Strains of the genus Delftia are poorly studied microorganisms. In this work, the complete genome of the naphthalene-degrading Delftia tsuruhatensis strain ULwDis3 isolated from seawater of the Gulf of Finland of the Baltic Sea was assembled. For the first time, genes encoding naphthalene cleavage pathways via salicylate and gentisate were identified in a strain of the genus Delftia. The genes are part of one operon (nag genes). Three open reading frames (ORFs) were found in the genome of D. tsuruhatensis strain ULwDis3 that encode gentisate 1.2-dioxygenase. One of the ORFs is part of the nag operon. The physiological and biochemical characteristics of the strain ULwDis3 when cultured in mineral medium with naphthalene as the sole source of carbon and energy were also studied. It was found that after 22 h of growth, the strain stopped consuming naphthalene, and at the same time, naphthalene 1.2-dioxygenase and salicylate 5-hydroxylase activities were not detected. Later, a decrease in the number of living cells and the death of the culture were observed. Gentisate 1.2-dioxygenase activity was detected from the time of gentisate formation until culture death.

Abstract Bovine mastitis is one of the most economically important diseases in cattle. Infectious mastitis has a viral or bacterial origin. The most common bacterial agents are Staphylococcus , Streptococcus , coliforms, and Bacillus species. These are opportunistic microorganisms that can switch to a pathogenic form, using various virulence factors with follow various pathologies, both animal and human. Three stable microbial consortia, each composed of Bacillus paranthracis and Staphylococcus haemolyticus strains, were isolated from milk of cows diagnosed with mastitis in three geographically remote regions of Russia. The composition of these consortia remained stable following multiple passages on culture media. Apparently, this stability is due to the structure of the microbial biofilms formed by the communities. The virulence of the consortia depended on the B. paranthracis strains. It seems plausible that the ability of the consortia to cause mastitis in cattle was affected by mutations of the cytK gene of B. paranthracis .

Hydrocarbon-decomposing microorganisms identified as representatives of the genera Pseudomonas, Rhodococcus, Acinetobacter, Kocuria, Raoultella, and Candida have been isolated from the oil-contaminated soil samples of the Middle Ob region. They have been screened for the ability to decompose various classes of hydrocarbons in a wide temperature range (6–37°C), in acid media (up to pH 4), and at increased salinity (up to 3%), for the ability to produce biosurfactants, and for the presence of genes encoding enzymes responsible for hydrocarbon decomposition. A microbial consortium has been suggested as the basis of a biological preparation for bioremediation of oil-contaminated soils in the Middle Ob region, including strains of Candida fluviatilis 24p-51, Rhodococcus erythropolis 24-44, Acinetobacter calcoaceticus 7-43, and Pseudomonas extremaustralis 7-31. The modes of cultivation and lyophilization of biomass have been determined for these microorganisms. The efficiency of degradation of oil hydrocarbons by the developed microbial consortium has been evaluated in laboratory model systems. The degree of oil degradation by the microbial consortium in the liquid mineral medium was 56%; in the model soil, 22% in 10 days at 24°C.

In this study, we investigated antibiotic-resistant microorganisms isolated by the direct plating method from 6 playgrounds in the city of Pushchino, Moscow Region, with different types of coating: sand, soil with sand, grass and a modern playground coating made of pressed rubber crumb. According to the results of the study, sand is the cleanest type of coating, both in terms of the total count of cultivated microorganisms (8 × 105/g of substrate) and in terms of the content of resistant strains. The most contaminated both in terms of the total count of cultivated microorganisms (1.2–1.9 × 109/g of substrate) and in terms of the content of antibiotic-resistant strains was the coating of pressed rubber crumb. We isolated 65 antibiotic-resistant strains of fluorescent pseudomonads. Nine Pseudomonas strains were found to contain antibiotic resistance plasmids (one belongs to P-1 incompatibility group, seven to IncP-7 and one to unidentified incompatibility group). For the first time, we discovered a conjugative plasmid pD4A-46 conferring tetracycline resistance and belonging to the P-7 incompatibility group. Taking into account the results obtained under this study, it can be recommended to periodically treat the crumb rubber coating with non-toxic antiseptics, i.e. hydrogen peroxide or chlorhexidine.

— The work presents characterization of antibiotic-resistant strains isolated by direct plating of five samples collected at different treatment stages from the Pushchino water treatment facilities in April 2015. Primary analysis of resistance of the collection (~800 strains) to the following antibiotics was carried out: carbenicillin, kanamycin, streptomycin, amikacin, tobramycin, chloramphenicol, rifampicin, gentamicin, tetracycline, ceftazidime, cefepime, and meropenem. Antibiotic-resistant bacteria most common in the Pushchino wastewater treatment facilities were found to belong to the genera Pseudomonas and Alcaligenes . Occurrence of tetracycline resistance genes was investigated, and predominance of the tetA / tetC genes responsible for active transport of this antibiotic from the cell were found to be predominant among the studied strains. The strains containing the genes associated with type I integrons ( intI1, qacE/qacE Δ 1, and sul1 ) constituted 25% of the studied ones. Four Pseudomonas strains were found to contain the IncN plasmids, while seven strains of this genus contained plasmids of the P-9 incompatibility group (ε-subgroup). Three IncP-9 plasmids were conjugative and carried simultaneously the determinants of tetracycline, streptomycin, and gentamicin resistance, which has not been previously reported for the ε-subgroup of IncP-9 plasmids.

Searching for new microorganisms with great potential for the synthesis of high-molecular exopolysaccharides possessing some useful traits is very important in the scope of certain industries. The bacterial strain Pantoea cypripedii 4A isolated by direct plating on a rich agar medium was studied in this work as a potential producer of extracellular polysaccharides. This strain was isolated from forest litter mixed with the topsoil of the M.A. Zablotsky Prioksko-Terrasny Reserve. The Pantoea cypripedii 4A strain is capable of synthesizing EPS that was confirmed by the Podobedov-Molish reaction (a qualitative reaction to carbohydrates in the medium) on a medium supplemented with 5% sucrose. Gel permeation chromatography confirmed that the isolated strain produces an exopolysaccharide with a molecular weight of about 1.69 MDa on a medium supplemented with 5% sucrose. However, the presence of two lower molecular weight peaks may indicate that the resulting product has heterogeneous structure. The yield of dry biopolymer when growing the strain on a mineral medium with sucrose at a final concentration of 5% without adding additional components, such as microelements, was 8.5 g/l. One of the important characteristics of EPS is the viscosity of their aqueous solutions. The measured dynamic viscosity of a 10% EPS solution synthesized by Pantoea cypripedii 4A was 1.728 mPa s. Despite the fact that the production of extracellular polysaccharides is often enhanced under stress conditions, neither reduced oxygen concentration, nor low temperature conditions did affect the EPS biosynthesis by the studied strain.

Исследовано распространение антибиотикоустойчивых микроорганизмов и генов резистентности к антибиотикам в очистных сооружениях г. Пущино. Обнаружены и охарактеризованы плазмиды резистентности к антибиотикам как возможные векторы для распространения генов устойчивости в окружающей среде. Продемонстрирована роль катаболических плазмид в биодеградации углеводородов нефти. Исследован горизонтальный перенос плазмид в лабораторных условиях и в открытой окружающей среде в процессе утилизации полициклических ароматических углеводородов. Исследованы ризосферные бактерии рода Pseudomonas, относящиеся к уникальной группе PGPR. Штаммы продуцируют широкий спектр биологически активных метаболитов, включая сидерофоры, феназины, 2,4-диацетилфлороглюцин, пиолютеорин, пирролнитрин, оомицин А, цианогенные гликозиды, синтезируют фитогормоны, включая индолил-3-уксусную кислоту (ИУК) и стимулируют корнеобразование у растений. На основе одного из таких штаммов P. chlororaphis (ранее P. aureofaciens) BS1393 разработан биопрепарат «Псевдобактерин-2», обладающий высокой эффективностью против целого ряда заболеваний растений. The dissemination of antibiotic-resistant microorganisms and antibiotic resistance genes in treatment facilities of Pushchino was studied. The antibiotic resistance plasmids were isolated and characterized as possible vectors for the spread of resistance genes in the environment. The role of catabolic plasmids in the biodegradation of oil hydrocarbons was demonstrated. The horizontal transfer of plasmids was studied under laboratory conditions and in an open environment during the utilization of polycyclic aromatic hydrocarbons. The rhizospheric bacteria of the genus Pseudomonas belonging to the unique PGPR group were studied. The strains produce a wide range of biologically active metabolites, including siderophores, phenazines, 2,4-diacetylphloroglucin, pyoluteorin, pyrrolnitrin, oomycin A, hydrocyanic acid, synthesize phytohormones, including indolyl-3-acetic acid (IAA), and stimulate root formation in plants. Based on one of these strains of P. chlororaphis (formerly P. aureofaciens) BS1393, the biopreparation Pseudobacterin-2 was developed, which is highly effective against a number of plant diseases.

Staphylococcus aureus is a causative agent of different infectious processes, food poisoning, and autoimmune disorders. The horizontal transfer of pathogenic strains can occur from animal to human under both house and farm conditions, and the spread of strains with antibiotic resistance is an existing problem. In addition to the spread of antibiotic-resistant strains in clinics, this problem also exists in veterinary medicine. It is especially important to monitor antibiotic resistance on farms where antibiotics are the standard treatment of animals, which may trigger the spread of antibiotic-resistant strains among animals and to the human population, and these strains can also be distributed in milk products produced by these farms (milk, cheese, and butter). In this work, we investigated 21 S. aureus isolates using whole-genome sequence analysis and tried to establish a relationship between these isolates with the development of bovine mastitis in seven regions of Western Russia. An S. aureus virulence profile was identified. We identified two groups of S. aureus associated with subclinical mastitis, namely, the enterotoxin-positive and enterotoxin-negative groups. The most prevalent factor associated with bovine mastitis in Russia was cytotoxins, including hemolysins and leukocidins. Multidrug resistance strains were investigated, and antibiotic resistance genes were identified. We identified S. aureus ST 97 type as the most common type in the regions in Western Russia. To the best of our knowledge, this is the first in-depth study of a range S. aureus isolates originating from cattle infections in Russia.

The Baltic Sea is vulnerable to environmental changes. With the increasing shipping activities, the risk of oil spills remains high. Archaea are widely distributed in many environments. However, the distribution and the response of archaeal communities to oil contamination have rarely been investigated in brackish habitats. Hence, we conducted a survey to investigate the distribution, diversity, composition, and species interactions of indigenous archaeal communities at oil-contaminated sites along the coast of the Gulf of Finland (GoF) using high-throughput sequencing. Surface water and littoral sediment samples were collected at presumably oil-contaminated (oil distribution facilities) and clean sites along the coastline of the GoF in the winter 2015 and the summer 2016. Another three samples of open sea surface water were taken as offshore references. Of Archaea, Euryarchaeota dominated in the surface water and the littoral sediment of the coast of the GoF, followed by Crenarchaeota (including Thaumarchaeota, Thermoprotei, and Korarchaeota based on the Greengenes database used). The unclassified sequences accounted for 5.62% of the total archaeal sequences. Our study revealed a strong dependence of the archaeal community composition on environmental variables (e.g., salinity, pH, oil concentration, TOM, electrical conductivity, and total DNA concentration) in both littoral sediment and coastal water in the GoF. The composition of archaeal communities was season and ecosystem dependent. Archaea was highly diverse in the three ecosystems (littoral sediment, coastal water, and open sea water). Littoral sediment harbored the highest diversity of archaea. Oil was often detected in the littoral sediment but rarely detected in water at those presumably contaminated sites. Although the composition of archaeal community in the littoral sediment was sensitive to low-input oil contamination, the unchanged putative functional profiles and increased interconnectivity of the archaeal core species network plausibly revealed resilience and the potential for oil degradation. Halobacteriaceae and putative cytochrome P450 pathways were significantly enriched in the oil-contaminated littoral sediment. The archaeal taxa formed highly interconnected and interactive networks, in which Halobacteriaceae, Thermococcus, and methanogens were the main components, implying a potential relevant trophic connection between hydrocarbon degradation, methanogenesis, sulfate reduction, and/or fermentative growth.

Mastitis, a major veterinary problem widespread in many regions, is caused mainly by Staphylococcus spp. However, there is no current reliable information about the role of Staphylococcus aureus and their toxins in the development of mastitis in cows in the territory of the Russian Federation. The aim of this investigation was to determine the profile of exotoxins of S. aureus from cow milk from farms of Central Russia. A total of 60 isolates of S. aureus were obtained from milk samples of cows with the subclinical form of mastitis. The exotoxin genes were identified using 2 types of PCR assays. The diversity of enterotoxin genes was studied by multiplex PCR. The percentage occurrence of enterotoxin genes was as follows: sea, 53.3%; seb, 3.3%; sec, 50%; sed, 4%; see, 46.6%; seg, 70%; sei, 10%; selp, 3.3%; and tsst1, 1.6%. The seh gene was not detected. The genes of pore-forming toxins and phenol-soluble modulins were identified by singleplex PCR and consisted of the following: hlA, 70%; lucS, 46.6%; psmA, 81.6%; psmB, 95%; and hld, 78.3%. The most abundant genes were psm (psmB, 95%), which codes for pore-forming toxins, and seg (70%), which codes for enterotoxins. The production of some enterotoxins in bacterial culture medium was detected by ELISA. The level of toxin production was near 1 ng/mL for SEA, SEE, SEG, SEI, SELP, and TSST-1 and reached a maximal level of 18 ng/mL for SEE. In the present work, we show that subclinical mastitis in cows is associated with S. aureus in the central region of the Russian Federation. Most of the isolates containing enterotoxin genes also had cytotoxin genes.

Diversity of the oil-degrading microbial strains isolated from the water and sediments of the Gulf of Finland (Baltic Sea) in winter and in summer was studied. Substrate specificity of the isolates for aliphatic and aromatic hydrocarbons was studied. The isolates belonged to 32 genera of the types Proteobacteria (alpha-, beta-, and gammaproteobacteria), Actinobacteria,Firmicutes, and Bacteroidetes. Seasonal variations of the oil-degrading microbial communities was revealed. The presence of the known genes responsible for the degradation of oil aliphatic and aromatic hydrocarbons was determined. The alkB sequence of the alkane hydroxylase gene was found in ~16% of the studied strains. The sequence of the phnAc phenanthrene 3,4- dioxygenase was found in Sphingobacterium sp. and Arthrobacter sp. isolates retrieved in winter and summer. In five Pseudomonas sp. strains from winter samples, the classical operons of naphthalene degradation (nah) were localized in catabolic plasmids, of which three belonged to IncР-9, one, to IncР-7, and two to an unidentified incompatibility group. Burkholderia and Delftia strains contained the operons for naphthalene degradation via salicylate and gentisate (nag). The presence of nag genes has not been previously reported for Delftia spp. strains. The sequences of the nagG salicylate 5-hydroxylase gene were also found in Achromobacter, Sphingobacterium, and Stenotrophomonas strains.

A facultative methylotrophic bacterium, strain Lp-1, which was isolated from root nodules of lupine (Lupinus polyphyllus L.) on the medium with methanol as a carbon and energy source, exhibited high similarity of the 16S rRNA gene sequences to Delftia strains (94‒99.9%). The cells of Delftia sp. Lp-1 were motile gram-negative rods dividing by binary fission. Predominant fatty acids were C16:0 (34.2%), C16:1ω9 (14.5%), and C18:1ω7c (17.3%). Phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol were the dominant phospholipids. Q8 was the major ubiquinone. Optimal growth occurred at 24‒26°C and pH 7.1‒7.3; growth was inhibited by 1% NaCl. The organism oxidized methanol with the classical methanol dehydrogenase and used the ribulose bisphosphate pathway of C1 metabolism. Analysis of translated amino acid sequence of the large subunit of the MxaF methanol dehydrogenase revealed 85.5‒94% similarity to the sequences of such autotrophic methylotrophs of the class Alphaproteobacteria as Angulomicrobium, Starkeya, and Ancylobacter, indicating the possible acquisition of the mxaF gene via horizontal gene transfer. Delftia sp. Lp-1 (VKM B-3039, DSM 24446), the first methylotrophic member of the genus Delftia, was shown to be a plant symbiont, stimulating plant growth and morphogenesis, increasing the level of photosynthetic pigments and specific leaf weight. It possesses the nifH gene of nitrogen fixation, is capable of phosphate solubilization, synthesis of auxins and siderophores, and is antagonistic to plant pathogenic fungi and bacilli.

From the leaves of three urban trees (Tilia sp., Acer sp., and Fraxinus sp.), 180 strains degrading phenanthrene, naphthalene, and salicylate were isolated by direct plating and enrichment cultures. The leaves of each tree species were characterized by a specific profile of aromatic hydrocarbon-degrading microflora. Members of the type Actinobacteria were predominant in the case of direct plating on media with phenanthrene and naphthalene. Enrichment cultures with phenanthrene and salicylate were shown to yield microbial consortia, the composition of which changed with time. Members of the type Proteobacteria were predominant in these consortia. No plasmids of polycyclic aromatic hydrocarbon degradation of the P-7 and P-9 incompatibility groups were revealed in the studied strains.