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-ß-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.

Correction: Krivonogov et al. Microbial Diversity and Authigenic Mineral Formation of Modern Bottom Sediments in the Littoral Zone of Lake Issyk-Kul, Kyrgyz Republic (Central Asia). Biology 2023, 12, 642.

Sergei Krivonogov was not included as an author in the original publication [...].

Silver Vapor Supersonic Jets: Expansion Dynamics, Cluster Formation, and Film Deposition.

Supersonic jets of metal vapors with carrier gas are promising for producing nanostructured metal films at relatively low source temperatures and high deposition rates. However, the effects of the carrier gas on the jet composition and expansion dynamics, as well as on film properties, remain virtually unexplored. In this work, the free-jet expansion of a mixture of silver vapor with helium in a rarefied regime at an initial temperature of 1373 K is investigated through mass spectrometry and direct-simulation Monte Carlo methods. Introducing the carrier gas into the source is found to result in a transition from a collisionless to a collision-dominated expansion regime and dramatic changes in the Ag jet, which becomes denser, faster, and more forward-directed. The changes are shown to be favorable for the formation of small Ag clusters and film deposition. At a fairly high helium flow, silver Ag2 dimers are observed in the jet, both in the experiment and the simulations, with a mole fraction reaching 0.1%. The terminal velocities of silver atoms and dimers are nearly identical, indicating that the clusters are likely formed due to the condensation of silver vapor in the expanding jet. A high potential of supersonic Ag-He jets for the deposition of nanostructured silver films is demonstrated. The deposited jet Ag2 dimers appear to serve as nucleation centers and, thus, allow for controlling the size of the produced surface nanostructures.

Microbial Diversity and Authigenic Mineral Formation of Modern Bottom Sediments in the Littoral Zone of Lake Issyk-Kul, Kyrgyz Republic (Central Asia).

This article presents geochemical, mineralogical and microbiological characteristics of five samples of modern bottom sediments in the littoral zone of the high-mountain salty lake Issyk-Kul. The 16S rRNA gene sequencing method shows that the microbial community consists of organic carbon degraders (representatives of phyla: Proteobacteria, Chloroflexi, Bacteroidota and Verrucomicrobiota and families Anaerolineaceae and Hungateiclostridiaceae), photosynthetic microorganisms (representatives of Chloroflexi, phototrophic Acidobacteria, purple sulphur bacteria Chromatiaceae and cyanobacteria) and bacteria of the reducing branches of the sulphur biogeochemical cycle (representatives of Desulfobacterota, Desulfosarcinaceae and Desulfocapsaceae). The participation of microorganisms in processes in the formation of a number of authigenic minerals (calcite, framboidal pyrite, barite and amorphous Si) is established. The high diversity of microbial communities indicates the presence of labile organic components involved in modern biogeochemical processes in sediments. The active destruction of organic matter begins at the water-sediment interface.

Adaptive Mechanisms of Shewanella xiamenensis DCB 2-1 Metallophilicity.

The dose-dependent effects of single metals (Zn, Ni, and Cu) and their combinations at steady time-actions on the cell viability of the bacteria Shewanella xiamenensis DCB 2-1, isolated from a radionuclide-contaminated area, have been estimated. The accumulation of metals by Shewanella xiamenensis DCB 2-1 in single and multi-metal systems was assessed using the inductively coupled plasma atomic emission spectroscopy. To estimate the response of the bacteria's antioxidant defense system, doses of 20 and 50 mg/L of single studied metals and 20 mg/L of each metal in their combinations (non-toxic doses, determined by the colony-forming viability assay) were used. Emphasis was given to catalase and superoxide dismutase since they form the primary line of defense against heavy metal action and their regulatory circuit of activity is crucial. The effect of metal ions on total thiol content, an indicator of cellular redox homeostasis, in bacterial cells was evaluated. Genome sequencing of Shewanella xiamenensis DCB 2-1 reveals genes responsible for heavy metal tolerance and detoxification, thereby improving understanding of the potential of the bacterial strain for bioremediation.

Characterization of Enrichment Cultures of Anammox, Nitrifying and Denitrifying Bacteria Obtained from a Cold, Heavily Nitrogen-Polluted Aquifer.

Anammox bacteria related to Candidatus Scalindua were recently discovered in a cold (7.5 °C) aquifer near sludge repositories containing solid wastes of uranium and processed polymetallic concentrate. Groundwater has a very high level of nitrate and ammonia pollution (up to 10 and 0.5 g/L, respectively) and a very low content of organic carbon (2.5 mg/L). To assess the potential for bioremediation of polluted groundwater in situ, enrichment cultures of anammox, nitrifying, and denitrifying bacteria were obtained and analyzed. Fed-batch enrichment of anammox bacteria was not successful. Stable removal of ammonium and nitrite (up to 100%) was achieved in a continuous-flow reactor packed with a nonwoven fabric at 15 °C, and enrichment in anammox bacteria was confirmed by FISH and qPCR assays. The relatively low total N removal efficiency (up to 55%) was due to nonstoichiometric nitrate buildup. This phenomenon can be explained by a shift in the metabolism of anammox bacteria towards the production of more nitrates and less N2 at low temperatures compared to the canonical stoichiometry. In addition, the too high an estimate of specific anammox activity suggests that N cycle microbial groups other than anammox bacteria may have contributed significantly to N removal. Stable nitrite production was observed in the denitrifying enrichment culture, while no "conventional" nitrifiers were found in the corresponding enrichment cultures. Xanthomonadaceae was a common taxon for all microbial communities, indicating its exclusive role in this ecosystem. This study opens up new knowledge about the metabolic capabilities of N cycle bacteria and potential approaches for sustainable bioremediation of heavily N-polluted cold ecosystems.

Effect of Mineral Carriers on Biofilm Formation and Nitrogen Removal Activity by an Indigenous Anammox Community from Cold Groundwater Ecosystem Alone and Bioaugmented with Biomass from a "Warm" Anammox Reactor.

The complex pollution of aquifers by reduced and oxidized nitrogen compounds is currently considered one of the urgent environmental problems that require non-standard solutions. This work was a laboratory-scale trial to show the feasibility of using various mineral carriers to create a permeable in situ barrier in cold (10 °C) aquifers with extremely high nitrogen pollution and inhabited by the Candidatus Scalindua-dominated indigenous anammox community. It has been established that for the removal of ammonium and nitrite in situ due to the predominant contribution of the anammox process, quartz, kaolin clays of the Kantatsky and Kamalinsky deposits, bentonite clay of the Berezovsky deposit, and zeolite of the Kholinsky deposit can be used as components of the permeable barrier. Biofouling of natural loams from a contaminated aquifer can also occur under favorable conditions. It has been suggested that the anammox activity is determined by a number of factors, including the presence of the essential trace elements in the carrier and the surface morphology. However, one of the most important factors is competition with other microbial groups that can develop on the surface of the carrier at a faster rate. For this reason, carriers with a high specific surface area and containing the necessary microelements were overgrown with the most rapidly growing microorganisms. Bioaugmentation with a "warm" anammox community from a laboratory reactor dominated by Ca. Kuenenia improved nitrogen removal rates and biofilm formation on most of the mineral carriers, including bentonite clay of the Dinozavrovoye deposit, as well as loamy rock and zeolite-containing tripoli, in addition to carriers that perform best with the indigenous anammox community. The feasibility of coupled partial denitrification-anammox and the adaptation of a "warm" anammox community to low temperatures and hazardous components contained in polluted groundwater prior to bioaugmentation should be the scope of future research to enhance the anammox process in cold, nitrate-rich aquifers.

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.

Photochemical Synthesis of Silver Hydrosol Stabilized by Carbonate Ions and Study of Its Bactericidal Impact on Escherichia coli: Direct and Indirect Effects.

The great attention paid to silver nanoparticles is largely related to their antibacterial and antiviral effects and their possible use as efficient biocidal agents. Silver nanoparticles are being widely introduced into various areas of life, including industry, medicine, and agriculture. This leads to their spreading and entering the environment, which generates the potential risk of toxic effect on humans and other biological organisms. Proposed paper describes the preparation of silver hydrosols containing spherical metal nanoparticles by photochemical reduction of Ag+ ions with oxalate ions. In deaerated solutions, this gives ~10 nm particles, while in aerated solutions, ~20 nm particles with inclusion of the oxide Ag2O are obtained. Nanoparticles inhibit the bacterium Escherichia coli and suppress the cell growth at concentrations of ~1 × 10-6-1 × 10-4 mol L-1. Silver particles cause the loss of pili and deformation and destruction of cell membranes. A mechanism of antibacterial action was proposed, taking into account indirect suppressing action of Ag+ ions released upon the oxidative metal dissolution and direct (contact) action of nanoparticles on bacterial cells, resulting in a change in the shape and destruction of the bacteria.

Biogeochemical Factors of Cs, Sr, U, Pu Immobilization in Bottom Sediments of the Upa River, Located in the Zone of Chernobyl Accident.

Laboratory modeling of Cs, Sr, U, Pu immobilization by phytoplankton of the river Upa, affected after the Chernobyl accident, has been carried out. Certain conditions are selected for strong fixation of radionuclides in bottom sediments due to biogeochemical processes. The process of radionuclide removal from the water phase via precipitation was based on their accumulation by phytoplankton, stimulated by nitrogen and phosphorus sources. After eight days of stimulation, planktonic phototrophic biomass, dominated by cyanobacteria of the genus Planktothrix, appears in the water sample. The effectiveness of U, Pu and Sr purification via their transfer to bottom sediment was observed within one month. The addition of ammonium sulfate and phosphate (Ammophos) led to the activation of sulfate- and iron-reducing bacteria of the genera Desulfobacterota, Desulfotomaculum, Desulfosporomusa, Desulfosporosinus, Thermodesulfobium, Thiomonas, Thiobacillus, Sulfuritallea, Pseudomonas, which form sulphide ferrous precipitates such as pyrite, wurtzite, hydrotroillite, etc., in anaerobic bottom sediments. The biogenic mineral composition of the sediments obtained under laboratory conditions was verified via thermodynamic modeling.

Bio-zeolite use for metal removal from copper-containing synthetic effluents.

The adsorption capacity of biologically modified zeolite with respect to copper-containing effluents (Cu(II)-Fe(III), Cu(II)-Fe(III)-Ni(II), Cu(II)-Fe(II)-Zn(II), and Cu(II)-Fe(II)-Ni(II)-Zn(II)) has been investigated in order to apply it for industrial effluents treatment. Obtained bio-zeolite was characterized using neutron activation analysis, confocal laser scanning microscopy, and scanning electron microscopy. The efficiency of metal ions removal was determined as a function of pH, copper concentration, time, and temperature. The metal sorption in analyzed systems showed to be pH-dependent. The equilibrium adsorption data were interpreted using Freundlich and Langmuir isotherms and the adsorption mechanism was investigated by kinetic studies. The sorption of Cu(II) and Zn(II) fitted well pseudo-first and pseudo-second-order models, while Ni(II) sorption was better described by the Elovich model. The thermodynamic parameters, ∆G°, ∆H°, and ∆S were evaluated to understand the nature of the sorption process. Obtained results show that bio-zeolite is of interest for heavy metal ions removal from industrial effluents. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40201-021-00694-x.

Zinc-Containing Effluent Treatment Using Shewanella xiamenensis Biofilm Formed on Zeolite.

The sorption properties of Shewanella xiamenensis biofilm formed on zeolite (mineral-organic sorbent) as a sorbent have been investigated aiming to determine its suitability for complex zinc-containing effluent treatment. The optimum conditions for metal sorption from synthetic solutions were evaluated by changing the pH, zinc concentration, temperature, and time of sorption. The highest removal of metal ions was attained at pH range 3.0-6.0 within 60-150 min of sorbent-sorbate contact. The results obtained from the equilibrium studies were described using the Langmuir, Freundlich, and Temkin models. Maximum sorption capacity of the sorbent calculated from the Langmuir model changed from 3.4 to 6.5 mg/g. High coefficient of determination values calculated for pseudo-second-order and Elovich models indicate the predominant role of chemisorption in metal removal. Gibbs energy and ∆H° values point at the spontaneous and endothermic character of the sorption. The effect of pH and biosorbent mass on Zn(II) sorption from industrial effluent with an initial Zn(II) concentration of 52.8 mg/L was tested. Maximum removal of zinc ions (85%) was achieved at pH 6.0 by applying a two-step treatment system.

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.

Investigation of materials for reactive permeable barrier in removing cadmium and chromium(VI) from aquifer near a solid domestic waste landfill.

The sorption characteristics of raw and biofilm-coated materials: vermiculite, lightweight expanded clay aggregate (LECA), perlite, zeolite, and shungite toward Cd and Cr(VI) ions were investigated to evaluate the possibility of their use as filtration barrier in the aquifer near a solid domestic waste landfill. The effectiveness of Cr(VI) removal by the raw materials changed in the following order: shungite > zeolite > perlite > vermiculite > LECA and for Cd: zeolite > shungite > vermiculite > perlite > LECA. After biofilm formation on the surface of the materials, the sorption capacity increased in some (perlite, LECA), while in others (zeolite) it was reduced. Four kinetic models were used to describe the experimental data. Mechanisms of metal removal were proposed: for Cr(VI), a characteristic combination of sorption processes was suggested, while the removal of Cd ions could occur by ion exchange and by complexation on the surface of the sorbent. Cr(VI) reduction by living bacterial cells forming a biofilm on the sorbent surface was assessed.

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

A denitrifying bacterium Pseudomonas veronii A-6-5 was isolated from a deep aquifer contaminated with nitrates and uranium. The O-polysaccharide (OPS) was isolated by mild acid degradation of the lipopolysaccharide of P. veronii A-6-5 and studied using sugar analysis and 1D and 2D 1H and 13C NMR spectroscopy. The trisaccharide O-repeating unit was found to have the following structure: [Formula: see text] [Formula: see text] where Hb is 3-hydroxybutanoyl. The genome of P. veronii A-6-5 was sequenced and a respective OPS gene cluster was identified. Functions of the proteins encoded in the gene cluster, including the enzymes involved in the O-polysaccharide biosynthesis and glycosyl transferases, were putatively assigned by comparison with available database sequences. Formation of a new coordination bond between uranyl and the O-polysaccharide from P. veronii A-6-5 was demonstrated using FTIR spectroscopy; it may affect uranyl migration in the groundwaters due to its immobilization on microbial biofilms. Applied importance of this work is that the structure of the O-polysaccharide of a strain isolated from uranium-contaminated groundwater was determined and the character of interaction between the polysaccharide and the uranyl ion was established. The data obtained are of importance for development of the biotechnologies for treatment of uranium-contaminated groundwater and activated sludge.

5,5-Di-chloro-6-hy-droxy-dihydro-pyrimidine-2,4(1H,3H)-dione: mol-ecular and crystal structure, Hirshfeld surface analysis and the new route for synthesis with Mg(ReO4)2 as a new catalyst.

The mol-ecular and crystal structures of the title compound, C4H4Cl2N2O3, were investigated by single-crystal X-ray diffraction and a Hirshfeld surface analysis. The title compound was synthesized by a new type of reaction using Mg(ReO4)2 as a new catalyst and a possible mechanism for this reaction is proposed. The six-membered ring adopts a half-chair conformation. In the crystal, hydrogen bonds connect the mol-ecules into double layers, which are connected to each other by halogen bonds. The Hirshfeld surface analysis revealed that the most important contributions for the crystal packing are from O⋯H/H⋯O (35.8%), Cl⋯Cl (19.6%), Cl⋯H/H⋯Cl (17.0%), H⋯H (8.3%), C⋯O/O⋯C (4.3%), Cl⋯O/O⋯Cl (4.2%) and O⋯O (4.1%) contacts.

Metal Removal from Nickel-Containing Effluents Using Mineral-Organic Hybrid Adsorbent.

Nickel is one of the most dangerous environmental pollutants and its removal from wastewater is an important task. The capacity of a mineral-organic hybrid adsorbent, consisting of Shewanella xiamenensis biofilm and zeolite (clinoptilolite of the Chola deposit), to remove metal ions from nickel-containing batch systems under different experimental conditions was tested. The obtained biosorbent was characterized using neutron activation, SEM, and FTIR techniques. It was established that maximum removal of cations, up to 100%, was achieved at pH 6.0. Several mathematical models were applied to describe the equilibrium and kinetics data. The maximum adsorption capacity of the hybrid biosorbent, calculated using the Langmuir model, varied from 3.6 to 3.9 mg/g. Negative Gibbs energy values and positive ∆H° values indicate the spontaneous and endothermic character of the biosorption process. The effects of several parameters (pH and biosorbent dosage) on Ni(II) removal from real effluent, containing nickel with a concentration of 125 mg/L, were investigated. The optimal pH for Ni(II) removal was 5.0-6.0 and an increase of sorbent dosage from 0.5 to 2.0 led to an increase in Ni(II) removal from 17% to 27%. At two times effluent dilution, maximum Ni(II) removal of 26% was attained at pH 6.0 and sorbent dosage of 1.0 g. A 12-fold effluent dilution resulted in the removal of 72% of Ni(II) at the same pH and sorbent dosage values. The obtained hybrid biosorbent can be used for Ni(II) removal from industrial effluents with low Ni(II) concentrations.

Syntheses and crystal structures of new aurate salts of adenine or guanine nucleobases.

Two new gold(III) complexes with adenine or guanine nitrogenous bases as counter-cations were synthesized. These are 6-amino-7H-purine-1,9-diium tetrachloridogold(III) chloride monohydrate, (C5H7N5)[AuCl4]Cl·H2O, 1, and 2-amino-6-oxo-6,7-dihydro-1H-purin-9-ium tetrachloridogold(III) hemihydrate, (C5H6N5O)[AuCl4]·0.5H2O, 2. Their crystal structures were studied using single-crystal X-ray diffraction and FT-IR spectroscopic techniques. The arrangement of species in the studied crystal structures implies π-stacking interactions, as well as concomitant C-H...π interactions, hydrogen bonds and other types of noncovalent interactions, which were studied qualitatively and quantitatively using the method of molecular Voronoi-Dirichlet polyhedra. The variation of the nitrogenous base from adenine to guanine results in evident differences in the packing of the species in the crystals of 1 and 2. The splitting and shifting of bands in the FT-IR spectra of the title compounds reveals several features representative of noncovalent interactions in their crystal structures.

Selective metal removal from chromium-containing synthetic effluents using Shewanella xiamenensis biofilm supported on zeolite.

A scheme of selective removal of metal ions from chromium-containing synthetic solutions with the following chemical composition, Cr (VI)-Fe (III), Cr (VI)-Fe (III)-Ni (II), Cr (VI)-Fe (III)-Ni (II)-Zn (II), and Cr (VI)-Fe (III)-Ni (II)-Zn (II)-Cu (II)) by Shewanella xiamenensis biofilm immobilized on a zeolite support, was proposed. Three biological processes, biosorption, bioaccumulation, and longtime bioreduction, were applied for metal removal. The process of Zn (II), Ni (II), and Cu (II) showed to be pH dependent. The maximum removal of Ni (II) was achieved during a 1-hour biosorption process at pH 5.0-6.0, of Zn (II) at pH 5.0, and of Cu (II) at pH 3.0. Chromium (VI) and Fe (III) ions were more efficiently removed by bioaccumulation. Chromium (VI) removal in the studied systems varied from 16.4% to 34.8 and of iron from 55.8 to 94.6%. In a long-term bioreduction experiment, it was possible to achieve complete reduction of Cr (VI) to Cr (III) ions by Shewanella xiamenensis in 42 days and by Shewanella xiamenensis biofilm on zeolite in 35 days. Shewanella oneidensis can be effectively used to remove metal ions from chemically complex effluents.