranes, cytoplasm, and inclusions. In yeast suspension, the first changes were observed after 15 min in the structure of pocket-like invaginations in the cytoplasmic membrane (CM): they were shortened and thickened. In the subsequent 30 to 60 min, CM ruptures were formed in the regions devoid of intramembrane protein particles and in the pocket-like invaginations. After 24 h, complete disintegration of the intracellular membrane structures and conglomeration of the ribosomal part of the cytoplasm occurred. Similar changes were observed on the exposure of gram-positive and gram-negative bacteria to AHB. However, the cell wall in all the microorganisms studied was not destroyed, and in Micrococcus luteusit was even thickened. These mummified forms were preserved as morphologically intact but nonviable cells for more than three years of observations. By their ultrastructural characteristics, these mummified forms of microorganisms were similar to the fossilized microorganisms discovered by us in fibrous kerite. The concept of micromummies was formulated. AHB are supposed to play an important role in the process of fossilization of microorganisms in nature.