Multiple driving factors contribute to the variations of typical antibiotic resistance genes in different parts of soil-lettuce system

Effect of meddling ARBs on ARGs dynamics in fungal infested soil and their selective dispersal along spatially distant mycelial networks

During the recent times, environmental antibiotic resistance genes (ARGs) and their potential transfer to other bacterial hosts of pathogenic importance are of serious concern. However, the dissemination strategies of such ARGs are largely unknown. We tested that saprotrophic soil fungi differentially enriched antibiotic resistant bacteria (ARBs) and subsequently contributed in spatial distribution of selective ARGs. Wafergen qPCR analysis of 295 different ARGs was conducted for manure treated pre-sterilized soil incubated or not with selected bacterial-fungal consortia. The qPCR assay detected unique ARGs specifically found in the mycosphere of ascomycetous and basidiomycetous fungi. Both fungi exerted potentially different selection pressures on ARBs, resulting in different patterns of ARGs dissemination (to distant places) along their respective growing fungal highways. The relative abundance of mobile genetic elements (MGEs) was significantly decreased along fungal highways compared to the respective inoculation points. Moreover, the decrease in MGEs and ARGs (along fungal highways) was more prominent over time which depicts the continuous selection pressure of growing fungi on ARBs for enrichment of particular ARGs in mycosphere. Such data also indicate the potential role of saprotrophic soil fungi to facilitate horizontal gene transfer within mycospheric environmental settings. Our study, therefore, advocates to emphasize the future investigations for such (bacteria-fungal) interactive microbial consortia for potential (spatial) dissemination of resistance determinants which may ultimately increase the exposure risks of ARGs.

Effects of nitrogen fertilization on the fate of high-risk antibiotic resistance genes in reclaimed water-irrigated soil and plants

High-risk antibiotic resistance genes (ARGs) in reclaimed water-irrigated soil pose a potential threat to ecosystem and human health. Inorganic fertilization - including with nitrogen, a key ingredient in agricultural production - may affect the ARG profile in soil. However, little is known about nitrogen fertilization's influence on ARGs profiles in the soil-plant system. This study investigated the effects of different nitrogen fertilizer types (CO(NH2)2, NO3--N (NaNO3) and NH4+-N (NH4HCO3)) and different nitrogen fertilizer application rates (low, medium, high) on the distribution of high-risk ARGs in reclaimed water-irrigated soil and plants using quantitative PCR, high-throughput sequencing and metagenomic sequencing. Soil microcosms results revealed that nitrogen fertilization significantly affected the pattern of high-risk ARGs in soil, and also affected high-risk ARGs abundance and transfer capacity in plants. Compared with nitrogen fertilizer application rate, nitrogen fertilizer types significantly contributed to enhancing the soil resistome, with the order of CO(NH2)2 > NO3--N ≈ NH4+-N. The medium application of NO3--N and NH4+-N significantly reduced high-risk ARGs abundance in the leaf endophyte. Bacterial community mainly drove the variation of ARGs in nitrogen-fertilized soil-plant system, and class I integron and metal resistance genes (MRGs) also had direct effects on these high-risk ARGs. A similar high-risk ARGs pattern was also found in field plot experiments, and several dangerous pathogens were observed as the main high-risk ARGs potential hosts in nitrogen-fertilized soil. Based on an economic assessment, application of NH4+-N (NH4HCO3) could reduce costs by $1,312.83 ha-1 compared with NO3--N (NaNO3). These results showed that the more important role of nitrogen type might be an effective and economical way to control high-risk ARGs spread in soil-plant system under reclaimed water irrigation.

Spread of plasmids carrying antibiotic resistance genes in soil-lettuce-snail food chain

Fertilization can change the composition of antibiotic resistance genes(ARGs) and their host bacteria in agricultural fields, while complex microbial activities help ARGs into crops and transmit them to humans through agricultural products.Therefore, this study constructed a farmland food chain with soil-lettuce-snail as a typical structure, added genetically engineered Pseudomonas fluorescens containing multidrug-resistant plasmid RP4 to track its spread in the farmland food chain, and used different fertilization methods to explore its influence on the spread and diffusion of ARGs and intl1 in the farmland food chain. It was found that exogenous Pseudomonas can enter plants from soil and pass into snails' intestines, and there is horizontal gene transfer phenomenon of RP4 plasmid in bacteria. At different interfaces of the constructed food chain, the addition of exogenous drug-resistant bacteria had different effects on the total abundance of ARGs and intl1. Fertilization, especially manure, not only promoted the spread of Pseudomonas aeruginosa and the transfer of RP4 plasmid levels, but also significantly increased the total abundance of ARGs and intl1 at all interfaces of the constructed food chain. The main ARGs host bacteria in the constructed food chain include Proteobacteria, Bacteroides, and Firmicutes, while Flavobacterium of Bacteroides is the unique potential host bacteria of RP4 plasmid. In conclusion, this study provides a reference for the risk assessment of ARGs transmitted to the human body through the food chain, and has important practical significance to reduce the antibiotic resistance contamination of agricultural products and ensure the safety of vegetable basket.

Community coalescence and plant host filtering determine the spread of tetracycline resistance genes from pig manure into the microbiome continuum of the soil-plant system

The spread of livestock manure-borne antibiotic resistance genes (ARGs) into agroecosystems through manure application poses a potential threat to human health. However, there is still a knowledge gap concerning ARG dissemination in coalescing manure, soil and plant microbiomes. Here, we examined the fate of tetracycline resistance genes (TRGs) originating from pig manure microbiomes and spread in the soil-A thaliana system and explored the effects of microbial functions on TRGs spread at different interfaces. Our results indicate that the TRGs abundances in all microbiome continuum of the soil-A. thaliana system were significantly increased with the application of a living manure microbiome, although the addition of manure with both an active and inactive microbiome caused a shift in the microbial community composition. This was attributed to the increasing relative abundances of tetA, tetL, tetM, tetO, tetW and tolC in the system. The application of living manure with DOX residues resulted in the highest relative abundance of total TRGs (3.30×10-3 copies/16S rRNA gene copies) in the rhizosphere soil samples. Community coalescence of the manure and soil microbiomes increased the abundance of Firmicutes in the soil and root microbiome, which directly explains the increase in TRG abundance observed in these interfaces. In contrast, the leaf microbiome differed markedly from that of the remaining samples, indicating strong plant host filtering effects on Firmicutes and TRGs from pig manure. The random forest machine learning model revealed microbial functions and their significant positive correlation with TRG abundance in the microbiome continuum of the system. Our findings revealed that community coalescence is the main driver of TRG spread from manure to the soil and root microbiomes. Plant host filtering effects play a crucial role in allowing certain microbial groups to occupy ecological niches in the leaves, thereby limiting the establishment of manure-borne TRGs in aboveground plant tissues.

Antibiotics and antibiotic resistance change bacterial community compositions in marine sediments

Emerging contaminants, including antibiotics, antibiotic-resistant bacteria (ARB), and extracellular antibiotic resistance genes (eARGs), have been detected in large numbers in the aquatic environment. The effects of emerging contaminants on bacterial communities in marine sediments are not well studied. In this study, the effects of emerging contaminants (antibiotics, ARB, and eARGs) on the variations of bacterial populations in marine sediments of the Bohai Sea, Yellow Sea, East China Sea, and South China Sea were investigated. The results showed that the abundance of the host bacterial phylum Probacteria in the marine sediments of the Bohai Sea was the lowest among the four seas after exposure to different antibiotics, ARB, and eARGs. The inputs of exogenous antibiotics and resistance genes significantly affected the community function, resulting in significant differences in community abundance at the genus level. The abundance of Halomonas, Sulfitobacter, and Alcanivorax in the four sea areas displayed noteworthy differences in response to the addition of exogenous antibiotics and eARGs. These findings contribute to a more comprehensive understanding of the intricate interplay between emerging contaminants and the dynamics of bacterial communities in natural ecosystems.

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.

Metagenomics insights into the performance and mechanism of soil infiltration systems on removing antibiotic resistance genes in rural sewage

The removal of antibiotic resistance genes (ARGs) in sewage is of great concern, but advanced sewage treatment technologies are not suitable for rural areas, so the multi-layer soil infiltration system (MSL) has been developed for rural sewage treatment. However, little is known about the performance and function of MSL in the treatment of ARGs in rural sewage. Here, we optimized the matrix composition and structure of MSL and explored the efficacy and mechanism of MSL systems for ARG removal under different hydraulic conditions. The ARGs removal rate of MSL ranged from 41.51% to 99.67%, in which MSL with the middle hydraulic load, high pollution load, and continuous inflowing conditions showed the best removal performance. In addition, this system can operate stably and resist the temperature fluctuation, which showed an equivalent removal rate of ARGs in warm and cold seasons, amounting to 69.0%. The structural equation model revealed that microorganisms in sewage could significantly affect ARG removal (path coefficient = 0.91), probably owing to their interspecies competition. As for the internal system, the reduction of ARGs was mainly driven by microorganisms in the system matrix (path coefficient = 0.685), especially soil-mixture-block (SMB) microorganisms. The physicochemical factors of the matrix indirectly reduce ARGs by affecting the microorganisms that adhere to the matrices. Note that the pairwise alignment of nucleotide analysis demonstrated that the system matrix, especially biochar in the SMB, adsorbed ARGs and their hosts from the sewage, and in turn eliminated them by inhibiting the spread and colonization of hosts, thereby reducing the abundance of ARGs. Collectively, this study provides a deeper insight into the removal of ARGs from rural sewage by MSL, which can help improve sewage treatment technologies.

Ecotoxic side-effects of allelochemicals on submerged plant and its associated microfloras effectively relieved by sustained-release microspheres

Harmful algae bloom caused by water eutrophication is a burning question worldwide. Allelochemicals sustained-release microspheres (ACs-SMs) exhibited remarkable inhibition effect on algae, however, few studies have focused on the ecotoxic side-effects of ACs-SMs on submerged plant and its associated microfloras. Herein the effects of different exposure situations including single high-concentration ACs (15 mg/L, SH-ACs), repeated low-concentration ACs (3 × 5 mg/L, RL-ACs) and ACs-SMs containing 15 mg/L ACs on morphological indexes, chlorophyll content, lipid peroxidation, enzymatic activity, and chlorophyll fluorescence indexes of submerged plant Vallisneria natans and the richness and diversity of its associated microfloras (epibiotic microbes and sediment microbes) were studied. The results showed that pure ACs (RL-ACs and SH-ACs groups) had negative effects on plant height, mean leaf number and area of V. natans, but promoted the increase of mean leaf length. In addition, pure ACs caused lipid peroxidation, activated the antioxidant defense system, decreased chlorophyll content, and damaged photosynthetic system in leaves. Interestingly, ACs-SMs not only had barely negative effects on above indexes of V. natans, but had certain positive effects at the later experiment stage (days 50-60). Pure ACs and ACs-SMs all reduced the richness and diversity of microfloras in each group, and promoted the increase of relative abundance of dominant bacteria Pseudomonas, leading to a simpler community structure. Significantly, V. natans leaves diminished the effects of pure ACs and ACs-SMs on epibiotic microbes, and the plant rhizosphere was beneficial to the increase of dominant bacteria that promoted plant growth. Thus, sustained-release microspherification technology can effectively relieve the ecotoxic side-effects of pure ACs on submerged plant and its associated microfloras. This study fills the gap on the ecological safety knowledge of ACs-SMs and provides primary data for evaluating the feasibility and commercialization prospects of ACs-SMs as algae inhibitor in aquatic ecosystem.

Doxycycline Attenuates Pig Intestinal Microbial Interactions and Changes Microbial Metabolic Pathways

Doxycycline is a therapeutic veterinary antibiotic commonly used in pig breeding. In this study, 27 fattening pigs of 33.5 ± 0.72 kg were divided equally into 3 groups. Doxycycline at 0, 3, and 5 mg/kg body weight was added to the feed in groups CK, L and H. The medication and withdrawal periods were set at 5 and 28 days. The results showed that the doxycycline average concentrations in groups L and H during the medication period were 117.63 ± 13.54 and 202.03 ± 24.91 mg/kg dry matter, respectively. Doxycycline levels were lower than the detection limit after 20 days. Doxycycline did not affect the diversity of the intestinal microbial community structure. The relative abundances of Streptococcus were significantly higher in treatment groups than that in group CK, and Alishewanella, Vagococcus, Cloacibacterium, and Campylobacter abundances were significantly positively correlated with doxycycline concentration. Interestingly, the microbiota cooccurrence network suggested that high doxycycline concentration weakened the interactions among bacteria until day 33. Functional prediction showed that doxycycline significantly altered metabolic pathways related to the cell membrane. The results revealed that the use of doxycycline during pig breeding can affect bacterial abundance during the withdrawal period, and it may affect interactions among bacteria and change the intestinal metabolic pathways.

Bioaccumulation of antibiotics and resistance genes in lettuce following cattle manure and digestate fertilization and their effects on soil and phyllosphere microbial communities

The degradation and bioaccumulation of selected antibiotics such as the sulfonamide sulfamethoxazole (SMX) and the fluoroquinolones enrofloxacin (ENR) and ciprofloxacin (CIP) were investigated in soil microcosm experiments where Lactuca sativa was grown with manure or digestate (1%) and spiked with a mixture of the three antibiotics (7.5 mg/kg each). The soil, rhizosphere and leaf phyllosphere were sampled (at 0 and 46 days) from each microcosm to analyze the antibiotic concentrations, main resistance genes (sul1, sul2, qnrS, aac-(6')-Ib-crand qepA), the intI1and tnpA mobile genetic elements and the microbial community structure.Overall results showed that SMX and CIP decreased (70-85% and 55-79%, respectively), and ENR was quite persistent during the 46-day experiment. In plant presence, CIP and ENR were partially up-taken from soil to plant. In fact the bioaccumulation factors were > 1, with higher values in manure than digestate amended soils. The most abundant gene in soil was sul2 in digestate- and aac-(6')-Ib-cr in the manure-amended microcosms. In soil, neither sulfamethoxazole-resistance (sul1 and sul2), nor fluoroquinolone-resistance (aac-(6')-Ib-cr, qepA and qnrS) gene abundances were correlated with any antibiotic concentration. On the contrary, in lettuce leaves, the aac-(6')-Ib-cr gene was the most abundant, in accordance with the fluoroquinolone bioaccumulation. Finally, digestate stimulated a higher soil microbial biodiversity, introducing and promoting more bacterial genera associated with antibiotic degradation and involved in soil fertility and decreased fluoroquinolone bioaccumulation.

Distribution and driving factors of antibiotic resistance genes in treated wastewater from different types of livestock farms

Treated wastewater from livestock farms is an important reservoir for antibiotic resistance genes (ARGs), and is a main source of ARGs in the environment. However, the distribution and driving factors of ARGs in treated wastewater from different types of livestock farms are rarely reported. In this study, treated wastewater from 69 large-scale livestock farms of different types, including broiler, layer, and pig farms, was collected, and 11 subtypes of ARGs, 2 mobile genetic elements (MGEs) and bacterial community structure were analyzed. The results revealed detection rates of NDM-1 and mcr-1 of 90 % and 43 %, respectively, and the detection rates of other ARGs were 100 %. The relative abundance of ARGs, such as tetA, tetX and strB, in broiler farms was significantly higher than that in layer farms, but the bacterial α diversity was significantly lower than that in other farm types. Furthermore, although the treatment process had a greater impact on the physicochemical properties of the treated wastewater than the livestock type, livestock type was the main factor affecting the bacterial community in the treated wastewater. The analysis of potential host bacteria of ARGs revealed significant differences in the host bacteria of ARGs in treated wastewater from different types of livestock farms. The host bacteria of ARGs in broiler farms mainly belonged to Actinobacteria, layer farms mainly belonged to Proteobacteria, and pig farms mainly belonged to Firmicutes. Additionally, redundancy analysis showed that the distribution of ARGs may have resulted from the combination of multiple driving factors in different types of livestock farms, among which tnpA and NH₄⁺-N were the main influencing factors. This study revealed multiple driving factors for the distribution of typical ARGs in treated wastewater from different types of livestock farms, providing basic data for the prevention and control of ARG pollution in agricultural environments.