Inhibition of free DNA degradation by the deformation of DNA exposed to trace polycyclic aromatic hydrocarbon contaminants

Interaction between polycyclic aromatic hydrocarbons and thymine (T)-base induces double-strand DNA distortion in different species

Polycyclic aromatic hydrocarbons (PAHs) are potent inhibitors of DNA that can induce genetic damage, abnormal gene expression, and metabolic disorders upon interfacing with biological macromolecules. However, the mechanism of their interactions with DNA remains elusive. Therefore, this study selected three representative PAHs, including phenanthrene (Phen), pyrene (Pyre), and benzo[a]pyrene (B[a]P), and explored their binding mechanisms with the double-strand DNA (dsDNA) from different species, including 1J1V (Escherichia coli), 6J5B (Arabidopsis thaliana), and 6Q1V (Homo sapiens). The results revealed that binding between PAHs and dsDNA occurred in the groove via van der Waals forces and π-π stacking, with the carboxyl oxygen atom of the thymine (T)-base within dsDNA being the key binding site. This result was further confirmed by the spectroscopic experiments, where significant changes in the peak of the T-base were observed after PAHs-dsDNA binding. More interestingly, the total binding energies of Pyre with the three dsDNA were -138.800 kJ/mol (Pyre-1J1V), -105.523 kJ/mol (Pyre-6J5B), and -127.567 kJ/mol (Pyre-6Q1V), respectively, all of which were higher than those of Phen and B[a]P. This suggests that that Pyre has the strongest dsDNA binding ability. Additionally, analysis of the thermodynamic parameters indicated that the interactions between the three PAHs and dsDNA were exothermic reactions. In contrast, the Pyre-dsDNA interaction predominantly involved van der Waals forces and hydrogen bonding due to the enthalpy change (∆H) < 0 and entropy change (∆S) < 0, while the Phen-dsDNA and B[a]P-dsDNA interactions predominantly involved hydrophobic forces due to ∆H > 0 and ∆S > 0. Furthermore, Pyre caused local distortion of dsDNA, which was more pronounced under atomic force microscopy (AFM). In summary, this study has unveiled a new phenomenon of binding between PAHs and dsDNA. This sheds light on the carcinogenic potential and environmental impacts of PAHs pollution.

Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review

Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.

Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC)

High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from 13C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from 13C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.

Insights into the enzymatic degradation of DNA expedited by typical perfluoroalkyl acids

Perfluoroalkyl acids (PFAAs) are considered forever chemicals, gaining increasing attention for their hazardous impacts. However, the ecological effects of PFAAs remain unclear. Environmental DNA (eDNA), as the environmental gene pool, is often collected for evaluating the ecotoxicological effects of pollutants. In this study, we found that all PFAAs investigated, including perfluorohexanoic acid, perfluorooctanoic acid, perfluorononanoic acid, and perfluorooctane sulfonate, even at low concentrations (0.02 and 0.05 mg/L), expedited the enzymatic degradation of DNA in a nonlinear dose-effect relationship, with DNA degradation fragment sizes being lower than 1,000 bp and 200 bp after 15 and 30 min of degradation, respectively. This phenomenon was attributed to the binding interaction between PFAAs and AT bases in DNA via groove binding. van der Waals force (especially dispersion force) and hydrogen bonding are the main binding forces. DNA binding with PFAAs led to decreased base stacking and right-handed helicity, resulting in loose DNA structure exposing more digestion sites for degrading enzymes, and accelerating the enzymatic degradation of DNA. The global ecological risk evaluation results indicated that PFAA contamination could cause medium and high molecular ecological risk in 497 samples from 11 contamination-hot countries (such as the USA, Canada, and China). The findings of this study show new insights into the influence of PFAAs on the environmental fates of biomacromolecules and reveal the hidden molecular ecological effects of PFAAs in the environment.

Degradation and adsorption of synthetic DNA water tracers in environmental matrices

Synthetic DNA tracers are gaining interest as tools for tracking contamination pathways and hydraulic connections in surface water and groundwater systems. However, few quantitative data exist that describe DNA tracer degradation and adsorption in environmental matrices. We undertook laboratory experiments to quantify the degradation of multiple double-stranded DNA tracers in stream water, groundwater, and domestic and dairy-shed effluent, and adsorption to stream sediments, soils, coastal sand aquifer media and alluvial sandy gravel aquifer media. Faster DNA tracer degradation seemed to be associated with high bacterial concentrations in the liquid phase. Overall, the degradation of the 352 base pair (bp) DNA tracers in the aqueous phase was significantly (P = 0.018) slower than that of the 302 bp DNA tracers. Although the tracers' internal amplicon lengths were similar, the longer non-amplified flanking regions of the 352 bp tracers may better protect them from environmental degradation. Thermodynamic analysis suggests that longer flanking regions contribute to greater tracer stability. This finding may explain our previous field observations that 352 bp tracer mass reductions were often lower than 302 bp tracer mass reductions. The 2 sets of DNA tracers did not differ significantly regarding their adsorption to stream sediment-stream water or aquifer media-groundwater mixtures (P > 0.067), but the 352 bp tracers showed significantly less adsorption to soil-effluent mixtures than the 302 bp tracers (P = 0.005). The DNA tracers' adsorption to soil-effluent mixtures was comparatively less than their adsorption to the aquifer media-groundwater and stream sediment-stream water mixtures, suggesting that DNA tracers may compete with like-charged organic matter for adsorption sites. These findings provide insights into the fate of DNA tracers in the environment. The DNA tracers' degradation rate constants determined in this study for a range of environmental conditions could assist the design of future field investigations.

Accelerated spread of antibiotic resistance genes (ARGs) induced by non-antibiotic conditions: Roles and mechanisms

The global spread of antibiotic resistance genes (ARGs) has wreaked havoc with the treatment efficiency of antibiotics and, ultimately, anti-microbial chemotherapy, and has been conventionally attributed to the abuse and misuse of antibiotics. However, the ancient ARGs have alterative functions in bacterial physiology and thus they could be co-regulated by non-antibiotic conditions. Recent research has demonstrated that many non-antibiotic chemicals such as microplastics, metallic nanoparticles and non-antibiotic drugs, as well as some non-antibiotic conditions, can accelerate the dissemination of ARGs. These results suggested that the role of antibiotics might have been previously overestimated whereas the effects of non-antibiotic conditions were possibly ignored. Thus, in an attempt to fully understand the fate and behavior of ARGs in the eco-system, it is urgent to critically highlight the role and mechanisms of non-antibiotic chemicals and related environmental factors in the spread of ARGs. To this end, this timely review assessed the evolution of ARGs, especially its function alteration, summarized the non-antibiotic chemicals promoting the spread of ARGs, evaluated the non-antibiotic conditions related to ARG dissemination and analyzed the molecular mechanisms related to spread of ARGs induced by the non-antibiotic factors. Finally, this review then provided several critical perspectives for future research.

Dynamics, gene transfer, and ecological function of intracellular and extracellular DNA in environmental microbiome

Extracellular DNA (eDNA) and intracellular DNA (iDNA) extensively exist in both terrestrial and aquatic environment systems and have been found to play a significant role in the nutrient cycling and genetic information transmission between the environment and microorganisms. As inert DNA sequences, eDNA is able to present stability in the environment from the ribosome enzyme lysis, therein acting as the historical genetic information archive of the microbiome. As a consequence, both eDNA and iDNA can shed light on the functional gene variety and the corresponding microbial activity. In addition, eDNA is a ubiquitous composition of the cell membrane, which exerts a great impact on the resistance of outer stress from environmental pollutants, such as heavy metals, antibiotics, pesticides, and so on. This study focuses on the environmental dynamics and the ecological functions of the eDNA and iDNA from the perspectives of environmental behavior, genetic information transmission, resistance to the environmental contaminants, and so on. By reviewing the status quo and the future vista of the e/iDNAs research, this article sheds light on exploring the ecological functioning of the e/iDNAs in the environmental microbiome.

Biochar effectively inhibits the horizontal transfer of antibiotic resistance genes via transformation

The rapid spread of antibiotic resistance genes (ARGs) has posed a risk to human health. Here, the effects of biochar (BC) on the horizontal transfer of ARG-carrying plasmids to Escherichia coli via transformation were systematically investigated. BC could significantly inhibit the transformation of ARGs and the inhibition degree increased with pyrolysis temperature. Rice straw-derived BC showed a stronger inhibitory effect on the transformation of ARGs than that of peanut shell-derived BC from the same pyrolysis temperature. The inhibitory effect of BC from low pyrolysis temperature (300 ℃) was mainly caused by BC dissolutions, while it was mainly attributed to BC solids for high pyrolysis temperature (700 ℃) BC. BC dissolutions could induce intramolecular condensation and even agglomeration of plasmids, hindering their transformation into competent bacteria. The cell membrane permeability was slightly decreased in BC dissolutions, which might also contribute to the inhibitory effect. Plasmid can be adsorbed by BC solids and the adsorption increased with BC pyrolysis temperature. Meanwhile, BC-adsorbed plasmid could hardly be transformed into E. coli. BC solids could also deactivate E. coli and thereby inhibit their uptake of ARGs. These findings provide a way using BC to limit the spread of ARGs in the environment.

Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil

Exploring the metabolic characteristics of indigenous PAH degraders is critical to understanding the PAH bioremediation mechanism in the natural environment. While stable-isotopic probing (SIP) is a viable method to identify functional microorganisms in complex environments, the metabolic characteristics of uncultured degraders are still elusive. Here, we investigated the naphthalene (NAP) biodegradation of petroleum polluted soils by combining SIP, amplicon sequencing and metagenome binning. Based on the SIP and amplicon sequencing results, an uncultured Gammaproteobacterium sp. was identified as the key NAP degrader. Additionally, the assembled genome of this uncultured degrader was successfully obtained from the ¹³ C-DNA metagenomes by matching its 16S rRNA gene with the SIP identified OTU sequence. Meanwhile, a number of NAP degrading genes encoding naphthalene/PAH dioxygenases were identified in this genome, further confirming the direct involvement of this indigenous degrader in the NAP degradation. The degrader contained genes related to the metabolisms of several carbon sources, energy substances and vitamins, illuminating potential reasons for why microorganisms cannot be cultivated and finally realize their cultivation. Our findings provide novel information on the mechanisms of in situ PAH biodegradation and add to our current knowledge on the cultivation of non-culturable microorganisms by combining both SIP and metagenome binning.

Binding Force and Site-Determined Desorption and Fragmentation of Antibiotic Resistance Genes from Metallic Nanomaterials

Interfacial interactions between antibiotic resistance genes (ARGs) and metallic nanomaterials (NMs) lead to adsorption and fragmentation of ARGs, which can provide new avenues for selecting NMs to control ARGs. This study compared the adsorptive interactions of ARGs (tetM-carrying plasmids) with two metallic NMs (ca. 20 nm), i.e., titanium dioxide (nTiO₂) and zero-valent iron (nZVI). nZVI had a higher adsorption rate (0.06 min^-1) and capacity (4.29 mg/g) for ARGs than nTiO₂ (0.05 min^-1 and 2.15 mg/g, respectively). No desorption of ARGs from either NMs was observed in the adsorptive background solution, isopropanol or urea solutions, but nZVI- and nTiO₂-adsorbed ARGs were effectively desorbed in NaOH and NaH₂PO₄ solutions, respectively. Molecular dynamics simulation revealed that nTiO₂ mainly bound with ARGs through electrostatic attraction, while nZVI bound with PO₄^3- of the ARG phosphate backbones through Fe-O-P coordination. The ARGs desorbed from nTiO₂ remained intact, while the desorbed ARGs from nZVI were splintered into small fragments irrelevant to DNA base composition or sequence location. The ARG removal by nZVI remained effective in the presence of PO₄^3-, natural organic matter, or protein at environmentally relevant concentrations and in surface water samples. These findings indicate that nZVI can be a promising nanomaterial to treat ARG pollution.

Enrichment of antibiotic resistance genes (ARGs) in polyaromatic hydrocarbon-contaminated soils: a major challenge for environmental health

Polyaromatic hydrocarbons (PAHs) are widely spread ecological contaminants. Antibiotic resistance genes (ARGs) are present with mobile genetic elements (MGE) in the bacteria. There are molecular evidences that PAHs may induce the development of ARGs in contaminated soils. Also, the abundance of ARGs related to tetracycline, sulfonamides, aminoglycosides, ampicillin, and fluoroquinolones is high in PAH-contaminated environments. Genes encoding the efflux pump are located in the MGE and, along with class 1 integrons, have a significant role as a connecting link between PAH contamination and enrichment of ARGs. The horizontal gene transfer mechanisms further make this interaction more dynamic. Therefore, necessary steps to control ARGs into the environment and risk management plan of PAHs should be enforced. In this review, influence of PAH on evolution of ARGs in the contaminated soil, and its spread in the environment, has been described. The co-occurrence of antibiotic resistance and PAH degradation abilities in bacterial isolates has raised the concerns. Also, presence of ARGs in the microbiome of PAH-contaminated soil has been discussed as environmental hotspots for ARG spread. In addition to this, the possible links of molecular interactions between ARGs and PAHs, and their effect on environmental health has been explored.

Water tracking in surface water, groundwater and soils using free and alginate-chitosan encapsulated synthetic DNA tracers

Investigating contamination pathways and hydraulic connections in complex hydrological systems will benefit greatly from multi-tracer approaches. The use of non-toxic synthetic DNA tracers is promising, because unlimited numbers of tracers, each with a unique DNA identifier, could be used concurrently and detected at extremely low concentrations. This study aimed to develop multiple synthetic DNA tracers as free molecules and encapsulated within microparticles of biocompatible and biodegradable alginate and chitosan, and to validate their field utility in different systems. Experiments encompassing a wide range of conditions and flow rates (19 cm/day-39 km/day) were conducted in a stream, an alluvial gravel aquifer, a fine coastal sand aquifer, and in lysimeters containing undisturbed silt loam over gravels. The DNA tracers were identifiable in all field conditions investigated, and they were directly detectable in the stream at a distance of at least 1 km. The DNA tracers showed promise at tracking fast-flowing water in the stream, gravel aquifer and permeable soils, but were unsatisfactory at tracking slow-moving groundwater in the fine sand aquifer. In the surface water experiments, the microencapsulated DNA tracers' concentrations and mass recoveries were 1-3 orders of magnitude greater than those of the free DNA tracers, because encapsulation protected them from environmental stressors and they were more negatively charged. The opposite was observed in the gravel aquifer, probably due to microparticle filtration by the aquifer media. Although these new DNA tracers showed promise in proof-of-concept field validations, further work is needed before they can be used for large-scale investigations.

Enzymatic degradation of extracellular DNA exposed to chlorpyrifos and chlorpyrifos-methyl in an aqueous system

The persistence of extracellular DNA (eDNA) is crucial for ensuring species diversity and ecological function in aquatic systems. However, scarce information exists about the impact of pesticides on eDNA, although they often co-exist in the aquatic environment. Using a variety of spectroscopic analyses, eDNA degradation and the associated alterations in DNA secondary structure was investigated by exposing DNase I to tested DNA in the presence of chlorpyrifos, a commonly used organophosphate pesticide. Molecular dynamics simulation was used to explore the weak interactions between the tested DNA and chlorpyrifos. The results indicated that chlorpyrifos significantly enhanced DNA degradation without affecting the enzyme activity of DNase I in an aqueous system. Spectroscopic experiments confirmed that chlorpyrifos and the analog chlorpyrifos-methyl could bind with DNA to cause the bases noncovalent stacking interaction. Molecular simulations further demonstrated that pesticide binding with DNA molecules caused widening of the DNA grooves and destruction of the hydrated layer, which enhanced DNA degradation. The findings presented herein provide novel insight into the genotoxicity and ecotoxicity of chlorpyrifos and chlorpyrifos-methyl, as well as their impacts on DNA persistence in aquatic environments.

Stable-Isotope Probing-Enabled Cultivation of the Indigenous Bacterium Ralstonia sp. Strain M1, Capable of Degrading Phenanthrene and Biphenyl in Industrial Wastewater

To identify and obtain the indigenous degraders metabolizing phenanthrene (PHE) and biphenyl (BP) from the complex microbial community within industrial wastewater, DNA-based stable-isotope probing (DNA-SIP) and cultivation-based methods were applied in the present study. DNA-SIP results showed that two bacterial taxa (Vogesella and Alicyclobacillus) were considered the key biodegraders responsible for PHE biodegradation only, whereas Bacillus and Cupriavidus were involved in BP degradation. Vogesella and Alicyclobacillus have not been linked with PHE degradation previously. Additionally, DNA-SIP helped reveal the taxonomic identity of Ralstonia-like degraders involved in both PHE and BP degradation. To target the separation of functional Ralstonia-like degraders from the wastewater, we modified the traditional cultivation medium and culture conditions. Finally, an indigenous PHE- and BP-degrading strain, Ralstonia pickettii M1, was isolated via a cultivation-dependent method, and its role in PHE and BP degradation was confirmed by enrichment of the 16S rRNA gene and distinctive dioxygenase genes in the DNA-SIP experiment. Our study has successfully established a program for the application of DNA-SIP in the isolation of the active functional degraders from an environment. It also deepens our insight into the diversity of indigenous PHE- and BP-degrading communities.IMPORTANCE The comprehensive treatment of wastewater in industrial parks suffers from the presence of multiple persistent organic pollutants (POPs), such as polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), which reduce the activity of activated sludge and are difficult to eliminate. Characterizing and applying active bacterial degraders metabolizing multiple POPs therefore helps to reveal the mechanisms of synergistic metabolism and to improve wastewater treatment efficiency in industrial parks. To date, SIP studies have successfully investigated the biodegradation of PAHs or PCBs in real-world habitats. DNA-SIP facilitates the isolation of target microorganisms that pose environmental concerns. Here, an indigenous phenanthrene (PHE)- and biphenyl (BP)-degrading strain in wastewater, Ralstonia pickettii M1, was isolated via a cultivation-dependent method, and its role in PHE and BP degradation was confirmed by DNA-SIP. Our study provides a routine protocol for the application of DNA-SIP in the isolation of the active functional degraders from an environment.

Biphenyl-Metabolizing Microbial Community and a Functional Operon Revealed in E-Waste-Contaminated Soil

Primitive electronic waste (e-waste) recycling activities release massive amounts of persistent organic pollutants (POPs) and heavy metals into surrounding soils, posing a major threat to the ecosystem and human health. Microbes capable of metabolizing POPs play important roles in POPs remediation in soils, but their phylotypes and functions remain unclear. Polychlorinated biphenyls (PCBs), one of the main pollutants in e-waste contaminated soils, have drawn increasing attention due to their high persistence, toxicity, and bioaccumulation. In the present study, we employed the culture-independent method of DNA stable-isotope probing to identify active biphenyl and PCB degraders in e-waste-contaminated soil. A total of 19 rare operational taxonomic units and three dominant bacterial genera ( Ralstonia, Cupriavidus, and uncultured bacterium DA101) were enriched in the ¹³C heavy DNA fraction, confirming their functions in PCBs metabolism. Additionally, a 13.8 kb bph operon was amplified, containing a bphA gene labeled by ¹³C that was concentrated in the heavy DNA fraction. The tetranucleotide signature characteristics of the bph operon suggest that it originated from Ralstonia. The bph operon may be shared by horizontal gene transfer because it contains a transposon gene and is found in various bacterial species. This study gives us a deeper understanding of PCB-degrading mechanisms and provides a potential resource for the bioremediation of PCBs-contaminated soils.

DNA Facilitates the Sorption of Polycyclic Aromatic Hydrocarbons on Montmorillonites

The sorption of polycyclic aromatic hydrocarbons (PAHs) to montmorillonites is largely influenced by their interactions with dissolved organic matter (DOM). However, the role of DOM rather than humic and fulvic acids (e.g., extracellular DNA) in the PAH sorption to soil clays is little known. Here, we demonstrate that extracellular double-stranded salmon testes DNA substantially increased the sorption of phenanthrene and pyrene to Na-, Ca-, and Fe-modified montmorillonites. All PAH sorption isotherms fitted the linear and Freundlich models reasonably well ( R² = 0.918-0.999). Distribution coefficients were increased from 0.0458-0.103 and 0.0493-0.141 L/g at 0 mg/L DNA to 0.413-0.589 and 0.385-0.560 L/g at 10 mg/L DNA for phenanthrene and pyrene, respectively. Spectroscopic and computational chemistry analyses confirmed that PAHs were first inserted into DNA by binding with the nucleobases via van der Waals and π-π electron donor-acceptor interactions. Compared to PAHs, the DNA-PAH complex can be more easily sorbed to cation-modified montmorillonites by complexation between DNA phosphate and exchangeable cations in addition to intercalation into clay interlayers. This work highlights the importance of understanding the control on contaminant sorption by many organic compounds that are ubiquitous in soils but not represented by humic and fulvic acids.

A DNA Tracer System for Hydrological Environment Investigations

To monitor and manage hydrological pollution effectively, tracing sources of pollutants is of great importance and also is in urgent need. A variety of tracers have been developed such as isotopes, silica, bromide, and dyes; however, practical limitations of these traditional tracers still exist such as lack of multiplexed, multipoint tracing and interference of background noise. To overcome these limitations, a new tracing system based on DNA nanomaterials, namely DNA tracer, has already been developed. DNA tracers possess remarkable advantages including sufficient species, specificity, environmental friendly, stable migration, and high sensitivity as well as allowing for multipoints tracing. In this review article, we introduce the molecular design, synthesis, protection and signal readout strategies of DNA tracers, compare the advantages and disadvantages of DNA tracer with traditional tracers, and summarize the-state-of-art applications in hydrological environment investigations. In the end, we provide our perspective on the future development of DNA tracers.

Nature and Value of Freely Dissolved EPS Ecosystem Services: Insight into Molecular Coupling Mechanisms for Regulating Metal Toxicity

Extracellular polymeric substances (EPSs) dispersed in natural waters play a significant role in relieving impacts to microbial survival associated with heavy metal release, yet little is known about the association of freely dissolved EPS ecosystem services with metal transformation in natural waters. Here, we demonstrate that dispersive EPSs mitigate the metal toxicity to microbial cells through an associative coordination reaction. Microtitrimetry coupled with fluorescence spectroscopy ascribes the combination of freely dissolved EPSs from Escherichia coli (E. coli) with Cu²⁺/Cd²⁺ to a coordination reaction associated with chemical static quenching. Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and computational chemistry confirm that carboxyl residues in protein-like substances of the EPSs are responsible for the coordination. Frontier molecular orbitals (MOs) of a deprotonated carboxyl integrate with the occupied d orbitals of Cu²⁺ and/or d, s orbitals of Cd²⁺ to form metal-EPS complexes. Microcosmic systems show that because the metal-EPS complexes decrease cellular absorbability of metals, E. coli survivals increase by 4.3 times for Cu²⁺ and 1.6 times for Cd²⁺, respectively. Based on bonding energies for six metals-EPS coordination, an associative toxic effect further confirms that increased bonding energies facilitate retardation of metals in the EPS matrix, protecting against E. coli apoptosis.

Alkali-earth metal bridges formed in biofilm matrices regulate the uptake of fluoroquinolone antibiotics and protect against bacterial apoptosis

Bacterially extracellular biofilms play a critical role in relieving toxicity of fluoroquinolone antibiotic (FQA) pollutants, yet it is unclear whether antibiotic attack may be defused by a bacterial one-two punch strategy associated with metal-reinforced detoxification efficiency. Our findings help to assign functions to specific structural features of biofilms, as they strongly imply a molecularly regulated mechanism by which freely accessed alkali-earth metals in natural waters affect the cellular uptake of FQAs at the water-biofilm interface. Specifically, formation of alkali-earth-metal (Ca²⁺ or Mg²⁺) bridge between modeling ciprofloxacin and biofilms of Escherichia coli regulates the trans-biofilm transport rate of FQAs towards cells (135-nm-thick biofilm). As the addition of Ca²⁺ and Mg²⁺ (0-3.5 mmol/L, CIP: 1.25 μmol/L), the transport rates were reduced to 52.4% and 63.0%, respectively. Computational chemistry analysis further demonstrated a deprotonated carboxyl in the tryptophan residues of biofilms acted as a major bridge site, of which one side is a metal and the other is a metal girder jointly connected to the carboxyl and carbonyl of a FQA. The bacterial growth rate depends on the bridging energy at anchoring site, which underlines the environmental importance of metal bridge formed in biofilm matrices in bacterially antibiotic resistance.

Sequestration of nanoparticles by an EPS matrix reduces the particle-specific bactericidal activity

Most artificial nanomaterials are known to exhibit broad-spectrum bactericidal activity; however, the defence mechanisms that bacteria use based on extracellular polymeric substances (EPS) to detoxify nanoparticles (NPs) are not well known. We ruled out the possibility of ion-specific bactericidal activity by showing the lack of equivalent dissolved zinc and silicon toxicity and determined the particle-specific toxicity of ZnO and SiO2 nanoparticles (ZnONPs/SiO2NPs) through dialysis isolation experiments. Surprisingly, the manipulation of the E. coli EPS (i.e., no EPS manipulation or EPS removal by sonication/centrifugation) showed that their particle-specific bactericidal activity could be antagonized by NP-EPS sequestration. The survival rates of pristine E. coli (no EPS manipulation) reached 65% (ZnONPs, 500 mg L(-1)) and 79% (SiO2NPs, 500 mg L(-1)), whereas survival rates following EPS removal by sonication/centrifugation were 11% and 63%, respectively. Transmission electron microscopy (TEM) combined with fluorescence micro-titration analysis and Fourier-transform infrared spectroscopy (FTIR) showed that protein-like substances (N-H and C-N in amide II) and secondary carbonyl groups (C=O) in the carboxylic acids of EPS acted as important binding sites that were involved in NP sequestration. Accordingly, the amount and composition of EPS produced by bacteria have important implications for the bactericidal efficacy and potential environmental effects of NPs.

Noncovalent Binding of Polycyclic Aromatic Hydrocarbons with Genetic Bases Reducing the in Vitro Lateral Transfer of Antibiotic Resistant Genes

In current studies of noncovalent interactions of polycyclic aromatic hydrocarbons (PAHs) with genetic units, the impact of such interactions on gene transfer has not been explored. In this study, we examined the association of some widely occurring PAHs (phenanthrene, pyrene, benzo[g,h,i]perylene, and other congeners) with antibiotic resistant plasmids (pUC19). Small molecular PAHs (e.g., phenanthrene) bind effectively with plasmids to form a loosely clew-like plasmid-PAH complex (16.5-49.5 nm), resulting in reduced transformation of ampicillin resistance gene (Ampr). The in vitro transcription analysis demonstrated that reduced transformation of Ampr in plasmids results from the PAH-inhibited Ampr transcription to RNA. Fluorescence microtitration coupled with Fourier transform infrared spectroscopy (FTIR) and theoretical interaction models showed that adenine in plasmid has a stronger capacity to sequester small Phen and Pyre molecules via a π-π attraction. Changes in Gibbs free energy (ΔG) suggest that the CT-PAH model reliably depicts the plasmid-PAH interaction through a noncovalently physical sorption mechanism. Considering the wide occurrence of PAHs and antibiotic resistant genes (ARGs) in the environment, our findings suggest that small-sized PAHs can well affect the behavior of ARGs via above-described noncovalent interactions.

Bacterial diversity losses: A potential extracellular driving mechanism involving the molecular ecological function of hydrophobic polycyclic aromatic hydrocarbons

The DNA transformation is vital to the horizontal gene transfer (HGT). The low-efficiency transformation of bare plasmid exposed to hydrophobic polycyclic aromatic hydrocarbons (PAHs) decreases the gene transfer level, and is possibly related to the loss of bacterial diversity at present. PAHs have great affinity for bare DNA through dispersion force and π–π overlap between PAHs and bases. These noncovalent interactions between PAHs and bases reduced the transformational efficiency of plasmid into bacterial recipients. Meanwhile these low-efficiency transformations for plasmid are controlled by the ions like Ca²⁺ in environment, in turn, presence of 0.5 mmol L⁻¹ Ca²⁺ recovered the efficiency from 3.2 (phenanthrene), 3.5 (pyrene) to about 4.45 and 4.75, respectively. The combination of Ca²⁺ with the —POO⁻— groups in DNA forms strong electrovalent bonds, weakening the molecular effect of DNA on PAHs and in turn promoting the gene transfer exposed to PAHs.

Oxidation of polycyclic aromatic hydrocarbons by horseradish peroxidase in water containing an organic cosolvent

Polycyclic aromatic hydrocarbons (PAHs) are environmental contaminants that are toxic, mutagenic, and carcinogenic. We investigated the horseradish peroxidase (HRP)-catalyzed oxidation of PAHs in water containing N,N-dimethylformamide. Four PAHs (anthracene, phenanthrene, pyrene, and fluoranthene) were investigated using single-PAH and mixed-PAH systems. The results provide useful information regarding the preferential oxidation of anthracene over other PAHs regardless of the reaction time, enzyme dosage, and hydrogen peroxide concentration. The removal of PAHs was found to be very strongly correlated with the ionization potential (IP), and much greater PAH oxidation was observed at a lower IP. The oxidation of anthracene was specifically pH- and temperature-dependent, with the optimal pH and temperature being 8.0 and 40 °C, respectively. The redox mediators 1-hydroxybenzotriazole and veratryl alcohol promoted the transformation of anthracene by HRP; 9,10-anthraquinone was the main product detected from the anthracene oxidation system. The results of this study not only provide a better understanding of the oxidation of PAHs by utilizing a plant biocatalyst, but also provide a theoretical basis for establishing the HRP-catalyzed treatment of PAH-contaminated wastewater.

Ca2+ promoted the low transformation efficiency of plasmid DNA exposed to PAH contaminants

The effects of interactions between genetic materials and polycyclic aromatic hydrocarbons (PAHs) on gene expression in the extracellular environment remain to be elucidated and little information is currently available on the effect of ionic strength on the transformation of plasmid DNA exposed to PAHs. Phenanthrene and pyrene were used as representative PAHs to evaluate the transformation of plasmid DNA after PAH exposure and to determine the role of Ca²⁺ during the transformation. Plasmid DNA exposed to the test PAHs demonstrated low transformation efficiency. In the absence of PAHs, the transformation efficiency was 4.7 log units; however, the efficiency decreased to 3.72–3.14 log units with phenanthrene/pyrene exposures of 50 µg·L^–1. The addition of Ca²⁺ enhanced the low transformation efficiency of DNA exposed to PAHs. Based on the co-sorption of Ca²⁺ and phenanthrene/pyrene by DNA, we employed Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and mass spectrometry (MS) to determine the mechanisms involved in PAH-induced DNA transformation. The observed low transformation efficiency of DNA exposed to either phenanthrene or pyrene can be attributed to a broken hydrogen bond in the double helix caused by planar PAHs. Added Ca²⁺ formed strong electrovalent bonds with “–POO^––” groups in the DNA, weakening the interaction between PAHs and DNA based on weak molecular forces. This decreased the damage of PAHs to hydrogen bonds in double-stranded DNA by isolating DNA molecules from PAHs and consequently enhanced the transformation efficiency of DNA exposed to PAH contaminants. The findings provide insight into the effects of anthropogenic trace PAHs on DNA transfer in natural environments.

Ascorbic acid enhances the accumulation of polycyclic aromatic hydrocarbons (PAHs) in roots of tall fescue (Festuca arundinacea Schreb.)

Plant contamination by polycyclic aromatic hydrocarbons (PAHs) is crucial to food safety and human health. Enzyme inhibitors are commonly utilized in agriculture to control plant metabolism of organic components. This study revealed that the enzyme inhibitor ascorbic acid (AA) significantly reduced the activities of peroxidase (POD) and polyphenol oxidase (PPO), thus enhancing the potential risks of PAH contamination in tall fescue (Festuca arundinacea Schreb.). POD and PPO enzymes in vitro effectively decomposed naphthalene (NAP), phenanthrene (PHE) and anthracene (ANT). The presence of AA reduced POD and PPO activities in plants, and thus was likely responsible for enhanced PAH accumulation in tall fescue. This conclusion is supported by the significantly enhanced uptake of PHE in plants in the presence of AA, and the positive correlation between enzyme inhibition efficiencies and the rates of metabolism of PHE in tall fescue roots. This study provides a new perspective, that the common application of enzyme inhibitors in agricultural production could increase the accumulation of organic contaminants in plants, hence enhancing risks to food safety and quality.

Hydrological tracers using nanobiotechnology: proof of concept

In order to answer questions that involve differentiating among multiple and potentially interacting hydrological flowpaths, it would be ideal to use multiple tracers with identical transport properties that can nonetheless be distinguished from each other. This paper describes the development and proof of concept of a new kind of engineered tracer system that allows a large number of individual tracers to be simultaneously distinguished from one another. This new tracer is composed of polylactic acid (PLA) microspheres into which short strands of synthetic DNA and paramagnetic iron oxide nanoparticles are incorporated. The synthetic DNA serves as the "label" or "tag" in our tracers that allow us to distinguish one tracer from another, and paramagnetic iron oxide nanoparticles are included in the tracer to facilitate magnetic concentration of the tracers in potentially dilute water samples. Some potential advantages of this tracer concept include: virtually limitless uniquely labeled tracers, highly sensitive detection, and relatively moderate expense. Three proof-of-concept experiments at scales ranging from orders of 10 cm to 100 m demonstrated the use of the tracer system.