Main genome characteristics of butanol-producing Clostridium sp. UCM В-7570 strain.

The rapid development of new molecular methods and approaches, sequencing technologies, has provided new insights into genetic and structural features of bacterial genomes. Information about the genetic organization of metabolic pathways and their regulatory elements has greatly contributed to the increase in the number of studies related to the construction of new bacterial strains with improved characteristics. In this study, the entire genome of the producing strain Clostridium sp. UCM В-7570 from the "Collection of producing strains of microorganisms and plant lines for food and agricultural biotechnology" of Institute of Food Biotechnology and Genomics of the National Academy of Sciences of Ukraine was sequenced and characterized. The genome was assembled into the scaffold with a total size of 4,470,321 bp and a GC content of 29.7%. The total number of genes identified was 4262, of which 4057 encoded proteins, 10 were rRNA operons, and 80 were tRNA genes. The genes of the sequenced genome encoding enzymes involved in butanol fermentation were found and analyzed. They were organized into cluster structures, and their protein sequences were found to be similar to the corresponding strains of C. acetobutylicum, C. beijerinckii, and C. pasteurianum type strains with the highest similarity to the latter. Thus, Clostridium sp. UCM В-7570 producing strain was identified as C. pasteurianum and suggested for metabolic engineering purposes.

Bacterial sulfidogenic community from the surface of technogenic materials in vitro: composition and biofilm formation.

Microbial biofilms of sulfate-reducing bacteria Desulfovibrio oryzae SRB1 and SRB2 were evaluated on polyethylene terephthalate in mono- and associative bacterial cultures. Bacillus velesensis strains C1 and C2b suppressed both the formation of biofilm and reduced the number of sulfate-reducing bacteria in the biofilm on the polyethylene terephthalate during the 50-day experiment. A decrease in the number of sulfate-reducing bacteria compared to the monoculture was also noted in association of D. oryzae SRB1 + Sat1 (bacterium-satellite of the sulfate-reducing bacteria). The strain Sat1 was identified as Anaerotignum (Clostridium) propionicum based on some microbiological, physiological and biochemical, genetic features. The importance of studying existing interactions between microorganisms in the ferrosphere and plastisphere is emphasized.

Antifungal Activity and Effect of Plant-Associated Bacteria on Phenolic Synthesis of Quercus robur L.

Europe's forests, particularly in Ukraine, are highly vulnerable to climate change. The maintenance and improvement of forest health are high-priority issues, and various stakeholders have shown an interest in understanding and utilizing ecological interactions between trees and their associated microorganisms. Endophyte microbes can influence the health of trees either by directly interacting with the damaging agents or modulating host responses to infection. In the framework of this work, ten morphotypes of endophytic bacteria from the tissues of unripe acorns of Quercus robur L. were isolated. Based on the results of the sequenced 16S rRNA genes, four species of endophytic bacteria were identified: Bacillus amyloliquefaciens, Bacillus subtilis, Delftia acidovorans, and Lelliottia amnigena. Determining the activity of pectolytic enzymes showed that the isolates B. subtilis and B. amyloliquefaciens could not cause maceration of plant tissues. Screening for these isolates revealed their fungistatic effect against phytopathogenic micromycetes, namely Fusarium tricinctum, Botrytis cinerea, and Sclerotinia sclerotiorum. Inoculation of B. subtilis, B. amyloliquefaciens, and their complex in oak leaves, in contrast to phytopathogenic bacteria, contributed to the complete restoration of the epidermis at the sites of damage. The phytopathogenic bacteria Pectobacterium and Pseudomonas caused a 2.0 and 2.2 times increase in polyphenol concentration in the plants, respectively, while the ratio of antioxidant activity to total phenolic content decreased. Inoculation of Bacillus amyloliquefaciens and Bacillus subtilis isolates into oak leaf tissue were accompanied by a decrease in the total pool of phenolic compounds. The ratio of antioxidant activity to total phenolic content increased. This indicates a qualitative improvement in the overall balance of the oak leaf antioxidant system induced by potential PGPB. Thus, endophytic bacteria of the genus Bacillus isolated from the internal tissues of unripe oak acorns have the ability of growth biocontrol and spread of phytopathogens, indicating their promise for use as biopesticides.

Inhibition of heterotrophic bacterial biofilm in the soil ferrosphere by Streptomyces spp. and Bacillus velezensis.

The soil microbiome is involved in the processes of microbial corrosion, in particular, by the formation of biofilm. It has been proposed that an environmentally friendly solution to this corrosion might be through biological control. Bacillus velezensis NUChC C2b, Streptomyces gardneri ChNPU F3 and S. canus NUChC F2 were investigated as potentially 'green' biocides to prevent attachment to glass as a model surface and the formation of heterotrophic bacterial biofilm which participates in the corrosion process. Results showed high antagonistic and antibiofilm properties of S. gardneri ChNPU F3; which may be related to the formation of secondary antimicrobial metabolites by this strain. B. velezensis NUChC C2b and S. gardneri ChNPU F3 could be incorporated into green biocides - as components of antibiofilm agents that will protect material from bacterial corrosion or as agents that will prevent historical heritage damage.

Correction to: a new Rhodococcus aetherivorans strain isolated from lubricant-contaminated soil as a prospective phenol-biodegrading agent.

The published online version contains mistake in Table 3.

A new Rhodococcus aetherivorans strain isolated from lubricant-contaminated soil as a prospective phenol-biodegrading agent.

Microbe-based decontamination of phenol-polluted environments has significant advantages over physical and chemical approaches by being relatively cheaper and ensuring complete phenol degradation. There is a need to search for commercially prospective bacterial strains that are resistant to phenol and other co-pollutants, e.g. oil hydrocarbons, in contaminated environments, and able to carry out efficient phenol biodegradation at a variable range of concentrations. This research characterizes the phenol-biodegrading ability of a new actinobacteria strain isolated from a lubricant-contaminated soil environment. Phenotypic and phylogenetic analyses showed that the novel strain UCM Ac-603 belonged to the species Rhodococcus aetherivorans, and phenol degrading ability was quantitatively characterized for the first time. R. aetherivorans UCM Ac-603 tolerated and assimilated phenol (100% of supplied concentration) and various hydrocarbons (56.2-94.4%) as sole carbon sources. Additional nutrient supplementation was not required for degradation and this organism could grow at a phenol concentration of 500 mg L-1 without inhibition. Complete phenol assimilation occurred after 4 days at an initial concentration of 1750 mg L-1 for freely-suspended cells and at 2000 mg L-1 for vermiculite-immobilized cells: 99.9% assimilation of phenol was possible from a total concentration of 3000 mg L-1 supplied at daily fractional phenol additions of 750 mg L-1 over 4 days. In terms of phenol degradation rates, R. aetherivorans UCM Ac-602 showed efficient phenol degradation over a wide range of initial concentrations with the rates (e.g. 35.7 mg L-1 h-1 at 500 mg L-1 phenol, and 18.2 mg L-1 h-1 at 1750 mg L-1 phenol) significantly exceeding (1.2-5 times) reported data for almost all other phenol-assimilating bacteria. Such efficient phenol degradation ability compared to currently known strains and other beneficial characteristics of R. aetherivorans UCM Ac-602 suggest it is a promising candidate for bioremediation of phenol-contaminated environments.

Prospects of a new antistaphylococcal drug batumin revealed by molecular docking and analysis of the complete genome sequence of the batumin-producer Pseudomonas batumici UCM B-321.

Meticillin-resistant Staphylococcus aureus (MRSA) is a serious public health threat causing outbreaks of clinical infection around the world. Mupirocin is a promising anti-MRSA drug, however mupirocin-resistant strains of S. aureus are emerging at an increasing rate. The newly discovered antibiotic batumin may contribute to anti-MRSA therapy. The objective of this work was to identify possible molecular targets for batumin as well as mechanisms of its antistaphylococcal activity using computational molecular docking and by analysing the complete genome sequence of the batumin-producer Pseudomonas batumici UCM B-321. It was found that batumin acted very similarly to mupirocin by inhibiting aminoacyl tRNA synthetases. A previous hypothesis considering the trans-enoyl-CoA reductase FabI as a prime molecular target of batumin was rejected. However, indirect inhibition of fatty acid biosynthesis in sensitive bacteria does take place as a part of stringent response repression triggered by accumulation of uncharged tRNA molecules. Paralogues of diverse leucine-tRNA synthetases in the genome of P. batumici indicated that this protein might be the prime target of batumin. A batumin biosynthesis operon comprising 28 genes was found to be acquired through horizontal gene transfer. It was hypothesised that, in contrast to mupirocin, batumin could inhibit a broader range of aminoacyl tRNA synthetases and that acquired resistance to mupirocin might not endow S. aureus strains with resistance against batumin.

Peculiarities of Alteromonas macleodii strains reflects their deep/surface habitation rather than geographical distribution.

The phenotypic, chemotaxonomic and genetic peculiarities of 5 deep strains of Alteromonas macleodii (isolated from Adriatic and Ionian Sea water from a depth of 1,000-3,500 m) and 5 strains of the same species isolated from the surface layer of Aegean, Andaman, Black Sea and Atlantic Ocean water near the British shore have been studied. Electron microscopy has shown that the deep strains' cells were, on average, two times longer (2.1±0.2×0.7±0.1 µm) than the surface strains' (1.1±0.1×0.6±0.1 µm). Using fatty acid analysis (particularly the mono-unsaturated C16:1 and C18:1 fatty acids contents) the deep and surface isolates were clearly separated into two clusters. Distinctions between them were also found in different lectin binding capacity, which is probably determined by the structure of their extracellular polysaccharide matrix. Analysis of the results of PCR with primers to repeated nucleotide sequences revealed a higher level of genetic polymorphism in surface strains in comparison with the deep isolates. This division was confirmed by the cluster analysis method though it was not as clear as in the fatty acids analysis. The described peculiarities are probably reflective of specific conditions in which A. macleodii strains live on the surface or in the depth of the world's oceans.