[The history and the present of the Department of Biology of Extremophilous Microorganisms].

The priority results obtained during 35 years, when studying biology of methane-oxidizing bacteria, are presented. There is more profound representation of the results obtained for the recent 5 years of the Department activity: phylogenetic classification of methylotrophic bacteria, biodiversity of microorganisms in the typical biotopes of the Antarctica, resistance of extremophilous Antarctical microorganisms to heavy metals, etc. A method of thermodynamic prediction of the microorganisms interaction with xenobiotics (synthetic organic compounds, toxical metals and radionuclides) has been developed for creating new universal nature-protective biotechnologies. Optimal methods of xenobiotics detoxication have been realized. The ways of intensification of biosynthesis of exopolysaccharide and surfactants have been found.

[Reclassification of thermophylic methane-oxidizing bacteria with the use of sequence-analysis of 16S rRNA genes].

The authors have performed sequence-analysis of 16S rRNA genes of thermophylic methane-oxidizing bacteria UCM B-3026, UCM B-3032, UCM B-3109, UCM B-3014 which were isolated from sludge pond of different regions in Ukraine and deposited at Ukrainian Collection of Microorganisms (UCM) as Methylococcus thermophilus and "M. gracilis". A comparative analysis of 16S rRNA gene sequences of the studied bacteria with those sequences of various strains of bacteria in the GenBank databases has shown that the level of similarity of the strains UCM B-3026, UCM B-3032, UCM B-3109 with Methylocaldum szegediense was 98.0-98.7%, strain UCM B-3014 with Methylocaldum gracile--99.1%, that allows to relate them to these species. As to other species of the genus Methylocaldum, these strains had a lower level of similarity (94.8-97.2 %) and with Methylococcus thermophilus ACM 3585T (= IMV-B-3037T = UCM B-3037T)--less than 90%. Thus, the strains UCM B-3026, UCM B-3032, UCM-3109 were reclassified as Methylocaldum szegediense, strain UCM B-3014--as Methylocaldum gracile. When constructing phylogenetic tree based on the comparison of 16S rRNA genes with the use of various algorithms realized in the packages of programs Tree View (version 1.5.2) and ClastalX (version 1.81) certain clusters have formed genera Methylocaldum, Methylococcus and Methylomonas. Genera Methylobacter and Methylomicrobium have formed three clusters, one of the clusters contained two species of Methylobacter and two species of Methylomicrobium. Apparently, the taxonomy of genera Methylobacter and Methylomicrobium is to be specified.

[Classification of Methylomonas rubra sp. nov].

Strain Methylomonas rubra 15sh(T), deposited in several collections of microorganisms (NCIMB 11913(T) = UCM B-3075(T) = ACM 3303(T)), is the subject of numerous studies. However, the name of this strain is not valid, primarily due to the phenotypic similarity of the species M. rubra to the species M. methanica. The results of the present study and data available in the literature indicate that M. rubra deserves the status of a separate species. Strains of M. rubra differ from strains of M. methanica in a number of properties, such as the ability to reduce nitrates to nitrites, the structure of intracytoplasmic membranes, and the presence of a new coenzyme Q. The distinctions between the species M. rubra and M. methanica were confirmed by comparison of electrophoretic patterns of their cellular proteins, by results of DNA-DNA hybridization, and by the data from 16S rRNA gene sequencing (the level of phylogenetic homology between these two species was below 95%). Phylogenetic and phenotypic analyses showed that strains of M. rubra cannot be assigned to any species of the genus Methylomonas. Results of polyphasic analysis suggest an independent taxonomic status of strain Methylomonas rubra 15sh(T). This paper contains description of Methylomonas rubra sp. nov. with the type strain 15sh(T) = NCIMB 11913T = UCM B-3075(T) = ACM 3303(T). The nucleotide sequence of the 16S rRNA gene of strain 15sh(T) has been deposited with the GenBank database under the accession number AY995198.

[Search for psychrophilic methylotrophic bacteria in biotopes of the Antarctica].

Psychrotolerant bacteria which use obligately methane were found in the moss samples and in soil-vegetation samples in the island part of the Antarctica during the VII expedition (2003) at the station "Akademik Vernadsky". The number of methane-oxidizing bacteria in the samples from the Antarctica (101- 10(3)/g of the sample) was lower than in the samples from the regions with moderate climate (10(2)- 106/g of the sample). Psychrotolerant strains of Methylobacteriium genus which use facultatively methanol were found in the bottom sediments of the fresh-water and Krasnoye lakes, as well as in the soil-plant samples. The psychrophilic strain which is probably a new species of the genus Methylobacterium has been isolated from one soil-plant sample from the Antarctica at 10 degrees C. It is established that most collection mesophilic strains of Methylobacterium, which have been isolated from the soil and plant phyllosphere in Ukraine, also could grow at 10 degrees C.

[Effect of UV-radiation and drying on bacterium diversity in soil]. / Vplyv UF-oprominennia ta vysushuvannia na riznomanitnist' bakterii u hruntakh.

It has been shown that after DNA-injuring factors (UV irradiation or drying) action on soil one could observe the decrease of the total quantity of bacteria and the number of species, i.e., the decrease of microbe diversity. At the same time not numerous species were found in soils after their action. Thus the drying or UV-irradiation makes it possible to estimate more completely the microbe diversity in soils as well as to find resistant bacteria. It has been established that the strain Methylobacterium extorquens, M. mesophilicum, Bacillus subtilis, B. cereus, which were isolated after UV irradiation or drying of oil samples, were characterized by high resistance to gamma-irradiation (LD99.99--5-10 kGr). Bacteria (representatives of Pseudomonas genus) sensitive to drying or UV-irradiation were also sensitive to ionizing radiation (LD99.99--0.09 kGr). Nocardieforms and representatives of Myxococcus occupied intermediate position between representatives of genera Methylobacterium and Pseudomonas as to resistance to the above-mentioned stress agents.

[Thirty-five years of the Department of Biology of Gas-oxidizing Microorganisms of the D.K. Zabolotnyi Institute of Microbiology and Virology of the Academy of Sciences of Ukraine]. / Otdelu biologii gazookisliaiushchikh mikroorganizmov Instituta mikrobiologii i virusologii im. D.K. Zabolotnogo NAN Ukrainy--35 let.

The basic trends of the department scientific activity are presented. The priority results of investigations of methaneoxidizing bacteria biology are given. The biothechnological development of the department (obtaining of products of microbial synthesis: protein, polysaccharides, antialcoholic and antinarcotic preparations) are considered in detail. Possible areas of their application are presented.

[Actual problems of bacteria phylogenetic classification]. / Aktual'nye problemy filogeneticheskoi klassifikatsii bakterii.

Historical aspects of development of phylogenetic bacteria taxonomy and essence of species in systematics of bacteria are considered. Comparative analysis of phenotypic and phylogenic classification of bacteria is conducted. Basic results of 16S rRNA gene sequence for bacteria are adduced. Comparative estimation of molecular biological methods in microbiologic researches and also estimation of potentialities and shortcomings of 16S rRNA gene sequence-analysis in systematics of bacteria are conducted.

[Soil drying as a model for the action of stress factors on the natural bacterial population]. / Vysushivanie pochvy: model' deistviia stressovykh faktorov na prirodnye populiatsii bakterii.

The drying of soil samples reduced the abundance (especially of predominant species) and the diversity of bacteria isolated from these samples, making easier the isolation of rare bacterial species. Some bacterial species that were minor before soil drying became dominant in dried soil samples. In general, soil drying allowed the diversity of soil bacteria to be determined more adequately. The bacteria that were isolated from dried soil samples turned out to be resistant to gamma radiation (with LD90 = 2.8-4.6 kGy) and desiccation. It is concluded that soil drying may serve as a model for the action of stress factors on natural bacterial populations. The hypothesis that periodic desiccation was the primary cause of formation of bacterial radioresistance in nature is discussed.

[Stability of genetic markers in methane-oxidizing bacteria]. / Stabil'nost' geneticheskikh markerov u metanokisliaiushchikh bakterii.

A number of Methylococcus thermophilus 111p clones have been obtained which have acquired resistance to tetracycline. The stability of maintenance of marker resistance in these clones and also in already designed Methylomonas rubra 15sh mutants has been investigated. Chromosomal markers resistance to antibiotics or formaldehyde were maintained in the marked strains Methylococcus thermophilus 111p and Methylomonas rubra 15sh after storage in nonselective conditions. The markers of resistance to antibiotics, which were coded by plasmids (pAS8-121 and pULB113), were not always preserved in Methylomonas rubra and Methylococcus thermophilus. The stability of maintenance of chromosomal markers in the investigated methane oxidizing bacteria testifies to the fact that they can be used in laboratory and industrial practice for testing the marked bacteria on selective media. The collection of the marked bacteria-mutants Methylomonas rubra 15sh and Methylococcus thermophilus 111p has been created. These strains stably support the marker resistance to various antibiotics or formaldehyde in unselective conditions.

[The effect of gamma-radiation and desiccation on the viability of the soil bacteria isolated from the alienated zone around the Chernobyl Nuclear Power Plant]. / Vliianie gamma-izlucheniia i degidratatsii na vyzhivaemost' bakterii, izolirovannykh iz zony otchuzhdeniia Chernobyl'skoi AES.

Methylobacterium extorquens, M. mesophilicum, and Bacillus subtilis strains were found to be resistant to gamma-radiation, irrespective of whether they were isolated from the alienated zone around the Chernobyl Nuclear Power Plant or outside this zone. The LD90 of Methylobacterium and B. subtilis strains with respect to gamma-radiation was 2.0-3.4 and 3.7-4.4 kGy, respectively, whereas their LD99.99 values were 4.5-6.9 and more than 10 kGy, respectively. The high threshold levels of gamma-radiation for Methylobacterium and B. subtilis imply the efficient functioning of DNA repair systems in these bacteria. Unlike Bacillus polymyxa cells, the cells of M. extorquens, M. mesophilicum, and B. subtilis were also resistant to desiccation. Pseudomonas sp., Nocardia sp., and nocardioform actinomycetes were sensitive to both gamma-radiation and desiccation. Similar results were obtained when the bacteria studied were exposed to hydrogen peroxide and ultraviolet radiation. The results obtained indicate that the bacteria that are resistant to gamma-radiation are also resistant to desiccation, UV radiation, and hydrogen peroxide. The possibility of using simple laboratory tests (such as the determination of bacterial resistance to UV light and desiccation) for the evaluation of bacterial resistance to gamma-radiation is discussed.

[Strategy of obtaining microbial exopolysaccharides possessing stable preset properties]. / Stratehiia oderzhannia mikrobnykh ekzopolisakharydiv zi stabil'nymy zadanymy vlastyvostiamy.

Basing on the development of approaches to the controlled regulation of synthesis of the complex polysaccharide preparation ethapolan (producer Acinetobacter sp.) the strategy of obtaining microbial exopolysaccharides (EPS) with stable composition and properties was determined. The strategy is based on the following principles of regulation of composition, physico-chemical properties and synthesis intensification of EPS: 1) to find out EPS functional groups determining their physico-chemical properties and factor providing synthesis of EPS with certain functional groups; 2) to study changes of EPS composition and properties during producer cultivation and to determine growth phase in which the synthesis of EPS possessing necessary properties occurs; 3) to investigate interrelation between EPS physico-chemical properties and their protective functions and to determine cultivation conditions necessary for development of EPS protective functions; 4) analysis of metabolic pathways of EPS synthesis, elucidation of "bottlenecks" in producer's metabolism and search for ways toward their elimination.

[Peculiarities of ethanol metabolism in an Acinetobacter sp. mutant strain defective in exopolysaccharide synthesis]. / Nekotorye osobennosti metabolizma étanola u mutantnogo shtamma Acinetobacter sp., ne obrazuiushchego ékzopolisakharidy.

Activities of the key enzymes of ethanol metabolism were assayed in ethanol-grown cells of an Acinetobacter sp. mutant strain unable to synthesize exopolysaccharides (EPS). The original EPS-producing strain could not be used for enzyme analysis because its cells could not to be separated from the extremely viscous EPS with a high molecular weight. In Acinetobacter sp., ethanol oxidation to acetaldehyde proved to be catalyzed by the NAD(+)-dependent alcohol dehydrogenase (EC 1.1.1.1.). Both NAD+ and NADP+ could be electron accepters in the acetaldehyde dehydrogenase reaction. Acetate is implicated in the Acinetobacter sp. metabolism via the reaction catalyzed by acetyl-CoA-synthetase (EC 6.2.1.1.). Isocitrate lyase (EC 4.1.3.1.) activity was also detected, indicating that the glyoxylate cycle is the anaplerotic mechanism that replenishes the pool of C4-dicarboxylic acids in Acinetobacter sp. cells. In ethanol metabolism by Acinetobacter sp., the reactions involving acetate are the bottleneck, as evidenced by the inhibitory effect of sodium ions on both acetate oxidation in the intact cells and on acetyl-CoA-synthetase activity in the cell-free extracts, as well as by the limitation of the C2-metabolism by coenzyme A. The results obtained may be helpful in developing a new biotechnological procedure for obtaining ethanol-derived exopolysaccharide ethapolan.

[Ethanol formation by methane-utilizing bacteria at ethane co-metabolism]. / Obrazovanie étanola metanispol'zuiushchimi bakteriiami pri kometabolizme étana.

It was established, that EDTA (1.0 mM) and formamide (100 mM) are inhibitors of methanol dehydrogenase in Methylobacter luteus 12b, Methylomonas rubra 15sh and Methylococcus thermophilus 111p. The investigated strains co-metabolised ethane with the use of formate as the co-substrate. The application of formamide (or EDTA) as inhibitors of methanol dehydrogenase prevented from further transformation of ethanol and resulted in accumulation of extracellular ethanol. It was shown, that M. rubra 15sh accumulated extracellular ethanol under cultivation in a chemostate. The carried out researches have shown a regulation path of co-metabolism process of hydrocarbons by methane utilizing bacteria. Using the specific inhibitors of methanol dehydrogenase and a source of reducing agent (energy) for methane monooxygenase with the help of the cells of methane-oxidizing bacteria it is possible to obtain from ethane or other hydrocarbons the products of their monooxygenation--alcohols.

[A two-stage technique for producing the microbial exopolysaccaride ethapolan with improved rheological properties]. / Dvukhstadiinyi sposob polucheniia mikrobnogo ékzopolisakharida étaponala s uluchshennymi reologicheskimi svoistvami.

A two-stage technique was proposed for cultivating producers of microbial exopolysaccharide ethapolan. The practical value of ethapolan is determined by its rheological properties. The use of a formaldehyde-supplemented medium at the second stage of cultivation improved the rheological properties of ethapolan without reducing its yield. This effect of formaldehyde was due to its binding to the exopolysaccharide, which altered the molecular-mass characteristics of the latter and protected the cells against the toxic action of formaldehyde. At all stages of its purification, ethapolan had improved rheological properties, suggesting that it was tightly bound to formaldehyde.

[Processes of plant colonization by Methylobacterium strains and some bacterial properties ]. / Puti kolonizatsii rastenii shtammami Methylobacterium i ikh nekotorye svoistva.

The pink-pigmented facultative methylotrophic bacteria (PPFMB) of the genus Methylobacterium are indespensible inhabitants of the plant phyllosphere. Using maize Zea mays as a model, the ways of plant colonization by PPFMB and some properties of the latter that might be beneficial to plants were studied. A marked strain, Methylobacterium mesophilicum APR-8 (pULB113), was generated to facilitate the detection of the methylotrophic bacteria inoculated into the soil or applied to the maize leaves. Colonization of maize leaves by M. mesophilicum APR-8 (pULB113) occurred only after the bacteria were applied onto the leaf surface. In this case, the number of PPFMB cells on inoculated leaves increased with plant growth. During seed germination, no colonization of maize leaves with M. mesophilicum cells occurred immediately from the soil inoculated with the marked strain. Thus, under natural conditions, colonization of plant leaves with PPFMB seems to occur via soil particle transfer to the leaves by air. PPFMB monocultures were not antagonistic to phytopathogenic bacteria. However, mixed cultures of epiphytic bacteria containing Methylobacterium mesophilicum or M. extorquens did exhibit an antagonistic effect against the phytopathogenic bacteria studied (Xanthomonas camprestris, Pseudomonas syringae, Erwinia carotovora, Clavibacter michiganense, and Agrobacterium tumifaciens). Neither epiphytic and soil strains of Methylobacterium extorquens, M. organophillum, M. mesophilicum, and M. fujisawaense catalyzed ice nucleation. Hence, they cause no frost injury to plants. Thus, the results indicate that the strains of the genus Methylobacterium can protect plants against adverse environmental factors.

[Structure of an acylated exopolysaccharide synthesized by Acinetobacter sp]. / Struktura atsyl'ovanoho ekzopolisakharydu, syntezovanoho bakteriiamy Acinetobacter sp.

The complex preparation ethapolan synthesized by Acinetobacter sp. consists of neutral (minor component) and two acidic exopolysaccharides (EPS) one of which is acylated. On the basis of chemical modification of EPS, solvolysis with anhydrous hydrogen fluoride resulting in a penta- and octasaccharide fragments, Smith degradation, 1H- and 13C NMR analysis the following structure of the acylated polysaccharide repeating unit has been established (scheme): It is suggested that in the acylated EPS at least one glucose residue and the galactose residue are O-acylated.

[Unique properties of highly radioresistant bacteria]. / Unikal'nye svoistva vysokoradioustoichivykh bakterii.

In connection with the Chernobyl Nuclear Power Plant (ChNPP) accident and the negative ecological after-effects for biota in this zone the interest has arisen to radioresistant bacteria, as to the most dynamic model of the given ecosystem, and to mechanisms which provide resistance of bacteria to ionizing radiation. The analysis of published data has shown that the radioresistant bacteria are not interrelated taxonomically and phylogenetically. The extreme radioresistant bacteria are represented by the Deinococcus species, which form a group phylogenetically close to the line Thermus-Meiothermus. Other radioresistant bacteria are the representatives of the genera Rubrobacter, Methylobacterium, Kocuria, Bacillus and some archebacteria. Data on natural habitats, of radioresistant bacteria are not numerous. In a number of cases it is difficult to distinguish their natural habitats, as they were isolated from the samples which were previously exposed to X-ray or gamma-irradiation, or from the ecosystems with the naturally raised radioactivity. To understand the strategy of survival of radioresistant bacteria, we briefly reviewed the mechanism of action of various species of radiation on cells and macromolecules; physiological signs of the cell damage caused by radiation; mechanisms eliminating (repairing) these damages. More details on mechanisms of the DNA repair in D. radiodurans are described. The extreme resistance of D. radiodurans to the DNA damaging factors is defined by 1) repair mechanisms which fundamentally differ from those in other procaryotes; 2) ability to increase the efficiency of a standard set of the DNA repairing proteins. Literary and own data on the effect of radiation on survival of various groups of bacteria in natural ecosystems are summarized. The ecological consequences of the ChNPP accident for soil bacteria in this region were estimated. The reduction of the number of soil bacteria and recession of microbial diversity under the effect of anthropogenic radiation was shown.

[Isolation and study of Acinetobacter sp. mutant strains defective in production of exopolysaccharides]. / Poluchenie i issledovanie mutantnykh shtammov Acinetobacter sp.,ne obrazuiushchikh ékzopolisakharidy.

Nitrosoguanidine-induced mutants of Acinetobacter sp. defective in exopolysaccharide biosynthesis did not differ from the parent strain in distinguishing physiological and biochemical properties, such as requirements for growth factors, utilization of mono- and disaccharides, and resistance to antibiotics. The genetic relation of parent and mutant strains was shown by 16S rRNA PCR analysis. The comparative study of parent and mutant strains with respect to resistance to unfavorable environmental factors confirmed our hypothesis that Acinetobacter sp. exopolysaccharides perform protective functions. Hybridization experiments revealed the conjugal transfer of plasmid R68.45 from Pseudomonas putida BS228 (R68.45) to mutant but not to the parent Acinetobacter sp. strains. The role of the Acinetobacter sp. exopolysaccharides in providing the genetic stability of this bacterium is discussed.

[Sensitivity of soil bacteria isolated from the alienated zone around the Chernobyl Nuclear Power Plant to various stress factors]. / Chuvstvitel'nost' k stressovym faktoram pochvennykh bakterii, izolirovannykh iz zony otchuzhdeniia Chernobyl'skoi AES.

Seventy strains of chemoorganotrophic bacteria isolated by our group in 1993-1994 from soil sampled in the zone around the Chernobyl Nuclear Power Plant (ChNPP) were studied with respect to their sensitivity to various stress factors damaging DNA. Bacillus subtilis, B. cereus (both spores and vegetative cells), Methylobacterium extorquens, M. mesophilicum, and unidentified pigmented bacteria were found to be the most resistant to ultraviolet (UV) radiation, exhibiting LD90 values of 40 to more than 211 J/m2. The same bacteria, as well as Bacillus polymyxa, were tolerant to hydrogen peroxide (lethal concentrations of H2O2 ranged from 0.3 to 1.0 M); i.e., UV-resistant strains were also tolerant to hydrogen peroxide and vice versa. Fluorescent pseudomonads were the most sensitive to both UV radiation and H2O2, showing LD90 from 6 to 18 J/m2 and a lethal concentration of H2O2 lower than 0.1 M. All of the soil samples collected in the alienated zone around the ChNPP, where the radioactivity of the soil had decreased from 1000 to 2 microCi/kg soil over the period from 1987 to 1995, contained not only resistant bacteria but also a small number of bacteria sensitive to UV radiation and H2O2.