Metagenomic profiles of antibiotic resistance genes in paddy soils from South China

Distribution, source apportionment, and ecological risk assessment of soil antibiotic resistance genes in urban green spaces

Urban green spaces play a crucial role in cities by providing near-natural environments that greatly impacts the health of residents. However, these green spaces have recently been scrutinized as potential reservoirs of antibiotic resistance genes (ARGs), posing significant ecological risks. Despite this concern, our understanding of the distribution, sources, and ecological risks associated with ARGs remains limited. In this study, we investigated the spatial distribution of soil ARGs using spatial interpolation and auto-correlation analysis. To apportion the source of soil ARGs in urban green spaces of Tianjin, Geo-detector method (GDM) was employed. Furthermore, we evaluated the ecological risk posed by ARGs employing risk quotients (RQ). The results of our study showed a significantly higher abundance of Quinolone resistance genes in the soil of urban green spaces in Tianjin. These genes were mainly found in the northwest, central, and eastern regions of the city. Our investigation identified three main factors contributing to the presence of soil ARGs: antibiotic production, precipitation, livestock breeding, and hospital. The results of ecological risk in RQ value showed a high risk associated with Quinolone resistance genes, followed by Aminoglycoside, Tetracycline, Multidrug, MLSB, Beta Lactam, Sulfonamide, and Chloramphenicol. Mantel-test and correlation analysis revealed that the ecological risk of ARGs was greatly influenced by soil properties and heavy metals. This study provides a new perspective on source apportionment and the ecological risk assessment of soil ARGs in urban green spaces.

The effect of information provision on consumers' risk perceptions of, support for a ban, and behavioral intention towards the preventive use of antibiotics in food animals

BACKGROUND

Antibiotics have been widely used in feed and drinking water for food animals to prevent them from getting sick. Such preventive use of antibiotics has become a contributor to increasing antibiotic resistance and thus poses threats to human health. However, consumers have little knowledge about this practice and the associated health risks of increasing transmission of antibiotic residues and antibiotic resistant bacteria. This study aimed to examine the effect of information provision on consumers' risk perceptions, support for a ban, and behavioral intention regarding the preventive use of antibiotics in food animals. Especially, the study sought to test two competing hypotheses which were informed by two theoretical perspectives of fear appeal theory - the linear model and the plateau effect model. The former suggested that providing information on the health risks of both antibiotic residues and antibiotic resistant bacteria would have a stronger effect compared to providing information on only one of them, while the latter posited that providing information on both risks might not have additional influence, as the effect of information on either risk could reach the plateau.

METHODS

An experimental study with four conditions was conducted where participants read different information on the health risks associated with the preventive use first and then answered questions regarding consumers' risk perceptions, support for a ban, and behavioral intention regarding the preventive use. Condition 1 was the control condition, where basic information about antibiotics, antibiotic resistance, and the preventive use was provided. Condition 2 and Condition 3 further added information on the health risk of antibiotic residues (Condition 2) and antibiotic resistant bacteria (Condition 3) due to the preventive use, respectively. Condition 4 provided all information contained in the first three conditions.

RESULTS

The results showed that compared to participants in the control condition, participants in Conditions 2-4 reported higher risk perceptions, stronger support for a ban on the preventive use, and a higher intention to buy meat produced without the preventive use of antibiotics. However, there were no significant differences in these factors between Conditions 2-4, indicating that providing information on the health risk of either antibiotic residues, or antibiotic resistant bacteria, or both, has similar effect on these variables. That is, the hypothesis based on the plateau effect model was supported.

CONCLUSIONS

The findings suggested that informing the public with the health risk of either antibiotic residues or antibiotic resistant bacteria associated with the preventive use is effective enough to reach plateau effect in increasing risk perceptions, support for a ban, and behavioral intention, which has important implications for policymakers and livestock industries to develop effective communication strategies to promote responsible antibiotic use in food animals.

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

BACKGROUND

Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS

After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION

Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.

Soil type and moisture content alter soil microbial responses to manure from cattle administered antibiotics

Growing concerns about the global antimicrobial resistance crisis require a better understanding of how antibiotic resistance persists in soil and how antibiotic exposure impacts soil microbial communities. In agroecosystems, these responses are complex because environmental factors may influence how soil microbial communities respond to manure and antibiotic exposure. The study aimed to determine how soil type and moisture alter responses of microbial communities to additions of manure from cattle treated with antibiotics. Soil microcosms were constructed using two soil types at 15, 30, or 45% moisture. Microcosms received biweekly additions of manure from cattle given cephapirin or pirlimycin, antibiotic-free manure, or no manure. While soil type and moisture had the largest effects on microbiome structure, impacts of manure treatments on community structure and individual ARG abundances were observed across varying soil conditions. Activity was also affected, as respiration increased in the cephapirin treatment but decreased with pirlimycin. Manure from cattle antibiotics also increased NH4+ and decreased NO3- availability in some scenarios, but the effects were heavily influenced by soil type and moisture. Overall, this work demonstrates that environmental conditions can alter how manure from cattle administered antibiotics impact the soil microbiome. A nuanced approach that considers environmental variability may benefit the long-term management of antibiotic resistance in soil systems.

Metagenomic analysis reveals the microbial response to petroleum contamination in oilfield soils

The response of the microbes to total petroleum hydrocarbons (TPHs) in three types of oilfield soils was researched using metagenomic analysis. The ranges of TPH concentrations in the grassland, abandoned well, working well soils were 1.16 × 102-3.50 × 102 mg/kg, 1.14 × 103-1.62 × 104 mg/kg, and 5.57 × 103-3.33 × 104 mg/kg, respectively. The highest concentration of n-alkanes and 16 PAHs were found in the working well soil of Shengli (SL) oilfield compared with those in Nanyang (NY) and Yanchang (YC) oilfields. The abandoned well soils showed a greater extent of petroleum biodegradation than the grassland and working well soils. Α-diversity indexes based on metagenomic taxonomy showed higher microbial diversity in grassland soils, whereas petroleum-degrading microbes Actinobacteria and Proteobacteria were more abundant in working and abandoned well soils. RDA demonstrated that low moisture content (MOI) in YC oilfield inhibited the accumulation of the petroleum-degrading microbes. Synergistic networks of functional genes and Spearman's correlation analysis showed that heavy petroleum contamination (over 2.10 × 104 mg/kg) negatively correlated with the abundance of the nitrogen fixation genes nifHK, however, in grassland soils, low petroleum content facilitated the accumulation of nitrogen fixation genes. A positive correlation was observed between the abundance of petroleum-degrading genes and denitrification genes (bphAa vs. nirD, todC vs. nirS, and nahB vs. nosZ), whereas a negative correlation was observed between alkB (alkane- degrading genes) and amo (ammonia oxidation), hao (nitrification). The ecotoxicity of petroleum contamination, coupled with petroleum hydrocarbons (PH) degradation competing with nitrifiers for ammonia inhibited ammonia oxidation and nitrification, whereas PH metabolism promoted the denitrification process. Moreover, positive correlations were observed between the abundance of amo gene and MOI, as well as between the abundance of the dissimilatory nitrate reduction gene nirA and clay content. Thus, improving the soil physicochemical properties is a promising approach for decreasing nitrogen loss and alleviating petroleum contamination in oilfield soils.

The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum

The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.

Pig manure-derived fulvic acid more strongly drives the fate of arsenic and antibiotic resistance genes in paddy soil

Antibiotic resistance genes (ARGs) can threaten the clean production of rice owing to continuous selective pressure in heavy metal-antibiotic co-contaminated paddy soils. As an important soil carbon reservoir, the role of humic substances from different types of manure in the regulation of soil ARGs remains unclear. In this study, fulvic acid (FA) and humic acid (HA) were extracted from pig manure (PM), cow dung (CD), and chicken manure (CM). The influence of their characteristics and doses on the fate of ARGs was investigated in arsenic (As)-antibiotic co-contaminated paddy soils. The release of As and degradation of antibiotics were promoted in 1% PM-FA treatment, with increases of 4.8%-5.6% and 8.3%-8.8% compared with CM-FA and CD-FA treatments, respectively. The coexistence of FA/HA, Fe, As, and antibiotics in soil pore water affected the environmental behavior of ARGs, with FA showing a more positive effect. Species including Bacillus, Geobacter, Desulfitobacterium, and Christensenellaceae_R-7_group were considered potential hosts of ARGs, and their resistance to co-contamination increased after the addition of FA. Membrane transport is a potential strategy for host bacteria of ARGs to cope with As-antibiotic complex pressure. These results demonstrate the coupling mechanisms of As, antibiotics, and ARGs regulated by different humic substances in co-contaminated paddy soils, which could support the clean production of rice in agricultural practice.

Nanobiotics and the One Health Approach: Boosting the Fight against Antimicrobial Resistance at the Nanoscale

Antimicrobial resistance (AMR) is a growing public health concern worldwide, and it poses a significant threat to human, animal, and environmental health. The overuse and misuse of antibiotics have contributed significantly and others factors including gene mutation, bacteria living in biofilms, and enzymatic degradation/hydrolyses help in the emergence and spread of AMR, which may lead to significant economic consequences such as reduced productivity and increased health care costs. Nanotechnology offers a promising platform for addressing this challenge. Nanoparticles have unique properties that make them highly effective in combating bacterial infections by inhibiting the growth and survival of multi-drug-resistant bacteria in three areas of health: human, animal, and environmental. To conduct an economic evaluation of surveillance in this context, it is crucial to obtain an understanding of the connections to be addressed by several nations by implementing national action policies based on the One Health strategy. This review provides an overview of the progress made thus far and presents potential future directions to optimize the impact of nanobiotics on AMR.

Microbial community structure and antibiotic resistance profiles in sediments with long-term aquaculture history

The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in response to the reintroduction of antibiotics, as well as the presence of resistance genes in sediments from shrimp ponds that have been utilized for extended periods of 5, 15, and over 30 years. Results showed that the sediments exhibited a high prevalence of Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, and Oxyphotobacteria as the most abundant bacterial phyla, accounting for 70.35-77.43% of the total bacterial community. The five most abundant phyla of fungi detected in all sediments, namely Rozellomycota, Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota, constituted 24.26-32.54% of the total fungal community. It was highly probable that the Proteobacteria and Bacteroidetes phyla serve as the primary reservoir of antibiotic-resistant bacteria (ARB) in the sediment, which included various genera like Sulfurovum, Woeseia, Sulfurimonas, Desulfosarcina, and Robiginitalea. Among these genera, Sulfurovum appeared to be the most widespread in the sediment of aquaculture ponds that have been in operation for more than three decades, while Woeseia dominated in ponds that have been recently reclaimed and have a 15-year aquaculture history. Antibiotic resistance genes (ARGs) were categorized into seven distinct groups according to their mechanism of action. The prevalence of multidrug-resistant ARGs was found to be the highest among all types, with an abundance ranging from 8.74 × 10^-2 to 1.90 × 10^-1 copies per 16S rRNA gene copies. The results of a comparative analysis of sediment samples with varying aquaculture histories indicated that the total relative abundance of ARGs was significantly diminished in sediment with a 15-year aquaculture history as opposed to sediment with either a 5-year or 30-year aquaculture history. Another assessment of antibiotic resistances in aquaculture sediments involved an examination of the effects of reintroducing antibiotics on nitrogen metabolism processes. The findings revealed that the rates of ammonification, nitrification, and denitrification in the sediment with a history of 5 years and 15 years, decreased as the concentration of oxytetracycline increased from 1 to 300, and 2000 mg/kg, and inhibitory effects were found to be less pronounced in sediments with a 5-year history compared to those with a 15-year history. In contrast, oxytetracycline exposure led to a significant decrease in the rates of these processes in aquaculture pond sediments with a >30 years of aquaculture history across all the concentrations tested. The emergence and dissemination of antibiotic resistance profiles in aquaculture environments requires attention in future aquaculture management.

Diversity of enterobacterales in sediments of lagoons with fish farming activity and analysis of antibiotic resistance

The use of antibiotics in fish production can induce bacterial populations to develop resistance to multiple antibiotics and transfer antibiotic resistance genes to other bacteria, including clinically relevant bacteria. This study evaluated the diversity of Enterobacterales in sediment from lagoons with fish farming activity and analyzed antibiotic resistance in the central region of Peru. Sediment samples were collected from four fish-active ponds and transported to the laboratory for analysis. Bacterial diversity was analyzed using DNA sequencing and antibiotic resistance was tested using the disk diffusion method. The results showed variability of bacterial diversity in the ponds with fish farming activity. Simpson's index indicated that the Habascocha lagoon is the most diverse in bacterial species of the order Enterobacterales (0.8), but the least dominant. The Shannon-Wiener index revealed that it is the most diverse (2.93) and the Margalef index revealed that species richness in this lagoon is high (5.72). Similarity percentage analysis (SIMPER) allowed the identification of the main Enterobacterales with the highest percentage contribution in the frequencies of individuals. In general, the Enterobacterales species isolated showed multi-resistance to the antibiotics used and Escherichia coli was the most resistant.

Impacts of organic materials amendment on the soil antibiotic resistome in subtropical paddy fields

The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.

Soil antibiotic abatement associates with the manipulation of soil microbiome via long-term fertilizer application

The effects of different fertilization on microbial communities and resistome in agricultural soils with a history of fresh manure application remains largely unclear. Here, soil antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and microbial communities were deciphered using metagenomics approach from a long-term field experiment with different fertilizer inputs. A total of 541 ARG subtypes were identified, with Multidrug, Macrolides-Lincosamides-Streptogramins (MLS), and Bacitracin resistance genes as the most universal ARG types. The abundance of ARGs detected in manure (2.52 ARGs/16 S rRNA) treated soils was higher than chemical fertilizer (2.42 ARGs/16 S rRNA) or compost (2.37 ARGs/16 S rRNA) amended soils. The higher abundance of MGEs and the enrichment of Proteobacteria were observed in manure treated soils than in chemical fertilizer or compost amended soils. Proteobacter and Actinobacter were recognized as the main potential hosts of ARGs revealed by network analysis. Further soil pH was identified as the key driver in determining the composition of both microbial community and resistome. The present study investigated the mechanisms driving the microbial community, MGEs and ARG profiles of long-term fertilized soils with ARGs contamination, and our findings could support strategies to manage the dissemination of soil ARGs.

The source, fate and prospect of antibiotic resistance genes in soil: A review

Antibiotic resistance genes (ARGs), environmental pollutants of emerging concern, have posed a potential threat to the public health. Soil is one of the huge reservoirs and propagation hotspot of ARGs. To alleviate the potential risk of ARGs, it is necessary to figure out the source and fate of ARGs in the soil. This paper mainly reviewed recent studies on the association of ARGs with the microbiome and the transmission mechanism of ARGs in soil. The compositions and abundance of ARGs can be changed by modulating microbiome, soil physicochemical properties, such as pH and moisture. The relationships of ARGs with antibiotics, heavy metals, polycyclic aromatic hydrocarbons and pesticides were discussed in this review. Among the various factors mentioned above, microbial community structure, mobile genetic elements, pH and heavy metals have a relatively more important impact on ARGs profiles. Moreover, human health could be impacted by soil ARGs through plants and animals. Understanding the dynamic changes of ARGs with influencing factors promotes us to develop strategies for mitigating the occurrence and dissemination of ARGs to reduce health risks.

Impact of different manure-derived dissolved organic matters on the fate of arsenic-antibiotic in co-contaminated paddy soils

Manure application increases the transfer risk of antibiotic resistance to farmland. Especially, its impact remains unclear when it occurs in arsenic (As)-contaminated paddy soils, which is considered as a global environmental problem. In this work, we investigated the fate of antibiotic resistance genes (ARGs) in As-antibiotic co-contaminated paddy soils under the application of manure from different sources (pig manure, cow dung, and chicken manure). Differences in the aliphatic carbon and electron-donating capacities of these dissolved organic matters (DOM) regulated the transformation of iron and As by both biotic and abiotic processes. The regulation by pig manure was stronger than that by cow dung and chicken manure. DOM regulation increased the abundance of As-related functional genes (arsC, arrA, aioA, and arsM) in the soil and accelerated the transformation of As speciation, the highest proportion of As(III) being 45%-61%. Meanwhile, the continuous selection pressure provided by the highly toxic As(III) increased the risk of ARGs and mobile genetic elements (MGEs) via horizontal gene transfer. As-resistant bacteria, including Bacillus, Geobacter, and Desulfitobacterium, were finally considered as potential host bacteria for ARGs and MGEs. In summary, this study clarified the synergistic mechanism of As-antibiotic on the fate of ARGs in co-contaminated paddy soils, and provided practical guidance for the proper application of organic fertilizers.

Distribution and transfer of antibiotic resistance genes in different soil-plant systems

The extensive application of farm manure that is contaminated with pharmaceutical antibiotics not only causes substantial soil pollution but additionally leads to the input of antibiotic resistance genes (ARGs) into the soil. These ARGs would proliferate and affect human health via the food chain. The effects of cultivated crops and wild plants on ARGs in rhizosphere soil are unclear. Therefore, we chose potted plants of cultivated crops (pakchoi, lettuce, corn) and wild plants (barnyard grass, crabgrass, dog tail), and set up test groups, i.e., treatment group, antibiotic-contaminated soil; control group, no antibiotic-contaminated soil; and a blank group without plants. The aim was to explore differences in the distribution and transfer of ARGs in the soil-plant system between cultivated crops and wild plants and at the same time to explore the influence of bacterial community evolution on ARGs in the rhizosphere soil of cultivated crops and wild plants. We concluded that under the pressure of antibiotic selection, ARGs can be transferred to the root endophytes of plants through the soil and further to the phyllosphere of plants, and cultivated crops such as pakchoi and wild plants barnyard grass have a strong ability to transport ARGs. Regardless of cultivated crops or wild plants, the abundance of ARGs in rhizosphere soil can be substantially reduced by 66.53 ~ 85.35%. Redundancy analysis and network analysis indicated that bacterial community succession is the main mechanism affecting changes of ARGs in rhizosphere soil. The reduction of Firmicutes due to the plant was the main factor responsible for the reduction of the abundance of ARGs in rhizosphere soil. The tetA, tetG, tetX, sul2, and qnrS genes are highly related to some potential pathogens, and the health risks they bring are a red flag that deserves attention.

Validation and inhibition study for toxic expression of quinolone antibiotic resistance genes in agricultural soils of eastern China

With the extensive use of antibiotics, the problem of antibiotic resistance genes (ARGs) has gradually emerged. As agricultural soil is an important enrichment media of antibiotics and ARGs, it is particularly important to study the toxicity of ARGs, the effects of various nutrients and pollutants, and how to control them through source modification and process regulation. In this study, a combination of source modification and process regulation was used to weaken the toxic expression of Quinolones' (QNs') ARGs in soils from different agricultural areas. And the influence of soil nutrients and pollutants on this process will be explored. Protein-protein docking and molecular docking were used to construct a target protein complex for the toxic expression of QNs' ARGs and characterize the toxicity of QNs' ARGs. The two-dimensional and three-dimensional quantitative structure-activity relationships model construction and sensitivity analysis were used to molecular modification and related validation. Molecular dynamics simulations assisted by sampling survey method based on agricultural soils in Northeast China and the lower-middle reaches of the Yangtze River were carried out to generate four scenarios. The main results are: (a) A functionally improved and environmentally friendly quinolone derivative (ORB-19) was designed. It can effectively inhibit the expression of QNs' ARGs and weaken the antibiotic selection pressure risk. The application of ORB-19 in agricultural areas could significantly inhibit the toxic expression of QNs' ARGs (112.75%~169.59%); (b) QNs' ARGs have a stronger toxic expression in agricultural areas of Northeast China, which have higher nutrient elements; (c) The contribution of different types of agricultural pollution to suppressing the toxic expression of QNs' ARGs in agricultural soils varies; (d) The options of applied field measures given for the inhibition of QNs' ARG toxic expression varied between plots with different agricultural pollution types. This study provides theoretical support for inhibiting the toxic expression of QNs' ARGs in the soil environment, reducing the spread of ARGs in microbial populations, replacing green QNs derivatives, and sustainable development of agricultural soils.

Monitoring and evaluation of antibiotic resistance genes in three rivers in northeast China

Antibiotic resistance genes (ARGs) have become an important public health problem. In this study, we used metagenomic sequencing to analyze the composition of ARGs in selected original habitats of northeast China, comprising three different rivers and riverbank soils of the Heilongjiang River, Tumen River, and Yalu River. Twenty types of ARG were detected in the water samples. The major ARGs were multidrug resistance genes, at approximately 0.5 copies/16S rRNA, accounting for 57.5% of the total ARG abundance. The abundance of multidrug, bacitracin, beta-lactam, macrolide-lincosamide-streptogramin, sulfonamide, fosmidomycin, and polymyxin resistance genes covered 96.9% of the total ARG abundance. No significant ecological boundary of ARG diversity was observed. The compositions of the resistance genes in the three rivers were very similar to each other, and 92.1% of ARG subtypes were shared by all water samples. Except for vancomycin resistance genes, almost all ARGs in riverbank soils were detected in the river water. About 31.05% ARGs were carried by Pseudomonas. Opportunistic pathogenic bacteria carrying resistance genes were mainly related to diarrhea and respiratory infections. Multidrug and beta-lactam resistance genes correlated positively with mobile genetic elements (MGEs), indicating a potential risk of diffusion. The composition of ARGs in three different rivers was similar, indicating that climate plays an important role in ARG occurrence. ARG subtypes in river water were almost completely the same as those in riverbank soil. ARGs had no significant geographical distribution characteristics. Many ARGs were carried by human pathogenic bacteria related to diarrhea and respiratory infections, such as Pseudomonas aeruginosa and Aeromonas caviae. In general, our results provide a valuable dataset of river water ARG distribution in northeast China. The related ecological and geographical distribution characteristics should be further explored.

Antibiotic resistomes in water supply reservoirs sediments of central China: main biotic drivers and distribution pattern

Water supply reservoirs form one of the critical drinking water resources. Their water quality directly affects human health. However, reservoir sediments have not received adequate attention in antibiotic resistance genes (ARGs) dissemination, though they reflect long-term ARGs contamination of water supply reservoirs. Moreover, the physicochemical parameters in water supply reservoir sediments are generally better than those in the other media. Thus, the main ARGs biotic drivers of the media would demonstrate their unique characteristics. In this study, sediment samples were collected from 10 water supply reservoirs in central China, and the antibiotic resistomes were determined with the metagenomic method. As revealed from the results, 174 ARGs (18 ARG types) were detected in the reservoir sediment. Besides, multidrug-, sulfonamide-, and vancomycin-ARGs were the dominant ARGs in the sediment samples. The macrolide-resistant Microcystis was prevalent (100% detection frequency with 0.35% average percentage) in reservoir sediments and posed potential risks to human health. Furthermore, the results of the Mantel test and VPA demonstrated that mobile genetic elements (MGEs) were the more essential biotic drivers in ARG contents of reservoir sediments rather than the bacteria community.

Occurrence of Antimicrobial Resistance in the Environment in Germany, Austria, and Switzerland: A Narrative Review of Existing Evidence

(1) Background: This study summarizes the current research on antibiotic resistance (AR) in the environment conducted in Austria, Germany, and Switzerland; (2) Methods: A narrative systematic literature review of epidemiological studies based on searches in EMBASE and CAB abstracts (up to 16 June2021) was conducted. Environmental reservoirs included water sources, wastewater, animal husbandry, wildlife, soil, and sediment; (3) Results: Four hundred and four records were screened, and 52 studies were included. Thirteen studies examined aquatic environments, and eleven investigated wastewater. Eight studies investigated both wildlife and animal husbandry. Less evidence was available for sediments, soil, and air. Considerable heterogeneity in research focus, study design, sampling, and measurement of resistance was observed. Resistance to all categories of antimicrobials in the WHO CIA list was identified. Resistance to critically important and highly important substances was reported most frequently; (4) Conclusions: The current research scope presents data-gathering efforts. Usage of a unified protocol for isolate collection, selecting sampling sites, and susceptibility testing is required to provide results that can be compared between the studies and reservoirs. Epidemiological, environmental, and ecological factors should be considered in surveys of the environmental dissemination of AR. Systematic epidemiological studies investigating AR at the interface of human, animal, and environmental health are needed.

Metagenomic analysis of microbial communities and antibiotic resistance genes in spoiled household chemicals

Numerous attempts have been utilized to unveil the occurrences of antibiotic resistance genes (ARGs) in human-associated and non-human-associated samples. However, spoiled household chemicals, which are usually neglected by the public, may be also a reservoir of ARGs because of the excessive and inappropriate uses of industrial drugs. Based upon the Comprehensive Antibiotic Research Database, a metagenomic sequencing method was utilized to detect and quantify Antibiotic Resistance Ontology (AROs) in six spoiled household chemicals, including hair conditioner, dishwashing detergent, bath shampoo, hand sanitizer, and laundry detergent. Proteobacteria was found to be the dominant phylum in all the samples. Functional annotation of the unigenes obtained against the KEGG pathway, eggNOG and CAZy databases demonstrated a diversity of their functions. Moreover, 186 types of AROs that were members of 72 drug classes were identified. Multidrug resistance genes were the most dominant types, and there were 17 AROs whose resistance mechanisms were categorized into the resistance-nodulation-cell division antibiotic efflux pump among the top 20 AROs. Moreover, Proteobacteria was the dominant carrier of AROs with the primary resistance mechanism of antibiotic efflux. The maximum temperature of the months of collection significantly affected the distributions of AROs. Additionally, the isolated individual bacterium from spoiled household chemicals and artificial mixed communities of isolated bacteria demonstrated diverse resistant abilities to different biocides. This study demonstrated that there are abundant microorganisms and a broad spectrum profile of AROs in spoiled household chemicals that might induce a severe threat to public healthy securities and merit particular attention.

Characteristics changes on Applications of Antibiotics and Current Approaches to Enhance Productivity with Soil Microbiome

The contamination of environmental sully with antibiotics is regarded as a major problem today and predictable to attain more recognition in near future. However, human intervention resulting in antibiotic consumption is being enhancing all around the world. Our review of literature revealed the role of microbiome in sully and how antibiotic resistant genes raised. The structure of antibiotics basically influenced by natural components such as biotic and abiotic push which shifts based on different soils. Therefore, management of microbiome in soil and their expression studies were distinctively revealed. The assessment of antibiotic resistance genes with help of next generation sequencing provided a clear comprehension on genome and transcriptome of the bacterial genes. Thus, interaction of microbiome with soil can also be well understood. The current findings in our study will guide every researcher to follow logical protocol in analyzing microbiota composition is covered as well and also to understand its metagenomic and sequenced with next-generation sequencer which helps to comprehend the diverse micro-flora present in soil and its operation. Finally, later progresses in bioinformatics computer program, flow of work, and applications for analyzing metagenomic information are put in a nutshell.

Structure of the manure resistome and the associated mobilome for assessing the risk of antimicrobial resistance transmission to crops

In this study, the impact of bovine and poultry manure on the quantitative and qualitative composition of antibiotic resistance genes (ARGs) and the environmental mobilome associated with antimicrobial resistance in soil and crops was determined with the use of next generation sequencing methods. The aim of the study was to perform a metagenomic analysis of manure to estimate the risk of the transmission of ARGs and bacterial drug resistance carriers to fertilized soil and crops. The total copy number of ARGs was nearly four times higher in poultry manure (555 ppm) than in bovine manure (140 ppm), and this relationship was also noted in fertilized soil. Poultry manure induced a much greater increase in the concentrations of ARGs in the soil environment (196.4 ppm) than bovine manure (137.8 ppm) immediately after supplementation. The application of poultry manure led to the highest increase in the abundance of genes encoding resistance to tetracyclines (9%), aminoglycosides (3.5%), sulfonamides (3%), bacitracin (2%), chloramphenicol (2%), and macrolide-lincosamide-streptogramin antibiotics (1%). Heavy metals were stronger promoters of antibiotic resistance in the environment than antibiotics. Antibiotics exerted a greater influence on maintaining the diversity of ARGs than on increasing their abundance in soil. Large quantities of insertion sequences (IS), including those associated with the mobility of ARGs in the population of ESKAPEE pathogens, are introduced to soil with manure. These IS remain stable for up to several months, which indicates that manure, in particular poultry manure, significantly increases the risk of rapid ARG transfer to the environment. Manure also largely contributes to an increase in the diversity of the resistome and mobilome in the metagenome of bacteria isolated from crops. Bacteria of the phylum Proteobacteria appear to play a major role in the transmission of multiple ARGs in crops grown for human and animal consumption.

Film mulching reduces antibiotic resistance genes in the phyllosphere of lettuce

Phyllosphere is an important reservoir of antibiotic resistance genes (ARGs), but the transfer mechanism of ARGs from soil and air to phyllosphere remains unclear. This study demonstrated that soil-air-phyllosphere was the dominant ARG transfer pathway, and blocking it by film mulching can reduce typical phyllosphere ARGs in lettuce by 80.7% - 98.7% (89.5% on average). To further eliminate phyllosphere ARGs in lettuce grown with film mulching, the internal soil-endosphere-phyllosphere transfer pathway deserves more attention. We analyzed the ARG hosts and the resistome in lettuce rhizosphere and phyllosphere with film mulching via hybrid Illumina-Nanopore sequencing. Pseudomonas sp. 7SR1 was more abundant than other ARG hosts, accounting for 1.0% and 47.1% of the total bacteria in rhizosphere and phyllosphere, respectively. The species has flagella that can promote mobility and can excrete extracellular polymeric substances and/or surfactant-like microbial products, which benefits its colonization in the phyllosphere. Impeding the migration of Pseudomonas sp. 7SR1 via the soil-endosphere-phyllosphere pathway would be effective to further reduce ARGs in phyllosphere. Multidrug resistant genes were predominant in phyllosphere (40.3% of the total), and 87.6% of the phyllosphere ARGs were located on chromosomes, indicating relatively low horizontal gene transfer (HGT) potentials. This study provides insights into the transfer mechanism, hosts, and control strategies of phyllosphere ARGs in typical plants.

Identification and antimicrobial susceptibility of milk pathogen isolated from dairy production systems

Livestock has been recognized as a reservoir of antibiotic-resistant bacteria. Prevalence of resistance has been associated with herd size and intensification of animal production systems. Brazil is one of the emergent hotspots of bacterial resistance, which is also associated with animal husbandry. This study aimed to evaluate the resistance profile of pathogens that cause subclinical mastitis and the relationship between resistance status at farm level and different production systems. Milk samples from cows diagnosed with subclinical mastitis were collected from farms that adopt different husbandry systems with different production intensities, i.e., agroecological, low input, high input, Free-Stall and Compost-bedded pack barn. Etiological agents were isolated and microbiologically identified, and antibiotic susceptibility testing was conducted, using the disk diffusion method. The main isolated agents were Streptococcus spp. (n = 54, 30.5 %) and coagulase-positive Staphylococcus (CPS) (n = 54; 30.5 %). The recovered isolates displayed high antibiotic resistance against Sulfamethazine (80.2 %), Gentamicin (29.37 %), Penicillin (29.37 %), Oxacillin (28.82 %) and Ampicillin (26 %). Multidrug resistance was found for all agents and in all farming systems (39.54 %). Neither production systems (p = 0.26) nor farming systems (p = 0.24) significantly affected the resistance rates of samples. Therefore, intensive production systems may not be a root cause of increased rates of antimicrobial resistance in the milk production chain, suggesting that other environmental factors should be investigated. It is noteworthy that high levels of multidrug resistance were even found in bacteria earlier considered as minor pathogens. This development can be taken as a warning that environmental bacteria are potential transmitters of resistance genes to the environment.

Analysis of Antibiotic Resistance Genes, Environmental Factors, and Microbial Community From Aquaculture Farms in Five Provinces, China

The excessive use of antibiotics speeds up the dissemination and aggregation of antibiotic resistance genes (ARGs) in the environment. The ARGs have been regarded as a contaminant of serious environmental threats on a global scale. The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat bacterial infections; there is a universal concern about the environmental risk of ARGs in the aquaculture environment. In this study, a survey was conducted to evaluate the abundance and distributions of 10 ARGs, bacterial community, and environmental factors in sediment samples from aquatic farms distributed in Anhui (AP1, AP2, and AP3), Fujian (FP1, FP2, and FP3), Guangxi (GP1, GP2, and GP3), Hainan (HP1, HP2, and HP3), and Shaanxi (SP1, SP2, and SP3) Province in China. The results showed that the relative abundance of total ARGs was higher in AP1, AP2, AP3, FP3, GP3, HP1, HP2, and HP3 than that in FP1, FP2, GP1, GP2, SP1, SP2, and SP3. The sul1 and tetW genes of all sediment samples had the highest abundance. The class 1 integron (intl1) was detected in all samples, and the result of Pearson correlation analysis showed that the intl1 has a positive correlation with the sul1, sul2, sul3, bla_OXA, qnrS, tetM, tetQ, and tetW genes. Correlation analysis of the bacterial community diversity and environmental factors showed that the Ca²⁺ concentration has a negative correlation with richness and diversity of the bacterial community in these samples. Of the identified bacterial community, Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidota were the predominant phyla in these samples. Redundancy analysis showed that environmental factors (TN, TP, Cl^–, and Ca²⁺) have a positive correlation with the bacterial community (AP1, GP1, GP2, GP3, SP1, SP2, and SP3), and the abundance of ARGs (sul1, tetW, qnrS, and intl1) has a positive correlation with the bacterial community (AP2, AP3, HP1, HP2, and HP3). Based on the network analysis, the ARGs (sul1, sul2, bla_CMY, bla_OXA, qnrS, tetW, tetQ, tetM, and intl1) were found to co-occur with bacterial taxa from the phyla Chloroflexi, Euryarchaeota, Firmicutes, Halobacterota, and Proteobacteria. In conclusion, this study provides an important reference for understanding the environmental risk associated with aquaculture activities in China.

Termite mound formation reduces the abundance and diversity of soil resistomes

Termites are pivotal ecosystem engineers in tropical and subtropical habitats, where they construct massive nests ('mounds') that substantially modify soil properties and promote nutrient cycling. Yet, little is known about the roles of termite nesting activity in regulating the spread of antimicrobial resistance (AMR), one of the major Global Health challenges. Here, we conducted a large-scale (> 1500 km) investigation in northern Australia and found distinct resistome profiles in termite mounds and bulk soils. By profiling a wide spectrum of ARGs, we found that the abundance and diversity of antibiotic resistance genes (ARGs) were significantly lower in termite mounds than in bulk soils (P < 0.001). The proportion of efflux pump ARGs was significantly lower in termite mound resistome than in bulk soil resistome (P < 0.001). The differences in resistome profiles between termite mounds and bulk soils may result from the changes in microbial interactions owing to the substantial increase in pH and nutrient availability induced by termite nesting activities. These findings advance our understanding of the profile of ARGs in termite mounds, which is a crucial step to evaluate the roles of soil faunal activity in regulating soil resistome under global environmental change.

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems

BACKGROUND

Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively.

RESULTS

High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition.

CONCLUSIONS

Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.

Improved reduction of antibiotic resistance genes and mobile genetic elements from biowastes in dry anaerobic co-digestion

This study investigated the performance of anaerobic co-digestion (AcoD) of pig manure and food waste on the reduction of antibiotic resistomes under wet and dry AcoD conditions. High-throughput quantitative PCR technology was utilized for a comprehensive assessment of the performances of the two processes. The results show that dry AcoD with a total solids (TS) content of 20% effectively reduced total antibiotic resistance genes (ARGs) by 1.24 log copies/g wet sample, while only 0.54 log copies/g wet sample was reduced in wet AcoD with a TS content of 5%. Dry AcoD was more efficient in reduction of aminoglycosides, multidrug and sulfonamide resistance genes compared with the reduction of other classes of ARGs. Dry AcoD caused a significant reduction of ARGs with resistance mechanisms of efflux pump and antibiotic deactivation. In contrast, there was no obvious difference in reductions of ARGs with different resistance mechanisms in wet AcoD. Network analysis showed that ARGs were significantly correlated with mobile genetic elements (MGEs) (Spearman's r > 0.8, P < 0.05), as well as microbial communities. Enrichment of ARGs and MGEs was found at the early period of AcoD processes, indicating some ARGs and MGEs increased during the hydrolysis and acidogenesis stages. But after a long retention time, their abundances were effectively reduced by dry AcoD in the subsequent stages.

Eukaryotic community diversity and pathogenic eukaryotes in a full-scale drinking water treatment plant determined by 18S rRNA and metagenomic sequencing

In this study, 18S rRNA high-throughput sequencing was applied to investigate the eukaryotic community in a full-scale drinking water treatment plant. Eukaryotic species and microbial functions in raw water and filter biofilms were identified by metagenomic sequencing. The eukaryotic species richness and diversity presented declining trends throughout the treatment process. The lowest eukaryotic species richness was observed in disinfected water. Arthropoda, Ciliophora, Ochrophyta, and Rotifera were the dominant eukaryotic phyla and exhibited high variations in relative abundance among the different treatment units. Sedimentation significantly decreased the abundance of all eukaryotes except Arthropoda. Biological activated carbon (BAC) filtration and chlorine disinfection exerted strong effects on community composition. The eukaryotic communities in water were distinct from those in filter biofilms, as were the communities of different filter biofilms from each other. In contrast, communities were functionally similar among different filter biofilms, with the category metabolism being the dominant category represented, within which amino acid transport and metabolism (E) and energy production and conversion (C) dominated among subcategories. Seventy-one eukaryotic species pathogenic to humans were identified in raw water and filter biofilms. Quantitative PCR (qPCR) results showed that Acanthamoeba spp. and Vermamoeba vermiformis were present during some treatment processes, with concentrations of 12-1.2 × 10⁵ copies/mL and 1 copy/mL, respectively. Neither of the two pathogenic amoebae was found in disinfected water. Canonical correspondence analysis (CCA) showed that pH was the most important environmental factor affecting eukaryotic community composition. Overall, the results provide insights into the eukaryotic community diversity in drinking water treatment plants and the potential eukaryotic hazards involved in drinking water production.

Abundance, diversity and mobility potential of antibiotic resistance genes in pristine Tibetan Plateau soil as revealed by soil metagenomics

Widespread occurrence of antibiotic resistance genes (ARGs) has become an important clinical issue. Studying ARGs in pristine soil environments can help to better understand the intrinsic soil resistome. In this study, 10 soil samples were collected from a high elevation and relatively pristine Tibetan area, and metagenomic sequencing and bioinformatic analyses were conducted to investigate the microbial diversity, the abundance and diversity of ARGs and the mobility potential of ARGs as indicated by different mobile genetic elements (MGEs). A total of 48 ARG types with a relative abundance of 0.05-0.28 copies of ARG/copy of 16S rRNA genes were detected in Tibetan soil samples. The observed ARGs were mainly associated with antibiotics that included glycopeptide and rifamycin; the most abundant ARGs were vanRO and vanSO. Low abundance of MGEs and potentially plasmid-related ARGs indicated a low horizontal gene transfer risk of ARGs in the pristine soil. Pearson correlation and redundancy analyses showed that temperature and total organic carbon were the major environmental factors controlling both microbial diversity and ARG abundance and diversity.

Antimicrobial resistance in the farm-to-plate continuum: more than a food safety issue

Antimicrobial resistance (AMR) threatens to reverse the essential benefits of antibiotics, not only in humans, where decades of advancements in healthcare outcomes are endangered, but also in the food production industry. As the world moves toward Sustainable Development Goals, food safety is a critical element to improve and strengthen global health, and ensure sustainable development. Emergence of AMR in the food production industry represents a serious risk for exposed workers, their relatives and consumers. This perspective presents the challenge of AMR through the lens of food safety, by highlighting its multisectoral and multidimensional implications not only on the Sustainable Development Goals for food safety and public health but also on food security, animal health and welfare, the environment and climate, and socioeconomic development.

The changes in antibiotic resistance genes during 86 years of the soil ripening process without anthropogenic activities

This study aimed to reveal the baseline of natural variations in antibiotic resistance genes (ARGs) in soil without anthropogenic activities over the decades. Nine soil samples with different time of soil formation were taken from the Yancheng Wetland National Nature Reserve, China. ARGs and mobile genetic elements (MGEs) were characterized using metagenomic analysis. A total of 196 and 192 subtypes of ARGs were detected in bulk soil and rhizosphere, respectively. The diversity and abundance of ARGs were stable during 69 years probably due to the alkaline pH soil environment but not due to antibiotics. Increases in ARGs after 86 years were probably attributed to more migrant birds inhabited compared with other sampling sites. Multidrug was the most abundant type, and largely shared by soil samples. It was further shown that soil samples could not be clearly distinguished, suggesting a slow process of succession of ARGs in the mudflat. The variation partitioning analysis revealed that the ARG profile was driven by the comprehensive effects exhibited by the bacterial community, MGEs, and environmental factors. Besides, pathogenic bacteria containing ARGs mediated by migrant birds in the area with 86 years of soil formation history nearing human settlements needed special attention. This study revealed the slow variations in ARGs in the soil ripening process without anthropogenic activities over decades, and it provided information for assessing the effect of human activities on the occurrence and dissemination of ARGs.

Antibiotic resistance genes (ARGs) in agricultural soils from the Yangtze River Delta, China

As an important reservoir of intrinsic antimicrobial resistance, soil is subjected to increasing anthropogenic activities that creates sustained selection pressure for the prevalence of antibiotic resistance genes (ARGs), thus constituting an important environmental dissemination pathway to human exposure. This study investigated the levels and spatial distributions of three classes of ARGs in relation to a range of co-occurring chemical mixtures and soil properties at a regional scale of the Yangtze River Delta (YRD), China. The selected eight ARGs were all detected in 241 agricultural soil samples with relative abundances ranging from 1.01 × 10^-7 to 2.31 × 10^-1 normalized to the 16S rRNA gene. The sulII and tetG were the dominant ARGs with a mean relative abundance of 6.67 × 10^-3 and 5.25 × 10^-3, respectively. The ARGs were mainly present in agricultural soils alongside Taihu Lake and Shanghai municipality, the most agriculturally and economically vibrant area of the YRD region. Antibiotics, rather than other co-occurring pollutants and soil properties, remain to be the dominant correlate to the ARGs, suggesting their co-introduction into the soils via irrigation and manure application or the sustained selection pressure of antibiotics from these sources for the proliferation of ARGs in the soils. While the current dataset provided useful information to assess the ARGs pollution for mitigation, future studies are warranted to reveal the complete picture on the potential transfer of antimicrobial resistance from soil to agricultural produces to human consumption and associated health implications.

Metagenomic and 14 C tracing evidence for autotrophic microbial CO2 fixation in paddy soils

Autotrophic carbon dioxide (CO₂ ) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with ¹⁴ C-labelling to investigate all known autotrophic pathways and CO₂ assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%-82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of ¹⁴ C-CO₂ are assimilated into SOC (74.3-175.8 mg ¹⁴ C kg^-1 ) and microbial biomass (5.2-24.1 mg ¹⁴ C kg^-1 ) after 45 days incubation, where more than 70% of ¹⁴ C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.

ARGDIT: a validation and integration toolkit for Antimicrobial Resistance Gene Databases

MOTIVATION

Antimicrobial resistance is currently one of the main challenges in public health due to the excessive use of antimicrobials in medical treatments and agriculture. The advancements in high-throughput next-generation sequencing and development of bioinformatics tools allow simultaneous detection and identification of antimicrobial resistance genes (ARGs) from clinical, food and environment samples, to monitor the prevalence and track the dissemination of these ARGs. Such analyses are however reliant on a comprehensive database of ARGs with accurate sequence content and annotation. Most of the current ARG databases are therefore manually curated, but this is a time-consuming process and the resulting curation errors could be hard to detect. Several secondary ARG databases consolidate contents from different source ARG databases, and hence modifications in the primary databases might not be propagated and updated promptly in the secondary ARG databases.

RESULTS

To address these problems, a validation and integration toolkit called ARGDIT was developed to validate ARG database fidelity, and merge multiple primary ARG databases into a single consolidated secondary ARG database with optional automated sequence re-annotation. Experimental results demonstrated the effectiveness of this toolkit in identifying errors such as sequence annotation typos in current ARG databases and generating an integrated non-redundant ARG database with structured annotation. A toolkit-oriented workflow is also proposed to minimize the efforts in validating, curating and merging multiple ARG protein or coding sequence databases. Database developers therefore benefit from faster update cycles and lower costs for database maintenance, while ARG pipeline users can easily evaluate the reference ARG database quality.

AVAILABILITY AND IMPLEMENTATION

ARGDIT is available at https://github.com/phglab/ARGDIT.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Different Age-Induced Changes in Rhizosphere Microbial Composition and Function of Panax ginseng in Transplantation Mode

Transplantation is a cultivation mode widely applied in perennial plant growing. This method might be an effective way to alleviate problems associated with continuous cultivation (4-6 years) in ginseng production, but the alleviating mechanism and effects on soil microbial community is unclear. To study this issue, non-transplanted 2-year-old, and 5-year-old (transplantation mode: 2 + 3) and 9-year-old (transplantation mode: 3 + 3 + 3) ginseng rhizosphere soils were analyzed via MiSeq sequencing. The results showed that 9-year-old ginseng rhizosphere soil had lower available nitrogen and the lowest pH, available phosphorus, observed species and community diversity and richness (Chao1, and ACE) among all samples (p < 0.05). The abundances of some bacterial classes (Thermoleophilia, Bacilli, and Nitrospira) and fungal genera (Mortierella, Epicoccum, and Penicillium spp.) and functional richness associated with nutrient element cycles and antifungal activity decreased, while abundances of some fungal genera (Ilyonectria, Tetracladium, and Leptodontidium spp.) increased with increasing age of ginseng plants (p < 0.05 or p < 0.01). However, there was greater similarity between soil samples of 2-year-old and transplanted 5-year-old ginseng plants and the increase in cultivation time from 2 to 5 years did not significantly influence the microbial community, suggesting that transplantation is a viable strategy for suppressing soil-borne diseases in Panax ginseng plants over long growth periods.

Dynamics of metal(loid) resistance genes driven by succession of bacterial community during manure composting

Metal(loid) resistance genes (MRGs) play important roles in conferring resistance to metal(loid)s in bacterial communities. How MRGs respond to bacterial succession during manure composting remains largely unknown. Metagenomics was used in the present study to investigate the compositional changes of MRGs, their candidate hosts and association with integrons during thermophilic composting of chicken manures. MRGs conferring resistance to 20 metal(loid)s were detected, and their diversity and abundance (normalized to the abundance of 16S rRNA genes) were significantly reduced during composting. MRGs associated with integron were exclusively observed in proteobacterial species. Class 1 integron likely played an important role in maintaining mercury-resistance mer operon genes in composts. Escherichia coli harbored the most abundant MRGs in the original composting material, whereas species of Actinobacteria and Bacilli became more important in carrying MRGs during the late phases. There were significant linear relationships between the relative abundance of some specific bacterial species (E. coli, Actinobacteria species and Enterococcus faecium) and the abundance of MRGs they potentially harbored. The succession of these bacteria contributed to an overall linear regression between the relative abundance of all predicted candidate hosts and the abundance of total MRGs. Our results suggest that the succession of bacterial community was the main driver of MRG dynamics during thermophilic composting.

The persistence of antimicrobial resistance and related environmental factors in abandoned and working swine feedlots

Swine feedlots that have operated in the absence of adequate disposal facilities are being demolished under the new environmental protection policies in China. The environmental behavior and transmission risks of antimicrobial resistance genes (ARGs) are unclear for these abandoned swine feedlots. We examined 40 soil samples that originated from the soils adjacent to two abandoned and two working swine feedlots to explore: 1) the distribution patterns and vertical transmission of 17 ARGs and two integron genes and 2) the bacterial community as well as their correlation with environmental factors and target genes. We found that seven and nine out of forty-eight subtypes of veterinary antimicrobials (VAs) were detected in the soil near abandoned feedlots and working feedlots, respectively. Three tet genes (tetM, tetO and tetW) were particularly enriched in the soil adjacent to both abandoned and working feedlots. The tetM gene was a "hub" on the network of the topsoil. The relative abundance of Firmicutes ranged from 2.5 to 9% in the soil near two Beijing feedlots and was significantly higher than that in the upstream blank control (CK soil) (ANOVA, p < 0.05). Overall, the ARG distribution patterns in the soils adjacent to abandoned swine feedlots were similar to the working feedlots. This study offers basic information on the prevalence and transmission risk of ARGs in abandoned swine feedlots and provides a reference for the restoration and reuse of demolished feedlots.

Characterization of the Microbial Resistome in Conventional and "Raised Without Antibiotics" Beef and Dairy Production Systems

Metagenomic investigations have the potential to provide unprecedented insights into microbial ecologies, such as those relating to antimicrobial resistance (AMR). We characterized the microbial resistome in livestock operations raising cattle conventionally (CONV) or without antibiotic exposures (RWA) using shotgun metagenomics. Samples of feces, wastewater from catchment basins, and soil where wastewater was applied were collected from CONV and RWA feedlot and dairy farms. After DNA extraction and sequencing, shotgun metagenomic reads were aligned to reference databases for identification of bacteria (Kraken) and antibiotic resistance genes (ARGs) accessions (MEGARes). Differences in microbial resistomes were found across farms with different production practices (CONV vs. RWA), types of cattle (beef vs. dairy), and types of sample (feces vs. wastewater vs. soil). Feces had the greatest number of ARGs per sample (mean = 118 and 79 in CONV and RWA, respectively), with tetracycline efflux pumps, macrolide phosphotransferases, and aminoglycoside nucleotidyltransferases mechanisms of resistance more abundant in CONV than in RWA feces. Tetracycline and macrolide–lincosamide–streptogramin classes of resistance were more abundant in feedlot cattle than in dairy cow feces, whereas the β-lactam class was more abundant in dairy cow feces. Lack of congruence between ARGs and microbial communities (procrustes analysis) suggested that other factors (e.g., location of farms, cattle source, management practices, diet, horizontal ARGs transfer, and co-selection of resistance), in addition to antimicrobial use, could have impacted resistome profiles. For that reason, we could not establish a cause–effect relationship between antimicrobial use and AMR, although ARGs in feces and effluents were associated with drug classes used to treat animals according to farms’ records (tetracyclines and macrolides in feedlots, β-lactams in dairies), whereas ARGs in soil were dominated by multidrug resistance. Characterization of the “resistance potential” of animal-derived and environmental samples is the first step toward incorporating metagenomic approaches into AMR surveillance in agricultural systems. Further research is needed to assess the public-health risk associated with different microbial resistomes.

Distribution and Succession Feature of Antibiotic Resistance Genes Along a Soil Development Chronosequence in Urumqi No.1 Glacier of China

Primary succession of plant and microbial communities in the glacier retreating foreland has been extensively studied, but shifts of antibiotic resistance genes (ARGs) with the glacier retreating due to global warming remain elusive. Unraveling the diversity and succession features of ARGs in pristine soil during glacier retreating could contribute to a mechanistic understanding of the evolution and development of soil resistome. In this study, we quantified the abundance and diversity of ARGs along a 50-year soil development chronosequence by using a high-throughput quantitative PCR (HT-qPCR) technique. A total of 24 ARGs and two mobile genetic elements (MGEs) were detected from all the glacier samples, and the numbers of detected ARGs showed a unimodal pattern with an increasing trend at the early stage (0∼8 years) but no significant change at later stages (17∼50 years). The oprJ and mexF genes encoding multidrug resistance were the only two ARGs that were detected across all the succession ages, and the mexF gene showed an increasing trend along the succession time. Structural equation models indicated the predominant role of the intI1 gene encoding the Class 1 integron-integrase in shaping the variation of ARG profiles. These findings suggested the presence of ARGs in pristine soils devoid of anthropogenic impacts, and horizontal gene transfer mediated by MGEs may contribute to the succession patterns of ARGs during the initial soil formation stage along the chronosequence.

Understanding drivers of antibiotic resistance genes in High Arctic soil ecosystems

Soils in tropical and temperate locations are known to be a sink for the genetic potential of anthropogenic-driven acquired antibiotic resistance (AR). In contrast, accumulation of acquired AR is less probable in most Polar soils, providing a platform for characterizing background resistance and establishing a benchmark for assessing AR spread. Here, high-throughput qPCR and geochemistry were used to quantify the abundance and diversity of both antibiotic resistance genes (ARGs) and selected mobile genetic elements (MGEs) across eight soil clusters in the Kongsfjorden region of Svalbard in the High Arctic. Relative ARG levels ranged by over two orders of magnitude (10^-6 to 10^-4 copies/16S rRNA gene copy), and showed a gradient of potential human and wildlife impacts across clusters as evidenced by altered geochemical conditions and increased "foreign" ARG abundances (i.e., allochthonous), including bla_NDM-1. Impacted clusters exhibited 100× higher total ARGs and MGEs in tandem with elevated secondary nutrients, especially available P that is typically low and limiting in Arctic soils. In contrast, ARGs in less-impacted clusters correlated strongly to local soil lithology. The most plausible source of exogenous P and allochthonous ARGs in this region is bird and other wildlife guano, disseminated either by local human wastes or via direct carriage and deposition. Regardless of pathway, accumulation of apparent allochthonous ARGs and MGEs in High Arctic soils is concerning, highlighting the importance of characterizing Arctic sites now to establish benchmarks for tracking AR spread around the world.

Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: advances and applications

Our inability to cultivate most microorganisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and nonliving environments. As a result, reservoirs, sources and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes.

Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity

Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.

Prevalence of Antibiotic Resistance Genes in Air-Conditioning Systems in Hospitals, Farms, and Residences

High-throughput quantitative PCR combined with Illumina sequencing and network analysis were used to characterize the antibiotic resistance gene (ARG) profiles in air-conditioning filters from different environments. In total, 177 ARGs comprising 10 ARG types were determined. The detectable numbers and the relative abundance of ARGs in hospitals and farms were significantly higher than those in city and village residences. Compared to hospitals, farms had a higher level of tetracycline, multidrug, integrase, and macrolide⁻lincosamide⁻streptogramin (MLS) B resistance genes but a lower level of beta-lactam resistance genes. The bl3_cpha gene was the most abundant resistance gene subtype in hospital samples with an abundance of 2.01 × 10^-4 copies/16S rRNA, while a level of only 5.08 × 10^-12 copies/16S rRNA was observed in farm samples. There was no significant difference in bacterial diversity among the hospitals, farms, and residences, and Proteobacteria was the most abundant phylum. Network analysis revealed that Proteobacteria and Actinobacteria were possible hosts of the beta-lactam, MLSB, aminoglycoside, multidrug, sulfonamide, and tetracycline resistance genes. The results demonstrate that ARGs exist in indoor environments and that farms and hospitals are important sources. This study provides a useful reference for understanding the distribution patterns and risk management of ARGs in indoor environments.

DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples

High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes. It can also be used for experimental design, to estimate how many samples to use in future experiments, again with the advantage of being universally most powerful. We present three example analyses in the area of antimicrobial resistance. The first is to published data on bacterial communities and antimicrobial resistance genes (ARGs) in the environment; we show that there are significant changes in both ARG and community composition. The second is to new data on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep would provide sufficient power to observe significance of similar changes in further experiments. The third is to published data on bacterial communities surrounding rice crops. This is a much larger data set and is used to verify the new method. Our method has broad uses for statistical testing and experimental design in research on changing microbiomes, including studies on antimicrobial resistance.

Metagenomic analysis of antibiotic resistance genes (ARGs) during refuse decomposition

Landfill is important reservoirs of residual antibiotics and antibiotic resistance genes (ARGs), but the mechanism of landfill application influence on antibiotic resistance remains unclear. Although refuse decomposition plays a crucial role in landfill stabilization, its impact on the antibiotic resistance has not been well characterized. To better understand the impact, we studied the dynamics of ARGs and the bacterial community composition during refuse decomposition in a bench-scale bioreactor after long term operation (265d) based on metagenomics analysis. The total abundances of ARGs increased from 431.0ppm in the initial aerobic phase (AP) to 643.9ppm in the later methanogenic phase (MP) during refuse decomposition, suggesting that application of landfill for municipal solid waste (MSW) treatment may elevate the level of ARGs. A shift from drug-specific (bacitracin, tetracycline and sulfonamide) resistance to multidrug resistance was observed during the refuse decomposition and was driven by a shift of potential bacteria hosts. The elevated abundance of Pseudomonas mainly contributed to the increasing abundance of multidrug ARGs (mexF and mexW). Accordingly, the percentage of ARGs encoding an efflux pump increased during refuse decomposition, suggesting that potential bacteria hosts developed this mechanism to adapt to the carbon and energy shortage when biodegradable substances were depleted. Overall, our findings indicate that the use of landfill for MSW treatment increased antibiotic resistance, and demonstrate the need for a comprehensive investigation of antibiotic resistance in landfill.

Changes in bacterial community structure and antibiotic resistance genes in soil in the vicinity of a pharmaceutical factory

China is the largest global producer of antibiotics. With the demand for antibiotics increasing every year, it is necessary to assess potential environmental risks and the spread of antibiotic resistance genes (ARGs) associated with antibiotic production. Here, we investigated the occurrence and distribution of ARGs in soil in the vicinity of a pharmaceutical factory. The results showed that antibiotic concentrations were under the detection limit; however, ARGs were present in soil and tended to be enriched near the factory. A significant correlation between the relative abundance of intI-1 and tetracycline ARGs implied that horizontal gene transfer might play an important role in the spread of ARGs. The occurrence of these ARGs could be the results of previous antibiotic contamination. However, the soil bacterial community structure seemed to be more affected by nutrients or other factors than by antibiotics. Overall, this study supports the viewpoint that long-term pharmaceutical activity might have a negative effect on environmental health, thus, underscoring the need to regulate antibiotic production and management.

Comparative mangrove metagenome reveals global prevalence of heavy metals and antibiotic resistome across different ecosystems

The mangrove ecosystem harbors a complex microbial community that plays crucial role in biogeochemical cycles. In this study, we analyzed mangrove sediments from India using de novo whole metagenome next generation sequencing (NGS) and compared their taxonomic and functional community structures to mangrove metagenomics samples from Brazil and Saudi Arabia. The most abundant phyla in the mangroves of all three countries was Proteobacteria, followed by Firmicutes and Bacteroidetes. A total of 1,942 genes were found to be common across all the mangrove sediments from each of the three countries. The mangrove resistome consistently showed high resistance to fluoroquinolone and acriflavine. A comparative study of the mangrove resistome with other ecosystems shows a higher frequency of heavy metal resistance in mangrove and terrestrial samples. Ocean samples had a higher abundance of drug resistance genes with fluoroquinolone and methicillin resistance genes being as high as 28.178% ± 3.619 and 10.776% ± 1.823. Genes involved in cobalt-zinc-cadmium resistance were higher in the mangrove (23.495% ± 4.701) and terrestrial (27.479% ± 4.605) ecosystems. Our comparative analysis of samples collected from a variety of habitats shows that genes involved in resistance to both heavy metals and antibiotics are ubiquitous, irrespective of the ecosystem examined.