The paper describes a predatory Gram-negative bacterium from the genus Bdellovibrio, which was isolated from water of the Lyubozhikha River. As revealed by electron microscopy, the bacterium is an intracellular predator of Gram-negative microorganisms. Its prey range includes Pseudomonas tolaasii, the phytopathogen responsible for brown spot disease in the cultivated button mushroom (Agaricus bisporus). Based on the results of a 16S rRNA gene sequence analysis, the bacterium was identified as Bdellovibrio bacteriovorus strain LR3. We characterized the predator-prey dynamics between B. bacteriovorus LR3 and P. tolaasii, determining the optimal temperature and pH conditions for this interaction. Our results demonstrate the potential of B. bacteriovorus LR3 as a biocontrol agent against P. tolaasii in mushroom cultivation. The possibility of using B. bacteriovorus LR3 against clinical cases Salmonella and Escherichia infections is also addressed.

Phenolic compounds are an extensive group of natural and anthropogenic organic substances of the aromatic series containing one or more hydroxyl groups. The main sources of phenols entering the environment are waste from metallurgy and coke plants, enterprises of the leather, furniture, and pulp and paper industries, as well as wastewater from the production of phenol–formaldehyde resins, adhesives, plastics, and pesticides. Among this group of compounds, phenol is the most common environmental pollutant. One of the cheapest and most effective ways to combat phenol pollution is biological purification. However, the inability of bacteria to decompose high concentrations of phenol is a significant limitation. Due to the uncoupling of oxidative phosphorylation, phenol concentrations above 1 g/L are toxic and inhibit cell growth. This article presents data on the biodegradative potential of Rhodococcus opacus strain 3D. This strain is capable of decomposing a wide range of toxicants, including phenol. In the present study, cell growth with phenol, growth after rest, growth of immobilized cells before and after rest, phase contrast, and scanning microscopy of immobilized cells on fiber were studied in detail. The free-living and immobilized cells can decompose phenol concentrations up to 1.5 g/L and 2.5 g/L, respectively. The decomposition of the toxicant was catalyzed by the enzymes catechol 1,2-dioxygenase and cis,cis-muconate cycloisomerase. The role of protocatechuate 3,4-dioxygenase in biodegradative processes is discussed. In this work, it is shown that the immobilized cells can be stored for a long time (up to 2 years) without significant loss of their degradation activity. An assessment of the induction of genes potentially involved in this process was taken. Based on our investigation, we can conclude that this strain can be considered an effective destructor that is capable of degrading phenol at high concentrations, increases its biodegradative potential during immobilization, and retains this ability for a long storage time. Therefore, the strain can be used in biotechnology for the purification of aqueous samples at high concentrations from phenolic contamination.

Three strains, SL2, SL4-1, and SL4-2, were isolated from soil and assigned to the genus Rhodococcus. The strains can degrade toxic compounds: phenol and its chlorinated derivatives. It has been shown that the strains were sensitive to more than 25 antibiotics and could grow at a concentration of NaCl up to 120 g/L in the medium (strains SL4-1 and SL4-2). The viability of the cells during growth on phenol at different concentrations was investigated. The strain SL4-2 was able to grow in medium with phenol up to 1.5 g/L, while addition of phenol up to 2 g/L had a toxic effect on the cells. The isolates can be used as a basis for the development of biopreparations for environmental treatment of anthropogenic pollutants.

A gram-positive bacterium, strain Viol, belonging to the genus Microbacterium, was isolated from a sample of soddy-podzolic soil taken in the vicinity of Pushchino (Moscow oblast). The strain formed intensely colored colonies of violet or red-violet color on agar media, which was not typical for representatives of this genus. A feature of the fine structure of cells of the strain Viol was the presence of an extensive capsule, organized in the form of chaotically oriented ultrastructures resembling needle-shaped crystals surrounded by a polysaccharide matrix. A violet pigment was extracted from the cells of the novel isolate and characterized. The experimental data obtained indicate a new mechanism of intermicrobial antagonistic action, which is implemented by cells of the Viol strain in the presence of alien bacteria, which is probably a moderate predatory "wolf pack" lifestyle.

Biotechnologically significant strains of bacteria of the genus Pseudomonas were isolated from the rhizosphere of wild and cultivated cereals. They were able of both biocontrol of phytopathogenic fungi and bacteria and of degrading the herbicide glyphosate as the sole source of phosphorus (P. chlororaphis subsp. chlororaphis G16, P. chlororaphis subsp. aureofaciens G27, and P. protegens G23-4) and the herbicide Axial as the sole source of carbon (P. chlororaphis G27). These strains exhibited lipolytic and proteolytic activities; P. chlororaphis G27 also produced hydrogen cyanide possessing an antifungal effect. The strains studied in this research can be recommended as a basis for biopreparations for plant protection from phytopathogenic microorganisms, on soils treated with herbicides, in particular.

In our study, we investigated the bioaccumulation of T4 and RB43 bacteriophages by the bivalve mollusks U. pictorum and A. cygnea . Additionally, tests were conducted to determine the content of E. coli in the mollusks, and a comparison of the bioaccumulation activity of the viruses based on their diet was made. The results of the studies indicated that T4 and RB43 bacteriophages, despite differences in conditions and virus structure, exhibit a similar bioaccumulation model where their titers depend on the activity of the mollusk and their cyclical changes. The phage is reproduced by the natural microflora of the animal and can be retained due to its filtration feeding type. The activity of the mollusk is also influenced by its feeding characteristics.

The current study was carried out to characterize chalky soil bacteria obtained from the rhizosphere of Acacia species growing in Abardae, Maekel Region of Eritrea. This study collected three chalky soil samples from the rhizosphere of Acacia ethibica, Acacia origena, and non-rhizospheric soil. The samples contained 1.42 × 1010, 5.35 × 109, and 5.68 × 107 cfu/g of culturable bacteria, respectively. A total of 80 bacterial strains were isolated, with ten selected for further study based on their distinct morphology. The researchers examined the cell morphology and the antimicrobial and plant growth-promoting activity of the chosen bacterial isolates. The study’s findings identified that the aerial mycelium of the strain EAE-1 displayed a unique and previously unreported arrangement of hyphae-bearing spores. The antimicrobial test results also showed that bacterial strains EAE-1, EAE-3, EAE-14, EAE-15, EAE-40, and EAO-24 displayed a wide range of antimicrobial activity against the examined phytopathogens. Furthermore, the seed germination result showed that the majority of bacterial strains had a positive effect on wheat growth, with strains EAE-40 and EAO-17 particularly enhancing maize growth. To sum up, the substantial capabilities of these strains position them as promising candidates for biotechnological applications. This study also represents the preliminary analysis of the microbial composition of Eritrean soil.

Microbial degradation of pollutants is a safe and cost-effective way to clean the environment. However, little is known on changes at the cell ultrastructure level and on the mechanisms of adaptation in general to xenobiotics under conditions of their biodegradation. Rhodococcus sp. strain 7Ba is capable of preserving long-term viability and the ability to degrade when growing with phenol at up to 1 g/L. Destructive morphological changes at the ultrastructural level were not detected in the cells growing on phenol, which indicated rapid adaptation to it. Strain 7Ba cells formed a polysaccharide matrix under all experimental conditions. Investigation of the growth of spore-forming bacteria cells on glyphosate (0.5 g/L) showed that, although the substrate was not optimal, the cells were able to grow on it. The cells of Paenibacillus sp. GP5-2 and Rossellomorea sp. GP5-7 exhibited ultrastructural changes and a delay in spore formation (for strain GP5-2). The detected changes were adaptive, and further study will improve our understanding of their strategy ensuring the preservation of survival and the ability to degrade.

Microorganisms of various systematic groups, such as fungi, bacteria and actinomycetes, represent an inexhaustible source of biologically active substances that can be used in various fields of human activity [...]

Every year, people cause more and more harm to the environment as a result of their activities, so the search for new strains of pollutant destructors remains an urgent task. Microbial destructors are the inhabitants of various natural sources: soil, water, etc. We isolated four strains from soil (designated SL-1, 2, 3 and SL-4) and two from river sludge (designated IL-1 and IL-2). The isolation was carried out by the enrichment culture method on a mineral medium containing phenol at a concentration of 0.5 g/L as the sole source of energy and carbon. The pure cultures obtained were tested for their ability to grow on phenol at a concentration of 0.5–2 g/L. The studies showed that strain SL-4 was able to grow on phenol at concentrations of up to 2 g/L, while strains IL-1, SL-1, SL-2 and SL-3 were able to grow on phenol up to 1.5 g/L, and IL-1 was able to grow on phenol up to 0.5 g/L. The new isolates were further tested for their ability to degrade toluene (50 g/L), pinoxaden (50 g/L), a diesel + gasoline mixture, biphenyl and oil. The isolates showed growth on all the substrates used as sole carbon and an energy source, except for strains IL-1, IL-2, SL-1 and SL-3, which are incapable of toluene utilization. The strains were tested for their ability to grow at high salinity. Studies have shown that strain SL-4 is able to grow on a medium with up to 120 g/L of NaCl and the other isolates with up to 100 g/L. The studied strains were also tested for cell viability when growing at high concentrations of phenol and its chlorinated derivatives. The peculiarities of the physiology of isolates and the maintenance of cell viability in unfavorable conditions are important for their further use as a basis for biological products.

Microorganisms from various taxonomic groups play a crucial role in environmental cleanup, specifically in the bioremediation of contaminated soils and aquatic ecosystems by decomposing toxic pollutants or transforming them into less toxic substrates that can be easily recycled. Over 150 cultures were examined for their capability to utilize these substances as the only source of growth in a mineral medium, with phenol concentrations in the medium varying from 0.1 g/L to 2.5 g/L, oil at 1–2%, pinoxaden and toluene up to 0.5%, and carbon tetrachloride up to 10%. It was found that the isolated bacteria belonged to the genera Rhodococcus, Pseudomonas, Peribacillus, Microbacterium, and Bacillus. As a result, strains that can efficiently eliminate various pollutants were isolated and characterized.

Background: Microbial communities are essential in human health and environmental regulation, but present a challenge for the analytical science due to their diversity and dynamic range. Tandem mass spectrometry provides functional insights on microbial life cycle, but is time-consuming. MALDI TOF excels in rapid species identification, but not functional assessment. To address critical challenges in human health and environmental sustainability, microbiology needs advanced mass spectrometry methods and bioinformatic tools enabling both rapid identification and accurate assessment of functional activity of microbial communities. Results: We show for the first time that both identity and functional activity of microorganisms and their communities can be accurately determined in experiments as short as 7 min per sample, using the basic Orbitrap MS configuration without peptide fragmentation. The approach was validated using strain isolates, mock microbiomes composed of bacteria spiked at known concentrations and human fecal microbiomes. Our new bioinformatic algorithm identifies the bacterial species with an accuracy of 95 %, when no prior information on the sample is available. Microbiome composition was resolved at the genus level with the mean difference between the actual and identified components of 12 %. For mock microbiomes, Pearson coefficient of up to 0.97 was achieved in estimates of strain biomass change. By the example of Rhodococcus biodegradation of n-alkanes, phenols and its derivatives, we showed the accurate assessment of functional activity of strain isolates, compared with the standard label-free and label-based approaches. Significance: Our approach makes microbial proteomics fast, functional and insightful using the Orbitrap instruments even without employing peptide fragmentation technology. The approach can be applied to any microorganisms and can take a niche in routine functional assessment of microbial pathogens and consortiums in clinical diagnostics together with MALDI TOF MS and 16S rRNA gene sequencing.

Biodegradation of phenol is an effective method for removing this toxicant from contaminated sites. Phenol is a toxic compound for living cells, so many bacteria degrade phenol in relatively low concentrations, up to 0.75 g L−1. The Rhodococcus opacus strain 1CP is an effective destructor of a wide range of pollutants. In the absence of a carbon source in the medium, cells of the R. opacus 1CP strain easily form cyst-like resting cells (CLC). The purpose of this work was to evaluate the viability of cells during long-term storage and the efficiency of the process of phenol destruction by R. opacus 1CP cells germinating after dormancy. Resting cells were obtained by simple cultivation in a rich medium followed by storage under static conditions. This is a simple approach to obtain a large amount of biomass. Decomposition of phenol proceeded via catechol followed by ortho-cleavage of aromatic ring. The induction of three phenol hydroxylases was detected by RT-PCR in cells germinated in a mineral medium with phenol as the carbon source. The stability of the genome of cells germinating after dormancy is shown by box-PCR. Dormant R. opacus 1CP cells, both suspended and immobilized, can be directly used for the decomposition of phenol after 4–12 months storage. In addition to phenol, after 9 months of storage, immobilized germinating cells easily metabolized 4-chlorophenol and 2,4,6-trichlorophenol. The results demonstrate a potential and simple approach toward achieving long-term storage of cells for further use in bioremediation.

Phenol and its chlorinated derivatives are introduced into the environment with wastewater effluents from various industries, becoming toxic pollutants. Phenol-degrading bacteria are important objects of research; among them, representatives of the genus Rhodoccocus are often highlighted as promising. Strain 7Ba was isolated by enrichment culture. A new isolate was characterized using culturing, biochemistry, high-throughput sequencing, microscopy (including electron microscopy), and functional genome analysis. Rhodococcus erythropolis strain 7Ba is able to grow on phenol and chlorophenols without losing its properties during long-term storage. It was shown that strain 7Ba is able to form viable but nonculturable (VBNC) forms during long-term storage under nutrient limitation, preserving both cell viability and the ability to degrade phenols. The ultrastructural organization of the vegetative forms of cells and VBNC forms was characterized. The following distinctive features were found: modifications (thickening) of cell membranes, cell size reduction, nucleoid condensation. Functional analysis of the genome showed the presence of genes for the degradation of alkanes, and two branches of the β-ketoadipate pathway for the degradation of aromatic compounds. Also, the genome of strain 7Ba contains several copies of Rpf (resuscitation promoting factor) genes, a resuscitation factor of resting bacterial forms. The new isolate strain 7Ba is a promising biotechnological agent that can not only utilize toxic aromatic compounds but also remain viable during long-term storage. For this reason, its further application as an agent for bioremediation can be successful under changing conditions of climate and given the deficiency of nutrient compounds in nature. Minor biostimulation will allow the strain to recover its metabolic activity and effectively degrade pollution.

Biological protection is an important part of the strategy of the modern environmentally safe protection of agricultural plants from phytopathogens. The most promising in this regard are soil microorganisms, in particular representatives of the phylum Actinomycetota. Actinomycetes are producers of biological compounds of various chemical structures with antibacterial, antifungal, and antitumor effects. The authors have a collection of microorganisms (120 bacterial strains) isolated from soil and water sources. When analyzing isolates according to the morphological features of cells and mycelium, 25 bacterial cultures were selected from the collection. Studies of the ability to detect antimicrobial activity in the strains selected have been carried out. Five cultures were selected that effectively inhibit the growth of some phytopathogens. The bacterial strains were identified using the 16S rRNA gene, and their belonging to the Streptomyces genus was shown. The analysis of antibiotic resistance to 80 antibiotics showed that most antibiotics inhibited the growth of the studied strains of streptomyces. Data on the physiological characteristics of growth were obtained: the temperature optimum of growth for all strains is in the range of 24–30 °C, the optimum of NaCl concentration values for all strains is in the range of 0–3%, with the exception of the strain IPS92w, whose optimum range is wider and equal to 0–6%, and the optimum of pH values is in the range of 6–8. The strains selected have biotechnological potential for the development of a biological product with antimicrobial activity against phytopathogenic microorganisms.

Bacteria, designated as A1.1 and A1.2, were isolated from poultry waste based on the ability to form ammonia on LB nutrient medium. Whole genome sequencing identified the studied strains as Peribacillus frigoritolerans VKM B-3700D (A1.1) and Bacillus subtilis VKM B-3701D (A1.2) with genome sizes of 5462638 and 4158287 bp, respectively. In the genome of B. subtilis VKM B-3701D, gene clusters of secondary metabolites of bacillin, subtilisin, bacilisin, surfactin, bacilliacin, fengycin, sactipeptide, and ratipeptide (spore killing factor) with potential antimicrobial activity were identified. Clusters of coronimine and peninodin production genes were found in P. frigoritolerans VKM B-3700D. Information on coronimine in bacteria is extremely limited. The study of the individual properties of the strains showed that the cultures are capable of biosynthesis of a number of enzymes, including amylases. The B. subtilis VKM V-3701D inhibited the growth of bacterial test cultures and reduced the growth rate of the mold fungus Aspergillus unguis VKM F-1754 by 70% relative to the control. The antimicrobial activity of P. frigoritolerans VKM V-3700D was insignificant. At the same time, a mixture of cultures P. frigoritolerans VKM B-3700D/B. subtilis VKM B-3701D reduced the growth rate of A. unguis VKM F-1754 by 24.5%. It has been shown that strain A1.1 is able to use nitrogen compounds for assimilation processes. It can be assumed that P. frigoritolerans VKM V-3700D belongs to the group of nitrifying or denitrifying microorganisms, which may be important in developing methods for reducing nitrogen load and eutrophication.

In the process of evolution, living organisms develop mechanisms for population preservation to survive in unfavorable conditions. Spores and cysts are the most obvious examples of dormant forms in microorganisms. Non-spore-forming bacteria are also capable of surviving in unfavorable conditions, but the patterns of their behavior and adaptive reactions have been studied in less detail compared to spore-forming organisms. The purpose of this work was to study the features of transition from dormancy to active vegetative growth in one of the non-spore-forming bacteria, Gordonia polisoprenivorans 135, which is known as a destructor of such aromatic compounds as benzoate, 3-chlorobenzoate, and phenol. It was shown that G. polyisoprenivorans 135 under unfavorable conditions forms cyst-like cells with increased thermal resistance. Storage for two years does not lead to complete cell death. When the cells were transferred to fresh nutrient medium, visible growth was observed after 3 h. Immobilized cells stored at 4 °C for at least 10 months regenerated their metabolic activity after only 30 min of aeration. A study of the ultrathin organization of resting cells by transmission electron microscopy combined with X-ray microanalysis revealed intracytoplasmic electron-dense spherical membrane ultrastructures with significant similarity to previously described acidocalcisomas. The ability of some resting G. polyisoprenivorans 135 cells in the population to secrete acidocalcisome-like ultrastructures into the extracellular space was also detected. These structures contain predominantly calcium (Ca) and, to a lesser extent, phosphorus (P), and are likely to serve as depots of vital macronutrients to maintain cell viability during resting and provide a quick transition to a metabolically active state under favorable conditions. The study revealed the features of transitions from active growth to dormant state and vice versa of non-spore-forming bacteria G. polyisoprenivorans 135 and the possibility to use them as the basis of biopreparations with a long shelf life.

Microbial interactions play an important role in natural habitat. The long-term coevolution of various species leads to the adaptation of certain types of microorganisms as well as to the formation of a wide variety of interactions such as competitive, antagonistic, pathogenic and parasitic relationships. The aim of this work is a comprehensive study of a new ultramicrobacterium Microbacterium lacticum str. F2E, isolated from perennial oil sludge, which is characterized by high antimicrobial activity and a unique ultrastructural organization of the cell envelope, which includes globular surface ultrastructures with a high negative charge. A previously undescribed mechanism for the antagonistic action of the F2E strain against the prey bacterium is proposed. This mechanism is based on the ability to preferentially capture essential microelements, in which charge interactions and the property of phosphate accumulation may play a significant role. The revealed type of intermicrobial interaction can probably be attributed to the non-contact type antagonistic action in the absence of any diffuse factor secreted by the antagonistic bacteria.

Violacein is a biotechnologically significant secondary metabolite due to its antibacterial, antifungal, and other properties. Isolation, research, and identification of violacein producing strains are of interest for the development of biotechnological processes, in order to enhance the biosynthesis of this compound. The purpose of the present work was to study the properties of a newly isolated bacterium capable of synthesizing blue-purple pigment. An aboriginal bacterium was isolated from the coastal zone of the Vezelka River in the city of Belgorod. Based on chemical and spectrophotometric studies of the crude ethanol extract, the pigment was identified as violacein, and the isolate was assigned to the group of violacein-forming bacteria, which includes bacteria of the genera Chromobacterium, Iodobacter, Janthinobacterium, Duganella, Collimonas, and Massilia. Based on cultural, morphological, tinctorial, physiological, and biochemical properties, as well as analysis of the 16S rRNA gene sequence, the new isolated strain was assigned to the genus Janthinobacterium. The isolated strain is capable of suppressing the growth of a number of fungal and bacterial phytopathogens. For representatives of the genus Janthinobacterium, their inhibitory influence on cyanobacteria was shown for the first time.