Vol 93, No 6 (2024)

One of the major strategies for evolution of bacteria, accompanied by pronounced changes in their genetic organization, is the formation of symbioses with eukaryotes. They provide their micropartners with nutrients and ecological niches, in which bacteria implement trophic or protective functions used by their hosts. Acquisition of the ability for symbiosis is associated with formation of specialized sym gene systems, which is often accompanied by a modification in bacterial genome structure. In nodule bacteria (rhizobia) – N₂-fixing symbionts of leguminous plants, most of which belong to α-proteobacteria of order Hyphomicrobiales, the symbiogenic changes in genomes vary depending on the taxonomic position. In the evolutionarily primary rhizobia of family Bradyrhizobiaceae, which emerged directly from free-living N₂-fixers, transition to symbiosis is accompanied by a significant (1.5–2 times) increase in the genome size. However, their genomes retain a unitary structure: in the majority of Bradyrhizobium strains, more than 95% of genes are located in chromosomes. In the secondary rhizobia of family Phyllobacteriaceae (Mesorhizobium, Phyllobacterium), which emerged by transfer of sym genes into soil bacteria, various stages were revealed for formation of multipartite genome harboring a significant part of genes in extrachromosomal elements (ECE) – plasmids and chromids. The most pronounced multicomponent genome structure is found in the Rhizobiaceae family (Rhizobium, Sinorhizobium, Neorhizobium), in which the total size of ECEs containing sym genes can exceed the size of chromosome. In these bacteria, transfer from tropical to temperate ecosystems was accompanied by narrowing the host specificity, however, modification of genome structure was revealed only in Sinorhizobium, in which the proportion of ECE increases up to 51% of genome. Such genomes were also revealed in associative (rhizospheric, endophytic) N₂-fixers of genus Azospirillum, in which ECE comprise up to 60% of a genome. The irreversibly differentiated N₂-fixing cellular forms, bacteroids formed by rhizobia are included into the temporary organelles, symbiosomes considered as precursors of N₂ -fixing organelles which are revealed in some protists and are probably may be constructed for the crop plants.

A new methane-forming archaeon strain Z-7115^T was isolated from the bottom sediments of the freshwater Lake Baikal (Eastern Siberia, Russia). Morphologically, the strain is represented by non-motile coccoid cells 0.5–3 µm in size, collected in packets of 2–4 and their small aggregates. The strain uses methanol, mono-, di-, trimethylamine and acetate as energy substrates for methanogenesis. The cells grow at a temperature of 15–35°C (optimum 25°C), pH 6.3–7.5 (optimum pH 7.3) and are tolerant to NaCl concentrations < 0.1 M. The G + C content of genomic DNA is 40.76 mol. %. According to the 16S rRNA gene analysis, the new isolate belongs to the genus Methanosarcina, having a similarity level of 98.51% with the closest species of this genus M. siciliae T4/M^T . The average nucleotide similarity (ANI) between the genomes of strains Z-7115^T and M. siciliae T4/M^T was 83.8%. The virtual assessment of the hybridization of the genomes of these two strains was 23.3%. Based on the data of phylogenetic analysis and morpho-physiological properties, it is proposed to classify the isolated strain Z-7115^T (=JCM 39438, =VKM B-3565) as a new species Methanosarcina baikalica sp. nov.

The survival of the microbial population in constantly changing environmental conditions, including those unfavorable for growth, is ensured by: (1) the formation of a subpopulation of persister cells (P), maturing into ametabolic quiescent forms (RF); (2) protection of chromosomal DNA of stationary cells using the physicochemical mechanism of its co-crystallization with the nucleoid-associated protein Dps and the formation of a biocrystalline nucleoid (BN); (3) the ability of RF to germinate in a fresh environment with a mixed population of phenotypically different dissociators, one of which will be the most adaptive to it. This study addressed two questions: (1) how BN is structurally organized in prokaryotic RFs, and (2) how nucleoid biocrystallization is related to the phenotypic heterogeneity of populations growing from RFs. The work proposes a new model of BN decrystallization/recrystallization during heating/cooling of RF at sublethal temperatures in a non-growth environment, which reproduces the dynamics of BN formation in the model of nucleoid organization as a folded globule. Electron microscopic analysis of structural changes in BN in heated/cooled RFs, together with the determination of the dissociative spectra of the populations growing from them, allowed us to obtain the following new information. Biocrystallization of the nucleoid occurs in the following sequence: (1) the beginning co-crystallization of DNA-Dps is accompanied by the division of the nucleoid volume with the formation of a compacted nucleoid from superfolded DNA in the central region of the cell and loops of superfolded linear DNA extending from it; (2) co-crystallization of looped DNA-Dps with its different geometric arrangement – toroidal, lamellar, etc.; (3) crystallization of Dps-Dps, repeating the template folding of looped DNA-Dps and the formation of a multilayer structure of the Dps-Dps crystalline array. It was found that the actual heating of the PF (45‒700C, 15 min), leading to decrystallization of looped DNA-Dps while maintaining the structure of the compacted nucleoid, does not affect the dissociative (colonial-morphological) spectrum of the population growing from the PF. The change in its dissociative spectrum is influenced by the process of DNA-Dps recrystallization, during which, apparently, Dps binds not only to the former, but also to other DNA sites, also affinity for Dps and, possibly, partially occupied by other nucleoid-associated proteins, which influences changes in DNA topology and its transcription.

Biofilm formation is a widespread phenomenon in the world of microbes. They can affect human and animal health, cause damage to various industries, and at the same time can be useful in areas such as wastewater treatment or increasing the bioavailability of nutrients for plants. This actualizes the development of biofilm research methods. In this paper, an optical sensor method for indicating bacterial biofilm formation taking into account biological variability is described for the first time using the example of plant growth-stimulating rhizobacteria of the genus Azospirillum. A correlation was found between changes in the electrophysical parameters recorded by the sensor system and morphological features of bacteria from planktonic and/or biofilm cultures: the presence of motor organelles (flagella), polymorphism and ultrastructure of cellular forms. It was found that the profile of microbial cells recorded by the optical system in planktonic and biofilm forms differs significantly. When comparing cells of different strains (parent strain and its derivatives) or planktonic and biofilm bacteria, the variables recorded by the electro-optical sensor system are consistent with the changes in the micro- and ultrastructure of bacteria recorded by us using other methods. The results of the analysis of the electrophysical profiles of A. baldaniorum Sp245 can be used as a reference for identifying the specificity of the interaction of biofilm cells of this strain with various components of the root surface of the putative plant partner using an optical sensor system.

The goal of this work was to study the process of bioleaching of arsenic-containing polymetallic concentrate containing 16.0% Cu, 5.3% Zn and 1.7% As, under different conditions. The dependence of the leaching of non-ferrous metals on temperature (45 and 55°C) and the use of CO₂ and molasses bioreactors as carbon sources for the microbial population, as well as differences in the composition of microbial populations formed in different conditions were studied. Increasing temperatures led to the increase leaching of both copper and zinc. However, at a higher temperature (55°C), the use of additional carbon sources significantly affected the extraction of metals, while at 45°C, the extraction of metals did not differ significantly between different experimental variants. A study of the microbial populations of bioreactors showed that both temperature changes and additional carbon sources influenced the microbial populations that formed during the bioleaching process. When using carbon dioxide at 45°C, the total number of microbial cells was 1.4 times higher than in other variants, and at 55°C, it was 8 times higher. In addition, changes in the relationships between microorganisms in microbial populations were observed. At 45°C, microbial populations were dominated by iron-oxidizing heterotrophic archaea of the genus Ferroplasma, heterotrophic archaea of the genus Cuniculiplasma, sulfur-oxidizing autotrophic bacteria of the genus Acidithiobacillus, mixotrophic iron- and sulfur-oxidizing bacteria of the genus Sulfobacillus. At 55°C, the microbial populations were dominated by bacteria of the genus Sulfobacillus and iron-oxidizing bacteria of the genus Leptospirillum. The use of carbon dioxide led to the dominance of bacteria of the genus Sulfobacillus: the proportion of 16S rRNA gene fragment sequences of this genus was 99.9%.

Coagulase-negative staphylococci (CNS) isolated from clinical hospital environmental objects were screened for their ability to produce antibacterial compounds. It was shown that CNS strains with pronounced antagonistic activity were detected with a frequency of about 1.4%. The antibacterial activity of individual CNS strains was due to the release of low-molecular peptide compounds into the environment. The molecular weight of three isolated peptides was 2985, 2998, and 3004 Da. The peptide secreted by Staphylococcus hominis bacteria contains an unusual amino acid, methyllanthionine, and can be classified as a class I bacteriocin, a lantibiotic. The antibacterial activity of the isolated peptides was demonstrated against gram-positive bacteria of various genera that are phylogenetically unrelated to the producers.

A study of the metabolic group of iron-reducing prokaryotes that use the weakly crystalline mineral ferrihydrite as an electron acceptor has revealed its widespread distribution on Earth. However, the ability of iron reducers to develop in polyextreme conditions – at elevated pH values and temperatures – has not yet been demonstrated. To prove the existence of alkalithermophilic iron reducers, we studied water and sediment samples from the Goryachinsk nitrogen springs. These springs are confined to young tectonic faults of the Baikal rift zone, and their waters are characterized by low mineralization, high pH (8.8‒9.2) and temperature (53‒55°C). By adding synthesized ferrihydrite to water and bottom sediment samples from the Goryachinsk springs and incubating them under anaerobic conditions at temperatures of 50 and 55°C, enrichment cultures were obtained that reduce this mineral. Profiling of water and sediment samples and primary enrichment cultures by the 16S rRNA gene revealed their high phylogenetic diversity, represented almost exclusively by bacterial taxa. Further transfers with ferrihydrite and organic acids or hydrogen added as an electron donor allowed us to obtain stable enrichment cultures of organo- and lithotrophic alkalithermophilic iron reducers. From 30 to 50% of their total representation were representatives of the genus Parvivirga , one of the first cultivated representatives of the OPB41 group (now the order Anaerosomatales) of the phylum Actinomycetota.

The first data on the diversity and structure of bacterial communities in the Selenga River, its tributaries and delta waters (Selenga shallow water) during the summer high-water period of 2021 were obtained. A tendency towards a gradual decrease in chemical indicators (alkalinity, mineralization, concentrations of sulfate and chloride ions) was revealed downstream in the Russian part of the Selenga River. As before, the chemical composition of the Selenga River waters was determined by water content and anthropogenic load, while the influence of tributary waters was local. At a distance of 1 km from the mouths in the mixing zone of river water and lake water, the chemical composition and taxonomic structure of bacterial communities were close to those observed in the pelagic zone of Lake Baikal. In all analyzed 16S rRNA gene libraries, 9 common bacterial phyla were identified, with a predominance of Pseudomonadota (51.71–76.83%) in river communities and Actinomycetota (17.28–66.32%) in the communities of the Selenga shallows. The most significant differences in the taxonomic composition of bacterial communities were noted at the genus level. It is assumed that there is a stable bacterial community throughout the Selenga River, the main representatives of which are bacteria of the Limnohabitans, Pseudarcicella, Rhodoluna, and Polynucleobacter genera, which also dominate in the small rivers of Southern Baikal. Comparative analysis of the diversity of tributary communities did not reveal a significant impact on the microbiomes of the Selenga River and Lake Baikal: only a few river bacterial taxa were identified in the littoral and pelagic zones of the lake.

Bacillus thuringiensis subsp. israelensis (Bti) is a known subspicies of crystal-forming entomopathogenic bacteria used to control blood-sucking mosquitoes. In this work, we isolated three different strains of Bti 4369, 4929 and 4999 from the wild larvae midgut of blood-sucking mosquitoes Aedes flavescens . The bacterial isolates were identified by the 16S rRNA gene and serotype determination revealed that the strains belonged to Bt subsp. israelensis H14. The strains had differences in bacterial colony morphology, a number of biochemical characteristics and protein endotoxin profiles. The isolated strains Bti 4369 and 4999 showed high insecticidal activity against Culex pipiens pipiens and Aedes aegypti larvae, with LC₅₀ values of 1.47 ×10⁸ ‒2.26 × 10⁸ spores/ml 24 hours after treatment. The value for strain Bti 4929 LC₅₀ was 32.7‒35.9 × 10⁸ spores/ml. The new isolated strains of Bacillus thuringiensis subsp. israelensis have high potential for the development of ecological friendly bioinsecticides for the control of blood-sucking mosquitoes.

Methylococcus capsulatus MIR is a strain of methanotrophic bacteria that is potentially suitable for producing feed protein and other value-added products from methane. Genomic analysis did not reveal in Mc. capsulatus MIR known pathways of C3-carboxylation, necessary for the replenishment of intermediates of the tricarboxylic acid cycle and the full functioning of metabolism. The pepc gene encoding PEP carboxylase in Methylomonas rapida 12 was introduced into Mc. capsulatus MIR cells on a plasmid under the control of a medium-strength promoter. Expression of heterologous PEP carboxylase led to an increase in the content of glutamate, glycine and lysine in the cells of the recombinant strain, but did not increase to the growth rate of the culture. Consequently, the introduction of heterologous PEP carboxylase, which carries out the C3-carboxylation reaction, helps to increase the nutritional value of the methanotroph biomass.