Anastasia Ivanova

The efficiency of bioremediating oil-contaminated serozem (gray desert soil) of Southern Kazakhstan was investigated in the study. The first stage involved choosing hydrocarbon-degrading microorganisms suitable for the bioremediation of this desert soil. The second stage assessed the bioremediation potential of the selected microorganisms in laboratory microcosms. The final stage was a field trial experiment investigating oil removal under conditions of in situ natural attenuation, biostimulation (application of NPK fertilizer Nitroammophoska), reintroduction of indigenous oil-degrading microorganisms isolated from soils of the Aral Sea region and bioaugmentation using degrader strains from the laboratory collection. Additionally, the resulting native desert soil microbiomes were compared. Results showed that natural attenuation of the desert soil occurred over two months (with 68.5% of hydrocarbons removed), while biostimulation, reintroduction, and bioaugmentation were—as expected—also effective, achieving 89.4–97.0% oil removal. In the contaminated soil during the spring season, a significant increase in the proportion of Gammaproteobacteria within the soil microbiome was observed, with Alphaproteobacteria and Bacilli also representing significant fractions.

Adamantane is a unique tricyclic hydrocarbon with a rigid, diamond-like structure. It is widely distributed in natural hydrocarbons and has significant potential applications in medicine, materials science, and pharmaceuticals. Despite its high chemical stability, biocatalytic methods using cytochrome P450 enzymes and microorganisms, such as Pseudomonas strains and actinobacteria, demonstrate high regional specificity in the hydroxylation and modification of adamantane, primarily at tertiary C–H bonds. This review summarises the latest data on the mechanisms and pathways of the microbial transformation of adamantane and its derivatives, including the key metabolites and enzymatic systems involved. The advantages of biocatalysis—namely, high selectivity, environmental friendliness and mild reaction conditions—are highlighted as a promising approach to the synthesis of functional adamantane derivatives for use in the development of innovative drugs and materials. The limitations of current methods and prospects for development are also discussed, including searching for new microorganisms and regulating enzymatic activity to increase the efficiency of biotransformation.

Alkane-oxidizing bacteria play a crucial role in the global carbon cycle. Rhodococcus species are well-known hydrocarbon degraders, distinguished by the harboring of multiple homologs of AlkB family alkane monooxygenases. Although different types of rhodococcal AlkBs have been described, the overall picture of their diversity remains unclear, leaving gaps in the current classification. We conducted a phylogenetic analysis of all AlkBs identified in Rhodococcus (sensu lato) and examined the genomic context of the corresponding genes. The sequence clustering was well aligned with genomic neighborhoods, allowing both features to be used as criteria for proposing AlkB types that form distinct phylogenetic groups and have characteristic genomic contexts. Our approach allowed us to revise the classification of previously described AlkBs, identifying eight types on their basis, and to propose three new ones. Alkane monooxygenases whose genes are co-localized with rubredoxin genes can be considered a generalized AlkBR type, the most common among all Rhodococcus. In the AlkB0 type, which is a paralog of AlkBR, violations of conservativity in known alkane monooxygenase signature motifs were found. Our findings provide a more consistent classification framework for rhodococcal AlkB that prevents the over-reporting of “novel” types and contributes to a deeper understanding of alkane monooxygenase diversity.

Urban dust samples were collected in Moscow (Russia) in June 2021. The samples were collected in three functional zones of Moscow (traffic, residential, and recreational) and included air microparticles, leaf dust, and paved dust. Data on the taxonomic composition of bacterial communities were obtained for dust samples, and their functional characteristics were predicted using PICRUSt2 2.5.0 and FAPROTAX 1.8.0 software. The culturable part of the bacterial community was examined for the presence of antibiotic-resistant strains with respect to β-lactams, tetracyclines, amphenicols, and aminoglycosides. The presence of bacteria resistant to ceftazidime, cefepime, and tetracycline was detected in all dust samples. The presence of bacteria resistant to meropenem and amikacin was only observed in the dust collected from leaves in the residential and traffic zones. The overall abundance of cultured antibiotic-resistant bacteria from the total heterotrophs ranged from 0.03% to 1.88%, with the highest percentage observed in dust from the residential zone. Notably, strains resistant to all antibiotics tested were observed in the leaf dust bacterial community.

The elimination of hydrocarbon pollution is a critical environmental challenge, often addressed using biotechnological approaches. The study of alkane oxidizing bacteria is an important task, as it will allow developing new approaches to oil pollution treatment and improving existing ones. Representatives of the genus Rhodococcus are well-known hydrocarbon-oxidizing bacteria with high biotechnological potential. A distinctive feature of some Rhodococcus species is the presence of multiple homologous alkB genes within their genomes. However, the reasons behind this redundancy and the functional diversity of the alkane monooxygenases encoded by these genes remain unclear. Furthermore, despite the significant diversity of alkB genes even within this single genus, a comprehensive classification system has yet to be established. In this study, we conducted a phylogenetic analysis of all AlkB family alkane monooxygenases identified in Rhodococcus genomes and examined the genomic context of their corresponding genes. Our findings reveal a remarkable diversity of AlkB enzymes, refine the classification of previously described AlkB types, and propose three novel types.For the AlkB0 type, we identified deviations from previously reported signature amino acid motifs. Our results highlight the key role of colocalization of alkane monooxygenase alkB genes with rubredoxin rubB genes in the further functional classification of alkane monooxygenases.

Identifying the relationship between the microbiomes of urban dust particles from different biotopes is important because the state of microorganisms can be used to assess the quality of the environment. The aim of this work was to determine the distribution and interaction patterns of microorganisms of dust particles in the air and on leaf surfaces. Metabarcoding of bacterial and fungal communities, PAH, and metal content analyses and electron microscopy were used in this work. The results obtained allowed us to characterise the biological and chemical components of the dust particles. Some bacterial and fungal genera were correlated with benzanthracene, fluoranthene, and Cu, Ni, Co, Zn, and Mn contents. Bacterial communities were found to be more sensitive to all the pollutants studied. PM10 microbial communities circulated between biotopes and study areas due to air flows, as evidenced by the presence of similar ASVs in fungi and bacteria. The results could help to understand the effects of climate change and anthropogenic activities.

The complete genome of the naphthalene- and n-alkane-degrading strain Pseudomonas sp. strain OVF7 was collected and analyzed. Clusters of genes encoding enzymes for the degradation of naphthalene and n-alkanes are localized on the chromosome. Based on the Average Nucleotide Identity and digital DNA–DNA Hybridization compared with type strains of the group of fluorescent pseudomonads, the bacterium studied probably belongs to a new species. Using light, fluorescent, and scanning electron microscopy, the ability of the studied bacterium to form biofilms of different architectures when cultured in liquid mineral medium with different carbon sources, including naphthalene and n-dodecane, was demonstrated. When grown on a mixture of naphthalene and n-dodecane, the strain first consumed naphthalene and then n-dodecane. Cultivation of the strain on n-dodecane was characterized by a long adaptation phase, in contrast to cultivation on naphthalene and a mixture of naphthalene and n-dodecane.

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.

The impact of geographical factors, functional zoning, and biotope type on the diversity of microbial communities and chemical components in the dust of urban ecosystems was studied. Comprehensive analyses of bacterial and fungal communities, polycyclic aromatic hydrocarbons (PAHs), and metals in road and leaf dust in three urban zones of Murmansk and Moscow with contrasting anthropogenic load were conducted. We found that the structure of bacterial communities affected the functional zoning of the city, biotope type, and geographical components. Fungal communities were instead impacted only by biotope type. Our findings revealed that the structure of fungal communities was mostly impacted by PAHs whereas bacterial communities were sensitive to metals. Bacteria of the genus Sphingomonas in road and leaf dust as indicators of the ecological state of the urban ecosystems were proposed.

We performed a comparative study of the total bacterial communities and communities of cultivable polycyclic aromatic hydrocarbons (PAH)-degrading bacteria in different functional zones of Moscow and Murmansk that were formed under the influence of the PAH composition in road and leaf dust. The PAHs were determined by high-performance liquid chromatography (HPLC); the bacterial communities’ diversity was assessed by metabarcoding. The degraders were isolated by their direct plating on a medium with the PAHs. The PAH total quantity declined in the leaf dust from the traffic to the recreational zone. For the road dust, a negative gradient with pollution was observed for Rhodococcus and Acinetobacter degraders and for their relative abundance in the microbiome for the functional zones of Moscow. The opposite effect was observed in the Murmansk leaf dust for the Rothia and Pseudomonas degraders and in the Moscow road dust for Microbacterium. The PCA and linear regression analyses showed that the Micrococcus degraders in the dust were sensitive to anthropogenic pollution, so they can be used as a tool for monitoring anthropogenic changes in the biosphere. The data on the degraders’ and microbial communities’ diversity suggest that minor degrading strains can play a key role in PAH degradation.