Microbiology

While cytoskeletal proteins have long been considered to be present only in eukaryotes, but not in prokaryotes, homologs of the major cytoskeletal proteins, including tubulin, have been discovered in bacteria and archaea in the last 30 years. The properties of tubulin homologs, as well as of the cytoskeleton-like structures they form in prokaryotic cells, vary and differ significantly from the relevant properties of eukaryotic tubulins. The comparison of prokaryotic tubulin homologs with each other seems therefore to be an interesting task and thus is the goal of the current review. We consider such tubulin homologs found in bacteria and archaea as FtsZ, TubZ, PhuZ, BtubA/BtubB, CetZ, etc. The ability of various tubulin homologs to act as targets for pharmaceuticals, similar to the FtsZ protein, which is already a target for promising antibiotics, is also discussed.

The relic Lake Mogilnoe, separated from the Barents Sea by a sand and pebble dam, is located in the high Arctic on the Kildin island (Murmansk region). This lake is a classic example of a meromictic basin of marine origin. The data obtained during the 2018 expedition showed changes in the hydrochemical regime of the lake that have occurred over the past 20 years. Sulfide concentration in the monimolimnion of the lake was as high as 140 mg/L. A tendency for salinization of the surface waters to 7 g/L has been noted. The Lake Mogilnoe is characterized by a discrepancy between the halocline and thermocline levels. The chemocline zone in the lake is below the halocline level. In a narrow oxygen-containing layer between 3 and 7.5 m, aerobic microflora of the marine type and marine fauna were present. The bacterial plate was formed at the boundary of the sulfide layer at ~8 m and mainly consisted of green sulfur bacteria (GSB). Brown-colored GSB species containing bacteriochlorophyll e were predominant. The previously formed concept of anaerobic phototrophic bacteria (APB) biodiversity based on morphological characteristics was modified using metagenomic data obtained by analyzing DNA from two samples of lake water in the chemocline zone, and was also supplemented by identifying new GSB species. Molecular diagnostic data confirmed the absolute dominance of the brackish species of GSB Chlorobium phaeovibrioides. This is the first on isolation and identification of brown- and green-colored Prosthecochloris aestuarii morphotypes from Lake Mogilnoe and identified, as well as of bacteriochlorophyll c-containing Prosthecochloris sp. The taxonomic position of Pelodyction phaem, which was constantly present in the Lake Mogilnoe, is discussed in detail. Despite the partial isolation of the ecosystem of Lake Mogilnoe from the Barents Sea, the main properties of the dominant GSB species of GSB and Prosthecochloris aestuarii turned out to be similar to those of the phylotypes living in lakes on the White Sea coast of the, which remained connected with the Barents Sea.

Taxonomic diversity and quantitative distribution of cultured forms of Fe-and Mn-oxidizing microorganisms in Fe-Mn nodules of different sizes and fine earth of Gleyic Luvisols formed in the territory not affected by direct anthropogenic impact, were analyzed. The results were obtained using a combination of microbiological, molecular and analytical methods and noninvasive techniques. Most of the microorganisms which were cultured from the nodules were Mn oxidizers. Bacteria of the genera Bacillus, Rhodococcus, Lysinibacillus, Pseudomonas, and Priestia were identified in the nodules. Quantitative distribution of Fe-and Mn-oxidizing microorganisms in the outer and inner zones of the nodules of different sizes demonstrated that Mn-oxidizing microorganisms were involved in all stages of nodules formation and development, while Fe-oxidizing microorganisms participated in the initial phase of their formation. Spherules and porous structures of bacterial nature were observed in the studied nodules. The host fine earth was characterized by differences in the relative abundance of the dominant microbial groups in the profile. Manganese-oxidizing bacteria were represented in the soil fine earth by the genera Prestia and Methylobacterium.

Degradation of oil hydrocarbons artificially introduced into bottom sediments in a bioelectrochemical system of a membrane-free (silt) type was studied. Passive bioelectrochemical stimulation by means of electrodes connected by an external circuit with a resistance of 1 kΩ, with an average electric current of ~85 µA was found to cause an increase in degradation during two months from 23.0 to 57.9%. Contamination of bottom sediments with oil (1.32 g/kg) slightly decreased the current in the external circuit of the bioelectrochemical system. The relationship was revealed between the degree of oil degradation and predominant utilization of the lighter n-alkanes in the C₁₄H₃₀–C₃₀H₆₂ series, compared with both the original oil and the residual hydrocarbons of the control. An increase in the representation of the alkB alkane monooxygenase genes relative to the 16S rRNA gene in the total DNA isolated from the sediments was induced by the introduction of hexadecane, both in the case of electrochemical stimulation and in the control. The results may be of interest for the development of new methods of bioelectrochemical removal of organic pollutants from anaerobic environments.

The sources of thermophilic bacteria revealed in cold Lake Baikal sediments are considered. Comparative analysis of the taxonomic position of thermophilic microorganisms from four terrestrial hot springs at Lake Baikal coast and from the bottom sediments associated with hydrocarbon discharge was carried out. The sequences of thermophilic microorganisms with the same taxonomic position were revealed both in the hot springs and bottom sediments. Some microbial species occurred only in the hydrotherm samples or only in those from the sediments. Gas-saturated fluids from the hydrocarbon generation zone at the depth of 4‒6 km are the most probable source of thermophilic microorganisms in the bottom sediments.

A modified method for culturing, concentrating, and purifying phage ϕ24B preparations was developed. In particular, a new lysogenic phage-producing strain lacking flagella was used, induction conditions were optimized, and purification in a sucrose gradient and concentration by deposition on a Freon 113 cushion were used. Using this method, a preparation of the Stx-converting bacteriophage ϕ24B was obtained, which was suitable for direct analysis by the cryoEM method. Based on cryoEM data for this phage, the first primary three-dimensional reconstruction of its virions was performed. The structure of the phage ϕ24B tail is described. It was shown that the adsorption apparatus of this virus is represented by six thin lateral fibrils and an axial fibril located at the end of the tail. This arrangement of the tail structure is consistent with the previously proposed hypothesis based on analysis of the receptor binding proteins (RBPs) of this bacteriophage.

In bacteria F-type ATPase (F-ATPase) plays a key role in bioenergetics and couples ATP synthesis/hydrolysis with the transport of ions (H⁺ or Na⁺) across the membrane. The ion specificity of the enzyme is determined by the amino acid sequence of subunits c and а. Here, we introduced several mutations (7 in subunit c and 6 in subunit a) into F-ATPase of thermophilic bacterium Bacillus sp. PS3 in order to change the ion specificity of the enzyme from proton to sodium. The mutations did not affect the ATPase activity of the enzyme, but led to loss of proton conductivity and impaired the binding of subunit a to the c-subunit oligomer, rather than changed the ion specificity.

The vital enzyme of yeast metabolism, plasma membrane H+-ATPase (PMA1), is phosphorylated during folding and functioning. The main phosphorylation sites are Ser911 and Thr-912 in the C-terminal regulatory domain. The work used wild and mutant forms of the enzyme with substitutions of these amino acid residues with Ala or Asp to determine their role in the functioning of the ATPase and the distribution of polyphosphates (polyP) by fractions. Growth parameters, ATP content, and in situ polyP distribution were determined on whole cells. To determine the ATPase activity in vitro, plasma membranes containing wild-type enzyme and mutant forms were isolated. Mutants S911D, T912D and S911D/T912A had ATPase activity close to the wild type; mutant S911A had increased activity. The growth rate of strains S911D, T912D and S911D/T912A was 2.0‒3.0 times lower than that of the wild type, and the growth rate of S911A was close to the wild type. Mutations S911D and S911D/T912A caused a decrease in ATP content by 2.0‒2.5 times. All substitutions affected the distribution of polyP by fractions. The effect depended on the chemical nature of the substitution: in the case of replacement with Asp, which changes the type of phosphosite, there was a decrease in the polyR1 fraction and an increase in the polyR2 fraction; when replaced with Ala, which removes phosphosite, the effect was the opposite. The content of the polyP3 fraction increased in all mutants. The data indicate that the residues of Ser911 and Thr-912 are important not only for the normal functioning of the PMA of H+-ATPase, but also for the regulation of phosphorus and energy metabolism.

Bacterial strains isolated from root nodules of the legume plant Hedysarum arcticum B. Fedtsch growing on Samoylovsky Island in the Lena River delta (Arctic zone of Yakutia) were assigned to the genera Rhizobium (family Rhizobiaceae) and Mesorhizobium (Phyllobacteriaceae) of the order Hyphomicrobiales (class Alphaproteobacteria) according to the rrs gene sequencing data. According to phylogenetic analysis of concatemers of the atpD, dnaK, gyrB, and rpoB genes, the strains belonged to the species Rhizobium giardinii and Mesorhizobium norvegicum. The strains were shown to be facultative psychrotrophs growing at 5 and 28ºC. These microsymbionts are promising for further study of their symbiotic efficiency regarding other forage legume species, with an aim to establish highly productive agrophytocenoses in the Far North.