Microbiology
ISSN (print):0026-3656
Media registration certificate: No. 0110237 dated 02/09/1993
Founder: Russian Academy of Sciences, Institute of Microbiology RAS
Editor-in-Chief: Pimenov Nikolay Viktorovich
Number of issues per year: 6
Indexation: RISC, list of Higher Attestation Commissions, CrossRef, White List (level 2)
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Vol 92, No 6 (2023)
ЭКСПЕРИМЕНТАЛЬНЫЕ СТАТЬИ
Methylomonas Montana sp. nov., the First Unpigmented Methanotroph of the Genus Methylomonas, Isolated from Mountain River Sediments
Abstract
Abstract—
Aerobic methanotrophic bacteria of the genus Methylomonas inhabit a wide spectrum of habitats including freshwater bodies, river sediments, wetlands, rice paddies, landfill cover soils, and hydromorphic soils. Majority of the currently described species of this genus are represented by neutrophilic, motile, growing on methane rod-shaped bacteria, whose pigmentation varies from yellow to pink and red. This study reports characterization of a novel, unpigmented isolate of these bacteria, strain MW1T, which was obtained from sediments of the mountain river Khosta, Krasnodar region, Russia. Strain MW1T grew on methane and methanol within a temperature range of 8–37°C (optimum at 25–30°C) and at рН 5.5–7.5 (optimum at 6.3–7.0). The 16S rRNA gene sequence of strain MW1T displayed 95.48–98.47% similarity to those in earlier described Methylomonas. The closest taxonomically characterized phylogenetic relative of strain MW1T was M. fluvii EbBT, isolated from the river Elbe sediments. Complete genome sequence of strain MW1T was 4.6 Mb in size and contained three rRNA operons and about 4200 protein-encoding genes, including the gene cluster pmoCAB coding for membrane methane monooxygenase. Soluble methane monooxygenase was not encoded in the genome. The G+C DNA content was 52.4%. The average nucleotide identity of the genome of strain MW1T with those in earlier described representatives of the genus Methylomonas was 79.4–82.1%. We propose to classify this isolate as representing a novel species of the genus Methylomonas, M. montana sp. nov. Strain MW1T (=VKM 3737T = UQM 41536T) is the type strain of the newly proposed species.
535-544
Transcriptome Analysis of Escherichia coli Dormant Cystlike Cells
Abstract
Abstract—
The transcriptome of Esherichia coli cystlike dormant cells was investigated. RNA content in a single dormant cell was 0.26 fg, i.e., 13.5 times less than in a cell of a growing culture. The presence of mRNA in E. coli dormant cells has not been reported previously. The pools of gene reads for the dormant and growing cells were characterized, as well as the differential expression of all genes, calculated according to the special algorithm considering the average mRNA amount in a single cell. The notion of the genes active in every cell of the population was introduced. In each cell of the dormant and growing E. coli population, such genes were represented by the transcripts of 21 and 16% of the genes, respectively. The revealed cell heterogeneity in the set of active genes is one of the reasons (and forms) of heterogeneity of bacterial populations. Sixty genes were revealed, for which activity increased twice or more during formation of E. coli dormant cells. These were the genes responsible for genome activity, structure and properties of the cell envelope, cell proliferation, stress adaptation, biofilm formation and functioning, and collective behavior, as well as the genes providing for survival of the cell population during germination of the dormant cells.
545-563
Anoxygenic Phototrophic Bacteria of the Meromictic Lake Bol’shie Khruslomeny (Oleniy Island, Kandalaksha Gulf, Murmansk Oblast, Russia)
Abstract
Abstract—
The composition and structure of the anoxygenic phototrophic bacterial (APB) community in the water column of Lake Bol’shie Khruslomeny during winter were investigated. The community developed at the depth of 4.25 m, and its activity during the ice-covered period was very low (6.2 µmol C L–1 day–1). The water in the zone of highest development of phototrophic bacteria was of an unusual lemon-yellow color, probably due to the production and accumulation of polysulfides. The near-bottom water was also of lemon-yellow color and was resistant to oxidation by the air oxygen. In the zone of peak APB development the content of BChl d from green-colored green sulfur bacteria was considerably higher than that of BChl e from brown-colored green sulfur bacteria: 77 and 23%, respectively. The cultures of green and purple sulfur bacteria were isolated from lake water, and their physiological and genetic characteristics were determined. Two strains of green sulfur bacteria (brown-colored BrKhr17 and green-colored GrKhr17) contained gas vacuoles in their cells. Phylogenetically they were most closely related to the green-colored strain Chlorobium phaeovibrioides DSM 265 and were identified as new Chlorobium phaeovibrioides strains.
564-580
Phylogenetic Diversity of Prokaryotic Communities of the Upper Sediment Layers of the Kandalaksha Gulf, White Sea
Abstract
Abstract—
Microbial communities of the sediments of the Kandalaksha Gulf (White Sea) remain insufficiently studied. While the data on the rates of some microbial processes are available, very little is known of the microorganisms inhabiting these sediments. In the present work, high-throughput sequencing of variable regions of the 16S rRNA genes was used to characterize the microbial communities of 47 Kandalaksha Gulf sediment samples, collected at 10 cm below from the bottom surface. Pseudomonadota and Desulfobacterota were the most abundant phyla, which together comprised about a half of all prokaryotes. Determination of the dominant genus-level taxon proved impossible. The most represented chemoorganotrophic microorganisms were uncultured Sandaracinaceae (up to 10.8%) and Woeseia (up to 7.5%). Sulfate-reducing bacteria were important community components in the studied upper sediment layers, with uncultured groups SEEP-SRB1 (up to 7.0%) and Sva0081 (up to 5.9%) among the most abundant. In some samples, the genera Sulfurovum (up to 15.5%) and Thiohalophilus (up to 7.0%), involved in the oxidation of sulfur compounds, were important components of the community. Among the archaeal ASVs, the genus Nitrosopumilus, oxidizing ammonium to nitrite, exhibited the highest relative abundance (up to 6.9% of the total number of prokaryotes). Numerous sequences identified as the 16S rRNA gene fragments of chloroplasts were found in the samples, indicating that the rate of organic matter delivery to the upper sediment layers exceeded the rate of its degradation.
581-594
Microbial Community Composition as an Indicator of the State of Basins Located at the Sea Coast (Exemplified by the Kanda Bay, Kandalaksha Gulf, White Sea)
Abstract
Abstract—
Formation of the Kanda Bay resulted from construction of a railway dam (1916) and subsequent isolation of the sea lagoon from the main basin of the Kandalaksha Gulf, White Sea. Decreased action of tidal flows, which mix the water column of the lagoon, altered the hydrological regime of the basin. Decreased water exchange resulted in formation of oxygen-depleted near-bottom water and to sulfide contamination. A freshwater lake was, however, preserved in the southern part of the Kanda Bay. The composition of microbial communities was studied for the near-bottom water horizons at different sides of the Kanda Bay. The oxygen regime in this layer was found to change, with increasing concentrations of sulfide and methane and active processes of sulfate reduction and methane oxidation. The composition of the microbial community changed noticeably, with lower abundance of true marine and freshwater microorganisms and development of bacteria and archaea predominant in microbial communities of anoxic water in meromictic basins. Among the microbial diversity, indicator species with increased abundance were revealed. These are archaea of the genera Methanoregula and Methanosaeta (phylum Halobacterota). The sulfur cycle microorganisms, which were the indicators of stagnant marine water, included anoxygenic phototrophic bacteria of the class Chlorobia, (Chlorobium phaeovibrioides, Pelodictyon phaeoclathratiforme), Chloroflexi of the genus Chloronema, nonsulfur purple bacteria related to the genus Rhodoferax, colorless sulfur bacteria of the family Beggiatoaceae, and sulfur oxidizers of the genus Thiobacillus. Archaea of the genus Nitrosopumilus (phylum Crenarchaeota) and bacteria of the genus Woeseia may be considered opposites to the indicator microorganisms, since they were found only in the open sea water. In our opinion, stable water exchange through the dam will result in the stable composition of the Kanda Bay microbial community, with only seasonal variations and year-to-year fluctuations. The negative scenario supports prediction of conversion of the Kanda Bay into a stratified basin with anoxic near-bottom water and the microbial community similar to that found in meromictic lakes.
595-608
Effect of the Extracts from Lichens and Lichenophilic Fungi on in vitro Growth of Clinically Significant Microorganisms
Abstract
Abstract—
Activity of the ethanol extracts from lichens (LE), of the cultures of lichenophilic (endobiotic) fungi (LFE), and of ethanol extracts from these cultures was tested using the following test organisms: Escherichia coli, Salmonella typhimurium, Pseudomonas fluorescens, Staphylococcus aureus, Micrococcus luteus, Enterococcus faecium, Paenibacillus sp., and Candida parapsilosis. Selective activity of LE and LFE against yeasts and gram-positive and gram-negative bacteria was revealed. The extracts from Cladonia rangiferina exhibited no activity against any of the tested cultures. The previously reported locus effect on activity of metabolites of one lichen species was confirmed. Agar block technique was used to detect selective activity of 23 out of 61 analyzed fungal strains against gram-positive and gram-negative bacteria, and of 8 strains, against yeasts. Ethanol extracts of six cultures were shown to suppress growth of St. aureus, M. luteus, Paenibacillus sp., and E. coli. Strain NM10F28209 from the lichen Stereocaulon paschale, which exhibited inhibitory activity against Ca. parapsilosis was selected for priority development of an antifungal preparation.
609-616
Osmolytes and Lipids of the Conidia of the Xerohalophilic Micromycete Aspergillus penicillioides
Abstract
Abstract—
Investigation of the lipid and osmolyte composition in conidia of the xerohalophile Aspergillus penicilloides grown on media with high concentrations of NaCl and glycerol is important for the understanding of the functions of these compounds in the adaptation of the extremophile. Conidia of the fungus grown on a medium with glycerol contained up to 15% of the dry mass of carbohydrates and polyols (CaP) of the cytosol, with predominance of glycerol (60% of the total) in their composition, while on a medium with salt, the proportion of glycerol did not exceed 20%, and the amount of CaP was 10%. On both media, the proportion (20%) and amount (2.5%) of trehalose were the same; the proportion of polyols was thus about 80%, although their composition was different, indicating a possible synergy between trehalose and polyols in adaptation. Both variants of conidia were characterized by a low content of both membrane and storage lipids, represented mainly by triacylglycerides. Phosphatidylcholines and sterols were the predominant membrane lipids of the fungal conidia, regardless of the composition of the medium, which indicated high stability and conservatism of the lipid bilayer. The constancy of the composition of membrane and storage lipids and their low content, the high level of CaP, and significant differences in their composition indicate the key role of osmolytes in the adaptation of fungal conidia to various environmental conditions.
617-624
Occurrence of the Ability to Suppress the Growth of Related Strains in Rhizobia
Abstract
Abstract—
Screening of 1019 strains of rhizobia Rhizobium leguminosarum and Neorhizobium galegae from the “Symbiont” collection of symbiotic rhizospheric microorganisms of the Institute of Biochemistry and Genetics, Ufa Research Center, Russian Academy of Sciences, which have been isolated from root nodules of 20 leguminous species, for the ability to suppress the growth of related strains of rhizobia was carried out. Inhibition of the growth of competing bacteria by rhizobia was shown to be rather common. On average, when grown on rich media, ~10% of rhizobial strains released antibacterial substances into the medium. At the same time, when a live culture of rhizobia was applied to the lawn of bacteria, the percentage of suppression was higher. The percentage of strains synthesizing antibacterial substances correlated also, to some extent, with the level of genetic diversity of the population of legume microsymbionts. A weak signal of impaired protein synthesis was found in the study of the mechanism of action of metabolites of 20 strains of rhizobia R. leguminosarum bv. viciae from root nodules of Lathyrus palustris and Lathyrus vernus. In other cases, the nature of the antibacterial action of bacterial metabolites could not be determined using the DualRep2 system.
625-630
КРАТКИЕ СООБЩЕНИЯ
Effect of the Bacteriocin Subtylosin P19 on Bacillus Anthracis Spores
Abstract
Abstract—
This is the first report on electron microscopic investigation of the effect of bacteriocin on Bacillus anthracis dormant spores. The new bacteriocin, subtilosin P19, isolated from a natural Bacillus subtilis strain, effectively killed dormant B. anthracis spores at concentrations of 0.5‒35 µg/mL after 60-min exposure. Our data, combined with analysis of the known mechanisms of the action of bacteriocins, suggest that the mechanism of spore inactivation was apparently based on multiple disruptions of the integrity of the inner and outer membranes surrounding the cortex of the resting spore. It is also likely that the molecular configuration of subtilisin P19 allows it to penetrate through the outer integuments and to damage the vital membrane structures of the anthrax spores. Subtilosin P19 can serve as a promising basis for new antimicrobial preparations of natural origin.
631-636