Antagonistic activity of actinomycetes of Lake Baikal

It was demonstrated that actinomycetes of Lake Baikal are strong antagonists of other microorganisms. Representatives of the genera Streptomyces and Micromonospora inhibit the growth of bacteria isolated from the lake, as well as of antibiotic-resistant microorganisms causing various human diseases. Baikal actinomycetes display a wide range of antagonistic activity and are potential producers of new biologically active substances.     

Diversity of 16S rRNA genes in metagenomic community of the freshwater sponge Lubomirskia baicalensis

Phylogenetic analysis of the nucleotide sequences of 16S rRNA genes in the metagenomic community of Lubomirskia baicalensis has revealed taxonomic diversity of bacteria associated with the endemic freshwater sponge. Fifty-four operational taxonomic units (OTUs) belonging to six bacterial phyla (Actinobacteria, Proteobacteria (class ??-Proteobacteria and ??-Proteobacteria) Verrucomicrobia, Bacteroidetes, Cyanobacteria, and Nitrospira) have been identified. Actinobacteria, whose representatives are known as antibiotic producers, is the dominant phylum of the community (37%, 20 OTUs). All sequences detected shared the maximal homology with unculturable microorganisms from freshwater habitats. The wide diversity of bacteria closely coexisting with the Baikal sponge indicate the complex ecological relationships in the community formed under the unique conditions of Lake Baikal.     

Description of the lake baikal microorganism communities growing on a steel plate and in the natural water surrounding this substratum

This article presents an analysis of the microbial community growing on a stainless steel plate. A sample from this plate has been tested for the rpoC gene. Dominant biofilm species (clones) were identified with the help of molecular cloning and nucleotide sequencing of a 16S rRNA gene fragment. The activities of planktonic microorganisms and biofilm microorganisms attached to the plate were compared. Seven of nineteen sequences (37%) were found to belong to the Sphingobacteria group. Analysis of 16S rRNA gene sequences cloned from natural biofilms sampled from Lake Baikal showed a great variety of microorganisms in the biofilm. The following taxonomic groups were revealed among them: sphingobacteria, α-proteobacteria, cyanobacteria, verrucomicrobia, bacilli, γ-proteobacteria, flavobacteria, and β-proteobacteria. This kind of analysis was done in Lake Baikal for the first time.     

Study on the Lake Baikal microbial community in the areas of the natural oil seeps

We studied the composition of a natural microbial community, the distribution of different groups of microorganisms (including those able to degrade oil hydrocarbons) within the areas of natural oil seeps in the Lake Baikal. It was revealed that, in the bottom sediments, the oil-degrading microorganisms dominating the community have included the bacteria of g. Bacillus, while in the water column, dominating microbes are presented by species of genera Rhodococcus, Pseudomonas, and Micrococcus. Under the conditions of the model experiment, the potential activity of Baikal microbes towards utilization of n-alcanes has been assessed. Under such conditions it was shown that the concentration of n-alcanes decreases to 60% during 20 days of the experiment (the initial oil concentration was 0.5 mg/l, i.e., ten maximal permissible concentrations, MPC).     

Methodological aspects of assessing chitin utilization by soil microorganisms

A computational method for estimating specific activity of chitin decomposition by microorganisms is proposed. Spectrophotometric and gas chromatographic methods have been used to determine the rates of chitinase production, biomass accumulation, and carbon dioxide emission by pure cultures of microorganisms grown on a chitin-containing medium. Among dominants of the chitinolytic community of chernozem (Trichoderma viride, Stretomyces albolongus, Alcaligenes, and Arthrobacter), the highest chitinolytic activity is characteristic of prokaryotes. In brown desert-steppe soil, the main destructor prokaryotes are actinomycetes (S. roseolilacinus). The biomass of the fungus T. viride growth on the chitin-containing medium markedly exceeds that of prokaryotes, but the specific activity of respiration and chitinase production in actinomycetes S. roseolilacinus and S. albolongus is an order of magnitude higher than in T. viride.     

Isolation and characterization of antiprotozoal compound-producing Streptomyces species from Mongolian soils

Natural resources are recognized as important sources of potential drugs for treating various infections, and microorganisms are a rich natural source of diverse compounds. Among the world's microorganisms, actinomycetes, which are abundant in soil and marine, are the well-known producers of a wide range of bioactive secondary metabolites and antibiotics. In the present study, four actinomycetes (samples N25, N6, N18, and N12) were isolated from soil samples in Mongolia. Phylogenetic analysis of these isolates revealed that they share the highest similarity with Streptomyces canus (N25), S. cirratus (N6), S. bacillaris (N18) and S. peucetius (N12), based on 16S rRNA gene sequencing. Crude extracts were obtained from them using ethyl acetate, and the crude fractions were separated by thin layer chromatography. The fractions were then evaluated for their cytotoxicities and their anti-Toxoplasma and antimalarial activities in vitro. The S. canus (N25) crude extract was selected for further chemical characterization based on its antiprotozoal activities. Using liquid chromatography-high resolution mass spectrometry, phenazine-1-carboxylic acid (PCA) was detected and identified in the active fractions of the metabolites from strain N25. We next confirmed that commercially available PCA possesses antiprotozoal activity against T. gondii (IC₅₀: 55.5 μg/ml) and Plasmodium falciparum (IC₅₀: 6.4 μg/ml) in vitro. The results of this study reveal that soil actinomycetes are potential sources of antiprotozoal compounds, and that PCA merits further investigation as an anti-protozoal agent.     

Distribution of iron- and manganese-oxidizing bacteria in the bottom sediments of Lake Baikal

The specific features of the distribution, abundance, and taxonomic diversity of bacteria oxidizing iron and manganese in the bottom sediments sampled from different areas of Lake Baikal are studied. These bacteria are widespread in Baikal bottom sediments. Cultivated iron- and manganese-oxidizing microorganisms are ascribed to six genera: Metallogenium, Leptothrix, Siderocapsa, Naumaniella, Bacillus, and Pseudomonas. The surface layers of the ground and the border between oxidized and reduced sediments serve as ecological niches for iron- and manganese-oxidizing microorganisms. Redox conditions of the environment and the availability of dissolved forms of iron and manganese, as well as of organic matter, which are controlled by the conditions of sedimentation in the lake, are the main factors affecting the abundance and distribution of iron bacteria.     

Isolation and characterization of wastewater sand filter actinomycetes

One hundred twenty-two different actinomycete strains were isolated from sample collected from several depths of the Marrakech wastewater infiltration-percolation system. To evaluate the antimicrobial effect of the different actinomycetes recovered, eleven wastewater-associated micro-organisms known as human potential pathogens were used. Results showed that 44 isolates had an in vitro inhibitory effect toward at least seven of the indicator microorganisms while only five active strains inhibited all these pathogens. All five selected active isolates belonged to the genus Streptomyces. Three were identified as Streptomyces violaceorubidus. These isolates showed the broad activity spectrum against a wastewater-associated pathogenic yeast (Candida albicans), Gram-negative (Salmonella sp. CCMM B₁₇) and Gram-positive (Staphylococcus aureus CCMM B₃). These findings indicate the potential involvement of antagonistic actinomycetes in the removal of wastewater-associated pathogens.     

Comparative analysis of biodiversity in the planktonic and biofilm bacterial communities in Lake Baikal

Bacterial communities of the water and the biofilm formed during five years on an artificial substrate in Lake Baikal were studied by the pyrosequencing of 16S rRNA gene fragments; taxonomic diversity of bacterial communities and differences in their structure were revealed. The biofilm community contained mainly representatives of three phyla: Cyanobacteria, Bacteroidetes, and Proteobacteria; the amounts of other groups were within 1%. Bacterial community of the plankton was more heterogeneous; along with the dominant phyla (Bacteroidetes, Actinobacteria, and Proteobacteria) 15% of the members were of the other phyla. The use of pyrosequencing allowed to reveal 35 bacterial phyla in Lake Baikal, some of which were identified for the first time; moreover, minor groups of microorganisms (including only several sequences), which were not earlier determined by other molecular methods were found.     

Diketopiperazines from two strains of South China Sea sponge-associated microorganisms

The paper reports the isolation and structural elucidation of seven diketopiperazines from the title microorganisms. Although all isolates are known, three of which were isolated from the actinomycetes for the first time. And this is also the first report to isolate four DKPs from the D. avara-associated microorganism.     

Microbial community of the water column of the Selenga River-Lake Baikal biogeochemical barrier

The microbial communities of the estuarine zone and the mixing zone of river and lake waters in the Selenga River estuary were studied using the fluorescence in situ hybridization (FISH) method. The microorganisms belonging to the phylogenetic group Gammaproteobacteria were found to predominate in the river estuary, constituting up to 17% of the total bacterial community. Among cultivable microorganisms, organotrophic bacteria were predominant (2040 CFU/ml) in this zone, which results in high rates of microbial production (6.0 μg C/(l day). The microbial community structure changed with distance from the river estuary; representatives of the Alpha-, Beta-, and Gammaproteobacteria were present in equal proportions; psychrotolerant and oligotrophic bacteria were numerous. The rate of heterotrophic carbon dioxide assimilation decreased to 3.8 μg C/(l day). At 5–7 km from the river estuary, where the hydrologic, physical, and chemical conditions are similar to those of lake waters, members of the Betaproteobacteria, which are typical of the open waters of Lake Baikal, are the major representatives of planktonic microorganisms.     

Taxonomic composition of Lake Baikal bacterioneuston communities

The taxonomic composition of microbial communities of Lake Baikal surface microlayer was studied by pyrosequencing of the 16S rDNA amplicons. Statistically reliable differences were found between bacterioneuston of the shallow and deep-water stations. The shallow station community was characterized by higher diversity than the deep-water one. While bacterioneuston communities were shown to be less diverse than the water column communities, their diversity was comparable to that of other biofilm associations. Microbial communities of Lake Baikal surface microlayer were shown to be similar to those of the water column in the composition of predominant phyla, while differing considerably at the genus level. Bacterioneuston of Lake Baikal was comparable to microbial communities of the surface microlayer of other freshwater basins, although it was characterized by high abundance of the Alphaproteobacteria and Verrucomicrobia. High abundance of photoheterotrophs compared to the water column communities of other freshwater basins was another distinctive feature of Lake Baikal bacterioneuston. Our results showed the Lake Baikal surface microlayer to be a specific microbial community with low species diversity and relatively high abundance of photoheterotrophic microorganisms.     

Distribution of psychrophilic microorganisms in soils of Terra Nova Bay and Edmonson Point, Victoria Land and their biosynthetic capabilities

Microbiota of soil samples from Terra Nova Bay and Edmonson Point, Antarctica was observed by dilutions spread plate method. Variety of mesophilic and psychrophilic microorganisms was detected and isolated. Bacteria, actinomycetes, fungi, and microalgae occurred. Fungi genera Penicillium, Aspergillus, Paecilomyces, Cladosporium, Mortierella, Candida, Rhodotorula were found. By morphology and cell wall aminoacid composition the actinomycete genus Streptomyces was characterized. The bacteria and actinomycetes were screened for biologically active products. Some cultures formed enzymes, glycolipids and antibiotics. Psychrophilic strain Streptomyces sp. no. 8 was studied more detail and was established that it produced following antibiotics: azalomycin B, nigericin and non-polyenic macrolide antibiotic composed from two components that inhibited the growth of Gram-positive bacteria, yeasts, and phytopathogenic fungi.     

Microbial community associated with <Emphasis Type="Italic">Thioploca</Emphasis> sp. sheaths in the area of the posolsk bank methane seep,southern baikal

Bacterial mats formed by a colorless sulfur bacterium Thioploca sp. in the area of the Posolsk Bank cold methane seep (southern Baikal) were studied using electron microscopy and phylogenetic analysis. Morphologically the bacteria were identified as Thioploca ingrica. Confocal microscopy of DAPI-stained samples revealed numerous rod-shaped, filamentous, and spiral microorganisms in the sheaths, as well as inside and between the trichomes. Transmission electron microscopy revealed nonvacuolated bacteria and small cells without cell envelopes within the sheath. Bacteria with pronounced intracytoplasmic membranes characteristic of type I methanotrophs were observed at the outer side of the sheath. Based on analysis of the 16S rRNA gene sequences, the following phyla were identified in the sheath community: Bacteroidetes, Nitrospira, Chloroflexi, Planctomycetes, Verrucomicrobia, γ-, and δ-Proteobacteria, Euryarchaeota, Crenarchaeota, and Thaumarchaeota, as well as anammox bacteria. A hypothetical scheme of matter flows in the Lake Baikal bacterial mats was proposed based on the data on metabolism of the cultured homologues.     

Study on dynamic changes of microbial community and lignocellulose transformation mechanism during green waste composting

There are few reports on the material transformation and dominant microorganisms in the process of greening waste (GW) composting. In this study, the target microbial community succession and material transformation were studied in GW composting by using MiSeq sequencing and PICRUSt tools. The results showed that the composting process could be divided into four phases. Each phase of the composting appeared in turn and was unable to jump. In the calefactive phase, microorganisms decompose small molecular organics such as FA to accelerate the arrival of the thermophilic phase. In the thermophilic phase, thermophilic microorganisms decompose HA and lignocellulose to produce FA. While in the cooling phase, microorganisms degrade HA and FA for growth and reproduction. In the maturation phase, microorganisms synthesize humus using FA, amino acid and lignin nuclei as precursors. In the four phases of the composting, different representative genera of bacteria and fungi were detected. Streptomyces, Myceliophthora and Aspergillus, maintained high abundance in all phases of the compost. Correlation analysis indicated that bacteria, actinomycetes and fungi had synergistic effect on the degradation of lignocellulose. Therefore, it can accelerate the compost process by maintaining the thermophilic phase and adding a certain amount of FA in the maturation phase.     

Patterns of Formation of Microbial Communities of Alluvial Soils in the Selenga Estuary

Microbial communities of alluvial soils in the facies on islands in the Selenga estuary and near Stepnoi Dvorets and Istomino Settlements were studied. The distribution of the CFU-dominant microorganisms (Bacillus and Pseudomonas + Arthrobacter) has been revealed in the studied island soils. In addition, actinomycetes Streptomyces were found among the dominants in soils of the near-terrace floodplain. The quantitative distribution of microorganisms across soil layers was demonstrated. The effect of ecological factors in formation of microbial communities on the islands and central floodplain regions was revealed.     

Graylings of Baikal Lake basin (Thymallus, Thymallidae): Diversity of forms and their taxonomic status

The morphological characters, molecular-genetic features, and patterns of the dorsal fin in different subspecies and forms of Arctic grayling Thymallus arcticus populating Lake Baikal and its tributaries, Irkutsk Reservoir, and Lake Khubsugul have been studied. Three groups are discernable. The first includes the white and black Baikal graylings T. a. baicalensis, as well as the western Siberian T. a. arcticus; the second group is represented by the Kosogol grayling T. a. nigrescens, and the third is composed of T. arcticus ssp. from the Yakchii lakes (the Verkhnyaya Angara basin) with a phenotype close to graylings populating the upper reaches of the Lena River. All of them are distinguished by some morphological characters, elements of the dorsal fin pattern, and by body coloration. The populations of black Baikal graylings are genetically uniform, and their distinctions from white Baikal graylings are insignificant, which agrees with the absence of a considerable divergence of these forms by a complex of meristic characters. It is assumed that in the black and white Baikal graylings the exchange by genetic information has either ceased quite recently, or persists, although, insignificantly. Some genetic remoteness of the west Siberian grayling from Irkutsk Reservoir and Nizhnyaya Tunguska, closely related to the Baikal grayling, is recorded. The formation of the Khubsugul subspecies is possibly a result of the contact of grayling populations during the rearrangements of the river system in the last glaciation period in the upper reaches of Yenisei and Selenga in Mongolia. The habitation in the Baikal system of the Upper Lena graylings indicates a connection between the Lena and Baikal basins in the past. The results of a multivariate analysis of meristic characters and the sequences of mitochondrial DNA confirm the conclusion made by Svetovidov (1931, 1936), concerning the absence of grounds to assign a species status to the Baikal forms.     

The Biodiversity of Actinomycetes in Lake Baikal

The taxonomic analysis of 107 actinomycete strains isolated from the bottom sediments and water of Lake Baikal showed that most of the water isolates belong to the genus Streptomyces and most of the sediment isolates belong to the genus Micromonospora. In the sediments, the number of actinomycetes increased with depth (down to 200 m). Eight Streptomyces isolates were identified to a species level.     

Taxonomic characterization of the microorganisms associated with the cultivable diatom Synedra acus from Lake Baikal

Determination of the taxonomic position of microorganisms associated with diatoms was carried out using microscopic, microbiological, and phylogenetic methods. Examination of the cultures of the fresh-water diatom Synedra acus grown in Lake Baikal water by epifluorescence and electron microscopy revealed that bacterial cells colonized the mucilage surrounding the cells of living microalgae and their cell surfaces and penetrate into the frustules of dead diatoms. A total of 13 strains of heterotrophic bacteria were isolated in pure cultures and described. Based on the results of analysis of their morphological, physiological, and biochemical properties, as well as on data obtained by 16S rRNA gene analysis, the following strains were identified to the species level: Sphingomonas sp., Variovorax paradoxus, Pseudomonas fluorescens, Microbacterium trichothecenolyticum, Rhodococcus sp., Caulobacter vibrioides, and Brevundimonas vesicularis.