Characterization of the core bacteriobiome in the rhizosphere of greenhouse vegetables: taxonomic diversity and putative functions

The aim of the study. The aim was to profile 16S rRNA gene diversity and to assess functional potential of bacterial assemblages in the rhizosphere of some unconventional vegetables grown in protected greenhouse conditions in West Siberia. Location and time of the study. Novosibirsk, Russia, 2016. Methodology. At the end of the growing season in the middle of September the rhizosphere soil was collected from the plants of wax gourd (Benincasa hispida), bitter melon (Momordica charantia), kiwano (Cucumis metuliferus) and cowpea (Vigna unguiculata) grown on peat-based substrate in a polyethylene-protected greenhouse that has been in operation for more than 40 years. The metagenomic DNA was extracted and amplified with V3-V4 primers for 16S rRNA genes, and the amplicons sequenced with Illumina MiSeq. The obtained OTUs tables were used to predict putative functions by running through the FAPROTAX database. Main results. The rhizosphere bacteriobiome was dominated by Proteobacteria (32±11% of the total number of sequence reads), Acidobacteria (23±7%) and Actinobacteria (18±3%) phyla, together accounting for about three quarters of the rhizosphere bacteriobiome. In total 20 bacterial phyla were found. The rhizosphere bacteriobiome was surprisingly diverse with Shannon index ranging 7.0–7.5. The number of the observed operational taxonomic units (OTUs) per sample was very high, ranging 4,500–4,900, and the potential number of OTUs estimated as 5,100–5,700; all those OTUs were evenly and equitably represented in the bacteriobiome, and dominance indices (Simpson dominance and Berger-Parker) were very low. The main dominant OTU represented Bradyrhizobiaceae family and accounted for just 1% on average. Overall the study identified 27 OTUs belonging to the Bradyrhizobiaceae family, but only four of them were ascribed to nitrogen fixation by FAPROTAX. Function prediction by FAPROTAX also suggested that bacteriobiome had a marked potential for the carbon cycle, denitrification, aromatic compound and plant polymer degradation, but no plant pathogens. The biggest difference in rhizosphere bacteriobiome diversity was observed between the bitter melon and the other three vegetable crops: bitter melon had much increased abundance of Arthrobacter and Sphingomonas as compared with wax gourd, kiwano and cowpea, and increased number of bacterial species associated with aromatic compounds degradation. Conclusion. Based on the finding that the studied rhizosphere bacteriobiomes were very diverse, we conclude that the crops were able to recruit diverse microbiota from the peat-based soil substrate, which, in its turn, means that diverse soil substrate microbiota has been sustained over several decades of the greenhouse operation. All crops apparently shaped distinct bacteriobiomes in their rhizosphere, which ideally should be included into studies of plant-associated bacterial diversity profiles for breeding and sustainable production.The aim of the study. The aim was to profile 16S rRNA gene diversity and to assess functional potential of bacterial assemblages in the rhizosphere of some unconventional vegetables grown in protected greenhouse conditions in West Siberia. Location and time of the study. Novosibirsk, Russia, 2016. Methodology. At the end of the growing season in the middle of September the rhizosphere soil was collected from the plants of wax gourd (Benincasa hispida), bitter melon (Momordica charantia), kiwano (Cucumis metuliferus) and cowpea (Vigna unguiculata) grown on peat-based substrate in a polyethylene-protected greenhouse that has been in operation for more than 40 years. The metagenomic DNA was extracted and amplified with V3-V4 primers for 16S rRNA genes, and the amplicons sequenced with Illumina MiSeq. The obtained OTUs tables were used to predict putative functions by running through the FAPROTAX database. Main results. The rhizosphere bacteriobiome was dominated by Proteobacteria (32±11% of the total number of sequence reads), Acidobacteria (23±7%) and Actinobacteria (18±3%) phyla, together accounting for about three quarters of the rhizosphere bacteriobiome. In total 20 bacterial phyla were found. The rhizosphere bacteriobiome was surprisingly diverse with Shannon index ranging 7.0–7.5. The number of the observed operational taxonomic units (OTUs) per sample was very high, ranging 4,500–4,900, and the potential number of OTUs estimated as 5,100–5,700; all those OTUs were evenly and equitably represented in the bacteriobiome, and dominance indices (Simpson dominance and Berger-Parker) were very low. The main dominant OTU represented Bradyrhizobiaceae family and accounted for just 1% on average. Overall the study identified 27 OTUs belonging to the Bradyrhizobiaceae family, but only four of them were ascribed to nitrogen fixation by FAPROTAX. Function prediction by FAPROTAX also suggested that bacteriobiome had a marked potential for the carbon cycle, denitrification, aromatic compound and plant polymer degradation, but no plant pathogens. The biggest difference in rhizosphere bacteriobiome diversity was observed between the bitter melon and the other three vegetable crops: bitter melon had much increased abundance of Arthrobacter and Sphingomonas as compared with wax gourd, kiwano and cowpea, and increased number of bacterial species associated with aromatic compounds degradation. Conclusion. Based on the finding that the studied rhizosphere bacteriobiomes were very diverse, we conclude that the crops were able to recruit diverse microbiota from the peat-based soil substrate, which, in its turn, means that diverse soil substrate microbiota has been sustained over several decades of the greenhouse operation. All crops apparently shaped distinct bacteriobiomes in their rhizosphere, which ideally should be included into studies of plant-associated bacterial diversity profiles for breeding and sustainable production

Control of structurization processes in wood-cement systems at fixed pH

The paper presents a study of structurization processes in the wood-cement systemmixed with the buffer solutions and the improvement of service properties of products produced therefrom. Infrared spectroscopy, X-ray phase analysis, and pH measurements show that structurization processes in wood-cement systems depend on the acidity of aqueous solution, the behavior of hydration, neutralization, and polycondensation reactions with the formation of polymer products including those with cement grout components and functional groups of wood. It is shown that phosphate buffer solutions used for mixing wood-cement compositions improve their strength properties and reduce water absorption. The optimum acidity of the buffered medium for service properties of the wood-cement systemis pH = 4.8

Numerical Modeling of Radiation-Dominated and QED-Strong Regimes of Laser-Plasma Interaction

Ultra-strong laser pulses can be so intense that an electron in the focused beam loses significant energy due to gamma-photon emission while its motion deviates via the radiation back-reaction. Numerical methods and tools designed to simulate radiation-dominated and QED-strong laser-plasma interactions are summarized here.Comment: 12 pages, 6 figure

Dynamics of Emitting Electrons in Strong Electromagnetic Fields

We derive a modified non-perturbative Lorentz-Abraham-Dirac equation. It satisfies the proper conservation laws, particularly, it conserves the generalized momentum, the latter property eliminates the symmetry-breaking runaway solution. The equation allows a consistent calculation of the electron current, the radiation effect on the electron momentum, and the radiation itself, for a single electron or plasma electrons in strong electromagnetic fields. The equation is applied to a simulation of a strong laser pulse interaction with a plasma target. Some analytical solutions are also provided.Comment: The original form of this paper was submitted to Phys. Rev. Lett. on August 3, 2008. The current version of the paper is substantially extended and includes modifications resulting from points raised during the review proces

THE EFFECT OF DEXTRANAL ON THE GUT BACTERIOBIOME OF CALVES

Background. The search for more efficient pro- and prebiotics to improve calves’ health, including decreasing the incidence of intestinal infections and increasing biomass production, has been very actual. The effect of prebiotics, however, is poorly, especially as related to gut microbiome biodiversity.  The aim of this work was to study the influence of dextranal on the growth of calves and their gut(rectum) bacteriobiome. Materials and Methods. Bacteriobiome composition and structure was assessed in the control group (K, conventional diet) and dextranal-receiving group (D) in 18-20 days aged calves  by 16S metabarcoding (V3-V4, Illumina MiSeq). Results. Overall, we found 377 operational taxonomic units (OTU) from 168 genera, 91 families, 55 orders, 30 classes and 11 phyla, with more than the half of the total number of identifies OTUs belonging to the Firmicutes phylum, followed by Bacteroidetes and Actinobacteria. The relative abundance of the phylum-specific nucleotide sequences followed the same order of dominance. Dextranal addition resulted in the increased (11.9 kg/calf, or 15%) of the living body mass of the two-months old calves in group D as compared with group K: consequently, the dextranal-related difference in the calves’ gut bacteriobiome composition and structure can be viewed as beneficial. It primarily concerns the decreased abundance of the opportunistic pathogen Escherichia/Shigella (Gammaproteobacteria) in group D. Overall 73 OTUs, including six dominant ones, were found to be differentially abundant in the groups. However, changes in the relative abundance of some OTUs were difficult to interpret, most likely due to the low strain/species resolution by 16S rRNA gene fragments’ sequences. As for the α- biodiversity, there were no differences between the groups, but the overall trend directed to the increasing α- biodiversity of the calves’ gut bacteriobiome after dextranal treatment. Conclusion. This study reports the first attempt to inventory the gut bacteriobiome of the cattle in the region, and the obtained results provide the basis for a more detailed and taxonomically targeted further research

колективна монографія

Кримінальний процесуальний кодекс 2012 року: ідеологія та практика правозастосування: колективна монографія / за заг. ред. Ю. П. Аленіна ; відпов. за вип. І. В. Гловюк. - Одеса : Видавничий дім «Гельветика», 2018. - 1148 с

Potato Tuber Yield and Quality Under Different Potassium Application Rates and Forms in West Siberia

Potato cultivars have different strategies for dealing with potassium (K) deficiency in soil, and their response to different forms and rates of K fertilisation may vary because of differences in soil K availability. This study was performed to evaluate the effect of K fertilisation rates (0, 30, 60, 90, 120 and 150 kg K/ha) on tuber yield and quality (dry matter, starch, sugar and ascorbic acid content, taste) of two potato cultivars (Roco and Rosara) grown in the microplot field experiment on Luvisol in the forest-steppe zone in southern West Siberia, Russia (NL 54.422106, EL 83.160257). The tuber yield of both potato cultivars increased with increase in K application rate up to 2.1 and 2.9 kg/m2 for Roco and Rosara, respectively. Sugar content, averaging 3.5%, was mostly determined by cultivar; however, in both cultivars it tended to decrease with increasing K application rate. The application of K fertiliser in the form of sulphate as compared to chloride increased dry matter content from 22.4 to 23.8% and ascorbic acid content from 13.2 to 14.6 mg/100 g fresh mass. Starch content of potato tubers averaged 59.7 ± 4.8% over all K fertilisation variants, with cultivar responses being different. Potassium application rate did not affect Roco tubers’ taste, while improving Rosara tubers’ taste under moderate application rates. The results underscore the importance to adjust fertiliser recommendations concerning potassium application rates and source on the basis of biological requirements and intended utilization of individual potato cultivar

Characterization of the core bacteriobiome in the rhizosphere of greenhouse vegetables: taxonomic diversity and putative functions

The aim of the study. The aim was to profile 16S rRNA gene diversity and to assess functional potential of bacterial assemblages in the rhizosphere of some unconventional vegetables grown in protected greenhouse conditions in West Siberia. Location and time of the study. Novosibirsk, Russia, 2016. Methodology. At the end of the growing season in the middle of September the rhizosphere soil was collected from the plants of wax gourd (Benincasa hispida), bitter melon (Momordica charantia), kiwano (Cucumis metuliferus) and cowpea (Vigna unguiculata) grown on peat-based substrate in a polyethylene-protected greenhouse that has been in operation for more than 40 years. The metagenomic DNA was extracted and amplified with V3-V4 primers for 16S rRNA genes, and the amplicons sequenced with Illumina MiSeq. The obtained OTUs tables were used to predict putative functions by running through the FAPROTAX database. Main results. The rhizosphere bacteriobiome was dominated by Proteobacteria (32±11% of the total number of sequence reads), Acidobacteria (23±7%) and Actinobacteria (18±3%) phyla, together accounting for about three quarters of the rhizosphere bacteriobiome. In total 20 bacterial phyla were found. The rhizosphere bacteriobiome was surprisingly diverse with Shannon index ranging 7.0–7.5. The number of the observed operational taxonomic units (OTUs) per sample was very high, ranging 4,500–4,900, and the potential number of OTUs estimated as 5,100–5,700; all those OTUs were evenly and equitably represented in the bacteriobiome, and dominance indices (Simpson dominance and Berger-Parker) were very low. The main dominant OTU represented Bradyrhizobiaceae family and accounted for just 1% on average. Overall the study identified 27 OTUs belonging to the Bradyrhizobiaceae family, but only four of them were ascribed to nitrogen fixation by FAPROTAX. Function prediction by FAPROTAX also suggested that bacteriobiome had a marked potential for the carbon cycle, denitrification, aromatic compound and plant polymer degradation, but no plant pathogens. The biggest difference in rhizosphere bacteriobiome diversity was observed between the bitter melon and the other three vegetable crops: bitter melon had much increased abundance of Arthrobacter and Sphingomonas as compared with wax gourd, kiwano and cowpea, and increased number of bacterial species associated with aromatic compounds degradation. Conclusion. Based on the finding that the studied rhizosphere bacteriobiomes were very diverse, we conclude that the crops were able to recruit diverse microbiota from the peat-based soil substrate, which, in its turn, means that diverse soil substrate microbiota has been sustained over several decades of the greenhouse operation. All crops apparently shaped distinct bacteriobiomes in their rhizosphere, which ideally should be included into studies of plant-associated bacterial diversity profiles for breeding and sustainable production.The aim of the study. The aim was to profile 16S rRNA gene diversity and to assess functional potential of bacterial assemblages in the rhizosphere of some unconventional vegetables grown in protected greenhouse conditions in West Siberia. Location and time of the study. Novosibirsk, Russia, 2016. Methodology. At the end of the growing season in the middle of September the rhizosphere soil was collected from the plants of wax gourd (Benincasa hispida), bitter melon (Momordica charantia), kiwano (Cucumis metuliferus) and cowpea (Vigna unguiculata) grown on peat-based substrate in a polyethylene-protected greenhouse that has been in operation for more than 40 years. The metagenomic DNA was extracted and amplified with V3-V4 primers for 16S rRNA genes, and the amplicons sequenced with Illumina MiSeq. The obtained OTUs tables were used to predict putative functions by running through the FAPROTAX database. Main results. The rhizosphere bacteriobiome was dominated by Proteobacteria (32±11% of the total number of sequence reads), Acidobacteria (23±7%) and Actinobacteria (18±3%) phyla, together accounting for about three quarters of the rhizosphere bacteriobiome. In total 20 bacterial phyla were found. The rhizosphere bacteriobiome was surprisingly diverse with Shannon index ranging 7.0–7.5. The number of the observed operational taxonomic units (OTUs) per sample was very high, ranging 4,500–4,900, and the potential number of OTUs estimated as 5,100–5,700; all those OTUs were evenly and equitably represented in the bacteriobiome, and dominance indices (Simpson dominance and Berger-Parker) were very low. The main dominant OTU represented Bradyrhizobiaceae family and accounted for just 1% on average. Overall the study identified 27 OTUs belonging to the Bradyrhizobiaceae family, but only four of them were ascribed to nitrogen fixation by FAPROTAX. Function prediction by FAPROTAX also suggested that bacteriobiome had a marked potential for the carbon cycle, denitrification, aromatic compound and plant polymer degradation, but no plant pathogens. The biggest difference in rhizosphere bacteriobiome diversity was observed between the bitter melon and the other three vegetable crops: bitter melon had much increased abundance of Arthrobacter and Sphingomonas as compared with wax gourd, kiwano and cowpea, and increased number of bacterial species associated with aromatic compounds degradation. Conclusion. Based on the finding that the studied rhizosphere bacteriobiomes were very diverse, we conclude that the crops were able to recruit diverse microbiota from the peat-based soil substrate, which, in its turn, means that diverse soil substrate microbiota has been sustained over several decades of the greenhouse operation. All crops apparently shaped distinct bacteriobiomes in their rhizosphere, which ideally should be included into studies of plant-associated bacterial diversity profiles for breeding and sustainable production

Undisturbed Soil Pedon under Birch Forest: Characterization of Microbiome in Genetic Horizons

Vast areas of land in the forest-steppe of West Siberia are occupied by birch forests, the most common ecosystems there. However, currently, little is known about the microbiome composition in the underlying soil, especially along a sequence of soil genetic horizons. The study aimed at inventorying microbiome in genetic horizons of a typical Phaeozem under undisturbed birch forest in West Siberia. Bacteria and fungi were studied using 16S rRNA genes’ and ITS2 amplicon sequencing with Illumina MiSeq. Proteobacteria and Acidobacteria together accounted for two-thirds of the operational taxonomic units (OTUs) numbers and half of the sequences in each genetic horizon. Acidobacteria predominated in eluvial environments, whereas Proteobacteria, preferred topsoil. The fungal sequences were dominated by Ascomycota and Basidiomycota phyla. Basidiomycota was the most abundant in the topsoil, whereas Ascomycota increased down the soil profile. Thelephoraceae family was the most abundant in the A horizon, whereas the Pyronemataceae family dominants in the AEl horizon, ultimately prevailing in the subsoil. We conclude that soil genetic horizons shape distinct microbiomes, therefore soil horizontation should be accounted for while studying undisturbed soils. This study, representing the first description of bacterio- and mycobiomes in genetic horizons of the Phaeozem profile, provides a reference for future research

Rhizosphere Bacteriobiome of the Husk Tomato Grown in the Open Field in West Siberia

The composition and structure of rhizosphere bacteriobiome of the husk tomato (Physalis philadelphica Lam.) plants grown on Phaeozem in the open field in West Siberia, Russia (55°15’ NL, 83°31’ EL) were studied using Illumina MiSeq sequencing of the V3-V4 hypervariable region of 16S rRNA genes. In total 5898 OTUs (Operational Taxonomic Units) were found in the study, representing 20 phyla and 53 identified and 15 non-identified (below the phylum level) classes. The most OTU-rich phyla were Proteobacteria, Acidobacteria and Actinobacteria, their relative abundance in the total number of sequence reads being 26, 22 and 19%, respectively. Bacteroidetes, Gemmatimonadetes and Verrucomicrobia phyla each accounted for 2 ‒ 4%. The rest 14 of the identified phyla were quite negligible, contributing less than 0.5% each. At the OTUs level, the structure was very even and equitable, as only 7 OTUs had relative abundance ranging from 0.5 to 1.1%. The main dominant OTU represented Bradyrhizobiaceae family, implying the importance of nitrogen-fixing bacteria for plant growth and development without any mineral fertilisation. The dominance biodiversity index was very low (0.001), while Shannon index was rather high (7.5). We believe the presented husk tomato rhizosphere bacteriobiome, as the first study using new generation sequencing platform for this species, will help get a better picture of Solanaceae microbiomes in different environments, thus contributing to a more comprehensive understanding of shaping microbial communities by plant roots