ATR–FTIR investigation of mechanisms of Bacillus subtilis adhesion onto variable- and constant-charge soil colloids

Significantly enhanced biodegradation of profenofos by Cupriavidus nantongensis X1T mediated by walnut shell biochar

The feasibility of using walnut shell biochar to mediate biodegradation of Cupriavidus nantongensis X1T for profenofos was investigated. The results of scanning electron microscopy, classical DLVO theory and Fourier transform infrared spectroscopy indicated that strain X1T was stably immobilized on biochar by pore filling, van der Waals attraction, and hydrogen bonding. Profenofos degradation experiments showed that strain X1T immobilized on biochar significantly decomposed profenofos (shortened the half-life by 5.2 folds) by promoting the expression of the degradation gene opdB and the proliferation of strain X1T. The immobilized X1T showed stronger degradation ability than the free X1T at higher initial concentration, lower temperature and pH. The immobilized X1T could maintain 83% of removal efficiency for profenofos after 6 reuse cycles in paddy water. Thus, X1T immobilized using walnut shell biochar as a carrier could be practically applied to biodegradation of organophosphorus pesticides present in agricultural water.

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.

Antimicrobial susceptibility testing using infrared attenuated total reflection (IR-ATR) spectroscopy to monitor metabolic activity

Fast and accurate detection of antimicrobial resistance in pathogens remains a challenge, and with the increase in antimicrobial resistance due to mis- and overuse of antibiotics, it has become an urgent public health problem. We demonstrate how infrared attenuated total reflection (IR-ATR) can be used as a simple method for assessment of bacterial susceptibility to antibiotics. This is achieved by monitoring the metabolic activities of bacterial cells via nutrient consumption and using this as an indicator of bacterial viability. Principal component analysis of the obtained spectra provides a tool for fast and simple discrimination of antimicrobial resistance in the acquired data. We demonstrate this concept using four bacterial strains and four different antibiotics, showing that the change in glucose concentration in the growth medium after 2 h, as monitored by IR-ATR, can be used as a spectroscopic diagnostic technique, to reduce detection time and to improve quality in the assessment of antimicrobial resistance in pathogens.

An experimental study of the effects of bacteria on asphaltene adsorption and wettability alteration of dolomite and quartz

The adsorption of asphaltene on the rock surface and the changes in its wettability are very relevant issues in flow assurance and oil recovery studies, and for carbonate reservoirs, they are even more important. During microbial enhanced oil recovery (MEOR) processes, wettability alteration is considered a crucial mechanism leading to improved oil recovery. Therefore, it is essential to understand the mechanisms of surface wettability changes by bacteria and biosurfactants and find new and reliable methods to prevent asphaltene adsorption. Hence, the main aim of this research was to investigate the effect of a mixture of thiobacillus thiooxidans and thiobacillus ferooxidans microorganisms with an optimum effective temperature of around 30 °C (referred to as mesophilic bacteria), as well as a mixture of two moderate thermophiles Sulfobacillus thermosulfidooxidans for operating temperatures around 50 °C (referred to as moderately thermophilic bacteria) on the adsorption of asphaltene samples isolated from two different crude oils onto main reservoir minerals (i.e., quartz and dolomite). The results indicated that after two weeks of mineral aging in moderate thermophilic bacteria, the adsorption of asphaltene on both minerals increased between 180 and 290%. Fourier-transform infrared spectroscopy (FTIR) analysis for quartz and dolomite samples demonstrated that after aging in bacterial solution, bonds related to the adsorption of bacterial cells and biosurfactant production appear, which are the main factors of change in wettability. Alteration in wettability towards hydrophilicity expands hydrogen bonds on the surface, thus improving asphaltene adsorption due to polar interaction. Asphaltene 1 changed the contact angle of dolomite from 53.85° to 90.51° and asphaltene 2 from 53.85° to 100.41°. However, both strains of bacteria caused a strong water-wetting effect on the dolomite rock samples. The influence of moderate thermophilic bacteria on surface wettability is more significant than that of mesophilic bacteria, which may be caused by the high protein content of these bacteria, which expands hydrogen bonding with the surface. Adsorption of asphaltenes on dolomite rocks previously aged with bacteria showed that the wetted rock samples retained their water-wet state. This study highlights the dual impact of the used microorganisms. On one hand, they significantly reduce contact angles and shift wettability towards a strongly water-wet condition, a crucial positive factor for MEOR. On the other hand, these microorganisms can elevate the adsorption of asphaltenes on reservoir rock minerals, posing a potential challenge in the form of formation damage, particularly in low-permeability reservoirs.

Effects of extracellular enzymes secreted by wild edible fungi mycelia on the surface properties of local soil colloids

The extracellular enzymes secreted by wild edible fungi mycelia participate in a series of physiochemical reactions in soil, thereby changing the surface properties of local soil colloids irreversibly. However, the reaction process and mechanism were generally ignored, leading to a misunderstanding of local soil functions. In this work, the soil samples collected from areas where growing wild edible fungi were selected as model substances, and the effects of extracellular enzymes (α-amylase, β-glucosidase, and peroxidase) secreted by wild edible fungi mycelia on the physicochemical properties of soil colloids were explored. After adding extracellular enzymes, the pores and fissures between the lamellar sheets were observed more obviously and the surface heights decreased significantly, especially after adding α-amylase. The addition of extracellular enzymes increased the electronegativity and the suspension stability of soil colloids owing to the decrease in their polarity and water solubility. The added extracellular enzymes might be adsorbed on the organic and inorganic components in soil colloids and could promote the decomposition of soil organic matter, thereby changing the physicochemical properties of soil colloids and improving the soil quality. The results will lay a theoretical foundation for understanding the soil function in the areas where growing wild edible fungi.

Physiological characteristics, geochemical properties and hydrological variables influencing pathogen migration in subsurface system: What we know or not?

The global outbreak of coronavirus infectious disease-2019 (COVID-19) draws attentions in the transport and spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in aerosols, wastewater, surface water and solid wastes. As pathogens eventually enter the subsurface system, e.g., soils in the vadose zone and groundwater in the aquifers, they might survive for a prolonged period of time owing to the uniqueness of subsurface environment. In addition, pathogens can transport in groundwater and contaminate surrounding drinking water sources, possessing long-term and concealed risks to human society. This work critically reviews the influential factors of pathogen migration, unravelling the impacts of pathogenic characteristics, vadose zone physiochemical properties and hydrological variables on the migration of typical pathogens in subsurface system. An assessment algorithm and two rating/weighting schemes are proposed to evaluate the migration abilities and risks of pathogens in subsurface environment. As there is still no evidence about the presence and distribution of SARS-CoV-2 in the vadose zones and aquifers, this study also discusses the migration potential and behavior of SARS-CoV-2 viruses in subsurface environment, offering prospective clues and suggestions for its potential risks in drinking water and effective prevention and control from hydrogeological points of view.

Decreased levels and ecological risks of disinfection by-product chloroform in a field-scale artificial groundwater recharge project by colloid supplement

To bolster freshwater supply, artificial groundwater recharge with recycled water has increasingly attracted research attentions and interests. However, artificial groundwater recharge has potential risks to groundwater quality, as recharge water disinfection is frequently used for pathogen inactivation and causes the concerns of disinfection by-products (DBPs). Colloid supplement is a good approach solving this problem, but its roles in mitigating DBPs remains unclear. In this study, we collected 20 groundwater and soil samples from a field-scale groundwater recharge project, and explored the impacts of silica colloids on chloroform migration and groundwater bacterial communities during the recharge process. Water physicochemical variables changed along the recharge time, and colloid supplement significantly reduced chloroform formation and slowed its migration in groundwater. Bacterial communities in groundwater, river water and recharge water were significantly different. Gammaproteobacteria in recharge water (71.7%) was more abundant than in river water (30.5%) and groundwater (33.5%), while Actinobacteria dominated groundwater (40.6%). After recharge, Gammaproteobacteria increased more with colloid supplement (75.7%) than without (52.6%), attributing to its dominance in soils (74.6%). Our results suggested more bacterial lineages released from soils into aquifer by silica colloid supplement, owing to the competitive adsorption encouraging microbial transfer, especially Gram-negative bacteria. Our findings unraveled the effects of colloid supplement on chloroform formation and migration during artificial groundwater recharge, which consequently altered groundwater bacterial communities, and offered valuable suggestions for the safety management of DBPs in aquifer recharge.

Inhibition of phosphate sorptions on four soil colloids by two bacteria

Ion sorption on soil and sediment has been reported to be potentially affected by bacteria which may interact both physically and chemically with solid surfaces. However, whether and how bacteria affect the sorption of inorganic phosphate (P) on soil colloids remains poorly known. Here, we comparably investigated the P sorption on four soil colloids (three highly weathered soils including two Oxisols and one Ultisol and one weakly weathered soil Alfisol) and their complexes with Bacillus subtilis and Pseudomonas fluorescens. Batch experiments showed a notable reduction in P sorption on the colloids of highly weathered soils by the two bacteria at varying P concentrations and pHs; whereas that on the colloids of Alfisol appeared to be unaffected by the bacteria. The inhibitory effect was confirmed by both greater decline in P sorption at higher bacteria dosages and the ability of the bacteria to desorb P pre-adsorbed on the colloids. Further evidence was given by isothermal titration calorimetric experiments which revealed an alteration in enthalpy change caused by the bacteria for P sorption on Oxisol but not for that on Alfisol. The B. subtilis was more efficient in suppressing P sorption than the P. fluorescens, indicating a dependence of the inhibition on bacterium type. After association with bacteria, zeta potentials of the soil colloids decreased considerably. The decrease positively correlated with the decline in P sorption, regardless of soil and bacterium types, demonstrating that the increment in negative charges of soil colloids by bacteria probably contributed to the inhibition. In addition, scanning electron microscopic observation and the Derjaguin-Landau-Verwey-Overbeek theory prediction suggested appreciable physical and chemical interactions between the bacteria and the highly weathered soil colloids, which might be another contributor to the inhibition. These findings expand our understandings on how bacteria mobilize legacy P in soils and sediments.

The mechanism for inhibiting acidification of variable charge soils by adhered Pseudomonas fluorescens

Acidification in variable charge soils is on the rise due to increased acid deposition and use of nitrogenous fertilizers. The associated low pH and cation exchange capacity make the soils prone to depleted base cations and increased levels of Al³⁺. Consequently, Al toxicity to plants and soil infertility decrease crop yield. This study was designed to investigate the effect of Pseudomonas fluorescens on the acidification of two Ultisols. The simulated acidification experiment demonstrated that the pH of bacteria-treated soil was higher than that of control under similar conditions, suggesting that the adhered bacteria inhibited soil acidification. This observation was attributed to the association of organic anions (RCOO^- or RO^-) on bacteria with H⁺ to form neutral molecules (RCOOH or ROH) and reducing the activity of H⁺ in solution. The bacteria also inhibited the increase in soil soluble Al and exchangeable Al during soil acidification. The adhesion of bacteria on the soils increased soil effective cation exchange capacity (ECEC) and exchangeable base cations at each pH compared to control. The release of exchangeable base cations from bacteria-treated soil, and the decrease in soil ECEC and exchangeable base cations with decreasing pH confirmed that protonation of organic anions on adhered bacteria was mainly responsible for the inhibition of soil acidification. The change of zeta potential of the bacteria with pH and the ART-FTIR analysis at various pH provided more evidence for this mechanism. Therefore, the bacteria in variable charge soils played an important role in retarding soil acidification.

Adhesion of Sphingomonas sp. GY2B onto montmorillonite: A combination study by thermodynamics and the extended DLVO theory

Bacterial adhesion on mineral surface are of fundamental importance in geochemical processes and biogeochemical cycling, such as mineral transformation and clay-mediated biodegradation. In this study, thermodynamics analysis combined with classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory as well as the extended DLVO (XDLVO) theory were employed to investigate the adhesion of the Gram-negative PAH-degrading bacteria Sphingomonas sp. GY2B on montmorillonite (Mt). Scanning electron microscopy (SEM), Fourier transform infrared spectra (FTIR) and X-ray photoelectron spectroscopy (XPS) indicated the affinity of GY2B for Mt, and the experimental results could be described well by pseudo-second-order (R2 = 0.997) and Langmuir model (R2 = 0.995). The thermodynamics analysis revealed the physical nature of bacterial adhesion onto Mt, which was confirmed by the XDLVO theory. The related surface properties (Zeta potential, hydrodynamic diameter and hydrophobicity) at different ionic strength were determined and the interaction energy between Mt and GY2B were also calculated using the DLVO and XDLVO theories in KCl or CaCl2 solution. At low ionic strength (≤ 20 mM), GY2B adhesion onto Mt was primarily driven by long-range DLVO forces (e.g. electrostatic repulsion), while short-range (separation distance < 5 nm) Van der Waals and hydrophobic interactions played more important roles in the bacterial adhesion at higher ionic strength (50-100 mM). In addition, Mt had a better adhesion capacity to bacteria in Ca2+ solution than that in K+ solution, owing to less negative charge and lower energy barrier in mineral-bacteria system in Ca2+ solution. Overall, the adhesion of bacteria onto Mt could be evaluated well on the basis of the XDLVO theory along with thermodynamics analysis. This study provides valuable insights into the clay-mediated microbial remediation of hydrophobic organic contaminants in the environment.

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.