Natalia E. Gogoleva

• PostDoc Position at University of Innsbruck

Mapping transcription start sites and determining their activity remain a challenging task even for well-studied organisms. Here, we present Cappable-seq RNA sequencing data of Escherichia coli K-12 MG1655 after treatment with three antibiotics with various spectra of action that may expand the range of mapped transcription start sites for this mod...

The Achromobacter insolitus LCu2 strain, isolated from the roots of alfalfa (Medicago sativa L.), utilized cinnamic acid, as well as its methoxy derivatives ‒ vanillic and ferulic acids ‒ as the only carbon source. Weak growth was observed on m-coumaric acid, but not on o- and p-coumaric acids. Growth on cinnamic acid was slow and diauxic. The loss...

The strain Achromobacter insolitus LCu2 isolated from the roots of alfalfa (Medicago sativa L.) utilized cinnamic acid and its methoxy derivatives (vanillic and ferulic acids) as the sole carbon source. Weak growth was observed with m-coumaric acid, but not on o- or p-coumaric acids. Growth on the cinnamic acid was slow and diauxic. The substrate d...

Karst caves, formed by the erosion of soluble carbonate rocks, provide unique ecosystems characterized by stable temperatures and high humidity. These conditions support diverse microbial communities, including wall microbial fouling, aquatic biofilms, and planktonic communities. This study discloses the taxonomic diversity of protists in aquatic b...

A rhizosphere strain, Achromobacter insolitus LCu2, was isolated from alfalfa (Medicago sativa L.) roots. It was able to degrade of 50% glyphosate as the sole phosphorus source, and was found resistant to 10 mM copper (II) chloride, and 5 mM glyphosate–copper complexes. Inoculation of alfalfa seedlings and potato microplants with strain LCu2 promot...

The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at t...

Some surface properties of carbonate speleothems from Kirillov’s, Pionerskaya and Yaschik Pandory caves in the Republic of Khakasia, as well as Yuryevskaya Cave in the Republic of Tatarstan were investigated. The types of the speleothem samples such as crusts, drips, corallites, and moon milk were studied. All the samples were collected in cave aph...

Background Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Sout...

Background A familial history of rheumatoid arthritis (RA) predisposes an individual to develop RA. This study aimed at investigating factors associated with this conversion from the Tatarstan cohort. Methods A total of 144 individuals, referred to as pre-RA and at risk for familial RA, were selected 2 years (range: 2–21 years) before conversion t...

Phytopathogenic microorganisms, being able to cause plant diseases, usually interact with hosts asymptomatically, resulting in the development of latent infections. Knowledge of the mechanisms that trigger a switch from latent to typical, symptomatic infection is of great importance from the perspectives of both fundamental science and disease mana...

Bacterial adaptation is regulated at the population level with the involvement of intercellular communication (quorum sensing). When the population density is insufficient for adaptation under starvation, bacteria can adjust it to a quorum level through cell divisions at the expense of endogenous resources. This phenomenon has been described for th...

Hot springs are known as highly adverse extreme environments where thermophilic and hyperthermophilic microorganisms can survive. We describe taxonomic diversity of several microbial biofilms collected along water temperature gradient in hot streams in the aquatic system of the Stolbovskie hot springs on Kunashir Island, Kurils, Russia. The taxonom...

Puctures for the report about our Hakasian expedition aimed to the collection of cave biofilms

Pink snow mold, caused by a phytopathogenic and psychrotolerant fungus, Microdochium nivale, is a severe disease of winter cereals and grasses that predominantly occurs under snow cover or shortly after its melt. Snow mold has significantly progressed during the past decade, often reaching epiphytotic levels in northern countries and resulting in d...

We report the discovery of a new abscisic acid (ABA) metabolite, found in the course of a mass spectrometric study of ABA metabolism by the rhizosphere bacterium Rhodococcus sp. P1Y. Analogue of (+)-ABA, enriched in tritium in the cyclohexene moiety, was fed in bacterial cells, and extracts containing radioactive metabolites were purified and analy...

The impact of histidine acid bacterial phytase from Pantoea brenneri AS3 as a feed additive (1000 U/kg feed) on the microbial ecology of the gastrointestinal tract was evaluated. The enzyme was obtained from the culture liquid of a recombinant yeast Pichia pastoris pPINK-HC (agpP) by ultrafiltration: a 3.5-fold phytase concentrate with a total acti...

Background: Laboratory experiments with starving cultures indicate that a wide range of microorganisms show genetic traits that improve stability for oligotrophic conditions. However, it remains unclear to what extent laboratory studies of starvation survival in pure or mixed cultures can be extrapolated to stable microbial ecosystems in nature. Mo...

Genomic safe harbors (GSHs) provide ideal integration sites for generating transgenic organisms and cells and can be of great benefit in advancing the basic and applied biology of a particular species. Here we report the identification of GSHs in a dry-preservable insect cell line, Pv11, which derives from the sleeping chironomid, Polypedilum vande...

Whole-genome sequencing of a soil isolate Bacillus pumilus, strain 7P, and its streptomycin-resistant derivative, B. pumilus 3-19, showed genome sizes of 3,609,117 bp and 3,609,444 bp, respectively. Annotation of the genome showed 3794 CDS (3204 with predicted function) and 3746 CDS (3173 with predicted function) in the genome of strains 7P and 3-1...

Microdochium nivale is a progressive and devastating phytopathogen that causes different types of cereal crop and grass diseases that are poorly characterized at the molecular level. Although rye (Secale cereale L.) is one of the most resistant crops to most of the phytopathogens, it is severely damaged by M. nivale. The recent high-quality chromos...

Garden pea (Pisum sativum L.) is a globally important legume crop. Like other legumes, it forms beneficial symbiotic interactions with the soil bacteria rhizobia, gaining the ability to fix atmospheric nitrogen. In pea nodules, the meristem is long-lasting and results in the formation of several histological zones that implicate a notable different...

The required amount of abscisic acid containing 4 – 5 D atoms ([2H]ABA) in the cyclohexene fragment of the molecule was produced via isotope exchange in 100% deuterated D2O at 220°C in the presence of diisopropyl ethylamine. The yield of labeled compound was 45 – 80%. A complex of biological studies was carried out using the D-labeled preparation....

The O-antigen (O-polysaccharide) is an essential component of lipopolysaccharide on the surface of Gram-negative bacteria and plays an important role in interaction with host organisms. In this study, we investigated the chemical structure and characterized the gene cluster of Enterobacter cloacae K7 O-antigen. As judged by sugar analyses along wit...

In recent years, the incidence of Fusarium wilt in potato plants has steadily increased, in the Middle Volga Region of Russia. The current work aimed to investigate the structure of root mycobiota of the Zhukovskij rannij potato cultivar and assess the effect of growth stage on Fusarium populations in different compartments of the potato root. Usin...

Siderophores produced by microorganisms to scavenge iron from the environment have been shown to contribute to virulence and/or stress resistance of some plant pathogenic bacteria. Phytopathogenic bacteria of Pectobacterium genus possess genes for the synthesis of siderophore enterobactin, which role in plant-pathogen interactions has not been eluc...

The bacterial pathogen Salmonella enterica, which causes enteritis, has a broad host range and extensive environmental longevity. In water and soil, Salmonella interacts with protozoa and multiplies inside their phagosomes. Although this relationship resembles that between Salmonella and mammalian phagocytes, the interaction mechanisms and bacteria...

Background and Aims Plant diseases caused by Pectobacterium atrosepticum are often accompanied by extensive rot symptoms. In addition, these bacteria are able to interact with host plants without causing disease for long periods, even throughout several host plant generations. There is, to date, no information on the comparative physiology/biochemi...

Ferritins comprise a conservative family of proteins found in all species and play an essential role in resistance to redox stress, immune response, and cell differentiation. Sponges (Porifera) are the oldest Metazoa that show unique plasticity and regenerative potential. Here, we characterize the ferritins of two cold-water sponges using proteomic...

Our study is the first to consider the changes in the entire set of matrix plant cell wall (PCW) polysaccharides in the course of a plant infectious disease. We compared the molecular weight distribution, monosaccharide content, and the epitope distribution of pectic compounds and cross-linking glycans in non-infected potato plants and plants infec...

Simple Summary We found that incubation with a solution containing ~50 mM neodymium (one of the rare-earth elements, REE) induces a rapid of active metabolism in mammalian cells. We have named this state REEbernation and found that the process involves a rapid replacement of calcium with neodymium in membranes and organelles of a cell, allowing it...

We investigated the effect of the strain Bacillus subtilis GM5 on growth, feed conversion, and the composition of cecum microbiota in broiler chickens. Half of which received a control diet, while the other half was fed a diet supplemented with GM5 spores. Cecal contents on days 1, 10, and 42 were subjected to metataxonomic analysis. Principal Comp...

Lactic acid bacteria are widespread in various ecological niches and are widely used in various biotechnological processes like dairy food and silage production. While a number industrial strains of Lactobacillus are available to the date, a screening of new ones is still challenging. The Lactobacillus fermentum AG8 strain was isolated from the 4-m...

The phytohormone abscisic acid (ABA) plays an important role in plant growth and in response to abiotic stress factors. At the same time, its accumulation in soil can negatively affect seed germination, inhibit root growth and increase plant sensitivity to pathogens. ABA is an inert compound resistant to spontaneous hydrolysis and its biological tr...

Pectobacterium versatile (formerly P. carotovorum) is a recently defined species of soft rot enterobacteria capable of infecting many plant hosts and damaging different tissues. Complex transcriptional regulation of virulence properties can be expected for such a versatile pathogen. However, the relevant information is available only for related sp...

A comparative analysis of transcriptomes at the vegetative and generative stages of the development of Lentinus edodes basidiomycetes was carried out. The nature of differential gene expression was described, and the activated/repressed metabolic pathways were visualized.

We propose an algorithm for RNA-Seq data analysis useful for revealing the “master regulators” of gene expression in experimental condition, as well as of cis-elements regulating transcript level of genes from certain groups.

Using laser capture microdissection, a comparative analysis of transcriptomes of three histological zones of pea nodules was performed.

Phytopathogenic pectobacteria produce extracellular low-molecular-weight phosphonates which possibly determine the strategy for the plant-microbe interaction.

We performed a genomic analysis of the presence and organization of oxygenases involved in the hydroxylation of various substrates, including the aromatic ring, and dioxygenases catalyzing a ring-cleavage of the formed hydroxylated intermediates in A. brasilense SR80.

There are “molecular switchers” that transform peaceful coexistence of plants with phytopathogenic pectobacteria to symptomatic infection. These switchers seem to be perspective “targets” for plant protection approaches.

Snow mold is a severe plant disease caused by psychrophilic or psychrotolerant fungi, of which Microdochium species are the most harmful. A clear understanding of Microdochium biology has many gaps; the pathocomplex and its dynamic are poorly characterized, virulence factors are unknown, genome sequences are not available, and the criteria of plant...

The ability of larvae of a non-biting midge Polypedilum vanderplanki (Chironomidae) to withstand complete desiccation is a remarkable natural example of adaptation to extreme environment. In anhydrobiosis the larvae lose up to 99.2% of water and stay in a dry form until rainfall in natural environment or up to several decades in laboratory maintain...

Lactic acid bacteria are widespread in various ecological niches with the excess of nutrients and have reduced capabilities to adapt to starvation. Among more than 280 Lactobacillus species known to the date, only five, including Lactobacillus hilgardii, carry in their genome the gene encoding for PII-like protein, one of the central regulators of...

Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological e...

Here we report the whole genome sequence of Lactobacillus fermentum HFD1 strain, the producer of antibacterial peptides. The genome consists of one circular chromosome with 2101878 bp in length and GC-content of 51.8%, and includes linear DNA with 5386 bp in length with 100% identity to bacteriophage phiX174. The analysis of the genome has revealed...

RNA-Seq transcriptome data for the wild type and phoP mutant strains of Pectobacterium versatile is described. P. versatile is a recently introduced name for a species of plant pathogenic bacteria that unites a group of strains previously embedded within the Pectobacterium carotovorum clade [1,2]. Little detail is available about how this pathogen...

Here we demonstrated that pillar[5]arenes with counterions I⁻ and Cl⁻ show the ability to plasmid compactization and increasing bacterial transformation efficiently. Pillar[5]arenes have been tested for binding with palindromic decamer oligonucleotide and interacting with plasmid DNA. The complexation of pillar[5]arene with oligonucleotide has been...

Salmonella enterica is an ubiquitous pathogen throughout the world causing gastroenteritis in humans and animals. Survival of pathogenic bacteria in the external environment may be associated with the ability to overcome the stress caused by starvation. The bacterial response to starvation is well understood in laboratory cultures with a sufficient...

The oral cavity is one of the most complex microbial environments; however, the complex nature of the salivary microbiota and the level of inorganic anions in the saliva of subjects with and without gastroesophageal reflux disease (GERD) are poorly understood. The primary goals of this pilot research were to assess differences in salivary bacterial...

The PhoPQ two-component system, originally described in pectobacteria as PehRS, was previously shown to regulate a single gene, pehA. Using an insertional phoP mutant of Pectobacterium versatile, we demonstrate that PhoP controls a regulon of at least 116 genes with a large fraction of regulon members specific for pectobacteria. The functions perfo...

In enteric bacteria, DNA supercoiling is highly responsive to environmental conditions. Host specific features of environment serve as cues for the expression of genes required for colonization of host niches via changing supercoiling [1]. It has been shown that substitution at position 87 of GyrA of Salmonella enterica str. SL1344 influences globa...

The study is based on the hypothesis that high taxonomic diversity of bacteria detectable on the eye surface by molecular genetic methods is attributed to the high level of its contamination by skin microflora. Such contamination would make it problematic to identify the fractions of real ocular surface microbiome, which remains behind the one-perc...

Intestinal microbes play a key role in the energy metabolism of broiler chickens, participate in the development of the gastrointestinal tract, including the regulation of intestinal epithelial proliferation, vitamin synthesis and ion absorption, fermentation of carbohydrates and proteins, biotransformation of bile acids, protection from pathogens...

The aim of study was to determine the regenerative effect of oxytocin on the expression of PAX6, MKI67, TAB3 genes, respectively, during experimental corneal erosion. Material and methods. The study involved experimental animals divided into three groups (6 rabbits total). Groups 1 and 2 were simulated erosion of the cornea 8mm in diameter. Animals...

Oligosaccharins, which are biologically active oligosaccharide fragments of cell wall polysaccharides, may regulate the processes of growth and development as well as the response to stress factors. We characterized the effect of the oligosaccharin that stimulates rhizogenesis (OSRG) on the gene expression profile in the course of IAA-induced forma...

Plant growth-promoting rhizobacteria (PGPR) improve plant productivity and stress resistance. The mechanisms involved in plant-microbe interactions include the modulation of plant hormone status. The Novosphingobium sp. strain P6W was previously described as the bacterium capable of abscisic acid (ABA) degradation, and its inoculation decreased ABA...

The impact of neodymium chloride on cell cultures in phosphate-free conditions. Introduction Information about the effects of rare earth compounds on cells in vitro is varying. Such phenomena as stimulation of proliferation and induction of apoptosis were described at the same time. In some cases the effect is dose dependent, in others cases observ...

Root-associated fungi and bacteria play a pivotal role in the plant–soil ecosystem by influencing both plant growth and immunity. The aim of this study was to unravel the biodiversity of the bacterial and fungal rhizosphere (RS) and rhizoplane (RP) microbiota of Zhukovskij rannij potato (Solanum tuberosum L.) cultivar growing in the Alfisol of Tata...

Ciliates are the largest group of ubiquitous aquatic bacterivorous protists, and many species are easily cultivated. However, only few studies reported prokaryotic communities naturally associated with ciliate cells. Herein, we analyzed the microbiome composition of several strains of Paramecium (Ciliophora) originating from different locations and...

Mechanisms of microbial catabolism of phytohormone abscisic acid (ABA) are still unknown. Here, we report the complete genome sequence of ABA-utilizing Rhodococcus sp. strain P1Y, isolated from the rice ( Oryza sativa L.) rhizosphere. The sequence was obtained using an approach combining Oxford Nanopore Technologies MinION and Illumina MiSeq sequen...

Bacteria in natural associations with agricultural crops are promising for use in the improvement of clonal micropropagation of plants. We clarified the taxonomic position of Ochrobactrum cytisi strain IPA7.2 and investigated its tolerance for salinity, high temperature, and glyphosate pollution. We also tested the strain’s potential to promote the...

The phytohormone abscisic acid (ABA) plays multiple roles in plant survival and fitness. Significant quantities of ABA are constantly introduced into soil via root exudation, root turnover and incorporation of abscised shoot tissues. In addition, some phytopathogenic fungi synthesize ABA in the course of plant–microbe interactions. The accumulation...

Phloem fibers are important elements of plant architecture and the target product of many fiber crops. A key stage in fiber development is intrusive elongation, the mechanisms of which are largely unknown. Integrated analysis of miRNA and mRNA expression profiles in intrusivelygrowing fibers obtained by laser microdissection from flax (Linum usitat...

A procedure for tritiation of predominantly the cyclohexene moiety of abscisic acid was developed. Tritium was introduced by isotope exchange reaction with 100% tritiated water at 220°C in the presence of diisopropylethylamine. The yield of abscisic acid was 50%, and the specific activity was 30.5 Ci/mmol. The labeled product was tested. It was sho...

Aim. To indicate potentially pathogenic bacteria in plankton of the brackish rivers flowing into the Elton Lake by high-throughput sequencing of 16S ssuRNA gene. Materials and methods. The water samples from brackish rivers Lantsug and Chernavka, flowing into the Elton Lake, were taken up in a volume of 50 ml, filtered through membrane filters (por...

The microbial gut communities associated with various xylophagous beetles offer great potential for different biotechnologies and elaboration of novel pest management strategies. In this research, the intestinal bacterial and fungal communities of various cerambycid larvae, including Acmaeops septentrionis, Acanthocinus aedilis, Callidium coriaceum...

Prokaryotic diversity was studied in the planktonic communities of six Sol-Iletsk lakes (Orenburg oblast, Russia) varying in salinity level using the Illumina technology of high-throughput sequencing. The extremely halophilic archaea of the phyla Euryarchaeota and Nanohaloarchaeota, as well as the bacterial phylum Bacteroidetes predominated in the...

Modern techniques of next-generation sequencing (NGS) allow obtaining expression profile of all genes and provide an essential basis for characterizing metabolism in the organism of interest on a broad scale. An important condition for obtaining a demonstrative physiological picture using high throughput sequencing data is the availability of the g...

Modern techniques of next-generation sequencing (NGS) allow obtaining expression profile of all genes and provide an essential basis for characterizing metabolism in the organism of interest on a broad scale. An important condition for obtaining a demonstrative physiological picture using high throughput sequencing data is the availability of the g...

In the present study, we have monitored the process of systemic plant colonization by the plant pathogenic bacterium Pectobacterium atrosepticum (Pba) using RNA-Seq analysis in order to compare bacterial traits under in planta and in vitro conditions and to reveal potential players that participate in switching from stealth to brute force strategy...