Interactions of extracellular DNA with aromatized biochar and protection against degradation by DNase I

The effects of climate and soil depth on living and dead bacterial communities along a longitudinal gradient in Chile

Soil bacterial communities play a critical role in shaping soil stability and formation, exhibiting a dynamic interaction with local climate and soil depth. We employed an innovative DNA separation method to characterize microbial assemblages in low-biomass environments such as deserts and distinguish between intracellular DNA (iDNA) and extracellular DNA (eDNA) in soils. This approach, combined with analyses of physicochemical properties and co-occurrence networks, investigated soil bacterial communities across four sites representing diverse climatic gradients (i.e., arid, semi-arid, Mediterranean, and humid) along the Chilean Coastal Cordillera. The separation method yielded a distinctive unimodal pattern in the iDNA pool alpha diversity, increasing from arid to semi-arid climates and decreasing in humid environments, highlighting the rapid feedback of the iDNA community to increasing soil moisture. In the arid region, harsh surface conditions restrict bacterial growth, leading to peak iDNA abundance and diversity occurring in slightly deeper layers than the other sites. Our findings confirmed the association between specialist bacteria and ecosystem-functional traits. We observed transitions from Halomonas and Delftia, resistant to extreme arid environments, to Class AD3 and the genus Bradyrhizobium, associated with plants and organic matter in humid environments. The distance-based redundancy analysis (dbRDA) analysis revealed that soil pH and moisture were the key parameters that influenced bacterial community variation. The eDNA community correlated slightly better with the environment than the iDNA community. Soil depth was found to influence the iDNA community significantly but not the eDNA community, which might be related to depth-related metabolic activity. Our investigation into iDNA communities uncovered deterministic community assembly and distinct co-occurrence modules correlated with unique bacterial taxa, thereby showing connections with sites and key environmental factors. The study additionally revealed the effects of climatic gradients and soil depth on living and dead bacterial communities, emphasizing the need to distinguish between iDNA and eDNA pools.

Fate and mitigation of antibiotics and antibiotic resistance genes in microbial fuel cell and coupled systems

Microbial fuel cells (MFCs), known for their low energy consumption, high efficiency, and environmental friendliness, have been widely utilized for removing antibiotics from wastewater. Compared to conventional wastewater treatment methods, MFCs produce less sludge while exhibiting superior antibiotic removal capacity, effectively reducing the spread of antibiotic resistance genes (ARGs). This study investigates 1) the mechanisms of ARGs generation and proliferation in MFCs; 2) the influencing factors on the fate and removal of antibiotics and ARGs; and 3) the fate and mitigation of ARGs in MFC and MFC-coupled systems. It is indicated that high removal efficiency of antibiotics and minimal amount of sludge production contribute the mitigation of ARGs in MFCs. Influencing factors, such as cathode potential, electrode materials, salinity, initial antibiotic concentration, and additional additives, can lead to the selection of tolerant microbial communities, thereby affecting the abundance of ARGs carried by various microbial hosts. Integrating MFCs with other wastewater treatment systems can synergistically enhance their performance, thereby improving the overall removal efficiency of ARGs. Moreover, challenges and future directions for mitigating the spread of ARGs using MFCs are suggested.

Negative impacts of perishable waste biochar to Escherichia coli and exploring potential damage factors

Agricultural application of pyrolysis‑carbonized perishable wastes can target reduction treatment and resource utilization of the wastes. However, potential undesirable impact has rarely been assessed. In this study, the adverse effect of perishable waste biochars (PWB) from different pyrolysis temperatures on Escherichia coli (E. coli) was explored and the potential risk factors were further analyzed. The results showed that PWBs pyrolyzed at 350, 500, and 650 °C inhibited the growth of E. coli, and PWB pyrolyzed at 500 °C showed the most inhibition. The exposure to PWB damaged the antioxidative system, as revealed by the concentration-dependent increasing of intracellular ROS. In addition, the toxicity at the gene level in terms of cell division and growth inhibition, the damage of cell membrane, antioxidant system disturbance, and DNA damage occurred, resulting in loss of the cell rules of morphology and eventual death. According to our results, the inhibitory effect on the growth of E. coli was mainly caused by PWB solids, accounting for >70 %. The membrane disruption and oxidative damage of E. coli by PWB were possibly induced by the direct physical interaction between cell and char particles. The growth of E. coli can be partly influenced by PWB extraction solutions that varied between PWB types, due to the differences in pH, released DOC and the production of extracellular ∙OH. The exploration of these potential hazards could provide new insights into the fate and toxicity of PWB in the environment and help guide the safe and sustainable applications for PWB.

New challenge: Mitigation and control of antibiotic resistant genes in aquatic environments by biochar

With an increase of diverse contaminants in the environment, particularly antibiotics, the maintenance and propagation of antibiotic resistance genes (ARGs) are promoted by co-selection mechanisms. ARGs are difficult to degrade, cause long-lasting pollution, and are widely transmitted in aquatic environments. Biochar is frequently used to remove various pollutants during environmental remediation. Thus, this review provides a thorough analysis of the current state of ARGs in the aquatic environment as well as their removal by using biochar. This article summarizes the research and application of biochar and modified biochar to remove ARGs in aquatic environments, in order to refine the following contents: 1) fill gaps in the research on the various ARG behaviors mediated by biochar and some influence factors, 2) further investigate the mechanisms involved in effects of biochar on extracellular ARGs (eARGs) and intracellular ARGs (iARGs) in aquatic environments, including direct and the indirect effects, 3) describe the propagation process and resistance mechanisms of ARGs, 4) propose the challenges and prospects of feasibility of application and subsequent treatment in actual aquatic environment. Here we highlight the most recent research on the use of biochar to remove ARGs from aquatic environments and suggest future directions for optimization, as well as current perspectives to guide future studies on the removal of ARGs from aquatic environments.

Negative plant-soil feedback in Arabidopsis thaliana: Disentangling the effects of soil chemistry, microbiome, and extracellular self-DNA

Nutrient deficiency, natural enemies and litter autotoxicity have been proposed as possible mechanisms to explain species-specific negative plant-soil feedback (PSF). Another potential contributor to negative PSF is the plant released extracellular self-DNA during litter decay. In this study, we sought to comprehensively investigate these hypotheses by using Arabidopsis thaliana (L.) Heynh as a model plant in a feedback experiment. The experiment comprised a conditioning phase and a response phase in which the conditioned soils underwent four treatments: (i) addition of activated carbon, (ii) washing with tap water, (iii) sterilization by autoclaving, and (iv) control without any treatment. We evaluated soil chemical properties, microbiota by shotgun sequencing and the amount of A. thaliana extracellular DNA in the differently treated soils. Our results showed that washing and sterilization treatments mitigated the negative PSF effect. While shifts in soil chemical properties were not pronounced, significant changes in soil microbiota were observed, especially after sterilization. Notably, plant biomass was inversely associated with the content of plant self-DNA in the soil. Our results suggest that the negative PSF observed in the conditioned soil was associated to increased amounts of soilborne pathogens and plant self-DNA. However, fungal pathogens were not limited to negative conditions, butalso found in soils enhancing A.thaliana growth. In-depth multivariate analysis highlights that the hypothesis of negative PSF driven solely by pathogens lacks consistency. Instead, we propose a multifactorial explanation for the negative PSF buildup, in which the accumulation of self-DNA weakens the plant's root system, making it more susceptible to pathogens.

New discovery of extremely high adsorption of environmental DNA on cuttlefish bone pyrolysis derivative via large pore structure and carbon film

Environmental DNA (eDNA) carrying antibiotic resistance gene (ARG) has attracted a great deal of attention because of its threat to the ecology and human health. Traditional porous adsorbents, such as microporous biochar and natural mineral, are low-effective in removing eDNA from sewage. This study used cuttlefish-bone (CB), a fishery waste, as an anticipated material to adsorb a model compound of eDNA from herring sperm (hsDNA). An interesting result was firstly observed that extremely high DNA adsorption on cuttlefish-bone pyrolysis derivative (CCB) was up to 88.7 mg/g, 3-10 folds higher than that of most other adsorbents in the existing literatures, which was attributed to the carbon film and large pores. To achieve an adsorption rate of 75 %, hsDNA adsorption took 96 h on CB but only 24 h on CCB, which was attributed to the fluent channel of CCB. The ligand exchange, Ca2+ bridge and π-π interaction were identified as dominated adsorption mechanisms, based on FTIR and phosphate competition experiments. This study exploited a high-efficient, environmentally friendly, and low-cost adsorbent for treating ARG-contaminated soil and water.

Effects of particle size and pyrolytic temperature of biochar on the transformation behavior of antibiotic resistance genes

Rampant use of antibiotics has caused a rapid dissemination of antibiotic resistance genes (ARGs) in environment, posing great threats to ecosystems and human health. Applying biochar (BC) in natural systems to combat the spread of ARGs arises as an attention-grabbing solution. Unfortunately, the effectiveness of BC is still unmanageable due to the incomprehensive knowledge over correlations between BC properties and extracellular ARGs transformation. To pinpoint the crucial factors, we primarily explored transformation behaviors of plasmid-mediated ARGs exposed to BC (in suspensions or extraction solutions), adsorption capacities of ARGs on BC, and growth inhibition of E. coli imposed by BC. Specifically, the effects of BC properties including particle size (large-particulate 150 μm and colloidal 0.45-2 μm) and pyrolytic temperature (300, 400, 500, 600, and 700 °C) on the ARGs transformation were emphasized. Results showed that both large-particulate BC and colloidal BC, irrespective of their pyrolytic temperature, would induce significant inhibitory effects on the ARGs transformation, while the BC extraction solutions showed little effect except BC pyrolyzed at 300 °C. Correlation analysis uncovered that the inhibition effect of BC on ARGs transformation was tightly correlated with its adsorption capacity towards plasmid. Accordingly, greater inhibitory effects from those BCs with higher pyrolytic temperatures and smaller particle sizes mainly originated from their greater adsorption capacities. Intriguingly, E. coli was unable to ingest the plasmid adsorbed on BC, which led to ARGs blocked outside the cell membrane, although this inhibitory effect was partially affected by survival inhibition of BC on E. coli. Particularly, significant plasmid aggregation could occur in the extraction solution of large-particulate BC pyrolyzed at 300 °C, leading to a significant inhibition of ARGs transformation. Overall, our findings complete the insufficient understanding over the effects of BC on ARGs transformation behavior, and potentially provide new insights to scientific communities in mitigating ARGs spreading.

Bacterial extracellular polymeric substances: Biosynthesis and interaction with environmental pollutants

Extracellular polymeric substances (EPS) are highly hydrated matrices produced by bacteria, containing various polymers such as polysaccharides, proteins, lipids, and DNA. Extracellular polymer concentrations, ions, and functional groups provide physical stability to the EPS. Constituents of EPS form the three-dimensional architecture and help acquire nutrition for the bacteria. Structural and functional diversity of the extracellular polymer depends on the specific glycosyltransferases, polymerase and transporter proteins. These enzymes are encoded by specific genes present in operons such as crd, alg, wca, and gum reported in Agrobacterium, Pseudomonas, Enterobacteriaceae, and Xanthomonas. The operons regulate the biosynthesis of extracellular polymers such as curdlan, alginate, colonic acid, and xanthan, respectively. Various functional groups in the EPS, such as carbonyl, hydroxyl, phosphoryl, and amide, provide the sorption site for interaction with environmental pollutants. Hydrophobic interactions and coordinate bonds mainly dominate the binding of EPS with environmental pollutants. EPS binds, emulsifies, and solubilizes the organic compounds, enhancing the degradation process. EPS binds with heavy metals through complexation, surface adsorption, precipitation, and ion exchange mechanisms. The biodegradability efficiency and nontoxicity properties of EPS make it an excellent biopolymer for decontaminating environmental pollutants. This review summarizes an overview of the biosynthetic mechanisms and interaction of the bacterial extracellular polymer with environmental pollutants. Interaction mechanisms of pollutants with EPS and EPS-mediated bioremediation will help develop removal applications. Moreover, understanding the genes responsible for EPS production, and implementation of new genetic methodology can be helpful for the enhanced biosynthesis of EPS to control pollution by sequestrating more environmental pollutants.

Roles of substrates in removing antibiotics and antibiotic resistance genes in constructed wetlands: A review

Antibiotics and corresponding antibiotic resistance genes (ARGs) are emerging pollutants in wastewater that pose a significant threat to the environment and human health. Constructed wetlands (CWs) are a cost-effective technology for eliminating these pollutants through substrates, plants, and microorganisms. Detailed reviews of the roles of CW substrates on antibiotic and ARG removal and recent progress in the field are lacking. This paper reviews the mechanisms influencing antibiotic and ARG (intracellular and extracellular) removal in CWs, and natural, biomass, chemical, modified, industrial, novel, and combined substrates on their removal efficiencies. Generally, substrates remove antibiotics and ARGs mainly through adsorption, biodegradation, chemical oxidation, and filtration. Other mechanisms, such as photolysis, may also contribute to removal. Natural substrates (e.g., gravel, zeolite) are more frequently employed than other types of substrates. The removal performance of antibiotics and intracellular ARGs by zeolite was better than that of gravel through enhanced substrate adsorption, filtration, and biodegradation processes. Moreover, Mn ore showed promising high capability to remove high concentration of antibiotics through various removal pathways. In addition, combined substrates of soil/sand/gravel and other substrates further facilitate antibiotic removal. Future research is suggested to explore the mechanisms of competitive adsorption and redox-controlled biodegradation, investigate the effect of Fe/Mn oxides on the removal of antibiotics and ARGs via chemical oxidation, evaluate the removal of extracellular ARGs by CWs with different substrates, and investigate the effect of substrates on removal of antibiotics and ARGs in full-scale CWs.

A review of antibiotics and antibiotic resistance genes (ARGs) adsorption by biochar and modified biochar in water

Antibiotics have been used in massive quantities for human and animal medical treatment, and antibiotic resistance genes (ARGs) are of great concern worldwide. Antibiotics and ARGs are exposed to the natural environment through the discharge of medical wastewater, causing great harm to the environment and human health. Biochar has been widely used as a green and efficient adsorbent to remove pollutants. However, pristine and unmodified biochars are not considered sufficient and efficient to cope with the current serious water pollution. Therefore, researchers have chosen to improve the adsorption capacity of biochar through different modification methods. To have a better understanding of the application of modified biochar, this review summarizes the biochar modification methods and their performance, particularly, molecular imprinting and biochar aging are outlined as new modification methods, influencing factors of biochar and modified biochar in adsorption of antibiotics and ARGs and adsorption mechanisms, wherein adsorption mechanism of ARGs on biochar is found to be different than that of antibiotics. After that, the directions of biochar and modified biochar worthy of research and the issues that need attention are proposed. It can be noted that under the current dual carbon policy, biochar may have wider application prospects in future.

Pyrolysis temperature affects the inhibitory mechanism of biochars on the mobility of extracellular antibiotic resistance genes in saturated porous media

The migration of extracellular antibiotic resistance genes (eARGs) in porous media is an important pathway for ARGs to spread to the subsoil and aquifer. Biochar (BC) has been widely used to reduce the mobility of soil contaminants, however, its effect on the mobility of eARGs in porous media and the mechanisms are largely unknown. Herein, the effects of BCs synthesized from wheat straw and corn straw at two pyrolysis temperatures (300 °C and 700 °C) on the transport of plasmids-carried eARGs in sand column were investigated. The BC amendments all significantly decreased the mobility of eARGs in the porous medium, but the mechanism varied with pyrolysis temperature. The higher temperature BCs had a stronger irreversible adsorption of plasmids and greatly enhanced the attachment and straining effects on plasmids during transport, thus more effectively inhibited the mobility of eARGs. The lower temperature BCs had weaker adsorption, attachment, and straining effects on plasmids, but induced generation of hydroxyl radicals in the porous medium and thereby fragmented the plasmids and hindered the amplification of eARGs. These findings are of fundamental significance for the potential application of BC in controlling the vertical spread of eARGs in soil and vadose zones.

Removal of extracellular deoxyribonucleic acid increases the permeability and mass transfer of anammox granular sludge with different sizes

As a key component of extracellular polymeric substances (EPS), extracellular deoxyribonucleic acid (eDNA) acts as a bridge in maintaining the structural stability of granular sludge. However, its ability of carrying antibiotic resistance genes (ARGs) promotes the gene horizontal transfer, raising a high risk for human health. In this study, a series of batch tests were performed to elucidate the response of anammox granular sludge (AnGS) with different sizes (S-AnGS with diameters lower than 0.9 mm and L-AnGS with diameters of 0.9-2 mm) to the removal of eDNA and corresponding mechanism. The results showed that the highest bioactivity of S-AnGS and L-AnGS was achieved by adding DNase I, and the absolute abundance of hzsA in the systems also increased. The dominant microorganism in each sludge was Candidatus Kuenenia, which maintained a higher relative abundance of 24% in S-AnGS. Settling experiments demonstrated that the permeability of AnGS was positively correlated with the addition of DNase I. The permeability index of granular sludge, Г, rose by 58.54% in S-AnGS and 11.79% in L-AnGS. The absence of eDNA is conducive to the increase in the permeability and porosity of AnGS. Similarity in the functional genes and microbial communities of intracellular and extracellular DNA implied the occurrence of gene transmembrane transfer. The findings enrich our knowledge of eDNA in anammox granules and provide a guidance for the specific control of gene transfer through reducing eDNA.

Exploring the effects of heavy metal passivation under Fenton-like reaction on the removal of antibiotic resistance genes during composting

This study aims to explore the succession of microbes carrying antibiotic resistance genes (ARGs), the relationship between heavy metal speciation and ARGs via Fenton-like reaction during composting. The results indicated that the passivation of Cu and Ni was more prominent, and the Fenton-like reaction promoted exceptionally the passivation of Zn, Ni and Mn. The removals of macrolides-lincosamids-streptogramins (MLS), aminoglycoside and tetracycline resistance genes were induced with the composting process, but the relative abundance of bacitracin resistance genes increased. Additionally, Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were main carriers and disseminators of ARGs, and the Fenton-like reaction improved the contribution degree of Proteobacteria to bacitracin, tetracycline and aminoglycoside resistance genes. Redundancy analysis revealed the passivation of heavy metal contributed to the removal of tetracycline, MLS and aminoglycoside resistance genes. Conclusively, the Fenton-like reaction promoted the passivation of Zn, Ni and Mn, and controlled the abundance of bacitracin resistance genes in composting.

Application of α-Fe2O3 nanoparticles in controlling antibiotic resistance gene transport and interception in porous media

Metal oxide nanoparticles (MONPs) with a large specific surface area are expected to bind with antibiotic resistance genes (ARGs), thereby controlling ARGs' contamination by reducing their concentration and mobilization. Here, adsorption experiments were carried out and it was found that α-Fe₂O₃ NPs could chemically bind with ARGs (tetM-carrying plasmids) in water with an adsorption rate of 0.04 min^-1 and an adsorption capacity of 7.88 g/kg. Mixing α-Fe₂O₃ NPs into quartz sand column markedly increased the interceptive removal of ARGs from inflow water. The interception rate of 1.0 μg/mL ARGs in ultrapure water (25 mL, 5 pore volumes) through the sand column (plexiglass, length 8 cm, internal diameter 1.4 cm) with 1 g/kg α-Fe₂O₃ NPs was 1.73 times of that through the pure sand column; the interception rate overall increased with increasing addition of α-Fe₂O₃ NPs, reaching 68.8% with 20 g/kg α-Fe₂O₃ NPs. Coexisting Na⁺ (20 mM), Ca²⁺ (20 mM), and acidic condition (pH 4.0) could further increase the interception rate of ARGs by 1 g/kg α-Fe₂O₃ NPs from 21.1% to 86.2%, 90.7%, and 96.2%, respectively. The presence of PO₄^3- and humic acid at environmentally relevant concentrations would not significantly affect the interception of ARGs. In the treatment groups with PO₄^3- and humic acid, the removal rate decreased by only 1.8% and 0.1%, respectively. In addition, the interceptive removal of ARGs by α-Fe₂O₃ NPs-incorporated sand column was even better in actual surface water samples (87.2%) than that in the ultrapure water (21.1%). The findings provide a promising approach to treat ARGs-polluted water.

The effects of biochar on antibiotic resistance genes (ARGs) removal during different environmental governance processes: A review

Antibiotic resistance genes (ARGs) pollution has been considered as one of the most significant emerging environmental and health challenges in the 21st century, many efforts have been paid to control the proliferation and dissemination of ARGs in the environment. Among them, the biochar performs a positive effect in reducing the abundance of ARGs during different environmental governance processes and has shown great application prospects in controlling the ARGs. Although there are increasing studies on employing biochar to control ARGs, there is still a lack of review paper on this hotspot. In this review, firstly, the applications of biochar to control ARGs in different environmental governance processes were summarized. Secondly, the processes and mechanisms of ARGs removal promoted by biochar were proposed and discussed. Then, the effects of biochar properties on ARGs removal were highlighted. Finally, the future prospects and challenges of using biochar to control ARGs were proposed. It is hoped that this review could provide some new guidance for the further research of this field.

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.

Upgrading residues from wastewater and drinking water treatment plants as low-cost adsorbents to remove extracellular DNA and microorganisms carrying antibiotic resistance genes from treated effluents

Wastewater treatment is challenged by the continuous emergence of chemical and biological contaminants. Disinfection, advanced oxidation, and activated carbon technologies are accessible in high-income countries to suppress them. Low-cost, easily implementable, and scalable solutions are needed for sanitation across regions. We studied the properties of low-cost absorbents recycled from drinking water and wastewater treatment plant residues to remove environmental DNA and xenogenetic elements from used water. Materials characteristics and DNA adsorption properties of used iron-oxide-coated sands and of sewage-sludge biochar obtained by pyrolysis of surplus activated sludge were examined in bench-scale batch and up-flow column systems. Adsorption profiles followed Freundlich isotherms, suggesting a multilayer adsorption of nucleic acids on these materials. Sewage-sludge biochar exhibited high DNA adsorption capacity (1 mg g^-1) and long saturation breakthrough times compared to iron-oxide-coated sand (0.2 mg g^-1). Selected antibiotic resistance genes and mobile genetic elements present on the free-floating extracellular DNA fraction and on the total environmental DNA (i.e., both extra/intracellular) were removed at 85% and 97% by sewage-sludge biochar and at 54% and 66% by iron-oxide-coated sand, respectively. Sewage-sludge biochar is attractive as low-cost adsorbent to minimize the spread of antimicrobial resistances to the aquatic environment while strengthening the role of sewage treatment plants as resource recovery factories.