Structure and Functional Potential of Arctic Sea Sediment Microbiota.

Arctic ecosystems are affected by negative influence of climate change, pollution, and overexploitation of resources. Microorganisms playing a key role in preserving extreme econiches are poorly studied and require the use of modern methods for studying both their biodiversity and physiological activity. We applied Illumina MiSeq to the high-throughput 16S rRNA sequencing study of four Laptev Sea sediments from 64 - 185 m depth, using next generation sequencing enables rapid analysis of composition and diversity of prokaryotic communities. Although the dominant phylum in all samples was Proteobacteria, only the deepest sample contained a high number of archaeal organisms (19%) with the predominance of Methanosarcinaceace family in comparison with less 1% in the other three samples. This deepest sample had the lowest biodiversity and richness indices. Comparison of functional profiles of communities using Global Mapper tool revealed similar average abundance of infectiousness, drug resistance and environmental adaptation determinants in all samples, and high functional abundance for xenobiotic degradation in two samples. Among cultivated bacteria which could be promising producers of secreted RNase the representatives of Bacillus and Lysinibacillus genera were found. Our results contribute to improve our understanding of richness and ecological role of Laptev Sea microbiota.

Polysiloxane Coatings Biodeterioration in Nature and Laboratory.

Objects and structures made of organic glass require protection from damage caused by external factors. Light, humidity, temperature, dust pollution and, undoubtedly, microorganisms lead to the deterioration of optical and mechanical properties. Polysiloxane-based protective coatings, consisting of silicon-oxygen backbones linked together with organic side groups attached to the silicon atoms, are widely used. However, the polysiloxane coatings themselves also cannot avoid deterioration during operation that implies the constant development of new protective materials. Here, we created a new cross-linked polysiloxane that covers organic glasses to enhance their resistance to aggressive external factors, and investigated its own resistance to damage induced by micromycetes in natural tropical conditions and in the laboratory. It has been established that the surface of coatings in the tropics is prone to fouling with micromycetes, mainly of the genera Aspergillus and Penicillium, which produce oxalic, malic, lactic, and citric acids contributing to the biodeterioration of polysiloxane. The testing of monolithic polycarbonate, polymethyl methacrylate, and triplex coated with polysiloxane showed that they retained significant resistance to abrasion and transparency at a level of more than 90% under aggressive natural conditions. Under artificial laboratory conditions, the infection of samples with micromycete spores also revealed their growth on surfaces and a similar trend of damage.

Bacillus pumilus proteome changes in response to 2,4,6-trinitrotoluene-induced stress.

2,4,6-Trinitrotoluene (TNT) is the most widely used nitroaromatic compound and is highly resistant to degradation. Most aerobic microorganisms reduce TNT to amino derivatives via formation of nitroso- and hydroxylamine intermediates. Although pathways of TNT degradation are well studied, proteomic analysis of TNT-degrading bacteria was done only for some individual Gram-negative strains. Here, we isolated a Gram-positive strain from TNT-contaminated soil, identified it as Bacillus pumilus using 16S rRNA sequencing, analyzed its growth, the level of TNT transformation, ROS production, and revealed for the first time the bacillary proteome changes at toxic concentration of TNT. The transformation of TNT at all studied concentrations (20-200 mg/L) followed the path of nitro groups reduction with the formation of 4-amino-2,6-dinitrotoluene. Hydrogen peroxide production was detected during TNT transformation. Comparative proteomic analysis of B. pumilus showed that TNT (200 mg/L) inhibited expression of 46 and induced expression of 24 proteins. Among TNT upregulated proteins are those which are responsible for the reductive pathway of xenobiotic transformation, removal of oxidative stress, DNA repair, degradation of RNA and cellular proteins. The production of ribosomal proteins, some important metabolic proteins and proteins involved in cell division are downregulated by this xenobiotic.

Another plea for 'best practice' in molecular approaches to trematode systematics: Diplostomum sp. clade Q identified as Diplostomum baeri Dubois, 1937 in Europe.

DNA sequence data became an integral part of species characterization and identification. Still, specimens associated with a particular DNA sequence must be identified by the use of traditional morphology-based analysis and correct linking of sequence and identification must be ensured. Only a small part of DNA sequences of the genus Diplostomum (Diplostomidae) is based on adult isolates which are essential for accurate identification. In this study, we provide species identification with an aid of morphological and molecular (cox1, ITS-5.8S-ITS2 and 28S) characterization of adults of Diplostomum baeri Dubois, 1937 from naturally infected Larus canus Linnaeus in Karelia, Russia. Furthermore, we reveal that the DNA sequences of our isolates of D. baeri are identical with those of the lineage Diplostomum sp. clade Q , while other sequences labelled as the 'D. baeri' complex do not represent lineages of D. baeri. Our new material of cercariae from Radix balthica (Linnaeus) in Ireland is also linked to Diplostomum sp. clade Q. We reveal that D. baeri is widely distributed in Europe; as first intermediate hosts lymnaeid snails (Radix auricularia (Linnaeus), R. balthica) are used; metacercariae occur in eye lens of cyprinid fishes. In light of the convoluted taxonomy of D. baeri and other Diplostomum spp., we extend the recommendations of Blasco-Costa et al. (2016, Systematic Parasitology 93, 295­306) for the 'best practice' in molecular approaches to trematode systematics. The current study is another step in elucidating the species spectrum of Diplostomum based on integrative taxonomy with well-described morphology of adults linked to sequences.

Morphological and molecular differentiation of Diplostomum spp. metacercariae from brain of minnows (Phoxinus phoxinus L.) in four populations of northern Europe and East Asia.

Metacercariae of trematodes from the genus Diplostomum are major helminth pathogens of freshwater fish, infecting the eye or the brain. The taxonomy of the genus Diplostomum is complicated, and has recently been based mainly on the molecular markers. In this study, we report the results of the morphological and molecular genetic analysis of diplostomid metacercaria from the brain of the minnow Phoxinus phoxinus from three populations in Fennoscandia (Northern Europe) and one population in Mongolia (East Asia). We obtained the data on the polymorphism of the partial mitochondrial cox1 gene and ribosomal ITS1-5.8S-ITS2 region of these parasites. РСА-based morphological analysis revealed that the parasites in the Asian and the European groups of Diplostomum sp. were distinctly different. Metacercariae from the brain of Mongolian minnows were much larger than those from the brain of Fennoscandian minnows but had much fewer excretory granules. Considering that the two study regions were separated by a distance of about 4500 km, we also tested the genetic homogeneity of their host, the minnow, using the mitochondrial cytb gene. It was shown that Diplostomum-infected minnows from Mongolia and Fennoscandia represented two previously unknown separate phylogenetic lineages of the genus Phoxinus. Both molecular and morphological analysis demonstrated that the parasites from Fennoscandia belonged the species Diplostomum phoxini, while the parasites from Mongolia belonged to a separate species, Diplostomum sp. MТ.Each of the two studied Diplostomum spp. was associated with a specific, and previously unknown, genealogical lineage of its second intermediate host, P. phoxinus.

The composition of microbial communities in inflammatory periodontal diseases in young adults Tatars.

Host susceptibility and environmental factors are important for the development of gingivitis and periodontitis, but bacterial biofilms attached to the teeth and gingival tissues play a crucial role. We have analyzed and compared the subgingival microbial communities between subjects with dental plaque biofilm-induced generalized chronic gingivitis (CG), localized initial (Stage I) periodontitis (IP) and healthy controls (HC) of young people aged 18-19 years permanently residing in the city of Kazan (Tatarstan, Russia). The results showed that the α-diversity in groups with CG and IP was higher than in the healthy group. In a course of periodontal disease, a decrease in the relative abundance of dominates genera Rothia and Streptococcus was observed along with increase of class TM7-3 (Candidatus Saccharibacteria phylum) representatives. Also, the increase of red complex representatives Porphyromonadeceae, Treponema and Tannerella was detected together with statistically significant increase of Filifactor, Parvimonas, Peptostreptococcaceae, Veillonellaceae, Tissierelaceae and Mogibacteriaceae. Analysis of our data suggests that transition from HC to IP may be accompanied by a decrease in microbial diversity and a reduction in the abundance of family Rs-045 (Candidatus Saccharibacteria phylum), Desulfovibrionaceae Corynebacterium, Campylobacter and Selenomonas in young adults Kazan Tatars.

Metabolic Activity of Micromycetes Affecting Urban Concrete Constructions.

Concrete resistance to the destructive action of microorganisms is considered as a measure of its durability and is increasingly being raised as an important issue. We focused our study on the biodeterioration of concrete specimens widely used as a building material of urban houses by micromycetes isolated from the inner wall surface of the former military hospital in Kazan city, Tatarstan, Russia. Fungal community consists of 9 Penicillium isolates, 6 Aspergillus, 2 Trichoderma, and 1 isolate of Alternaria. First, we have identified two dominant isolates, Aspergillus fumigatus and Penicillium brevicompactum, and characterized their destructive properties according to the radial growth rate, antagonistic activity towards bacterial habitants of concrete, and production of organic acids. Then, we have demonstrated that five tested brands of high-strength concrete differ in bioreceptivity. The alterations in concrete resistances to compression and flexure after fungal attack were recorded at the trend level, mainly due to a short exposure time of concrete to fungal destructors in tests recommended by national Russian standard. Finally, using scanning electron microscopy we have shown that colonization of concrete by the dominant fungi includes their penetration into the thickness of concrete and germination in cracks. Elementary analysis revealed the decrease of calcium content on about 41% after fungal growth on the concrete in liquid phase and on 32% by superficial growth in comparison with the samples without fungal treatment.

Nematodes in the mallard (Anas platyrhynchos Linnaeus, 1758) and the common goldeneye (Bucephala clangula Linnaeus, 1758) (Anatidae) from Northern Europe.

There are first data on nematodes of Anas platyrhynchos Linnaeus, 1758 (mallard) and Bucephala clangula Linnaeus, 1758 (common goldeneye) from Northern Europe (Ladoga Lake region). The ducks were found to be infected with nine nematode species. A. platyrhynchos hosted eight nematode species and B. clangula was host to four nematode species. All species except Capillaria anatis were found in the region for the first time. Nematodes Amidostomum acutum, Streptocara crassicauda, and Tetrameres fissispina parasitized on both hosts and were the most abundant. The biggest number of parasites revealed was biohelminths with a direct life cycle.

Brownian aggregation rate of colloid particles with several active sites.

We theoretically analyze the aggregation kinetics of colloid particles with several active sites. Such particles (so-called "patchy particles") are well known as chemically anisotropic reactants, but the corresponding rate constant of their aggregation has not yet been established in a convenient analytical form. Using kinematic approximation for the diffusion problem, we derived an analytical formula for the diffusion-controlled reaction rate constant between two colloid particles (or clusters) with several small active sites under the following assumptions: the relative translational motion is Brownian diffusion, and the isotropic stochastic reorientation of each particle is Markovian and arbitrarily correlated. This formula was shown to produce accurate results in comparison with more sophisticated approaches. Also, to account for the case of a low number of active sites per particle we used Monte Carlo stochastic algorithm based on Gillespie method. Simulations showed that such discrete model is required when this number is less than 10. Finally, we applied the developed approach to the simulation of immunoagglutination, assuming that the formed clusters have fractal structure.

Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold.

Imidazole glycerol-phosphate dehydratase (IGPD) catalyzes the sixth step of histidine biosynthesis. The enzyme is of fundamental biochemical interest, because it catalyzes removal of a non-acidic hydrogen atom in the dehydration reaction. It is also a potential target for development of herbicides. IGPD is a metalloenzyme in which transition metals induce aggregation and are required for catalysis. Addition of 1 equivalent of Mn(2+)/subunit is shown by analytical ultracentrifugation to induce the formation of 24-mers from trimeric IGPD. Two histidine-rich motifs may participate in metal binding and aggregation. The 2.3-A crystal structure of metal-free trimeric IGPD from the fungus Filobasidiella neoformans reveals a novel fold containing an internal repeat, apparently the result of gene duplication. The 95-residue alpha/beta half-domain occurs in a few other proteins, including the GHMP kinase superfamily (galacto-homoserine-mevalonate-phosphomevalonate), but duplication to form a compact domain has not been seen elsewhere. Conserved residues cluster at two types of sites in the trimer, each site containing a conserved histidine-rich motif. A model is proposed for the intact, active 24-mer in which all highly conserved residues, including the histidine-rich motifs in both the N- and C-terminal halves of the polypeptide, cluster at a common site between trimers. This site is a candidate for the active site and also for metal binding leading to aggregation of trimers. The structure provides a basis for further studies of enzyme function and mechanism and for development of more potent and specific herbicides.