Effect of pH on the mitigation of extracellular/intracellular antibiotic resistance genes and antibiotic resistance pathogenic bacteria during anaerobic fermentation of swine manure

Eliminating antibiotics by white-rot-fungi Trametes versicolor from manure solids and synthetic wastewater

Antibiotics have been abused in livestock as veterinary drug and feed additive. Their incomplete metabolization by animals resulted in heavy accumulation in livestock manure, and therefore they can pose a threat to the environment. In this study, the mechanism of three antibiotics (oxytetracycline (OTC), sulfadiazine (SDZ), enrofloxacin (ENR)) removal/biodegradation by Trametes versicolor pellets in air-pulse fluidized-bed reactor was explored, and the effects of wood immobilized T. versicolor on four antibiotics (OTC, SDZ, ENR and chloramphenicol (CAP)) removal in solid cow manures were evaluated. T. versicolor could remove OTC, SDZ, ENR through adsorption and biodegradation, with the removal efficiency at 92% and 98% in 21 hours and 98% after 68 hours, respectively. The removal kinetics of those three antibiotics fitted well with the first-order kinetic model, with the removal constant k at -0.238 h-1, -0.102 h-1 and -0.023 h-1, respectively. T. versicolor could biodegrade those three antibiotics using laccase and cytochrome P450 system with the order SDZ≈OTC>ENR. Furthermore, wood immobilized T. versicolor promoted SDZ, OTC, ENR and chloramphenicol (CAP) antibiotic biodegradation in cow manure, especially in high inoculation ratio (wood immobilized T. versicolor: solid cow manures=1:2). This study revealed the mechanism of simultaneous SDZ, OTC, ENR and CAP antibiotic removal/biodegradation by white-rot fungi T. versicolor even by wood immobilized T. versicolor in solid cow manures, which provide a theoretical basis for future application of biological removal of antibiotics present in wastewater and solid manures.

Microbial degradation and pollutant control in aerobic composting and anaerobic digestion of organic wastes: A review

Aerobic composting (AC) and anaerobic digestion (AD) are promising technologies for organic waste treatment, but their efficiency and safety are influenced by complex waste composition and persistent contaminants. This review identifies the advances in understanding microbial community dynamics, enzymatic degradation pathways, and the fate of contaminants during AC and AD processes. The findings indicate that substrate composition shapes dominant microbial populations and their degradative enzymes, with this correlation potentially useful for predicting functional microbial communities. Additionally, AC shows advantages in antibiotic elimination while AD excels in heavy metal immobilization, with both contributing to removing certain antibiotic resistance genes (ARGs). The strategic manipulation of environmental conditions, particularly temperature and oxygen levels, can drive microbial succession to optimize organic matter decomposition while minimizing ARG proliferation. Economic analyses reveal that AC offers lower operational costs and AD generates valuable by-products with potential energy recovery from organic waste. Case studies indicate that integrating both technologies can overcome individual limitations and enhance degradation efficiency compared to conventional single-technology approaches. This work proposes a comprehensive framework for developing coupled AC-AD systems to achieve more efficient and safer organic waste valorization than conventional single-technology approaches. This review has important implications for advancing sustainable waste management practices and mitigating the spread of antibiotic resistance in the environment.

The new strategies for high efficiency removal of antibiotics and antibiotic resistance genes by direct bio-drying of biogas slurry: Microbiological mechanisms

High levels of antibiotics and antibiotic resistance genes (ARGs) still exist in biogas slurry after anaerobic digestion of cow manure. In this study, direct bio-drying strategies of cow manure biogas slurry without solid-liquid separation for the removal of antibiotics and ARGs were explored. The results showed that, after direct bio-drying of biogas slurry, the moisture contents decreased to 25.2 %-31.5 %. The maximum temperatures of the piles reached 76.1-77.4 °C, which is close to ultra-high temperatures (>80 °C). Direct biogas slurry bio-drying (CK treatment) achieved efficient removal of antibiotics, ARGs, and mobile genetic elements (MGEs) (95.4 %, 98.6 % and 86.7 % removal, respectively). Compared to the CK treatment, molecular membrane covering (MMC) alone was the most effective in further significantly decreasing the antibiotic concentration and the abundance of ARGs and MGEs in the final bio-dried samples, followed by food waste hydrochar (FHC) addition alone. Methanogenic archaea were identified as potential hosts for ARGs based on Network analysis. FHC addition-MMC increased the abundance of potential hosts for ARGs and promoted the expression of microbial methane metabolism function relative to the CK treatment during the later stages of bio-drying, thereby decreasing the removal efficiency of ARGs. The results of structural equation model and redundancy analysis showed that MGEs had the most significant direct effect on ARGs and moisture content had the highest relative contribution to changes in ARGs. In summary, direct bio-drying strategies were able to efficiently remove antibiotics and ARGs from cow manure biogas slurry and also achieve biological dewatering of the biogas slurry.

Application of compost amended with biochar on the distribution of antibiotic resistance genes in a soil-cucumber system-from the perspective of high-dose fertilization

The transfer of antibiotic resistance genes (ARGs) from soils to vegetables negatively impacts human health. This study explored the effects of the high-dose (18.73 t/ha) application of traditional compost (TC) and composts produced through the co-composting of traditional materials with large-sized (5-10 mm) biochar-amended compost (LBTC) or small-sized (< 0.074 mm) biochar-amended compost (SBTC) on the distribution of ARGs in a soil-cucumber system were explored. Results indicated that the SBTC group had the highest soil nitrogen, phosphorus, and potassium contents, followed by the LBTC, TC, and control treatment groups. These findings aligned with the quality and weight of harvested cucumbers. Bacterial community diversity decreased in compost-fertilized soils. Compared with their preexperimental values in soils, the total absolute abundances of ARGs and mobile genetic elements (MGEs) increased by 23.88 and 6.66 times, respectively, in the control treatment group; by 5.59 and 5.23 times, respectively, in the TC group; by 5.50 and 1.81 times, respectively, in the LBTC group; and by 5.49 and 0.47 times, respectively, in the SBTC group. Compared with those in the control treatment group, the absolute abundance of ermB, ermT, gyrA, qnrS, tetC, and intI1 decreased by 6-100% in the soil of the SBTC group. Compost application to soils significantly decreased ARG abundance in cucumbers; SBTC had the most significant effect and reduced the number of host bacteria at the phylum level from four to three. Nutrient levels in soils were important factors influencing the migration of ARGs from soils to cucumbers. In summary, when compared to other composts, the high-dose (18.73 t/ha) application of SBTC is more effective at reducing the risk of the accumulation and transfer of ARGs in the soil-cucumber system.

Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions

Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.

Bacterial isolates from drinking water river sources exhibit multi-drug resistant trait

Freshwater habitat is a natural reservoir for antimicrobial resistance (AMR). AMR poses serious human, animal, and environmental public health threats. This study aimed to evaluate the physicochemical and microbiological quality of five selected rivers (Apitipiti 1, Apitipiti 2, Apitipiti 3, Sogidi, and Aba Apa Akinmorin) in Oyo town, Nigeria, as well as the antibiotic resistance pattern of isolated bacterial species, using conventional methods. Most physicochemical parameters were within WHO and NIS permissible limits. Pearson's correlation matrix indicated that there were significant (p < 0.05) interactions among pH, electrical conductivity, temperature, sulphate and chloride salts, and BOD and COD. A total of thirty-two (32) bacterial species were isolated and identified as: Aeromonas (9), Bacillus (2), Corynebacterium (13), Lactobacillus (1), Pseudomonas (2), Staphylococcus (4), and Streptococcus (1). Of the rivers, Sogidi had the highest microbial load (6.36 log CFU/mL) while Apititipiti 1 had the lowest (5.76 log CFU/mL). With regard to antibiotic sensitivity, 81.8% were multidrug-resistant, with Corynebacterium kutscheri and Aeromonas spp. isolated from Apitipiti 2 and Aba Apa Akinmorin rivers, respectively, exhibiting a relatively high antibiotic resistance of 90.9%. This study reveals that these rivers may be unfit for consumption as multidrug-resistant bacteria of public health risk were associated with them.

Unraveling the determinants of antibiotic resistance evolution in farmland under fertilizations

Organic fertilization is a major driver potentiating soil antibiotic resistance in farmland. However, it remains unclear how bacterial antibiotic resistance evolves in fertilized soils and even spreads to crops. Compared with no fertilizer and commercial fertilizer treatments, organic fertilizers markedly increased the abundance of soil antibiotic resistance genes (ARGs) but the relatively weaker transfer of resistance genes from soil to crops. The introduction of organic fertilizers enriches the soil with nutrients, driving indigenous microorganisms towards a K-strategy. The pH, EC, and nutrients as key drivers influenced the ARGs abundance. The neutral (pH 7.2), low salt (TDS 1.4 %) and mesotrophic (carbon content 3.54 g/L) habitats similar to the soil environment conditioned by organic fertilizers. These environmental conditions clearly prolonged the persistence of resistant plasmids, and facilitated their dissemination to massive conjugators soil microbiome but not to plant endophytes. This suggested that organic fertilizers inhibited the spread of ARGs to crops. Moreover, the composition of conjugators showed differential selection of resistant plasmids by endophytes under these conditions. This study sheds light on the evolution and dissemination of antibiotic resistance in farmlands and can aid in the development of antimicrobial resistance control strategies in agriculture.

Affecting factors and mechanism of removing antibiotics and antibiotic resistance genes by nano zero-valent iron (nZVI) and modified nZVI: A critical review

Antibiotics and antibiotic resistance genetic pollution have become a global environmental and health concern recently, with frequent detection in various environmental media. Therefore, finding ways to control antibiotics and antibiotic resistance genes (ARGs) is urgently needed. Nano zero-valent iron (nZVI) has shown a positive effect on antibiotics degradation and restraining ARGs, making it a promising solution for controlling antibiotics and ARGs. However, given the current increasingly fragmented research focus and results, a comprehensive review is still lacking. In this work, we first introduce the origin and transmission of antibiotics and ARGs in various environmental media, and then discuss the affecting factors during the degradation of antibiotics and the control of ARGs by nZVI and modified nZVI, including pH, nZVI dose, and oxidant concentration, etc. Then, the mechanisms of antibiotic and ARGs removal promoted by nZVI are also summarized. In general, the mechanism of antibiotic degradation by nZVI mainly includes adsorption and reduction, while promoting the biodegradation of antibiotics by affecting the microbial community. nZVI can also be combined with persulfates to degrade antibiotics through advanced oxidation processes. For the control of ARGs, nZVI not only changes the microbial community structure, but also affects the proliferation of ARGs through affecting the fate of mobile genetic elements (MGEs). Finally, some new ideas on the application of nZVI in the treatment of antibiotic resistance are proposed. This paper provides a reference for research and application in this field.

Enhanced nutrient recovery from anaerobically digested poultry wastewater through struvite precipitation by organic acid pre-treatment and seeding in a bubble column electrolytic reactor

Limited mineralization of organic phosphorus to phosphate during the anaerobic digestion process poses a significant challenge in the development of cost-effective nutrient recovery strategies from anaerobically digested poultry wastewater (ADPW). This study investigated the influence of organic acids on phosphorus solubilization from ADPW, followed by its recycling in the form of struvite using a bubble column electrolytic reactor (BCER) without adding chemicals. The impact of seeding on the efficiency of PO43- and NH3-N recovery as well as the size distribution of recovered precipitates from the acid pre-treated ADPW was also evaluated. Pre-treatment of the ADPW with oxalic acid achieved complete solubilization of phosphorus, reaching ∼100% extraction efficiency at pH 2.5. The maximum removal efficiency of phosphate and ammonia-nitrogen from the ADPW were 88.9% and 90.1%, respectively, while the addition of 5 and 10 g/L struvite seed to the BCER increased PO43- removal efficiency by 9.6% and 11.5%, respectively. The value of the kinetic rate constant, k, increased from 0.0176 min-1 (unseeded) to 0.0198 min-1, 0.0307 min-1, and 0.0375 min-1 with the seed loading rate of 2, 5, and 10 g/L, respectively. Concurrently, the average particle size rose from 75.3 μm (unseeded) to 82.1 μm, 125.7 μm, and 148.9 μm, respectively. Results from XRD, FTIR, EDS, and dissolved chemical analysis revealed that the solid product obtained from the recovery process was a multi-nutrient fertilizer consisting of 94.7% struvite with negligible levels of heavy metals.

Analysis of extracellular and intracellular antibiotic resistance genes in commercial organic fertilizers reveals a non-negligible risk posed by extracellular genes

Livestock manure is known to be a significant reservoir of antibiotic resistance genes (ARGs), posing a major threat to human health and animal safety. ARGs are found in both intracellular and extracellular DNA fractions. However, there has been no comprehensive analysis of these fractions in commercial organic fertilizers (COFs). The present study conducted a systematic survey of the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) and their contributing factor in COFs in Northern China. Results showed that the ARG diversity in COFs (i.e., 57 iARGs and 53 eARGs) was significantly lower than that in cow dung (i.e., 68 iARGs and 69 eARGs). The total abundance of iARGs and eARGs decreased by 85.7% and 75.8%, respectively, after compost processing, and there were no significant differences between iARGs and eARGs in COFs (P > 0.05). Notably, the relative abundance of Campilobacterota decreased significantly (99.1-100.0%) after composting, while that of Actinobacteriota and Firmicutes increased by 21.1% and 29.7%, respectively, becoming the dominant bacteria in COFs. Co-occurrence analysis showed that microorganisms and mobile genetic elements (MGEs) were more closely related to eARGs than iARGs in COFs. And structural equation models (SEMs) further verified that microbial community was an essential factor regulating iARGs and eARGs variation in COFs, with a direct influence (λ = 0.74 and 0.62, P < 0.01), following by similar effects of MGEs (λ = 0.59 and 0.43, P < 0.05). These findings indicate the need to separate eARGs and iARGs when assessing the risk of dissemination and during removal management in the environment.

Antibiotic resistome and associated bacterial communities in agricultural soil following the amendments of swine manure-derived fermentation bed waste

The practice of utilizing animal manures on land is widespread in agriculture, but it has raised concerns about the possible spread of antibiotic resistance genes (ARGs) and the potential risk it poses to public health through food production. Fermentation bed culture is an effective circular agricultural practice commonly utilized in pig farming that minimizes the environmental impact of livestock farming. However, this method generates a significant amount of fermentation bed waste (FBW), which can be turned into organic fertilizer for land application. The objective of this research was to examine the impacts of amending agricultural soil samples with swine manure-derived FBW on microbial communities, mobile genetic elements (MGEs), and ARG profiles over different periods. The study findings indicated that the amendment of swine manure-derived FBW significantly increased the diversity and abundance of ARGs and MGEs during the early stages of amendment, but this effect diminished over time, and after 12 months of FBW amendments, the levels returned to those comparable to control samples. The shift in the bacterial communities played a significant role in shaping the patterns of ARGs. Actinobacteriota, Proteobacteria, and Bacteroidetes were identified as the primary potential hosts of ARGs through metagenomic binning analysis. Furthermore, the pH of soil samples was identified as the most important property in driving the composition of the bacterial community and soil resistome. These findings provided valuable insights into the temporal patterns and dissemination risks of ARGs in FBW-amended agriculture soil, which could contribute to the development of effective strategies to manage the dissemination risks of FBW-derived ARGs.

River sediment microbial community composition and function impacted by thallium spill

Thallium (Tl) is widely used in various industries, which increases the risk of leakage into the environment. Since Tl is highly toxic, it can do a great harm to human health and ecosystem. In order to explore the response of freshwater sediment microorganisms to sudden Tl spill, metagenomic technique was used to elucidate the changes of microbial community composition and functional genes in river sediments. Tl pollution could have profound impacts on microbial community composition and function. Proteobacteria remained the dominance in contaminated szediments, indicating that it had a strong resistance to Tl contamination, and Cyanobacteria also showed a certain resistance. Tl pollution also had a certain screening effect on resistance genes and affected the abundance of resistance genes. Metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) were enriched at the site near the spill site, where Tl concentration was relatively low among polluted sites. When Tl concentration was higher, the screening effect was not obvious and the resistance genes even became lower. Moreover, there was a significant correlation between MRGs and ARGs. In addition, co-occurrence network analysis showed that Sphingopyxis had the most links with resistance genes, indicating that it was the biggest potential host of resistance genes. This study provided new insight towards the shifts in the composition and function of microbial communities after sudden serious Tl contamination.