Intraspecific and interspecific quorum sensing of bacterial community affects the fate of antibiotic resistance genes during chicken manure composting under penicillin G stress

A feasible regulation strategy for conjugation of antibiotic resistance genes based on different bacterial quorum sensing inhibition methods

The dissemination of antibiotic resistance genes (ARGs) poses global environmental issues, and plasmid-mediated conjugation contributes substantially to the spread of ARGs. Quorum sensing (QS), an important cell-cell communication system that coordinates group behaviors, has potential as a feasible regulation pathway to inhibit the conjugation process. We examined the promoting effects of QS signal on conjugation, and this study is the first to report that QS inhibitors 2(3H)-benzofuranone and acylase I effectively repressed conjugation frequency of RP4 plasmid to 0.32- and 0.13-fold compared with the control respectively. The investigation of underlying mechanisms of QS inhibitors revealed a significant decrease in cellular contact and the formation of transfer channels. The downregulation of sdiA gene regulating the expression of QS signal receptor contribute to conjugation inhibition. Importantly, the expression of genes related to the formation of conjugative pili, which plays a role in plasmid mating bridge formation was downregulated, indicating QS inhibitors affect conjugation mainly through regulation of the mating pair formation system. Furthermore, 2(3H)-benzofuranone and acylase I achieved 84.07% and 66.05% inhibitory effect on plasmid spread in activated sludge reactors. Collectively, our findings demonstrate the feasibility of using different bacteria quorum quenching methods to control the spread of ARGs.

Adsorption and biodegradation of butyl xanthate in mine water by Pseudomonas sp. immobilized on yak dung biochar

The butyl xanthate (BX) in mining wastewater poses significant environmental challenges due to its toxicity and persistence. This study aimed to evaluate the effectiveness of Pseudomonas sp. immobilized on yak dung biochar (Ps.@YDBC600) for BX degradation, emphasizing the synergistic effects of biochar adsorption and microbial degradation. BX removal efficiency of free Pseudomonas sp. cells was assessed under various environmental conditions, with optimal degradation observed at 30 °C and an initial pH of 5.0. Yak dung biochar prepared at 600 °C (YDBC600) was selected due to its high surface area, porosity, and favorable adsorption properties, enhancing the immobilization and activity of Pseudomonas sp. The absorption of BX by biochar followed a two-compartment first-order kinetic model and primarily involved hydrogen bonding, hydrophobic interactions, and pore filling. The primary crystalline mineral component of YDBC600 and Ps.@YDBC600 before and after the adsorption and degradation of BX was SiO₂. The Ps.@YDBC600 was shown to significantly enhance BX removal efficiency compared to free Pseudomonas sp. cells or biochar alone. Molecular studies indicated that biochar facilitated BX degradation by providing a stable environment for Pseudomonas sp. and optimizing metabolic resource allocation. The primary by-products, including CS₂, HS-, ROCOS-, ROCSSH and (ROCSS)₂ were effectively minimized (each by-product was reduced more than 80%), reducing secondary pollution. These findings demonstrated the potential of Pseudomonas sp. immobilized on biochar as an effective approach for treating BX-contaminated mining wastewater, offering a sustainable approach to environmental remediation and management.

Mechanisms and influencing factors of horizontal gene transfer in composting system: A review

Organic solid wastes such as livestock manure and sewage sludge are important sources and repositories of antibiotic resistance genes (ARGs). Composting, a solid waste treatment technology, has demonstrated efficacy in degrading various antibiotics and reducing ARGs. However, some recalcitrant ARGs (e.g., sul1, sul2) will enrich during the composting maturation period. These ARGs persist in compost products and spread through horizontal gene transfer (HGT). We analyzed the reasons behind the increase of ARGs during the maturation phase. It was found that the proliferation of ARG-host bacteria and HGT process play an important role. This article revealed that microbial physiological responses, environmental factors, pollutants, and quorum sensing (QS) can all influence the HGT process in composting systems. We examined the influence of these factors on HGT in the compost system and summarized potential mechanisms by analyzing the alterations in microbial communities. We comprehensively summarized the HGT hazards that these factors may present in composting systems. Finally, we summarized methods to inhibit HGT in compost, such as using additives, quorum sensing inhibitors (QSIs), microbial inoculation, and predicting HGT events. Overall, the HGT mechanism and driving force in complex composting systems are still insufficiently studied. In view of the current situation, using predictions to assess the risk of HGT in composting may be advisable.

Potassium persulfate enhances humification of chicken manure and straw composting: The perspective of rare and abundant microbial community structure and ecological interactions

Improper disposal of organic solid waste results in serious environmental pollution. Aerobic composting provides an environmentally friendly treatment method, but improving humification of raw materials remains a challenge. This study revealed the effect of different concentrations of potassium persulfate (PP) on humification of chicken manure and straw aerobic composting and the underlying microbial mechanisms. The results showed that when 0.6 % PP was added (PPH group), humus and the degree of polymerization were 80.77 mg/g and 2.52, respectively, which were significantly higher than those in 0.3 % PP (PPL group). As the concentration of PP was increased, the composition of rare taxa (RT) changed and improved in evenness, while abundant taxa (AT) was unaffected. Additionally, the density (0.037), edges (3278), and average degree (15.21) in the co-occurrence network decreased compared to PPL, while the average path (4.021) and modularity increased in PPH. This resulted in facilitating the turnover of matter, information, and energy among the microbes. Interestingly, cooperative behavior between microorganisms during the maturation period (24-60 d) occurred in PPH, but competitive relationships dominated in PPL. Cooperative behavior was positively correlated with humus (p < 0.05). Because the indices, such as higher degree, betweenness centrality, eigenvector centrality, and closeness centrality of the AT, were located in the microbial network center compared to RT, they were unaffected by the concentration of PP. The abundance of carbohydrate and amino acid metabolic pathways, which play an important role in humification, were higher in PPH. These findings contribute to understanding the relative importance of composition, interactions, and metabolic functionality of RT and AT on humification during chicken manure and straw aerobic composting under different concentrations of PP, as well as provide a basic reference for use of various conditioning agents to promote humification of organic solid waste.

Ecological succession of abundant and rare subcommunities during aerobic composting in the presence of residual amoxicillin

Aerobic composting increases the content of soluble nutrients and facilitates the safe treatment of livestock manure. Although different taxa play crucial roles in maintaining ecological functionality, the succession patterns of community composition and assembly of rare and abundant subcommunities during aerobic composting under antibiotic stress and their contributions to ecosystem functionality remain unclear. Therefore, this study used 16 S rRNA gene sequencing technology to reveal the response mechanisms of diverse microbial communities and the assembly processes of abundant and rare taxa to amoxicillin during aerobic composting. The results indicated that rare taxa exhibited distinct advantages in terms of diversity, community composition, and ecological niche width compared with abundant taxa, highlighting their significance in maintaining ecological community dynamics. In addition, deterministic (heterogeneous selection) and stochastic processes (dispersal limitation) play roles in the community succession and functional dynamics of abundant and rare subcommunities. The findings of this study may contribute to a better understanding of the relative importance of deterministic and stochastic assembly processes in composting systems, and the ecological functions of diverse microbial communities, ultimately leading to improved ecological environment.

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.

Antibiotics and antibiotic resistance gene dynamics in the composting of antibiotic fermentation waste - A review

Fate of antibiotics and antibiotic resistance genes (ARGs) during composting of antibiotic fermentation waste (AFW) is a major concern. This review article focuses on recent literature published on this subject. The key findings are that antibiotics can be removed effectively during AFW composting, with higher temperatures, appropriate bulking agents, and suitable pretreatments improving their degradation. ARGs dynamics during composting are related to bacteria and mobile genetic elements (MGEs). Higher temperatures, suitable bulking agents and an appropriate C/N ratio (30:1) lead to more efficient removal of ARGs/MGEs by shaping the bacterial composition. Keeping materials dry (moisture less than 30%) and maintaining pH stable around 7.5 after composting could inhibit the rebound of ARGs. Overall, safer utilization of AFW can be realized by optimizing composting conditions. However, further removal of antibiotics and ARGs at low levels, degradation mechanism of antibiotics, and spread mechanism of ARGs during AFW composting require further investigation.

Comprehensive insights into antibiotic resistance gene migration in microalgal-bacterial consortia: Mechanisms, factors, and perspectives

With the overuse of antibiotics, antibiotic resistance gene (ARG) prevalence is gradually increasing. ARGs are considered emerging contaminants that are broadly concentrated and dispersed in most aquatic environments. Recently, interest in microalgal-bacterial biotreatment of antibiotics has increased, as eukaryotes are not the primary target of antimicrobial drugs. Moreover, research has shown that microalgal-bacterial consortia can minimize the transmission of antibiotic resistance in the environment. Unfortunately, reviews surrounding the ARG migration mechanism in microalgal-bacterial consortia have not yet been performed. This review briefly introduces the migration of ARGs in aquatic environments. Additionally, an in-depth summary of horizontal gene transfer (HGT) between cyanobacteria and bacteria and from bacteria to eukaryotic microalgae is presented. Factors influencing gene transfer in microalgal-bacterial consortia are discussed systematically, including bacteriophage abundance, environmental conditions (temperature, pH, and nutrient availability), and other selective pressure conditions including nanomaterials, heavy metals, and pharmaceuticals and personal care products. Furthermore, considering that quorum sensing could be involved in DNA transformation by affecting secondary metabolites, current knowledge surrounding quorum sensing regulation of HGT of ARGs is summarized. In summary, this review gives valuable information to promote the development of practical and innovative techniques for ARG removal by microalgal-bacterial consortia.

Antibiotic resistance genes fate during food waste management - Comparison between thermal treatment, hyperthermophilic composting, and anaerobic membrane bioreactor

The fate of eight different antibiotic resistance genes (ARGs) in food waste (sul1, sul2, tetO, tetW, ermF, ermB, ampC, oxa-1), intI1, and rpoB were monitored during thermal treatment (pyrolysis and incineration), hyperthermophilic composting, and anaerobic membrane bioreactor (AnMBR) treatment. ARGs in food waste ranged from 2.9 × 106 to 3.5 × 109 copies/kg with ampC being the least abundant and sul1 being the most abundant. Thermal treatment achieved removal below detection limits of all ARGs. Only two ARGs (sul1 and ampC) persisted in hyperthermophilic composting. While all genes except for ermB decreased in the AnMBR effluent relative to the food waste feed, sul1 remained at relatively high abundance. Biosolids on the contrary, accumulated tetO, ampC and sul2 in all tested operating conditions. Thermal treatment, despite limited resource recovery, provides the most effective mitigation of ARG risk in food waste.

Quorum sensing in different subcommunities becomes the key factor affecting the humification of the aerobic composting system with sauerkraut fermentation wastewater

Aerobic composting is an effective and harmless method to treat Sauerkraut fermentation wastewater (SFW). Given the limited understanding of the effect of quorum sensing (QS) on humification in subcommunities under acidic environments, a large-scale analysis was conducted to identify features that impact the response of QS to humification in different subcommunities. The results showed that the addition of SFW directly affected humification in subcommunities A and C, and the abundances of functional genes related to carbon fixation and carbon degradation were significantly increased at 7 and 15 d, respectively. In addition, subcommunity B indirectly affected humus production but regulated carbon metabolic pathways such as glycolysis/gluconeogenesis and pentose phosphate by QS with subcommunities B. These findings provide a novel perspective for analysing the regulation of humification in aerobic composting and suggest that composting has potential applications in organic wastewater treatment.

Bacterial community dynamics and co-occurrence network patterns during different stages of biochar-driven composting

Bacterial communities were dynamically tracked at four stages of biochar-driven sheep manure pile composting, and the co-occurrence networks with keystone taxa were established. The succession of bacterial community obvious varied during the composting process, Proteobacteria predominant in initial stage (39%) then shifted into Firmicutes in thermophilic (41%) and mesophilic (27%) stages, finally the maturation stage dominant by Bacteroidota (26%). Visualizations of bacterial co-occurrence networks demonstrate more cooperative mutualism and complex interactions in the thermophilic and mesophilic phases. Noticeably, the 7.5 and 10% biochar amended composts shown highest connections (736 and 663 total links) and positive cooperation (97.37 and 97.13% positive link) as well as higher closeness centrality and betweenness centrality of keystone taxa. Overall, appropriate biochar addition alters bacterial community succession and strengthens connection between keystone taxa and other bacteria, with 7.5 and 10% biochar amended composts has intense mutualistic symbiosis among bacterial communities.

Response characteristics of Flax retting liquid addition during chicken manure composting: Focusing on core bacteria in organic carbon mineralization and humification

To explore the applicability of flax retting liquid (FRL) addition, the physicochemical properties, microbial community structure and function, carbon conversion and humus (HS) formation were assessed during chicken manure (CM) aerobic composting. Compared with the control group, the addition of FRL increased the temperature at thermophilic phase, while the microbial mass carbon content (MBC) in SCF and FRH groups raised to 96.1±0.25 g/Kg and 93.33±0.27 g/Kg, respectively. Similarly, FRL also improved the concent of humic acid (HA) to 38.44±0.85 g/Kg, 33.06±0.8 g/Kg, respcetively. However, fulvic acid (FA) decreased to 30.02±0.55g/Kg, 31.4±0.43 g/Kg, respectively and further reduced CO₂ emissions. FRL influenced the relative abundance of Firmicutes at thermophilic phase and Ornithinimicrobium at maturity phase. Additionally, FRL strengthen the association among flora and reduce the number of bacteria, which was negative correlated with HA and positive with CO₂ during composting. These findings offer powerful technological support for improving agricultural waste recycling.

The role and mechanism of quorum sensing on environmental antimicrobial resistance

As more environmental contaminants emerging, antibiotics and antibiotic resistance genes (ARGs) have caused a substantial increase of antimicrobial resistance (AMR) in environment. Quorum sensing (QS) is a bacterial cell-to-cell communication process that regulates many traits and gene expression, including ARGs and the related genes that contribute to AMR development. Herein, we summarize the role, physiology, and genetic mechanisms of bacterial QS in AMR development in the environment. First, the effect of QS on AMR is introduced. Next, the role of QS in bacterial physiological behaviors that promote AMR development, including membrane permeability, tactic movement, biofilm formation, persister formation, and small colony variants (SCVs), is systematically analyzed. Furthermore, the regulation of QS on the expression of ARGs, generation of reactive oxygen species (ROS), which affects ARGs formation, and horizontal gene transfer (HGT), which accelerates the transmission of ARGs, are discussed to reveal the molecular mechanism for AMR development. This review provides a reference for a better understanding of AMR evolution and novel insights into AMR prevention.

Manganese dioxide eliminates the phytotoxicity of aerobic compost products and converts them into a plant friendly organic fertilizer

This study mainly confirmed the exogenous substances (pomace, biochar, MnO₂) and the quorum sensing of bacterial communities jointly regulate the metabolic conversion of toxic substances in manures and agricultural wastes, and converts them into a plant-friendly organic fertilizer through aerobic composting and pot experiment. The results showed the composting products had positive performance in bacterial communities, physicochemical indicators, and phytotoxicity. Meanwhile, the addition of exogenous substances could significantly improve seed germination index, promote metabolites conversion, and optimize bacterial community structure. Furthermore, the exogenous substances mainly regulated the functions of the three bacterial communities by quorum sensing system, then promoted the beneficial metabolites, and inhibited the harmful metabolites. Finally, pot experiments suggested compost products could significantly promote plant growth. Thus, these important discoveries extend the knowledge of the previous work and provide an economical and simple method to convert wastes into organic fertilizers that are friendly to plants and soil.

Potential of Aromatic Plant-Derived Essential Oils for the Control of Foodborne Bacteria and Antibiotic Resistance in Animal Production: A Review

Antibiotic resistance has become a severe public threat to human health worldwide. Supplementing antibiotic growth promoters (AGPs) at subtherapeutic levels has been a commonly applied method to improve the production performance of livestock and poultry, but the misuse of antibiotics in animal production plays a major role in the antibiotic resistance crisis and foodborne disease outbreaks. The addition of AGPs to improve production performance in livestock and poultry has been prohibited in some countries, including Europe, the United States and China. Moreover, cross-resistance could result in the development of multidrug resistant bacteria and limit therapeutic options for human and animal health. Therefore, finding alternatives to antibiotics to maintain the efficiency of livestock production and reduce the risk of foodborne disease outbreaks is beneficial to human health and the sustainable development of animal husbandry. Essential oils (EOs) and their individual compounds derived from aromatic plants are becoming increasingly popular as potential antibiotic alternatives for animal production based on their antibacterial properties. This paper reviews recent studies in the application of EOs in animal production for the control of foodborne pathogens, summarizes their molecular modes of action to increase the susceptibility of antibiotic-resistant bacteria, and provides a promising role for the application of nanoencapsulated EOs in animal production to control bacteria and overcome antibiotic resistance.

Aerobic composting of chicken manure with penicillin G: Community classification and quorum sensing mediating its contribution to humification

Chicken manure containing antibiotics is a hazardous biological waste. The purpose of our study was to investigate how different concentrations of penicillin G alter the bacterial community to affect humification during aerobic composting of chicken manure. The effect of quorum sensing on the bacterial community was also evaluated. Penicillin G mainly affects low fold changes (within 4) for low-abundance (within 200) microbial genera. We found that the bacterial community cooperated to regulate humus and humic acid synthesis. The microbial genera that make up the bacterial community are different, but each bacterial community may have the same ecological function. Quorum sensing affects humic acid synthesis by regulating carbohydrate metabolism and amino acid metabolism in bacterial communities through mechanisms such as the pentose phosphate pathway and the shikimate pathway. This work presents an understanding of the impact of quorum sensing on the collaboration between bacterial communities during composting.