Structure and gene cluster of the O-polysaccharide from Pseudomonas veronii A-6-5 and its uranium bonding

Microbial and Monosaccharide Composition of Biofilms Developing on Sandy Loams from an Aquifer Contaminated with Liquid Radioactive Waste

The development of microbial biofilms increases the survival of microorganisms in the extreme conditions of ecosystems contaminated with components of liquid radioactive waste (LRW) and may contribute to the successful bioremediation of groundwater. The purpose of this work was to compare the composition of the microorganisms and the exopolysaccharide matrix of the biofilms formed on sandy loams collected at the aquifer from a clean zone and from a zone with nitrate and radionuclide contamination. The aquifer is polluted from the nearby surface repository for liquid radioactive waste (Russia). The phylogenetic diversity of prokaryotes forming biofilms on the sandy loams' surface was determined during 100 days using high-throughput sequencing of the V4 region of the 16S rRNA genes. Scanning electron microscopy was used to study the development of microbial biofilms on the sandy loams. The ratio of proteins and carbohydrates in the biofilms changed in the course of their development, and the diversity of monosaccharides decreased, depending on the contamination of the sites from which the rocks were selected. The presence of pollution affects biofilm formation and EPS composition along with the dominant taxa of microorganisms and their activity. Biofilms establish a concentration gradient of the pollutant and allow the microorganisms involved to effectively participate in the reduction of nitrate and sulfate; they decrease the risk of nitrite accumulation during denitrification and suppress the migration of radionuclides. These biofilms can serve as an important barrier in underground water sources, preventing the spread of pollution. Pure cultures of microorganisms capable of forming a polysaccharide matrix and reducing nitrate, chromate, uranyl, and pertechnetate ions were isolated from the biofilms, which confirmed the possibility of their participation in the bioremediation of the aquifer from nonradioactive waste components and the decrease in the radionuclides' migration.

Structure elucidation and gene cluster of the O-antigen of Shewanella xiamenensis strain DCB-2-1 containing an amide of d-glucuronic acid with d-alanine and its bonding with U, Cr and V

The aim of this work was to examine the structure and gene cluster of O-OPS of S. xiamenensis strain DCB-2-1 and survey its conceivability for chelating uranyl, chromate and vanadate ions from solution. O-polysaccharide (OPS, O-antigen) was isolated from the lipopolysaccharide of Shewanella xiamenensis DCB-2-1 and studied by 1D and 2D nuclear magnetic resonance (NMR) spectroscopy and sugar analysis. The following structure of the brunched pentasaccharide was established: where d-β-GlcpA(d-Ala) is d-glucuronic acid acylated with NH group of d-Ala. The OPS structure established is unique among known bacterial polysaccharide structures. Interestingly, that dN-(d-glucuronoyl)-d-alanine derivative is not found in bacterial polysaccharides early. The O-antigen gene cluster of Shewanella xiamenensis strain DCB-2-1 has been sequenced. The gene functions were tentatively assigned by comparison with sequences in the available databases and found to be in agreement with the OPS structure. Based on the analysis of the IR spectra of the isolated polysaccharide DCB-2-1 and the products of its interaction with UO2(NO3)2 ∗ 6H2O, NH4VO3 and K2Cr2O7, a method of binding them can be proposed. Laboratory experiments show that the use of polysaccharide can be effective in removing uranyl, chromate and vanadate from solution.

Genome analysis of Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., isolated from nitrate- and radionuclide-contaminated groundwater, and transfer of several Pusillimonas species into three new genera Allopusillimonas, Neopusillimonas, and Mesopusillimonas

Two facultatively anaerobic, chemoorganoheterotrophic bacterial strains, designated JR1/69-2-13^T and JR1/69-3-13^T, were isolated from nitrate- and radionuclide-contaminated groundwater (Ozyorsk town, South Urals, Russia). Both strains were found to be motile, Gram-stain negative rod-shaped neutrophilic, psychrotolerant bacteria that grow within the temperature range from 5-10 to 33 °C at 0-3 (0-5)% NaCl (w/v). The major cellular fatty acids were identified as C_16:0, C_16:1 ω7c, C_18:1 ω7c and C_17:0 cyclo. The major polar lipids were found to consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol and unidentified aminophospholipids. The genomic G + C content of strains JR1/69-2-13^T and JR1/69-3-13^T was determined to be 57.2 and 57.9%, respectively. The 16S rRNA gene sequences of the strains showed high similarity between each other (98.6%) and to members of the genera Pusillimonas (96.8-98.4%) and Candidimonas (97.1-98.0%). The average nucleotide identity and digital DNA-DNA hybridization (dDDH) values among genomes of the new isolates and Pusillimonas and Candidimonas genomes were below 84.5 and 28.8%, respectively, i.e., below the thresholds for species delineation. Based on the phylogenomic, phenotypic and chemotaxonomic characterisation, we propose assignment of strains JR1/69-3-13^T (= VKM B-3223^T = KCTC 62615^T) and JR1/69-2-13^T (= VKM B-3222^T = KCTC 62614^T) to a new genus Pollutimonas as the type strains of two new species, Pollutimonas subterranea gen. nov., sp. nov. and Pollutimonas nitritireducens sp. nov., respectively. As a result of the taxonomic revision of the genus Pusillimonas, three novel genera, Allopusillimonas, Neopusillimonas, and Mesopusillimonas are also proposed; and Candidimonas bauzanensis is reclassified as Pollutimonas bauzanensis comb. nov. Genome analysis of the new isolates suggested molecular mechanisms of their adaptation to an environment highly polluted with nitrate and radionuclides.

Risk of colloidal and pseudo-colloidal transport of actinides in nitrate contaminated groundwater near a radioactive waste repository after bioremediation

The possible role of biogeochemical processes in the transport of colloidal and pseudo-colloidal U, Np, and Pu during bioremediation of radionuclide- and nitrate-contaminated groundwater was investigated. In two laboratory experiments with water samples taken from contaminated aquifers before and post bioremediation, we found that microbial processes could cause clayed, ferruginous, and actinide colloids to coagulate. The main mechanisms are biogenic insoluble ferrous iron species formations (goethite, pyrrhotite, siderite, troilite, and ferrihydrite), the aggregation of clay particles by microbial metabolites, and the immobilization of actinides in the bacterial cells, large polymers, and iron and clayed sediments. This process decreases the risk of colloidal and pseudo-colloidal transport of actinides.

Synthesis, Crystal Structure, and Hirshfeld Surface Analysis of Hexachloroplatinate and Tetraclorouranylate of 3-Carboxypyridinium—Halogen Bonds and π-Interactions vs. Hydrogen Bonds

This work aimed to synthesize new platinum and uranium compounds with nicotinic acid. In this article we describe the synthesis of two new anionic complexes (HNic)2[PtCl6] and (HNic)2[UO2Cl4] using wet chemistry methods. The structure of the obtained single crystals was established by single-crystal X-ray diffraction. The Hirshfeld surface analysis of the obtained complexes and their analogue (HNic)2[SiF6] was carried out for the analysis of intermolecular interactions. Hydrogen bonds (H···Hal/Hal···H and O···H/H···O) make the main contribution to intermolecular interactions in all compounds. Other important contacts in cations in all compounds are H···H, C···H/H···C and C···Hal/Hal···C; in anions H···Hal/Hal···H. The Pt-containing complex has a halogen-π interaction and halogen bonds, but Si-containing complex has a π–π staking interaction; these types of interactions are not observed in the U-containing compound.

Structure elucidation and gene cluster annotation of the O-antigen of Pseudomonas veronii SHC-8-1 containing 2-acetamido-2,4,6-trideoxy-4-(3,5-dihydroxyhexanoylamino)-d-glucose

O-polysaccharide (O-antigen, OPS) was isolated from the lipopolysaccharide of Pseudomonas veronii SHC-8-1 and studied by component analyses and 1D and 2D NMR spectroscopy. The following structure of the O-polysaccharide was established: where QuipNAc4N(dHh) is 2,4-diamino-2,4,6-trideoxy-dglucose (Bacillosamine) in which N-2 is acetylated and N-4 is acylated with 3,5-dihydroxyhexanoic acid (dHh). The O-antigen gene cluster of Pseudomonas veronii SHC-8-1 has been sequenced. The gene functions were tentatively assigned by comparison with sequences in the available databases and found to be in agreement with the OPS structure.

Biogeochemical Modelling of Uranium Immobilization and Aquifer Remediation Strategies Near NCCP Sludge Storage Facilities

Nitrate is a substance which influences the prevailing redox conditions in groundwater, and in turn the behaviour of U. The study of groundwater in an area with low-level radioactive sludge storage facilities has shown their contamination with sulphate and nitrate anions, uranium, and some associated metals. The uranyl ion content in the most contaminated NO3–Cl–SO4–Na borehole is 2000 times higher (1.58 mg/L) than that in the background water. At the same time, assessment of the main physiological groups of microorganisms showed a maximum number of denitrifying and sulphate-reducing bacteria (e.g., Sulfurimonas) in the water from the same borehole. Biogenic factors of radionuclide immobilization on sandy rocks of upper aquifers have been experimentally investigated. Different reduction rates of NO3−, SO42−, Fe(III) and U(VI) with stimulated microbial activity were dependent on the pollution degree. Moreover, 16S rRNA gene analysis of the microbial community after whey addition revealed a significant decrease in microbial diversity and the activation of nonspecific nitrate-reducing bacteria (genera Rhodococcus and Rhodobacter). The second influential factor can be identified as the formation of microbial biofilms on the sandy loam samples, which has a positive effect on U sorption (an increase in Kd value is up to 35%). As PHREEQC physicochemical modelling numerically confirmed, the third most influential factor that drives U mobility is the biogenic-mediated formation of a sulphide redox buffer. This study brings important information, which helps to assess the long-term stability of U in the environment of radioactive sludge storage facilities.