ATR-FTIR spectroscopic evidence for biomolecular phosphorus and carboxyl groups facilitating bacterial adhesion to iron oxides

Glassy gels toughened by solvent

Glassy polymers are generally stiff and strong yet have limited extensibility1. By swelling with solvent, glassy polymers can become gels that are soft and weak yet have enhanced extensibility1-3. The marked changes in properties arise from the solvent increasing free volume between chains while weakening polymer-polymer interactions. Here we show that solvating polar polymers with ionic liquids (that is, ionogels4,5) at appropriate concentrations can produce a unique class of materials called glassy gels with desirable properties of both glasses and gels. The ionic liquid increases free volume and therefore extensibility despite the absence of conventional solvent (for example, water). Yet, the ionic liquid forms strong and abundant non-covalent crosslinks between polymer chains to render a stiff, tough, glassy, and homogeneous network (that is, no phase separation)6, at room temperature. Despite being more than 54 wt% liquid, the glassy gels exhibit enormous fracture strength (42 MPa), toughness (110 MJ m-3), yield strength (73 MPa) and Young's modulus (1 GPa). These values are similar to those of thermoplastics such as polyethylene, yet unlike thermoplastics, the glassy gels can be deformed up to 670% strain with full and rapid recovery on heating. These transparent materials form by a one-step polymerization and have impressive adhesive, self-healing and shape-memory properties.

Interfacial interactions between minerals and organic matter: Mechanisms and characterizations

Minerals and organic matter are essential components of soil, with minerals acting as the "bone" and organic matter as the "skin". The interfacial interactions between minerals and organic matter result in changes in their chemical composition, structure, functional groups, and physical properties, possessing a significant impact on soil properties, functions, and biogeochemical cycles. Understanding the interfacial interactions of minerals and organic matter is imperative to advance soil remediation technologies and carbon targets. Consequently, there is a growing interest in the physicochemical identification of the interfacial interactions between minerals and organic matter in the academic community. This review provides an overview of the mechanisms underlying these interactions, including adsorption, co-precipitation, occlusion, redox, catalysis and dissolution. Moreover, it surveys various methods and techniques employed to characterize the mineral-organic matter interactions. Specifically, the up-to-date spectroscopic techniques for chemical information and advanced microscopy techniques for physical information are highlighted. The advantages and limitations of each method are also discussed. Finally, we outline future research directions for interfacial interactions and suggests areas for improvement and development of characterization techniques to better understand the mechanisms of mineral-organic matter interactions.

A sustainable and highly efficient fossil-free carbon from olive stones for emerging contaminants removal from different water matrices

The olive stone is a large waste product of the olive oil extraction industry. The present study investigates developing activated carbon from olive stone waste (OSAC) to remove pharmaceuticals from water. Different temperatures and olive stone: KOH ratios were studied. The OSAC produced at 750 °C and 1:3 ratio was found to have the highest porosity and surface area and was tested in the adsorption process. Diclofenac and ciprofloxacin were selected as model contaminants. The adsorption process was optimized with regards to OSAC dosage, pH, temperature, and initial concentration of adsorbate. The OSAC was found to be effective for a wide pH range (2-11) with an optimum dosage of 1 g/L at 25 °C. The pharmaceuticals were almost completely removed in 75 min. The adsorption was endothermic and followed first-order kinetics with physical mechanisms such as electrostatic possibly being the main driver. The optimum conditions were applied to test the removal of diclofenac and ciprofloxacin in synthetic water, lake water (Lake Balaton, Hungary) and secondary wastewater for seven cycles. There was little difference between the removal of the tested water matrices highlighting the potency of OSAC as an adsorbent for pharmaceutical removal in industrial applications. The removal dropped from >99% for the first cycle to 20-30% for the seventh cycle.

In Situ ATR Spectroscopy Study of the Interaction of Acacia senegal Gum with Gold Nanoparticles Films at the Solid-Liquid Interface

The adsorption process of Acacia gum (A. senegal), a complex heteropolysaccharide, was followed by using a spectroscopic method to unravel the relative contribution of the protein moieties and the carbohydrate blocks on the adsorption process. In situ ATR-FTIR was used to investigate the kinetics and conformational changes associated with the adsorption of A. senegal gum on gold nanoparticle films (Au-NPs) at different pHs. The results of this thorough study highlighted the adsorption of A. senegal gum through its protein moieties, in particular, AGPs of low molecular weight and high protein content, close to the Au-NPs surface. Isotherm experiments, by gradually increasing the concentration, showed that the gum adsorption was heterogeneous and followed the Freundlich model for the amide part, while the polysaccharide part followed the Langmuir model. In addition, the hydration and structural organization of the gum layer depended on the gum concentration. A. senegal gum adsorbed irreversibly on Au-NPs whatever the pHs, but the adsorbed layer presented a different behavior depending on pH. A more aggregated and less hydrated structure was observed at acidic pH, while a very hydrated and continuous layer was detected at higher pH. The secondary structure analysis through amide III band revealed a change in the gum secondary structure at high pH with the increase in β-turn while random coil decreased.

Electrospun Fe3O4-chitosan/polyvinyl alcohol nanofibrous film for improved capture and elimination of foodborne pathogens

This study developed a new "capture and killing" antibacterial approach for efficient elimination of foodborne pathogens. Fe3O4-Chitosan (CS)/polyvinyl alcohol (PVA) nanofibrous films with improved antibacterial and mechanical properties were fabricated by a simple, environmentally friendly, and cost-effective electrospinning technique. The relationship between the physical properties (viscosity, surface tension, and conductivity) and spinnability of CS/PVA as fiber forming matrix was explored. Electrospun Fe3O4-CS/PVA films (0.03-0.12 mm) with smooth and bead-free nanofibrous structures (145-169 nm) were successfully obtained. Compared with the film electrospun from neat CS/PVA, incorporating Fe3O4 nanoparticles (NPs) (1.25-5 wt%) in CS/PVA nanofibrous film promoted bacterial attachment and increased the final inactivated efficiency, showing a difference with Fe3O4 loading and bacterial strain, which had the highest value against Escherichia coli (E. coli) and Staphyloccus aureus (S. aureus) being 90 % and 66.30 %, respectively. The tensile strength and elongation at break of Fe3O4-CS/PVA films enhanced by 46-192 % and 92-141 %, respectively. Results of the cytotoxicity test indicated that the resulting films had high biocompatibility. These promising findings provide a novel strategy for effective foodborne pathogens elimination, which could apply to sterilizing and food packaging to extend the shelf life of liquid food.

Importance of inner-sphere P-O-Fe bonds in natural and synthetic mineral-organic associations

Sorption of organic molecules on mineral surfaces can occur through several binding mechanisms of varying strength. Here, we investigated the importance of inner-sphere P-O-Fe bonds in synthetic and natural mineral-organic associations. Natural organic matter such as water extracted soil organic matter (WESOM) and extracellular polymeric substances (EPS) from liquid bacterial cultures were adsorbed to goethite and examined by FTIR spectroscopy and P K-edge NEXAFS spectroscopy. Natural particles from a Bg soil horizon (Gleysol) were subjected to X-ray fluorescence (XRF) mapping, NanoSIMS imaging, and NEXAFS spectro-microscopy at the P K-edge. Inner-sphere P-O-Fe bonds were identified for both, adsorbed EPS extracts and adsorbed WESOMs. Characteristic infrared peaks for P-O-Fe stretching vibrations are present but cannot unambiguously be interpreted due to possible interferences with mono- and polysaccharides. For the Bg horizon, P was only found on Fe oxides, covering the entire surface at different concentrations, but not on clay minerals. Linear combination fitting of NEXAFS spectra indicates that this adsorbed P is mainly a mixture of orthophosphate and organic P compounds. By combining atomic force microscopy (AFM) images with STXM-generated C and Fe distribution maps, we show that the Fe oxide surfaces were fully coated with organic matter. In contrast, clay minerals revealed a much lower C signal. The C NEXAFS spectra taken on the Fe oxides had a substantial contribution of carboxylic C, aliphatic C, and O-alkyl C, which is a composition clearly different from pure adsorbed EPS or aromatic-rich lignin-derived compounds. Our data show that inner-sphere P-O-Fe bonds are important for the association of Fe oxides with soil organic matter. In the Bg horizon, carboxyl groups and orthophosphate compete with the organic P compounds for adsorption sites.

Biochemical characterization and mercury methylation capacity of Geobacter sulfurreducens biofilms grown in media containing iron hydroxide or fumarate

Geobacter species are common in iron-rich environments and can contribute to formation of methylmercury (MeHg), a neurotoxic compound with high bioaccumulation potential formed as a result of bacterial and archaeal physiological activity. Geobacter sulfurreducens can utilize various electron acceptors for growth including iron hydroxides or fumarate. However, it remains poorly understood how the growth on these compounds affects physiological properties of bacterial cells in biofilms, including the capacity to produce MeHg. The purpose of this study was to determine changes in the biochemical composition of G. sulfurreducens during biofilm cultivation in media containing iron hydroxide or fumarate, and to quantify mercury (Hg) methylation capacity of the formed biofilms. Biofilms were characterized by Fourier-transform infrared spectroscopy in the attenuated total reflection mode (ATR-FTIR), Resonance Raman spectroscopy and confocal laser scanning microscopy. MeHg formation was quantified by mass spectrometry after incubation of biofilms with 100 nM Hg. The results of ATR-FTIR experiments showed that in presence of fumarate, G. sulfurreducens biofilm formation was accompanied by variation in content of the energy-reserve polymer glycogen over time, which could be cancelled by the addition of supplementary nutrients (yeast extract). In contrast, biofilms cultivated on Fe(III) hydroxide did not accumulate glycogen. The ATR-FTIR results further suggested that Fe(III) hydroxide surfaces bind cells via phosphate and carboxylate groups of bacteria that form complexes with iron. Furthermore, biofilms grown on Fe(III) hydroxide had higher fraction of oxidized cytochromes and produced two to three times less biomass compared to conditions with fumarate. Normalized to biofilm volume, the content of MeHg was similar in assays with biofilms grown on Fe(III) hydroxide and on fumarate (with yeast extract and without). These results suggest that G. sulfurreducens biofilms produce MeHg irrespectively from glycogen content and cytochrome redox state in the cells, and warrant further investigation of the mechanisms controlling this process.

Transport of double-stranded ribonucleic acids (dsRNA) and deoxyribonucleic acids (DNA) in sand and iron oxide-coated sand columns under varying solution chemistries

Assessing ecological risks associated with the use of genetically modified RNA interference crops demands an understanding of the fate of crop-released insecticidal double-stranded RNA (dsRNA) molecules in soils. We studied the adsorption of one dsRNA and two double-stranded DNA as model nucleic acids (NAs) during transport through sand- and iron oxide-coated sand (IOCS)-filled columns over a range of solution pH and ionic compositions. Consistent with NA-sand electrostatic repulsion, we observed only slight retention of NAs in sand columns. Conversely, pronounced NA retention in IOCS columns is consistent with strong and irreversible NA adsorption involving electrostatic attraction to and inner-sphere complex formation of NAs with iron oxide coatings. Adsorption of NAs to iron oxides revealed a fast and a slow kinetic adsorption regime, possibly caused by the excluded-area effect. Adsorption of NAs to sand and IOCS increased in the presence of dissolved Mg2+ and with increasing ionic strength, reflecting cation-bridging and screening of repulsive electrostatics, respectively. The co-solute phosphate and a pre-adsorbed dissolved organic matter isolate competitively suppressed dsRNA adsorption to IOCS. Similar adsorption characteristics of dsRNA and similarly sized DNA suggest that existing information on DNA adsorption to soil particles helps in predicting adsorption and fate of dsRNA molecules in soils.

Artificial Soil-Like Material Enhances CO2 Bio-Valorization into Chemicals in Gas Fermentation

Gas fermentation offers a carbon-neutral route for producing industrial feedstocks using autotrophic microbes to convert carbon dioxide (CO2) in waste gases, such as industrial emissions and biogas, into valuable chemicals or biofuels. However, slow microbial metabolism owing to low gaseous solubility causes significant challenges in gas fermentation. Although chemical or genetic manipulations have been explored to improve gas fermentation, they are either nonsustainable or complex. Herein, an artificial soil-like material (SLM) inspired by natural soil was fabricated to improve the growth and metabolism ofCupriavidus necatorfor enhanced poly-β-hydroxybutyrate (PHB) biosynthesis from CO2 and hydrogen (H2). Porous SLM comprises low-cost nanoclay, boehmite, and starch and serves as a biocarrier to facilitate the colonization of bacteria and delivery of CO2 to bacteria. With 3.0 g/L SLM addition, the solubility of CO2 in water increased by ∼4 times and biomass and PHB production boosted by 29 and 102%, respectively, in the 24 h culture. In addition, a positive modulation was observed in the metabolism of PHB biosynthesis. PHB biosynthesis-associated gene expression was found to be enhanced in response to the SLM addition. The concentrations of intermediates in the metabolic pathway of PHB biosynthesis, such as pyruvate and acetyl-CoA, as well as reducing energy (ATP and NADPH) significantly increased with SLM addition. SLM also demonstrated the merits of easy fabrication, high stability, recyclability, and plasticity, thereby indicating its considerable potential for large-scale application in gas fermentation.

Mediated biosynthesis of CdS QDs by EPS from Desulfovibrio desulfuricans sub sp. under carbon source-induced reinforcement

This paper describes a unique molecular mechanism for the EPS-mediated synthesis of CdS QDs by sulfate-reducing bacteria (SRB) under carbon source-induced reinforcement. Under the induced by carbon sources (HCOONa, CH3COONa and C6H12O6), there was a significant increase in EPS production of SRB, particularly in protein, and the capacity of Cd(II) adsorption was further enhanced. CdS QDs were extracellularly synthesized by adding S2- after Cd(II) adsorption. The results showed that CdS QDs were wrapped or adhered by EPS, and the most significant increase in Arg and Lys among basic amino acids in EPS after HCOONa-induced was 133.34% and 63.89%, respectively. This may serve as a biological template for QD synthesis, producing protein gels with a large number of microcavities and controlling the nucleation of CdS QDs. The highest yield of HCOONa-CdS was achieved after induction, with 23.59 g/g biomass per unit strain, which was 447.34% higher than that before induction and was at a high level in previous studies. The synthesized CdS QDs were uniform in size distribution and had higher luminescence activity and a larger specific surface area than those synthesized by the chemical synthesis route, provides a new idea for EPS treatment of heavy metal wastewater and metal biorecovery.

Atomic-Level Structural Differences between Fe(III) Coprecipitates Generated by the Addition of Fe(III) Coagulants and by the Oxidation of Fe(II) Coagulants Determine Their Coagulation Behavior in Phosphate and DOM Removal

In situ Fe(III) coprecipitation from Fe2+ oxidation is a widespread phenomenon in natural environments and water treatment processes. Studies have shown the superiority of in situ Fe(III) (formed by in situ oxidation of a Fe(II) coagulant) over ex situ Fe(III) (using a Fe(III) coagulant directly) in coagulation, but the reasons remain unclear due to the uncertain nature of amorphous structures. Here, we utilized an in situ Fe(III) coagulation process, oxidizing the Fe(II) coagulant by potassium permanganate (KMnO4), to treat phosphate-containing surface water and analyzed differences between in situ and ex situ Fe(III) coagulation in phosphate removal, dissolved organic matter (DOM) removal, and floc growth. Compared to ex situ Fe(III), flocs formed by the natural oxidizing Fe2+ coagulant exhibited more effective phosphate removal. Furthermore, in situ Fe(III) formed through accelerated oxidation by KMnO4 demonstrated improved flocculation behavior and enhanced removal of specific types of DOM by forming a more stable structure while still maintaining effective phosphate removal. Fe K-edge extended X-ray absorption fine structure spectra (EXAFS) of the flocs explained their differences. A short-range ordered strengite-like structure (corner-linked PO4 tetrahedra to FeO6 octahedra) was the key to more effective phosphorus removal of in situ Fe(III) than ex situ Fe(III) and was well preserved when KMnO4 accelerated in situ Fe(III) formation. Conversely, KMnO4 significantly inhibited the edge and corner coordination between FeO6 octahedra and altered the floc-chain-forming behavior by accelerating hydrolysis, resulting in a more dispersed monomeric structure than ex situ Fe(III). This research provides an explanation for the superiority of in situ Fe(III) in phosphorus removal and highlights the importance of atomic-level structural differences between ex situ and in situ Fe(III) coprecipitates in water treatment.

Spectral Detection of Nanophase Iron Minerals Produced by Fe(III)-Reducing Hyperthermophilic Crenarchaea

Mineral transformations by two hyperthermophilic Fe(III)-reducing crenarchaea, Pyrodictium delaneyi and Pyrobaculum islandicum, were examined using synthetic nanophase ferrihydrite, lepidocrocite, and akaganeite separately as terminal electron acceptors and compared with abiotic mineral transformations under similar conditions. Spectral analyses using visible-near-infrared, Fourier-transform infrared attenuated total reflectance (FTIR-ATR), Raman, and Mössbauer spectroscopies were complementary and revealed formation of various biomineral assemblages distinguishable from abiotic phases. The most extensive biogenic mineral transformation occurred with ferrihydrite, which formed primarily magnetite with spectral features similar to biomagnetite relative to a synthetic magnetite standard. The FTIR-ATR spectra of ferrihydrite bioreduced by P. delaneyi also showed possible cell-associated organics such as exopolysaccharides. Such combined detections of biomineral assemblages and organics might serve as biomarkers for hyperthermophilic Fe(III) reduction. With lepidocrocite, P. delaneyi produced primarily a ferrous carbonate phase reminiscent of siderite, and with akaganeite, magnetite and a ferrous phosphate phase similar to vivianite were formed. P. islandicum showed minor biogenic production of a ferrous phosphate similar to vivianite when grown on lepidocrocite, and a mixed valent phosphate or sulfate mineral when grown on akaganeite. These results expand the range of biogenic mineral transformations at high temperatures and identify spacecraft-relevant spectroscopies suitable for discriminating mineral biogenicity.

Antimicrobial Efficiency of Chitosan and Its Methylated Derivative against Lentilactobacillus parabuchneri Biofilms

Antimicrobial materials are considered potential alternatives to prevent the development of biofilm-associated contaminations. Concerns regarding synthetic preservatives necessitate the development of innovative and safe natural antimicrobials. In the present study, we discuss the in situ infrared attenuated total reflection spectroscopy (IR-ATR) investigations of the selective antimicrobial efficiency of chitosan in controlling the growth of Lentilactobacillus parabuchneri biofilms. The protonated charges of chitosan were additionally amplified by structural modification via methylation, yielding quaternized derivative TMC (i.e., N, N, N-trimethyl chitosan). To evaluate antimicrobial effectiveness against L. parab. biofilms, IR-ATR spectroscopy provided information on molecular mechanisms and insights into chemical changes during real-time biofilm inhibition studies. The integrated fiberoptic oxygen microsensors enabled monitoring oxygen (O₂) concentration gradients within biofilms, thereby confirming the metabolic oxygen depletion dropping from 4.5 to 0.7 mg L^-1. IR studies revealed strong electrostatic interactions between chitosan/its water-soluble derivative and bacteria, indicating that a few hours were sufficient to affect biofilm disruption. The significant decrease in the IR bands is related to the characteristic spectral information of amide I, II, III, nucleic acid, and extracellular polymeric matrix (EPS) produced by L. parabuchneri biofilms. Cell clusters of biofilms, microcolonies, and destabilization of the EPS matrix after the addition of biopolymers were visualized using optical microscopy. In addition, scanning electron microscopy (SEM) of biofilms grown on polystyrene and stainless-steel surfaces was used to examine morphological changes, indicating the disintegration of the biofilm matrix into individual cells. Quantification of the total biofilm formation correlated with the CV assay results, indicating cell death and lysis. The electrostatic interactions between chitosan and the bacterial cell wall typically occur between protonated amino groups and negatively charged phospholipids, which promote permeabilization. Biofilm growth inhibition was assessed by a viability assay for a period of 72 h and in the range of low MIC values (varying 0.01-2%). These results support the potential of chitosan and TMC for bacterial growth prevention of the foodborne contaminant L. parabuchneri in the dairy industry and for further implementation in food packaging.

Escherichia coli and phosphate interplay mediates transport of nanoscale zero-valent iron synthesized by green tea in water-saturated porous media

Green synthesized nano-zero-valent iron (GT-nZVI) has been considered an excellent material for in-situ soil remediation due to its high stability and environmental benignity. However, sufficient transportability of GT-nZVI downstream towards the contaminated sites, likely affected by the physicochemical properties of soil-groundwater, is required for improved in-situ remediation. Thus, the effect of soil components (i.e., bacteria and phosphate) on GT-nZVI transportability is significant. Hence, we studied the transport of GT-nZVI (Fe0 core wrapped by green tea polyphenols) with the existence of E. coli and phosphate in water-saturated porous sand media in NaCl and CaCl2 solutions at pHs 6.0 and 8.0. Also studied were the stability, surface characteristics, and two-site kinetics attachment modeling (TKAM) with Escherichia coli or/and phosphate. The results showed that phosphate could further enhance GT-nZVI co-transport with E. coli by increasing the negative charge on GT-nZVI at pH 6.0. However, E. coli reduced GT-nZVI mobility at pH 8.0 because the cell-cell interactions could mask the negative charges of pre-deposited GT-nZVI on E. coli, forming the large clusters between GT-nZVI and E. coli. Then, phosphate occurrence diminished E. coli inhibition by detaching GT-nZVI from nZVI-E. coli-phosphate polymers due to the stronger phosphate adsorption on E. coli than GT-nZVI at pH 8.0. Overall, TKAM describes the transport and retention of GT-nZVI adequately under various conditions, indicating the deposition order with k2str value as follows: GT-nZVI alone > with (w.) E. coli > w. phosphate > w. combined E. coli & phosphate at pH 6.0. By contrast, w. phosphate > w. E. coli > w. combined E. coli & phosphate > GT-nZVI alone ensued at pH 8.0. This investigation highlights the transport behavior of GT-nZVI associated with surface property changes in complex environments for effective in-situ remediation.

Controlling microbial arsenite oxidation and mobilization in arsenite-adsorbed iron minerals: The Influence of pH conditions and mineralogical composition

The oxidation of aqueous arsenite (As(III)) by As(III)-oxidizing bacteria is known to attenuate the mobilization and toxicity of arsenic, and is regarded as potential method for As(III)-pollution remediation. However, during the interactions between As(III)-oxidizing bacteria and different As(III)-adsorbed soil Fe-minerals, the oxidation and partitioning of solid-phase As(III), as well as the controlling mechanisms, remain unclear. In this study, we therefore incubated three As(III)-adsorbed Fe-minerals with a typical As(III)-oxidizing bacteria (Pseudomonas sp. HN-1) at different pH conditions. After microbial oxidation, the percentage of arsenate (As(V)) was significantly higher at pH 7 (15-94%) and 9 (12-89%) than at pH 4 (6-50%) in all Fe-minerals. Incubation of As(III)-oxidizing bacteria promoted As-immobilization under acidic-conditions but As-mobilization under alkaline-conditions. Arsenic-X-ray adsorption spectroscopy results showed that solid-phase As(V) fraction in goethite, hematite and magnetite was 27-64%, 5-12% and 50-91%, respectively. Compared with the corner-sharing As(III)-adsorption complexes formed on magnetite, the edge-sharing complexes on hematite were significantly more stable towards microbial-oxidation. Additionally, the strong adhesion between strain HN-1 and hematite probably limit bacterial-activity and mobility, thereby inhibiting microbial As(III)-oxidation. Our findings elucidate the controlling mechanisms of microbial As(III)-oxidation in different As(III)-adsorbed Fe-minerals and demonstrate strain HN-1 is an excellent candidate for As(III)-remediation in soils containing goethite and magnetite.

Biocatalytic conversion of sunlight and carbon dioxide to solar fuels and chemicals

This review discusses the progress in the assembly of photosynthetic biohybrid systems using enzymes and microbes as the biocatalysts which are capable of utilising light to reduce carbon dioxide to solar fuels. We begin by outlining natural photosynthesis, an inspired biomachinery to develop artificial photosystems, and the rationale and motivation to advance and introduce biological substrates to create more novel, and efficient, photosystems. The case studies of various approaches to the development of CO2-reducing microbial semi-artificial photosystems are also summarised, showcasing a variety of methods for hybrid microbial photosystems and their potential. Finally, approaches to investigate the relatively ambiguous electron transfer mechanisms in such photosystems are discussed through the presentation of spectroscopic techniques, eventually leading to what this will mean for the future of microbial hybrid photosystems.

The Multiple States of Environmental DNA and What Is Known about Their Persistence in Aquatic Environments

Increased use of environmental DNA (eDNA) analysis for indirect species detection has spurred the need to understand eDNA persistence in the environment. Understanding the persistence of eDNA is complex because it exists in a mixture of different states (e.g., dissolved, particle adsorbed, intracellular, and intraorganellar), and each state is expected to have a specific decay rate that depends on environmental parameters. Thus, improving knowledge about eDNA conversion rates between states and the reactions that degrade eDNA in different states is needed. Here, we focus on eukaryotic extraorganismal eDNA, outline how water chemistry and suspended mineral particles likely affect conversion among each eDNA state, and indicate how environmental parameters affect persistence of states in the water column. On the basis of deducing these controlling parameters, we synthesized the eDNA literature to assess whether we could already derive a general understanding of eDNA states persisting in the environment. However, we found that these parameters are often not being measured or reported when measured, and in many cases very few experimental data exist from which to draw conclusions. Therefore, further study of how environmental parameters affect eDNA state conversion and eDNA decay in aquatic environments is needed. We recommend analytic controls that can be used during the processing of water to assess potential losses of different eDNA states if all were present in a water sample, and we outline future experimental work that would help determine the dominant eDNA states in water.

Iron oxide minerals promote simultaneous bio-reduction of Cr(VI) and nitrate: Implications for understanding natural attenuation

Nitrate and Cr(VI) coexist in aquifers, posing a potential threat to ecological environment and public health. Iron oxide minerals (hematite and magnetite) exist ubiquitously in groundwater, which are hot spots for biogeochemical transformation. However, there is still a knowledge gap anout the effect of iron oxide minerals on bioreduction of nitrate and Cr(VI). Here we observed that iron oxide minerals can significantly improve the ability of microorganisms to simultaneously reduce nitrate and Cr(VI), the reduction rates of nitrate and Cr(VI) increased by 7.3 and 8.5 times, respectively. The addition of minerals reinforced biofilm formation and shaped microbial communities with a new dominant strain of Azoarcus. The expression levels of functional genes were also upregulated, including napA, narG, nfsA, yieF, POD, and CAT. Furthermore, nitrate and chromate reductases' activities increased by 11 and 5 folds, respectively. These results demonstrated that iron oxide minerals participated in the bio-transformation of nitrate and Cr(VI) co-contamination, alleviating oxidative stress, shaping the microbial community, and ultimately accelerating bio-transformation. These findings offer a window into the biological transformation of co-contamination in the presence of iron oxide minerals, and insights to reveal strategies for microbial detoxification and to develop promising approaches for dealing with complex pollution conditions.

Adsorption of double-stranded ribonucleic acids (dsRNA) to iron (oxyhydr-)oxide surfaces: comparative analysis of model dsRNA molecules and deoxyribonucleic acids (DNA)

Double-stranded ribonucleic acid (dsRNA) molecules are novel plant-incorporated protectants expressed in genetically modified RNA interference (RNAi) crops. Ecological risk assessment (ERA) of RNAi crops requires a heretofore-missing detailed understanding of dsRNA adsorption in soils, a key fate process. Herein, we systematically study the adsorption of a model dsRNA molecule and of two double-stranded deoxyribonucleic acid (DNA) molecules of varying lengths to three soil iron (oxyhydr-)oxides - goethite, lepidocrocite, and hematite - over a range of solution pH (4.5-10), ionic strength (I = 10-100 mM NaCl) and composition (0.5, 1, and 3 mM MgCl2) and in the absence and presence of phosphate (0.05-5 mM) as co-adsorbate. We hypothesized comparable adsorption characteristics of dsRNA and DNA based on their structural similarities. Consistently, the three nucleic acids (NAs) showed high adsorption affinities to the iron (oxyhydr-)oxides with decreasing adsorption in the order goethite, lepidocrocite, and hematite, likely reflecting a decrease in the hydroxyl group density and positive charges of the oxide surfaces in the same order. NA adsorption also decreased with increasing solution pH, consistent with weakening of NA electrostatic attraction to and inner-sphere complex formation with the iron (oxyhydr-)oxides surfaces as pH increased. Adsorbed NA concentrations increased with increasing I and in the presence of Mg2+, consistent with adsorbed NA molecules adopting more compact conformations. Strong NA-phosphate adsorption competition demonstrates that co-adsorbates need consideration in assessing dsRNA fate in soils. Comparable adsorption characteristics of dsRNA and DNA molecules to iron (oxyhydr-)oxides imply that information on DNA adsorption to soil particle surfaces can inform dsRNA ERA.

Antimony (V) Adsorption at the Hematite–Water Interface: A Macroscopic and In Situ ATR-FTIR Study

The environmental mobility of antimony (Sb) is largely unexplored in geochemical environments. Iron oxide minerals are considered major sinks for Sb. Among the different oxidation states of Sb, (+) V is found more commonly in a wide redox range. Despite many adsorption studies of Sb (V) with various iron oxide minerals, detailed research on the adsorption mechanism of Sb (V) on hematite using macroscopic, spectroscopic, and surface complexation modeling is rare. Thus, the main objective of our study is to evaluate the surface complexation mechanism of Sb (V) on hematite under a range of solution properties using macroscopic, in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopic, and surface complexation modeling. The results indicate that the Sb (V) adsorption on hematite was highest at pH 4–6. After pH 6, the adsorption decreased sharply and became negligible above pH 9. The effect of ionic strength was negligible from pH 4 to 6. The spectroscopic results confirmed the presence of inner- and outer-sphere surface complexes at lower pH values, and only outer-sphere-type surface complex at pH 8. Surface complexation models successfully predicted the Sb (V) adsorption envelope. Our research will improve the understanding of Sb (V) mobility in iron-oxide-rich environments.

Removal and Inactivation of an Enveloped Virus Surrogate by Iron Conventional Coagulation and Electrocoagulation

It is imperative to understand the behavior of enveloped viruses during water treatment to better protect public health, especially in the light of evidence of detection of coronaviruses in wastewater. We report bench-scale experiments evaluating the extent and mechanisms of removal and/or inactivation of a coronavirus surrogate (ϕ6 bacteriophage) in water by conventional FeCl₃ coagulation and Fe(0) electrocoagulation. Both coagulation methods achieved ∼5-log removal/inactivation of ϕ6 in 20 min. Enhanced removal was attributed to the high hydrophobicity of ϕ6 imparted by its characteristic phospholipid envelope. ϕ6 adhesion to freshly precipitated iron (hydr)oxide also led to envelope damage causing inactivation in both coagulation techniques. Fourier transform infrared spectroscopy revealed oxidative damages to ϕ6 lipids only for electrocoagulation consistent with electro-Fenton reactions. Monitoring ϕ6 dsRNA by a novel reverse transcription quantitative polymerase chain reaction (RT-qPCR) method quantified significantly lower viral removal/inactivation in water compared with the plaque assay demonstrating that relying solely on RT-qPCR assays may overstate human health risks arising from viruses. Transmission electron microscopy and computationally generated electron density maps of ϕ6 showed severe morphological damages to virus' envelope and loss of capsid volume accompanying coagulation. Both conventional and electro- coagulation appear to be highly effective in controlling enveloped viruses during surface water treatment.

Sorption and abiotic transformation of monensin by iron and manganese oxides

Monensin, an ionophore antibiotic, is commonly administered as a feed additive to cattle and poultry. A large percentage of the administered dose is excreted in animal waste, which is often applied to agricultural fields as fertilizer. The objective of this work is to gain insight into the fate of monensin in soil by investigating the interactions between monensin and common soil minerals, including sorption and transformation to unmonitored partial oxidation products. Batch sorption experiments across varying conditions (i.e., pH, ionic strength) and desorption experiments (i.e., methanol, PO₄^3-, methyl tert-butyl ether) were used to determine the extent to which a selection of common redox-active soil minerals [birnessite (δ-MnO₂), goethite (α-FeOOH), hematite (α-Fe₂O₃)] can bind and transform monensin. Monensin was bound by hematite (pH < 7.5, up to 7.5 mmol kg^-1), goethite (pH < 7.5, up to 3.4 mmol kg^-1), and birnessite (pH < 7, up to 0.1 mmol kg^-1). Combined sorption and transformation were the greatest for hematite and the lowest for birnessite. Sorption to hematite was more reversible than to goethite. Each desorption from goethite recovered <10% of sorbed monensin, whereas desorption from hematite recovered up to 69% of sorbed monensin, dependent on the solution. The potential for iron and manganese (hydr)oxides to abiotically transform monensin through reductive dissolution to partial oxidation products was evaluated by mass spectral analysis following sorption experiments. Additionally, the dominant sorption mechanism was inferred through ATR-FTIR spectroscopy, via examination of the carboxylate peak separation differences, on goethite and hematite to be bridging bidentate.

Inactivation of Pseudomonas aeruginosa Biofilms by 405-Nanometer-Light-Emitting Diode Illumination

Biofilm formation by Pseudomonas aeruginosa contributes to its survival on surfaces and represents a major clinical threat because of the increased tolerance of biofilms to disinfecting agents. This study aimed to investigate the efficacy of 405-nm light-emitting diode (LED) illumination in eliminating P. aeruginosa biofilms formed on stainless steel coupons under different temperatures. Time-dependent killing assays using planktonic and biofilm cells were used to determine the antimicrobial and antibiofilm activities of LED illumination. We also evaluated the effects of LED illumination on the disinfectant susceptibility, biofilm structure, extracellular polymeric substance (EPS) structure and composition, and biofilm-related gene expression of P. aeruginosa biofilm cells. Results showed that the abundance of planktonic P. aeruginosa cells was reduced by 0.88, 0.53, and 0.85 log CFU/ml following LED treatment for 2 h compared with untreated controls at 4, 10, and 25°C, respectively. For cells in biofilms, significant reductions (1.73, 1.59, and 1.68 log CFU/cm2) were observed following LED illumination for 2 h at 4, 10, and 25°C, respectively. Moreover, illuminated P. aeruginosa biofilm cells were more sensitive to benzalkonium chloride or chlorhexidine than untreated cells. Scanning electron microscopy and confocal laser scanning microscopic observation indicated that both the biofilm structure and EPS structure were disrupted by LED illumination. Further, reverse transcription-quantitative PCR revealed that LED illumination downregulated the transcription of several genes associated with biofilm formation. These findings suggest that LED illumination has the potential to be developed as an alternative method for prevention and control of P. aeruginosa biofilm contamination.IMPORTANCEPseudomonas aeruginosa can form biofilms on medical implants, industrial equipment, and domestic surfaces, contributing to high morbidity and mortality rates. This study examined the antibiofilm activity of 405-nm light-emitting diode (LED) illumination against mature biofilms formed on stainless steel coupons. We found that the disinfectant susceptibility, biofilm structure, and extracellular polymeric substance structure and composition were disrupted by LED illumination. We then investigated the transcription of several critical P. aeruginosa biofilm-related genes and analyzed the effect of illumination temperature on the above characteristics. Our results confirmed that LED illumination could be developed into an effective and safe method to counter P. aeruginosa biofilm contamination. Further research will be focused on the efficacy and application of LED illumination for elimination of complicated biofilms in the environment.

Chemical Functionalization of the Zinc Selenide Surface and Its Impact on Lactobacillus rhamnosus GG Biofilms

Bacteria grow on surfaces and form communities called biofilms. Bacterial adhesion and properties of the derived biofilms depend on, among others, the nature of the supporting substrate. Here, we report how the surface properties of the substrate affect the biofilm growth of probiotic Lactobacillus rhamnosus GG (LGG). Hydrophilic (OH), hydrophobic (CH₃), and positively charged (NH₃⁺) surfaces were obtained by the functionalization of a ZnSe crystal with alkanethiol self-assembled monolayers (SAM). The self-assembly of alkanethiols onto ZnSe was studied in situ using infrared spectroscopy in attenuated total reflection mode (ATR-FTIR). The organization of grafted SAMs was analyzed based on the results of ATR-FTIR, high-energy elastic backscattering spectrometry, and contact angle measurements. The kinetics and adhesion strength of LGG initial attachment as well as its physiological state on surfaces terminated by the different functional groups were assessed by the combination of ATR-FTIR, force measurements based on atomic force microscopy, and fluorescent staining of bacteria. The strength of interactions between LGG and the surface was strongly affected by the terminal group of the alkanethiol chain. The -NH₃⁺ groups displayed the highest affinity with LGG at the first stage of interaction. The surface properties also played an important role when LGG biofilms were further grown in a nutritive medium for 24 h under flow conditions. Notably, the analysis of the infrared spectra recorded during the biofilm cultivation revealed differences in the kinetics of growth and in the polysaccharide features of the biofilm depending on the substrate functionality. LGG biofilm was stable only on the positively charged surface upon rinsing. Findings of this work clearly show that the adhesion features and the growth of LGG biofilms are substrate-dependent.

Functional Group Distribution of the Carrier Surface Influences Adhesion of Methanothermobacter thermautotrophicus

Various support carriers are used for high-density retention of methanogenic archaea in anaerobic wastewater treatment systems. Although the physicochemical properties of carrier materials and microorganisms influence the adhesion of methanogenic archaea, details about the underlying mechanism remain poorly characterized. We applied seven types of chemical surface modifications to carbon felts to clarify the adhesion properties of Methanothermobacter thermautotrophicus, a representative thermophilic hydrogenotrophic methanogen. The relationship between carrier surface properties and methanogen adhesion was evaluated. M. thermautotrophicus adhesion was significantly increased up to 2.6 times in comparison with control on carbon felts treated with NaOH, HCl, H₂SO₄, or Na₂HPO₄. Treated carbon felts showed a lower water contact angle, but no correlation between the carrier surface contact angle and methanogen adhesion was observed. On the other hand, at the surface of the carrier that showed improved adhesion of methanogens, the ratio of -COOH : -OH was 1 : 0.65. Such a ratio was not observed with treated carriers for which methanogen adhesion was not improved. Therefore, in the adhesion of M. thermautotrophicus, the functional group abundance was important as well as physical surface properties such as the hydrophobicity. Hydrogenotrophic methanogens are involved in active methanation during the startup of anaerobic digestion. Additionally, these methanogenic archaea function as methanogenic cathode catalysts. Therefore, anaerobic digestion performance will greatly improve by controlling the adhesion of hydrogenotrophic methanogens such as M. thermautotrophicus.

Adhesion mediated transport of bacterial pathogens in saturated sands coated by phyllosilicates and Al-oxides

The current knowledge of bacterial migration is mainly derived from work using bare or Fe-coated quartz sands as porous media. However, mineral coatings on quartz by phyllosilicates and Al-oxides prevail in natural soils, and their effect on bacterial transport remains unknown. Herein, we systematically explored the transport of two bacterial pathogens (Escherichia coli and Staphylococcus aureus) through saturated bare quartz and those coated by kaolinite (KaoQuartz), montmorillonite (MontQuartz) or Al-oxides (AlQuartz) under various solution ionic strength (IS) and pH levels. Elevating IS or decreasing pH discouraged bacterial mobility in all cases, with one exception for the migration of S. aureus through AlQuartz at various IS levels. E. coli showed a higher mobility than S. aureus in all cases. All the three coatings, especially the Al-oxides inhibited bacterial transport through quartz. Overall, the two phyllosilicates-coated sands showed transport behaviors (mobility trends with IS, pH, and cell type) similar to those for the bare quartz which could be explained by the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Nevertheless, for transport within AlQuartz, there were deviations between the observations and the DLVO predictions, probably because of the existence of non-DLVO forces such as hydrophobic and chemical interactions. More importantly, the bacterial retention was found to correlate well with the adhesion regardless of the solution condition and the bacteria and media type, thereby revealing a central role of adhesion in mediating migration through mineral-coated sands. These findings highlight the significance of mineral coating and adhesion in pathogen dissemination in natural soils.

Size-Dependent Bacterial Toxicity of Hematite Particles

Submicron-sized iron oxide particles can influence the activity of bacteria, but the exact mechanisms of oxide toxicity toward bacteria remain elusive. By using atomic force microscopy (AFM), soft X-ray tomography (Nano-CT), and Fourier transform infrared (FTIR) spectrometry, we show how the size-dependent interfacial interactions between hematite particles and bacteria in the absence of any ligands contribute to the antimicrobial properties against Gram-positive and Gram-negative bacterial strains. We found that surface adhesion between hematite particles and bacterial cells is initially dominated by Lifshitz van der Waals and electrostatic forces. Subsequently, the rapid formation of P-O-Fe bonds occurs, followed by changes in the structures of membrane proteins in 2 h, resulting in the loss of the structural integrity of the membrane within 10 h. Thus, particles can migrate into the cells. After contact with bacterial cells, reactive oxygen species are generated on the surface of hematite particles, leading to cell permeabilization. G^- bacteria appear to be more susceptible to this process than G⁺ bacteria because the latter exhibit weaker adhesion forces toward hematite and benefit from the protective effects of the peptidoglycan layers. Our work revealed that hematite nanoparticles are more toxic to bacteria than microscaled particles due to their strong interfacial physicochemical interactions with the cells.

The role of positively charged sites in the interaction between model cell membranes and γ-Fe2O3 NPs

The various applications of iron oxide nanoparticles (NPs) in clinical care and wastewater treatment are rapidly developing, thus their biological safety is worth attention. The electrostatic interaction between cell membranes and NPs is the key mechanism behind membrane damage and membrane penetration. Cell membranes are generally negatively charged with a few positively charged domains. The role of the positively charged sites in the NP-membrane interaction needs further investigation. In this study, the ratio of the positively charged sites was adjusted in two model cell membranes: giant and small unilamellar vesicles (GUVs and SUVs). After exposure to negatively charged γ-Fe₂O₃ NPs, the adhesion of NPs on the membranes and the induced membrane disruption were studied by microscopic observation and quartz crystal microbalance (QCM) monitoring. γ-Fe₂O₃ NPs adhered to and disrupted the membranes containing even few positively charged sites, although the whole membrane exhibited a negative zeta potential and hence electrostatically repels the NPs. The number of adhered γ-Fe₂O₃ NPs increased remarkably on membranes with overall positive zeta potential, but more serious disruption happened to membranes with higher ratios of positively charged sites. Therefore, the membrane rupture was more correlated to the number of positively charged sites than to the zeta potential of the whole membrane. In addition, exposure to γ-Fe₂O₃ NPs decreased the order of the lipid molecules and hence increased the fluidity of the membrane phase, and the most significant phase change occurred in the negatively charged membrane with the highest ratio of positively charged sites. Infrared spectra indicated that γ-Fe₂O₃ NPs probably interact with the membranes via the phosphodiester and trimethylamine groups in the lipid head groups. Our research furthers our knowledge of the electrostatic interaction between NPs and cell membranes, which should help to predict the biological effects of γ-Fe₂O₃ NPs.

Characterizing Preferential Adsorption of Phosphate on Binary Sorbents of Goethite and Maghaemite using in situ ATR-FTIR and 2D Correlation Spectroscopy

Recent developments in analytics using infrared spectroscopy have enabled us to identify the adsorption mechanism at interfaces, but such methods are applicable only for simple systems. In this study, the preferential adsorption of phosphate on binary goethite and maghaemite was investigated. As a result, monodentate and bidentate complexes were the major complexes on goethite and maghaemite, respectively. A shrinking effect in goethite and a swelling effect in maghaemite were identified, and environmental perturbations caused a significant decrease in the integrated absorbance of phosphate complexes on maghaemite, while no effect was observed on goethite, which implies that different adsorption mechanisms were involved. Based on the results, a bridging complex was proposed, and the swelling effect is explained by the negatively charged maghaemite surface resulting from the bidentate complex. The isolation of phosphate by the shrinking effect explains the low phosphate bioavailability in the soil environment, while the colloidal properties of the bidentate complex on maghaemite are the reason for colloidal mobilization. To the best of our knowledge, this study not only addresses the shrinking and swelling properties of iron (hydr)oxide nanoparticles but also demonstrates preferential adsorption on binary sorbents using in situ ATR-FTIR for the first time.

Mechanism of Cu(II) and Cd(II) immobilization by extracellular polymeric substances (Escherichia coli) on variable charge soils

Extracellular polymeric substances (EPS) found in soils can reduce the mobility of heavy metals through the use of both electrostatic and non-electrostatic mechanisms. Their effects vary from one soil type to another. The influence of EPS from Escherichia coli on the adsorption behaviors of Cu(II) and Cd(II) by two bulk variable charge soils, Oxisol and Ultisol, was studied at constant and varied pH, and the results were compared to a constant charge Alfisol. The maximum adsorption capacities of the soils were significantly (P < 0.05) enhanced in the presence of EPS, with Cu(II) adsorption being greater. Interaction of EPS with soils made the soil surface charge more negative by neutralizing positive charges and shifting the zeta potentials in a negative direction: from -18.6 to -26.4 mV for Alfisol, +5.1 to -22.2 mV for Oxisol, and +0.3 to -28.0 mV for Ultisol at pH 5.0. The adsorption data fitted both the Freundlich and Langmuir isotherms well. Preadsorbed Cd(II) was more easily desorbed by KNO₃ than preadsorbed Cu(II) from both the control and EPS treated soils. The adsorption of both metals was governed by electrostatic and non-electrostatic mechanisms, although more Cu(II) was adsorbed through the non-electrostatic mechanism. The information obtained in this study will improve our understanding of the mechanisms involved in reducing heavy metals mobility in variable charge soils and hence, their bioavailability.

Iron and nitrogen cycling, bacterioplankton community composition and mineral transformations involving phosphorus stabilisation in the ferruginous hypolimnion of a post-mining lake

Lake Medard is an oligotrophic post-mining lake characterised by ferruginous bottom waters, with marked redox gradients resulting from iron (Fe) and nitrogen (N) speciation and accompanying depth-dependent variations in the abundance of volatile fatty acids (VFAs), pH and alkalinity. The lacustrine system is meromictic, featuring a dysoxic hypolimnion and an anoxic monimolimnion with relatively high concentrations of sulfate (SO42-, 19 ± 2 mM) and Fe(ii) (127 ± 17 μM). An increase in dissolved manganese is also observed with increasing depth, together with a general lack of sulfide, which can only be detected at the sediment-water interface at concentrations of ∼0.30 μM. In the hypolimnion, nitrate (NO3-) becomes progressively depleted and ammonium (NH4+) dominates the dissolved N inventory (up to 185 ± 13 μM). Here we describe the biogeochemical disequilibrium conditions governing critical mineralogical transformations involving Fe and phosphorus (P) co-precipitation in the dysoxic-to-anoxic bottom water column. A combination of mineral equilibrium modelling and synchrotron-based diffraction and spectroscopic techniques was applied to investigate the minerals comprising the upper anoxic sediments. The combined dataset indicates that elemental recycling on and below the hypolimnion promote the precipitation of FeOOH polymorphs that accumulate as heterogeneous mineral clusters. Changes in the relative abundance of bacterioplankton taxa with increasing water depth point to a link between the activity of certain members of Proteobacteria and the co-recycling of carbon (C), N, and Fe stocks. Such a redox recycling process seems to lead to P stabilisation into organic-rich Fe-(oxyhydr)oxides near and above the anoxic sediment-water interface (SWI).

Water-Based Black Phosphorus Hybrid Nanosheets as a Moldable Platform for Wound Healing Applications

Black phosphorus (BP) nanosheets with unique biocompatibility and superior optical performance have attracted enormous attention in material science. However, their instability and poor solution-processability severely limit their clinical applications. In this work, we demonstrate the use of silk fibroin (SF) as an exfoliating agent to produce thin-layer BP nanosheets with long-term stability and facile solution-processability. Presence of SF prevents rapid oxidation and degradation of the resultant BP nanosheets, enhancing their performance in physiological environment. The SF-modified BP nanosheets exhibit subtle solution-processability and are fabricated into various BP-based material formats. As superior photothermal agents, BP-based wound dressings effectively prevent bacterial infection and promote wound repair. Therefore, this work opens new avenues for unlocking current challenges of BP nanosheet applications for practical biomedical purposes.

Removing Escherichia coli from water using zinc oxide-coated zeolite

The removal of Escherichia coli (E. coli) from water by zinc oxide-coated zeolite (ZOCZ) and ZOCZ's antibacterial properties were examined in laboratory experiments using plate counting method and tests of cell apoptosis. Batch experiments showed that ZOCZ has a maximum removal capacity for E. coli of about 4.34 × 10⁶ CFU g^-1 at 25 °C. Element mappings confirm that zinc ions accumulate in the E. coli cells causing cell death. Pseudo-second-order kinetics and Freundlich isotherms were found to best describe the removal of E. coli, suggesting that a multilayer of E. coli cells forms on the surface of ZOCZ particles.

Adsorption mechanism of extracellular polymeric substances from two bacteria on Ultisol and Alfisol

The primary objective of this study was to identify the capacity and mechanism of extracellular polymeric substance (EPS) adsorption on soil colloids of Alfisol and Ultisol at different pH and ionic strengths. Two kinds of EPS were extracted from Bacillus subtilis and Pseudomonas fluorescens by centrifugation, and their adsorption on Ultisol and Alfisol was investigated using a batch adsorption experiment and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). The average diameter of EPS from B. subtilis and P. fluorescens was 1825 and 1288 nm, respectively, and both the EPS were negatively charged. The zeta potentials of the two EPS became more negative with increasing solution pH from 3 to 8 and less negative with increasing ionic strength from 0 to 80 mM. The maximum adsorption capacity of EPS-C and EPS-N on Alfisol was higher than that on Ultisol, whereas the maximum adsorption capacity of EPS-P on Alfisol was lower than that on Ultisol. The adsorption of EPS-C, EPS-N, and EPS-P of both the EPS on Ultisol and Alfisol decreased with increasing solution pH from 3 to 8. Adsorption of EPS-C, EPS-N, and EPS-P of both the EPS on Alfisol significantly increased with increasing ionic strength from 0 to 10 mM, whereas it remained constant, slightly increased, or reduced, when the ionic strength was increased from 10 to 80 mM. The adsorption of EPS-C, EPS-N, and EPS-P on Ultisol slightly increased with increasing ionic strength from 0 to 80 mM. Saturation coverage determined by ATR-FTIR showed that adsorption of whole EPS on Ultisol was higher than that on Alfisol at pH 6 after 60 min. Thus, electrostatic force between EPS and soil colloids played an important role in EPS adsorption. Besides, proteins and phosphate groups in EPS also contributed to EPS adsorption on soil colloids.

Preferential adhesion of surface groups of Bacillus subtilis on gibbsite at different ionic strengths and pHs revealed by ATR-FTIR spectroscopy

Adhesion of bacteria onto minerals is a ubiquitous process that plays a central role in many biogeochemical, microbiology and environmental processes in soil and sediment. Although bacterial adhesion onto soil minerals such as phyllosilicates and Fe-oxides have been investigated extensively, little is known about the mechanisms for bacterial attachment onto Al-oxides. Here, we explored the adhesion of Bacillus subtilis onto gibbsite (γ-AlOOH) under various ionic strengths (1, 10, 50, and 100 mM NaCl) and pHs (pH 4, 7, and 9) by in-situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. The time evolution of the peak intensities of the attached bacteria suggested that the adhesion underwent an initial rapid reaction followed by a slow pseudo-first-order kinetic stage. Spectral comparison between the attached and free cells, together with the interaction energy calculated with the Derjaguin, Landau, Verwey, and Overbeek (DLVO) theory and the micro-morphology of bacteria-gibbsite complexes, indicated that both electrostatic and chemical (bacterial groups such as phosphate and carboxyl covalently bind to gibbsite) interactions participated in the adhesion processes. Both solution ionic strength (IS) and pH impacted the spectra of attached bacteria, but the peak intensity of different bands changed differently with these two factors, showing a preferential adhesion of surface groups (phosphate, carboxyl, and amide groups) on gibbsite at different conditions. The diverse responses to IS and pH alteration of the forces (chemical bonds, electrostatic attractions, and the hydrophobic interactions) that essentially govern the adhesion might be responsible for the preferential adhesion. These results may help to better understand how bacteria adhere onto soil oxides at molecular scales.

ATP and NADPH coated iron oxide nanoparticles for targeting of highly metabolic tumor cells

The metabolic activity of tumor cells is known to be higher as compared to that of normal cells, which has been previously exploited to deliver nanomedicines to highly metabolic tumor cells. Unfortunately, current strategies, which are mostly based on complex energy sources, such as sugars, showed insufficient accumulation at the target sites. We here report the coating of IONPs with two essential units of cellular metabolism: adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH). ATP and NADPH were directly bound to the IONPs' surface using a simple aqueous method. Both molecules were used as coatings, i.e. as stabilizing agents, but also simultaneously as targeting molecules to deliver IONPs to highly metabolic tumor cells. Indeed, we found that the uptake of ATP-IONPs and NADPH-IONPs is correlated with the metabolic activity of tumor cells, especially regarding their cellular ATP levels and NADPH consumption. We also measured one of the highest MRI r₂ relaxivities for both ATP-IONPs and NADPH-IONPs. With the direct coating of IONPs with ATP and NADPH, we therefore provide an optimal platform to stabilize IONPs and at the same time promising properties for the targeting and detection of highly metabolic tumor cells.

Ironing Out Genes in the Environment: An Experimental Study of the DNA-Goethite Interface

DNA fate in soil plays an important role in the cycling of genetic information in the environment. Adsorption onto mineral surfaces has great impact on this function. This study probes the kinetics, equilibrium behavior and bonding mechanisms associated with adsorption of DNA onto goethite, a common soil mineral. Surface sensitive ATR-FTIR and XPS approaches are applied to directly characterize the DNA-goethite interface. Adsorption kinetics follow a pseudo-first-order model, suggesting adsorption rate is surface limited. Adsorption rate constants increase with DNA concentration, ranging from 3.29 × 10^-3 to 3.55 × 10^-1 min^-1. Equilibrium adsorption, as monitored by ATR-FTIR and XPS, follows the Langmuir model, with a high affinity of DNA for goethite observed (K = 1.25 × 10³ and 9.48 × 10² mL/mg for ATR-FTIR and XPS, respectively). ATR-FTIR and XPS characterization of the structure of surface adsorbed DNA demonstrates inner-sphere coordination between backbone phosphate groups of DNA and goethite. Furthermore, adsorbed DNA retains a B-form, suggesting the DNA helix adsorbs on goethite without degradation or alteration to helical structure, despite binding of backbone phosphate groups. This work advances our understanding of the environmental behavior of DNA by characterizing the mechanism of adsorption onto a prominent soil mineral.

Bacteria attenuation by iron electrocoagulation governed by interactions between bacterial phosphate groups and Fe(III) precipitates

Iron electrocoagulation (Fe-EC) is a low-cost process in which Fe(II) generated from an Fe(0) anode reacts with dissolved O2 to form (1) Fe(III) precipitates with an affinity for bacterial cell walls and (2) bactericidal reactive oxidants. Previous work suggests that Fe-EC is a promising treatment option for groundwater containing arsenic and bacterial contamination. However, the mechanisms of bacteria attenuation and the impact of major groundwater ions are not well understood. In this work, using the model indicator Escherichia coli (E. coli), we show that physical removal via enmeshment in EC precipitate flocs is the primary process of bacteria attenuation in the presence of HCO3(-), which significantly inhibits inactivation, possibly due to a reduction in the lifetime of reactive oxidants. We demonstrate that the adhesion of EC precipitates to cell walls, which results in bacteria encapsulation in flocs, is driven primarily by interactions between EC precipitates and phosphate functional groups on bacteria surfaces. In single solute electrolytes, both P (0.4 mM) and Ca/Mg (1-13 mM) inhibited the adhesion of EC precipitates to bacterial cell walls, whereas Si (0.4 mM) and ionic strength (2-200 mM) did not impact E. coli attenuation. Interestingly, P (0.4 mM) did not affect E. coli attenuation in electrolytes containing Ca/Mg, consistent with bivalent cation bridging between bacterial phosphate groups and inorganic P sorbed to EC precipitates. Finally, we found that EC precipitate adhesion is largely independent of cell wall composition, consistent with comparable densities of phosphate functional groups on Gram-positive and Gram-negative cells. Our results are critical to predict the performance of Fe-EC to eliminate bacterial contaminants from waters with diverse chemical compositions.

Adhesion of Shewanella oneidensis MR-1 to Goethite: A Two-Dimensional Correlation Spectroscopic Study

Bacterial adhesion to mineral surfaces is an important but underappreciated process. To decipher the molecular level process and mechanism, the adhesion of Shewanella oneidensis MR-1 cells to goethite was investigated using flow-cell attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy coupled with two-dimensional correlation spectroscopy (2D-COS) analysis. The FTIR results indicate that bacterial phosphate-moieties play an important role in the formation of mono- and bidentate inner-sphere complexes, whereas carboxylic groups on cell surface only have a minor contribution to its adhesion. The 2D-COS analysis in short-term (0-120 min) and long-term (2-18 h) stages reveal that the adhesion process was in the following sequence: change in H-bonds of proteins on cell surfaces > formation of monodentate inner-sphere surface complexes > formation of outer-sphere surface complexes > transformation of protein secondary structure on cell surfaces > formation of additional bridging bidentate surface complexes. In addition, the adhesion of MR-1 cells on goethite was pH dependent due to pH impacts on the cell structure and the interface charge. The in situ ATR-FTIR integrated with 2D-COS analysis highlights its great potential in exploring complex surface reactions with microbes involved. These results improve our understanding of microbe-mineral interactions at the molecular level and have significant implications for a series of biogeochemical processes.

Iron-mediated stabilization of soil carbon amplifies the benefits of ecological restoration in degraded lands

Recent observations across a 14-year restoration chronosequence have shown an unexpected accumulation of soil organic carbon in strip-mined areas of central Brazil. This was attributed to the rapid plant colonization that followed the incorporation of biosolids into exposed regoliths, but the specific mechanisms involved in the stabilization of carbon inputs from the vegetation remained unclear. Using isotopic and elemental analyses, we tested the hypothesis that plant-derived carbon accumulation was triggered by the formation of iron-coordinated complexes, stabilized into physically protected (occluded) soil fractions. Confirming this hypothesis, we identified a fast formation of microaggregates shortly after the application of iron-rich biosolids, which was characterized by a strong association between pyrophosphate-extractable iron and plant-derived organic matter. The formation of microaggregates preceded the development of macroaggregates, which drastically increased soil carbon content (-140 Mg C/ha) a few years after restoration. Consistent with previous theoretical work, iron-coordinated organic complexes served as nuclei for aggregate formation, reflecting the synergistic effect of biological, chemical, and physical mechanisms of carbon stabilization in developing soils. Nevertheless, iron was not the only factor affecting soil carbon content. The highest carbon accumulation was observed during the period of highest plant diversity (> 30 species; years 3-6), declining significantly with the exclusion of native species by invasive grasses (years 9-14). Furthermore, the increasing dominance of invasive grasses was associated with a steady decline in the concentration of soil nitrogen and phosphorus per unit of accumulated carbon. These results demonstrate the importance of interdependent ecological and biogeochemical processes, and the role of soil-plant interactions in determining the success of restoration efforts. In contrast with previous but unsuccessful attempts to restore mined areas through nutrient application alone, iron-mediated stabilization of vegetation inputs favored the regeneration of a barren stable state that had persisted for over five decades since disturbance. The effectiveness of coupled organic matter and iron "fertilization," combined with management of invasive species, has the possibility to enhance terrestrial carbon sequestration and accelerate the restoration of degraded lands, while addressing important challenges associated with urban waste disposal.

Label-free optical biosensors based on aptamer-functionalized porous silicon scaffolds

A proof-of-concept for a label-free and reagentless optical biosensing platform based on nanostructured porous silicon (PSi) and aptamers is presented in this work. Aptamers are oligonucleotides (single-stranded DNA or RNA) that can bind their targets with high affinity and specificity, making them excellent recognition elements for biosensor design. Here we describe the fabrication and characterization of aptamer-conjugated PSi biosensors, where a previously characterized his-tag binding aptamer (6H7) is used as model system. Exposure of the aptamer-functionalized PSi to the target proteins as well as to complex fluids (i.e., bacteria lysates containing target proteins) results in robust and well-defined changes in the PSi optical interference spectrum, ascribed to specific aptamer-protein binding events occurring within the nanoscale pores, monitored in real time. The biosensors show exceptional stability and can be easily regenerated by a short rinsing step for multiple biosensing analyses. This proof-of-concept study demonstrates the possibility of designing highly stable and specific label-free optical PSi biosensors, employing aptamers as capture probes, holding immense potential for application in detection of a broad range of targets, in a simple yet reliable manner.