Comparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution

Aeromonas salmonicida is a global distributed Gram-negative teleost pathogen, affecting mainly salmonids in fresh and marine environments. A. salmonicida strains are classified as typical or atypical depending on their origin of isolation and phenotype. Five subspecies have been described, where A. salmonicida subsp. salmonicida is the only typical subspecies, and the subsp. achromogenes, masoucida, smithia, and pectinolytica are considered atypical. Genomic differences between A. salmonicida subsp. salmonicida isolates and their relationship with the current classification have not been explored. Here, we sequenced and compared the complete closed genomes of four virulent strains to elucidate their molecular diversity and pathogenic evolution using the more accurate genomic information so far. Phenotypes, biochemical, and enzymatic profiles were determined. PacBio and MiSeq sequencing platforms were utilized for genome sequencing. Comparative genomics showed that atypical strains belong to the subsp. salmonicida, with 99.55 ± 0.25% identity with each other, and are closely related to typical strains. The typical strain A. salmonicida J223 is closely related to typical strains, with 99.17% identity with the A. salmonicida A449. Genomic differences between atypical and typical strains are strictly related to insertion sequences (ISs) activity. The absence and presence of genes encoding for virulence factors, transcriptional regulators, and non-coding RNAs are the most significant differences between typical and atypical strains that affect their phenotypes. Plasmidome plays an important role in A. salmonicida virulence and genome plasticity. Here, we determined that typical strains harbor a larger number of plasmids and virulence-related genes that contribute to its acute virulence. In contrast, atypical strains harbor a single, large plasmid and a smaller number of virulence genes, reflected by their less acute virulence and chronic infection. The relationship between phenotype and A. salmonicida subspecies’ taxonomy is not evident. Comparative genomic analysis based on completed genomes revealed that the subspecies classification is more of a reflection of the ecological niche occupied by bacteria than their divergences at the genomic level except for their accessory genome.

Nitrogen Metabolism of an Anoxygenic Filamentous Phototrophic Bacterium Oscillocholris trichoides Strain DG-6

Abstract— The possible nitrogen sources for Osc. trichoides DG6, a typical strain of the Oscillochloridaceae family, are ammonium, N2, glutamate, asparagine, glycine, and glutamine. The assimilation of molecular nitrogen occurs with the participation of nitrogenase, the structural gene of which, nifH, is located in the gene cluster which also includes the genes of the nifD and nifK nitrogenase subunits and the auxiliary nifB gene. Considering that nifHBDK clusters have been also annotated in the genomes of other members of the Oscillochloridaceae family, including uncultured and candidate taxa, it can be assumed that the ability to fix nitrogen is a property immanent for this entire family. The pathways for assimilating ammonium in the cells grown using different nitrogen sources may differ. Osc. trichoides DG6 growing in a medium containing ammonium assimilated it with the participation of glutamate dehydrogenase, which is determined by a single gene. The expression product of this gene has dual functionality and can be used to implement the reaction with both NAD and NADP. With the growth of Osc. trichoides DG6 on a medium with glutamate as the only nitrogen source all the enzymes necessary for the implementation of the GS‑GOGAT pathway were found in the cells. However, for the glutamine synthetase reaction, ammonium, which was absent in the growth medium, was required. The source of ammonium may be glutamate metabolized through glutamate dehydrogenase.

Detection of phytopathogenic bacteria damaging weeping birch (Betula Pendula) by molecular identification method and сreation of phylogenetic genealogy

The article discusses the morphological changes of birch trees (Betula pendula Roth.) due to bacterial cancer that grow in the artificial forest «Green Belt» surrounding the city of Nur — Sultan. Kernel samples were taken from diseased tree trunks, isolated bacterial cultures were grown in nutrient medium and given cultural and morphological characteristics. Extraction of cores from diseased birch trunks, isolation of pure strains of the pathogen, molecular identification of ribosomal RNA 16S nucleotide chains and comparison of these results with relevant data from the international database Gene Bank are carried out using modern methods in the field of bacteriology and botany. The molecular characteristics of the isolated bacterial strains corresponded to 96.72 % of the typical strain Dickeya dadantii based on the international Gene Bank.

Comparative Proteomic Profiles of Typical Strain and Genetically Altered Variant of Vibrio cholerae O1, Biovar El Tor

Objective of the study was to identify the differences in the production of proteins in typical strain and genetically altered variant of V. cholerae O1, biovar El Tor.Materials and methods. Natural strains M1062 (Astrakhan, 1970) and M1509 (Moscow, 2010) were used as model strains in this work. Strains were cultivated on Luria Bertani agar at 37 °C. Electrophoresis was performed in accordance with W.K. Laemmli technique (1970), mass-spectrometric profiling – the method described by A. Shevchenko et al.Results and discussion. Mass-spectrometric scanning of cell lysates of the examined strains showed significant similarity of their proteomes (615 common proteins). The identified differences pertained to high expression of proteins in the strain M1062, participating in biosynthesis of DNA/RNA, included into “purines, pyrimidines, nucleosides” group, as well as regulatory proteins. In M1509 strain, biosynthesis of the proteins responsible for pathogenesis, adaptation under the influence of unfavorable environmental factors, included into “co-factors, vitamins, pigments” group, involved in lipid, carbohydrate, and protein metabolism, cellular processes, as well as proteins-transporters was increased. It has been suggested that the wide dissemination of El Tor genovariants is probably due to enhanced pathogenic and adaptive properties and also to the considerable transformation of cell metabolism.

Evolution of ST-4821 clonal complex hyperinvasive and quinolone-resistant meningococci: the next meningococcal pandemic?

The expansion of quinolone-resistant Neisseria meningitidis clone ChinaCC4821-R1-C/B from ST-4821 clonal complex (cc4821) caused a serogroup shift from serogroup A to C in invasive meningococcal disease (IMD) in China. To establish the relationship among globally distributed cc4821 meningococci, we analysed whole genome sequence data from 173 cc4821 meningococci isolated in four continents from 1972-2019. These meningococci clustered into four sub-lineages (1-4), with sub-lineage 1 primarily comprising serogroup C IMD isolates (82%, 41/50). Most isolates from outside China formed a distinct sub-lineage (81.6%, 40/49, the Europe-USA cluster), with the typical strain designation B:P1.17-6,23:F3-36:ST-3200(cc4821) and harbouring mutations in penicillin-binding protein 2. These data show that the quinolone-resistant clone ChinaCC4821-R1-C/B has expanded to other countries. The increasing global distribution of B:cc4821 meningococci raises concern that cc4821 has the potential to cause a global pandemic and, this would be challenging to control though there is indirect evidence that Trumenba® vaccine might afford some protection.

Identification of agent of leaf spot desease of lupine based on the the syringomicin gene (syrD)

Aim. The detection of the phytotoxin syringomycin's secretion genes of (syrD) has been performed for the purpose of correct species and pathovar identification of isolated and collection strains of the agent of lupine's brown spottiness. Methods. It has been used microbiological and molecular genetic (PCR) methods. Results. The presence of phytotoxin syringomycin's secretion (syrD) genes in collection and isolated strains of the agent of lupine's brown spottiness and the typical strain Pseudomonas syringae pv. syringae UCM B-1027Т has been established. It has been shown that the amount of PCR product produced by collection strains "Pseudomonas lupini" varies and correlates with their pathogenic properties. Conclusions. Based on the results of the previous investigation and presented in this paper, the reclassification of the species "Pseudomonas lupini" finished and the strains previously belonging to this species were attributed to Pseudomonas syringae pv. syringae. Keywords: identification, syringomycin's secretion genes (syrD), agent of lupine's brown spottiness.

Single-Crystalline Si1−xGex (x = 0.5~1) Thin Films on Si (001) with Low Threading Dislocation Density Prepared by Low Temperature Molecular Beam Epitaxy

Single-crystalline Si1−xGex thin films on Si (100) with low threading dislocation density (TDD) are highly desired for semiconductor industrials. It is challenging to suppress the TDD since there is a large mismatch (4.2%) between Ge and Si—it typically needs 106–107/cm2 TDD for strain relaxation, which could, however, cause device leakage under high voltage. Here, we grew Si1−xGex (x = 0.5–1) films on Si (001) by low temperature molecular beam epitaxy (LT-MBE) at 200 °C, which is much lower than the typical temperature of 450–600 °C. Encouragingly, the Si1−xGex thin films grown by LT-MBE have shown a dramatically reduced TDD down to the 103–104/cm2 level. Using transmission electron microscopy (TEM) with atomic resolution, we discovered a non-typical strain relaxation mechanism for epitaxial films grown by LT-MBE. There are multiple-layered structures being introduced along out-of-plane-direction during film growth, effectively relaxing the large strain through local shearing and subsequently leading to an order of magnitude lower TDD. We presented a model for the non-typical strain relaxation mechanism for Si1−xGex films grown on Si (001) by LT-MBE.

REP-PCR analisis of single agent of cucumber bacterial diseases

Aim. For the purpose of correct species identification and estimation of population’s heterogeneity, the fingerprinting of the genome of isolated by us Pectobacterium sp., collection «Erwinia toxica» strains and typical representatives of certain species of Pectobacterium and Diskeya genera has been carried out. Methods. In the course of research, microbiological, molecular genetic (REP-PCR), mathematical-statistical methods of research were used. Results. On the basic of BOX, REP and ERIC profiles the significant affinity between isolated Pectobacterium sp. and collections «Erwinia toxica» strains with the typical P. carotovorum susp. carotovorum UCM B1075T has been established. Genetic heterogeneity of isolated Pectobacterium sp. and collections «Erwinia toxica» strains has been estimated. Conclusions. It has been found the significant relationship between isolates Pectobacterium sp. and the collection «Erwinia toxica» strains with the typical strain P. carotovorum susp carotovorum UCM B1075T on the basic of their BOX, REP and ERIC profiles. Most likely, this indicates that they belong to this species. The genetic homogeneity of isolated Pectobacterium sp. strains of and the genetic heterogeneity of the collection «Erwinia toxica» strains is probably due to the plant’s selection from similar or different region.Keywords: identification, genetic heterogeneity, REPPCR, «Erwinia toxica», Pectobacterium sp.

Hot Deformation and Dynamic Recrystallization Behavior of Fe-8Mn-6Al-0.2C Steel

Hot deformation and dynamic recrystallization (DRX) behaviors of Fe-8Mn-6Al-0.2C steel were investigated by means of single-pass compression experiments at temperature ranging from 850 °C to 1150 °C and different strain rate of 0.01~10 s-1. The flow strain curves were analysed and showed that the higher temperature and lower strain rate led to the smaller critical stress, which meant softening mechanism was easier to occur; The constitutive equation of experimental steel was established and the relationship between peak strain and Z parameter was figured out; A hot processing map of experimental steel was developed over a power dissipation map for the typical strain of 0.9, indicating the best region of high workability in the study conditions. DRX was promoted with increase of deformation temperature and decrease of strain rate, and the banded grains had been broken and grew up obviously.