Combined contamination of microplastic and antibiotic alters the composition of microbial community and metabolism in wheat and maize rhizosphere soil

The widespread application of antibiotics and plastic films in agriculture has led to new characteristics of soil pollution. The impacts of combined contamination of microplastics and antibiotics on plant growth and rhizosphere soil bacterial community and metabolisms are still unclear. We conducted a pot experiment to investigate the effects of polyethylene (0.2%) and norfloxacin/doxycycline (5 mg kg-1), as well as the combination of polyethylene and antibiotics, on the growth, rhizosphere soil bacterial community and metabolisms of wheat and maize seedlings. The results showed that combined contamination caused more serious damage to plant growth than individual contamination, and aggravated root oxidative stress responses. The diversity and structure of soil bacterial community were not markedly altered, but the composition of the bacterial community, soil metabolisms and metabolic pathways were altered. The co-occurrence network analysis indicated that combined contamination may inhibit the growth of wheat and maize seedings by simplifying the interrelationships between soil bacteria and metabolites, and altering the relative abundance of specific bacteria genera (e.g. Kosakonia and Sphingomonas) and soil metabolites (including sugars, organic acids and amino acids). The results help to elucidate the potential mechanisms of phytotoxicity of the combination of microplastic and antibiotics.

Difference of Microbial Community in the Stream Adjacent to the Mixed Antibiotic Effluent Source

Released antibiotics from source to stream can influence bacterial communities and potentially alter the ecosystem. This research provides a comprehensive examination of the sources, distribution, and bacterial community dynamics associated with varied antibiotic release sources adjacent to the stream. The residual of antibiotics from different sources was determined, and the bacterial community structure was examined to reveal the differences in the bacteria community in the stream. The residual of antibiotics was quantified with liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the Illumina MiSeq platform was utilized to sequence bacterial 16S rRNA genes, providing comprehensive insights into the bacterial community structure in the sediment across five different sites. Results indicated that the presence and distribution of antibiotics were significantly influenced by released sources. In the case of the bacterial community, the Proteobacteria and Firmicutes were the most dominant phyla in the sediment, and especially, the Firmicutes showed higher abundance in sites mostly affected by livestock sources. Additionally, livestock gut bacteria such as Clostridium saudiense, Proteiniclasticum ruminis, and Turicibacter sanguinis were prevalent in antibiotic-contaminated sites adjacent to livestock facilities. Overall, this study provides critical insights into the effect of antibiotic contamination by verifying the relationship between the occurrence of antibiotic residuals and the alteration in the bacterial community in the stream.

Soil microbiome engineering for sustainability in a changing environment

Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.

Bacterial Resistance to β-Lactam Antibiotics in Municipal Wastewater: Insights from a Full-Scale Treatment Plant in Poland

This study investigated enzymatic and genetic determinants of bacterial resistance to β-lactam antibiotics in the biocenosis involved in the process of biological treatment of wastewater by activated sludge. The frequency of bacteria resistant to selected antibiotics and the activity of enzymes responsible for resistance to β-lactam antibiotics were estimated. The phenomenon of selection and spread of a number of genes determining antibiotic resistance was traced using PCR and gene sequencing. An increase in the percentage of bacteria showing resistance to β-lactam antibiotics in the microflora of wastewater during the treatment process was found. The highest number of resistant microorganisms, including multi-resistant strains, was recorded in the aeration chamber. Significant amounts of these bacteria were also present in treated wastewater, where the percentage of penicillin-resistant bacteria exceeded 50%, while those resistant to the new generation β-lactam antibiotics meropenem and imipenem were found at 8.8% and 6.4%, respectively. Antibiotic resistance was repeatedly accompanied by the activity of enzymes such as carbapenemases, metallo-β-lactamases, cephalosporinases and β-lactamases with an extended substrate spectrum. The activity of carbapenemases was shown in up to 97% of the multi-resistant bacteria. Studies using molecular biology techniques showed a high frequency of genes determining resistance to β-lactam antibiotics, especially the blaTEM1 gene. The analysis of the nucleotide sequences of blaTEM1 gene variants present in bacteria at different stages of wastewater treatment showed 50-100% mutual similarity of.

Class 1 integron and Enterococcus spp. abundances in swine farms from the " Suckling piglets" to the "Fatteners" production category

Swine farms are considered a hotspot of antimicrobial resistance and may contribute to the spread of antibiotic-resistant and/or pathogenic bacteria into the environment as well as to farm workers. In this study, swine fecal samples have been collected over the primary production, selecting three categories, i.e., "Suckling piglets", "Weaning pigs" and "Fatteners", in six intensive swine farms, for two years. Feces were analysed for the detection and abundance of class 1 integrons (used as proxy of antibiotic resistance and of anthropogenic pollution), and of enterococci [fecal indicator bacteria (FIB) and potentially pathogenic for humans] by quantitative Real Time PCR. Furthermore, Enterococcus faecalis and Enterococcus faecium were isolated, analysed for the presence of the intI1 gene by Real Time PCR and genetically typed by Pulsed-Field Gel Electrophoresis. Both enterococci and class 1 integrons were significantly more abundant in the Suckling piglets (p = 0.0316 and 0.0242, respectively). About 8% of the isolated enterococci were positive for the intI1 gene by Real Time PCR. E. faecalis and E. faecium were found genetically heterogeneous and no specific pattern could be identified as the driver for their presence along the pig primary production. These findings suggest that the "Suckling piglets" category of production represents the key point where to mitigate the risk of transmission of enterococci and class 1 integrons with associated antibiotic resistance genes to humans and spread into the environment.

Can agricultural land use alter the responses of soil biota to antibiotic contamination?

Antibiotics accumulate in soils via various agricultural activities, endangering soil biota that play fundamental roles in maintaining agroecosystem function. However, the effects of land-use heterogeneity on soil biota tolerance to antibiotic stresses are not well understood. In this study, we explored the relationships between antibiotic residues, bacterial communities, and earthworm populations in areas with different land-use types (forest, maize, and peanut fields). The results showed that antibiotic levels were generally higher in maize and peanut fields than in forests. Furthermore, land use modulated the effects of antibiotics on soil bacterial communities and earthworm populations. Cumulative antibiotic concentrations in peanut fields were negatively correlated with bacterial diversity and earthworm abundance, whereas no significant correlations were detected in maize fields. In contrast, antibiotics improved bacterial diversity and richness in forest soils. Generally, earthworm populations showed stronger tolerance to antibiotics than did soil bacterial communities. Agricultural land use differentially modified the responses of the soil bacterial community and earthworm population to antibiotic contamination, and earthworms might provide an alternative for controlling antibiotic contamination.

Organic fertilizer potentiates the transfer of typical antibiotic resistance gene among special bacterial species

The propagation of antibiotic resistance genes (ARGs) in environments has evoked many attentions, however, how to identify their host pathogenic bacteria in situ remains a great challenge. Here we explored the bacterial host distribution and dissemination of a typical ARG, sul1 gene, in agricultural soils through the simultaneous detection of sul1 and its host 16S rRNA gene by emulsion paired isolation and concatenation PCR (epicPCR). Compared to chemical fertilizer, organic fertilizer (chicken manure) led to a higher prevalence of sul1 gene in the soil, and dominant bacterial hosts of sul1 gene were classified into Proteobacteria and Bacteroidetes phyla. Additionally, significant higher diversity of antibiotic resistance bacteria (ARB), higher rate of horizontal gene transfer (HGT), higher rate of mobile genetic elements (MGE) and higher proportion of pathogens were all observed in the treatment of organic fertilizer. This study alerts potential health risks of manure applications in agricultural soils.

Toxicity assessment and microbial response to soil antibiotic exposure: differences between individual and mixed antibiotics

Increasing amounts of antibiotics are introduced into soils, raising great concerns on their ecotoxicological impacts on the soil environment. This work investigated the individual and joint toxicity of three antibiotics, tetracycline (TC), sulfonamide (SD) and erythromycin (EM) via a whole-cell bioreporter assay. TC, SD and EM in aqueous solution demonstrated cytotoxicity, whilst soil exposure showed genotoxicity, indicating that soil particles possibly affected the bioavailability of antibiotics. Toxicity of soils exposed to TC, SD and EM changed over time, demonstrating cytotoxic effects within 14-d exposure and genotoxic effects after 30 days. Joint toxicity of TC, SD and EM in soils instead showed cytotoxicity, suggesting a synergetic effect. High-throughput sequencing suggested that the soil microbial response to individual antibiotics and their mixtures showed a different pattern. Soil microbial community composition was more sensitive to TC, in which the abundance of Pseudomonas, Pirellula, Subdivision3_genera_incertae_sedis and Gemmata varied significantly. Microbial community functions were significantly shifted by EM amendments, including signal transduction mechanisms, cytoskeleton, cell wall/membrane/envelope biogenesis, transcription, chromatin structure and dynamics, and carbohydrate transport and metabolism. This work contributes to a better understanding of the ecological effects and potential risks of individual and joint antibiotics on the soil environment.

Veterinary antibiotics can reduce crop yields by modifying soil bacterial community and earthworm population in agro-ecosystems

Veterinary antibiotics are intensively and widely used in animal farming to treat or prevent diseases, as well as improve growth rate and feed efficiency. Animal manure is an important reservoir of veterinary antibiotics due to their high excretion rates, and thus manure application has been a critical source of veterinary antibiotics in agro-ecosystems. However, how veterinary antibiotics affect agroecosystem functions is still unclearly understood. In this study, we evaluated the effects of veterinary antibiotics on soil bacteria and earthworms in agricultural land with long-term manure application. The potential mechanisms of antibiotic-induced changes in crop yields were also revealed. The results showed that the increasing prevalence of veterinary antibiotics in agro-ecosystems inhibited earthworm abundance and bacterial diversity, and then decreased the bioavailability of soil nutrients. Furthermore, high-dose exposure to veterinary antibiotics improved the abundance of plant pathogenic bacteria. Analysis indicated that veterinary antibiotics played an important underlying role in driving the negative effects on peanut grain yields via disturbing microbe- and earthworm-mediated soil available nutrient contents. The direct toxicity effects of antibiotics on peanut relative yields were stronger than their indirect mediating effects. Additionally, the tradeoffs between antibiotics and agroecosystem functions increased at low exposure levels and then decreased at high exposure levels, which indicated the effects of antibiotics on agroecosystem functions were dose-dependent, except for earthworm biomass. Antibiotic contamination which will impose threats to agricultural sustainability was highlighted and should be paid more attention.

Occurrence of antibiotics and antibiotic resistance genes and their correlations in river-type drinking water source, China

The occurrence and distribution of antibiotics and antibiotic resistance genes (ARGs) in natural water has attracted worldwide attention. Antibiotic and ARG pollution in the surface water of drinking water sources might directly/indirectly affect human health. In this study, the distribution of 38 antibiotics, 10 ARGs, 2 integrons, and 16S r DNA in river-type water sources in a large city of China were monitored in winter, which was a period with high level of antibiotic pollution. The results showed that 20 antibiotics were detected with different detection frequencies. The antibiotic pollution in December 2019 was relatively high, with the total concentrations of antibiotics ranging from 281.95 to 472.42 ng/L, followed by that in January 2020 (191.70-337.29 ng/L) and November 2019 (161.25-309.72 ng/L). Sulfacetamide was dominant in November 2019 (23.52-219.00 ng/L) and in January 2020 (113.18-209 ng/L), while norfloxacin in December 2019 (146.72-290.20 ng/L). All the target antibiotics posed low or medium risk for aquatic organisms, and posed low health risk for mankind. Sul1 and erm36 were the predominant ARGs, and intI1 was the predominant integron in drinking water sources. Only tetA showed positive correlations with its corresponding antibiotic (tetracycline). The rest of ARGs showed no correlations with antibiotics or positive / negative correlations with their non-corresponding antibiotics. Overall, the antibiotics and ARG pollution in these water sources was relatively low. These findings provided some reference data for the distribution of antibiotics and ARGs in river-type drinking water sources of large cities in China.

Polystyrene microplastics alleviate the effects of sulfamethazine on soil microbial communities at different CO2 concentrations

Microplastics were reported to adsorb antibiotics and may modify their effects on soil systems. But there has been little research investigating how microplastics may affect the toxicities of antibiotics to microbes under future climate conditions. Here, we used a free-air CO₂ enrichment system to investigate the responses of soil microbes to sulfamethazine (SMZ, 1 mg kg^-1) in the presence of polystyrene microplastics (PS, 5 mg kg^-1) at different CO₂ concentrations (ambient at 380 ppm and elevated at 580 ppm). SMZ alone decreased bacterial diversity, negatively affected the bacterial structure and inter-relationships, and enriched the sulfonamide-resistance genes (sul1 and sul2) and class 1 integron (intl1). PS, at both CO₂ conditions, showed little effect on soil bacteria but markedly alleviated SMZ's adverse effects on bacterial diversity, composition and structure, and inhibited sul1 transmission by decreasing the intl1 abundance. Elevated CO₂ had limited modification in SMZ's disadvantages to microbial communities but markedly decreased the sul1 and sul2 abundance. Results indicated that increasing CO₂ concentration or the presence of PS affected the responses of soil microbes to SMZ, providing new insights into the risk prediction of antibiotics under future climate conditions.

CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

Antibiotrophy: Key Function for Antibiotic-Resistant Bacteria to Colonize Soils-Case of Sulfamethazine-Degrading Microbacterium sp. C448

Chronic and repeated exposure of environmental bacterial communities to anthropogenic antibiotics have recently driven some antibiotic-resistant bacteria to acquire catabolic functions, enabling them to use antibiotics as nutritive sources (antibiotrophy). Antibiotrophy might confer a selective advantage facilitating the implantation and dispersion of antibiotrophs in contaminated environments. A microcosm experiment was conducted to test this hypothesis in an agroecosystem context. The sulfonamide-degrading and resistant bacterium Microbacterium sp. C448 was inoculated in four different soil types with and without added sulfamethazine and/or swine manure. After 1 month of incubation, Microbacterium sp. (and its antibiotrophic gene sadA) was detected only in the sulfamethazine-treated soils, suggesting a low competitiveness of the strain without antibiotic selection pressure. In the absence of manure and despite the presence of Microbacterium sp. C448, only one of the four sulfamethazine-treated soils exhibited mineralization capacities, which were low (inferior to 5.5 ± 0.3%). By contrast, manure addition significantly enhanced sulfamethazine mineralization in all the soil types (at least double, comprised between 5.6 ± 0.7% and 19.5 ± 1.2%). These results, which confirm that the presence of functional genes does not necessarily ensure functionality, suggest that sulfamethazine does not necessarily confer a selective advantage on the degrading strain as a nutritional source. 16S rDNA sequencing analyses strongly suggest that sulfamethazine released trophic niches by biocidal action. Accordingly, manure-originating bacteria and/or Microbacterium sp. C448 could gain access to low-competition or competition-free ecological niches. However, simultaneous inputs of manure and of the strain could induce competition detrimental for Microbacterium sp. C448, forcing it to use sulfamethazine as a nutritional source. Altogether, these results suggest that the antibiotrophic strain studied can modulate its sulfamethazine-degrading function depending on microbial competition and resource accessibility, to become established in an agricultural soil. Most importantly, this work highlights an increased dispersal potential of antibiotrophs in antibiotic-polluted environments, as antibiotics can not only release existing trophic niches but also form new ones.

Reponses of microbial community and antibiotic resistance genes to the selection pressures of ampicillin, cephalexin and chloramphenicol in activated sludge reactors

High concentrations of antibiotics can exert strong selection pressures on the microbial community and promote the emergence and dissemination of antibiotic resistance genes (ARGs). The activated sludge reactors treating ampicillin, cephalexin and chloramphenicol production wastewater were established to investigate the responses of microbial community, ARGs and mobile genetic elements (MGEs) to antibiotics. Antibiotic selection pressures significantly declined the microbial diversity and changed microbial community structures. Based on metagenomic analysis, a total of 500 ARG subtypes affiliated with 18 ARG types were identified and 63 ARGs were shared by all samples. The substantial increase of ARG abundance and the shifts of ARG profiles were significantly correlated with antibiotic types and concentrations. The evident enrichment of non-corresponding ARG types suggested the strong co-selection effects of the target antibiotics. Additionally, metagenomic analysis revealed the occurrence of 104 MGEs belonging to various types and the five dominant MGEs were tnpA, intI1, tniA, tniB and IS91. The ARG-MGE co-occurrence associations implied the potential mobility of ARGs. Network analysis also demonstrated that five ARG types (aminoglycoside, beta-lactam, chloramphenicol, multidrug and tetracycline resistance genes) tended to co-occur internally and the obvious co-occurrence patterns among different ARG types indicated the potential for resistance co-selection. Moreover, 15 bacterial genera were speculated as the hosts of diverse ARGs. This study provides a comprehensive overview of the occurrence of ARGs and MGEs and is valuable for the risk assessment and management of antibiotic resistance.

Enhanced removal of ciprofloxacin and reduction of antibiotic resistance genes by earthworm Metaphire vulgaris in soil

Antibiotic residues could promote the dissemination of antibiotic resistance genes (ARGs) in the environments, and biodegradation represent a major route for antibiotic removal. Previous studies have showed that earthworm could enhance the degradation of certain organic contaminants, however, its effectiveness in ciprofloxacin removal and ARG reduction in soil remains unclear. In the present study, high-performance liquid chromatography, 16S rRNA gene sequencing and high-throughput quantitative PCR were employed to explore the effects of earthworm addition on ciprofloxacin removal and ARG abundance in ciprofloxacin-amended soil. Ciprofloxacin removal was significantly higher in earthworm cast as compare to control soil, and ARG abundance in earthworm cast was significantly lower than that of control soil. Procrustes analysis together with Mantel test showed that the ARG profiles were strongly associated with bacterial communities, indicating that the lower abundance of ARGs in cast samples could be attributed to changes in bacterial community compositions by earthworm activity. Flavobacterium and Turicibacter were enriched in cast samples, which were negatively correlated with ciprofloxacin concentration (p < 0.05), implying their potential roles in ciprofloxacin removal. These results suggested that earthworm gut is a hotspot for ciprofloxacin removal, and could be an option for mitigation of antibiotic pollution in soil.

Characteristics of microbial community of soil subjected to industrial production of antibiotics

Ecosystems worldwide are exposed to pollutants connected to the industrial production of pharmaceuticals. The objective of this study was to study the composition and characteristics of the soil microbial communities that had been exposed to long-term selection pressure caused by the industrial production of penicillin G. Soil samples from four sites among the penicillin G production plant were analysed using 16S rRNA profiling via Illumina MiSeq platform and were compared with the control samples from four sites outside the plant. Total metagenomic DNA from the impacted soil was also used for the preparation of E. coli T1R-based fosmid library which was consequently qualitatively tested for the presence of penicillin G acylase (PGA)-encoding genes using the method of sequence homology. Analyses of alpha diversity revealed that the long-term antibiotic presence in the soil significantly increased the microbial diversity and richness in terms of Shannon diversity index (p = 0.002) and Chao estimates (p = 0.004). Principal component analysis showed that the two types of communities (on-site and control) could be separated at the phylum, class and genus level. The on-site soil was enriched in Betaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Acidobacteria and Planctomycetia, while a significant decrease in Actinobacteria was observed. Metagenomic fosmid library revealed high hit rates in identifying PGAs (14 different genes identified) and confirmed the biotechnological potential of soils impacted by anthropogenic activity. This study offers new insights into the changes in microbial communities of soils exposed to anthropogenic activity as well as indicates that those soils may represent a hotspot for biotechnologically interesting targets.

Impacts of multi-year field exposure of agricultural soil to macrolide antibiotics on the abundance of antibiotic resistance genes and selected mobile genetic elements

Exposure of environmental bacteria to antibiotics may be increasing the global resistome. Antibiotic residues are entrained into agricultural soil through the application of animal and human wastes, and irrigation with reclaimed water. The impact of a mixture of three macrolide antibiotics on the abundance of selected genes associated with antibiotic resistance and genetic mobility were determined in a long-term field experiment undertaken in London, Canada. Replicated plots received annual applications of a mixture of erythromycin, clarithromycin and azithromycin every spring since 2010. Each antibiotic was added directly to the soil at a concentration of either 0.1 or 10 mg kg soil^-1 and all plots were cropped to soybeans. By means of qPCR, no gene targets were enriched in soil exposed to the 0.1 mg kg soil^-1 dose compared to untreated control. In contrast, the relative abundance of several gene targets including int1, sul2 and mphE increased significantly with the annual exposure to the 10 mg kg soil^-1 dose. By means of high-throughput qPCR, numerous gene targets associated with resistance to aminoglycosides, sulfonamides, trimethoprim, streptomycin, quaternary ammonium chemicals as well as mobile genetic elements (tnpA, IS26 and IS6100) were detected in soil exposed to 10 mg kg soil^-1, but not the lower dose. Overall, exposure of soil to macrolide antibiotics increased the relative abundance of numerous gene targets associated with resistance to macrolides and other antibiotics, and mobile genetic elements. This occurred at an exposure dose that is unrealistically high, but did not occur at the lower more realistic exposure dose.

Fate of pirlimycin and antibiotic resistance genes in dairy manure slurries in response to temperature and pH adjustment

Quantifying the fate of antibiotics and antibiotic resistance genes (ARGs) in response to physicochemical factors during storage of manure slurries will aid in efforts to reduce the spread of resistance when manure is land-applied. The objectives of this study were to determine the effects of temperature (10, 35, and 55 °C) and initial pH (5, 7, 9, and 12) on the removal of pirlimycin and prevalence of ARGs during storage of dairy manure slurries. We collected and homogenized feces and urine from five lactating dairy cows treated with pirlimycin and prepared slurries by mixing manure and sterile water. Aliquots (200 mL) of slurry were transferred and incubated in 400 mL glass beakers under different temperatures (10, 35, and 55 °C) or initial pH (5, 7, 9, and 12). Pirlimycin concentration and abundances of 16S rRNA, mefA, tet(W), and cfxA as indicators of total bacteria and ARGs corresponding to macrolide, tetracycline, and β-lactam resistance, respectively, were analyzed during manure incubation. The thermophilic environment (55 °C) increased the deconjugation and removal of pirlimycin, while the acidic shock at pH 5 increased deconjugation but inhibited removal of pirlimycin, suggesting that the chemical stability of pirlimycin could be affected by temperature and pH. The thermophilic environment decreased mefA relative abundance on day 7 and 28 (P = 0.02 and 0.04), which indicates that the bacteria that encoded mefA gene were not thermotolerant. Although mefA relative abundance was greater at the pH 9 shock than the rest of pH treatments on day 7 (P = 0.04), no significant pH effect was observed on day 28. The tet(W) abundance under initial pH 12 shock was less than other pH shocks on day 28 (P = 0.01), while no temperature effect was observed on day 28. There was no significant temperature and initial pH effect on cfxA abundance at any time point during incubation, implying that the bacteria that carrying cfxA gene are relatively insensitive to these environmental factors. Overall, directly raising temperature and pH can facilitate pirlimycin removal and decrease mefA and tet(W) relative abundances during storage of manure slurries.

A framework to bridge scales in distribution modeling of soil microbiota

Creating accurate habitat suitability and distribution models (HSDMs) for soil microbiota is far more challenging than for aboveground organism groups. In this perspective paper, we propose a conceptual framework that addresses several of the critical issues holding back further applications. Most importantly, we tackle the mismatch between the broadscale, long-term averages of environmental variables traditionally used, and the environment as experienced by soil microbiota themselves. We suggest using nested sampling designs across environmental gradients and objectively integrating spatially hierarchic heterogeneity as covariates in HSDMs. Second, to incorporate the crucial role of taxa co-occurrence as driver of soil microbial distributions, we promote the use of joint species distribution models, a class of models that jointly analyze multiple species’ distributions, quantifying both species-specific environmental responses (i.e. the environmental niche) and covariance among species (i.e. biotic interactions). Our approach allows incorporating the environmental niche and its associated distribution across multiple spatial scales. The proposed framework facilitates the inclusion of the true relationships between soil organisms and their abiotic and biotic environments in distribution models, which is crucial to improve predictions of soil microbial redistributions as a result of global change.

A slurry microcosm study on the interaction between antibiotics and soil bacterial community

Antibiotics released in the environment have attracted great attention. The environmental emission control of antibiotics should be based on the degree of their negative impacts on the environment and ecology. Here, we conducted a series of soil slurry microcosm experiments to investigate the interactions between antibiotics and the soil bacterial community. In the soil slurry, distinctive behaviors were observed for different antibiotics. Beta-lactams (ampicillin and ceftriaxone) experienced fast biodegradation. Kanamycin was adsorbed on soil particles soon after its addition. Nalidixic acid was stable throughout the experimental period (164 h). The main inactivation mechanism of tetracycline was deduced to be hydrolysis. Bacterial communities in slurries with or without antibiotic-treatment were profiled via high-throughput Illumina sequencing of the 16S rRNA gene. Unstable (ceftriaxone) and adsorbed (kanamycin) antibiotics show minor or negligible influences on the soil bacterial community. Stable antibiotics (nalidixic acid and tetracycline) have significantly affected the structure of the bacterial community. Most of enriched bacterial genera by various antibiotics belong to the same phylum, Proteobacteria. Inhibited bacterial phyla by nalidixic acid are Firmicutes and Bacteroidetes, while those inhibited by tetracycline are Firmicutes, Bacteroidetes and Cyanobacteria. According to the PICRUSt prediction of metagenome, influence of antibiotics on overall metabolic function of the bacterial community is rather limited. This study has provided valuable information, from a phylogenetic viewpoint, about the influence of high concentration of antibiotics on soil bacterial community.

An innovative modeling approach of linking land use patterns with soil antibiotic contamination in peri-urban areas

Due to the intensive use and continuous release, high and persistent concentrations of antibiotics are found in soils worldwide. This severe contamination elevates the risks associated with antibiotic exposure and resistance for soil ecosystems and human health. Estimating antibiotic concentrations in soils is a complex and important challenge because the limited information is available on antibiotic use and emission and the high exposure risk to human health occurred in peri-urban areas. In this study, soil antibiotic contamination was linked with land use patterns in a data-scarce peri-urban area in four different seasons, and we established a modeling framework based on land use to estimate spatially explicit distribution of antibiotics in soils. The soil antibiotic concentration was found to be substantially affected by surrounding land use patterns in buffer zones with a radius of 350 m. Agricultural land was the main source of antibiotics entering the soil. Notably, road networks also had considerable impacts on antibiotic residues in soils. Then, a statistical model was developed in describing the linkage between land use patterns and soil antibiotic concentration. Model evaluation suggested that the proposed model successfully simulated the variation of antibiotics in soil with good statistical performance (R² > 0.7). Finally, the model was extrapolated to investigate detailed distribution of antibiotics in soils. Clear spatial and seasonal dynamics can be found in soil antibiotic concentration. To our knowledge, this was the first attempt to adopt a model focusing on land use pattern to estimate the spatially explicit distribution of antibiotics in soils. Despite of some uncertainties, the research provides a land-use-based modeling approach as a reference for preventing and controlling soil antibiotic contamination in the future.

Dissipation of the antibiotic sulfamethoxazole in a soil amended with anaerobically digested cattle manure

The application of anaerobically digested cattle manure on agricultural land for both improving its quality and recycling a farm waste is an increasingly frequent practice in line with the circular economy. However, knowledge on the potential risk of spreading antibiotic resistance through this specific practice is quite scarce. The antibiotic sulfamethoxazole (SMX) is one of the most heavily prescribed in veterinary medicine. In this study, SMX dissipation and the possible effects on natural microorganisms were investigated in a soil amended with an anaerobically digested cattle manure produced from a biogas plant inside a livestock farm. Microcosm experiments were performed using amended soil treated with SMX (20 mg/kg soil). During the experimental time (61 days), soil samples were analysed for SMX and N4-acetylsulfamethoxazole, microbial abundance, activity and structure. Furthermore, the prevalence of the intI1 gene was also determined. The overall results showed that, although there was an initial negative effect on microbial abundance, SMX halved in about 7 days in the digestate-amended soil. The intI1 gene found in both the digestate and amended soil suggested that the use of anaerobically digested cattle manure as fertilizer can be a source of antibiotic resistant bacteria (ARBs) and genes (ARGs) in agroecosystems.

Bacterial community shift and antibiotics resistant genes analysis in response to biodegradation of oxytetracycline in dual graphene modified bioelectrode microbial fuel cell

This study explored the biodegradation mechanisms of oxytetracycline (OTC/O) and electrochemical characteristics from the perspective of bacterial community shift and OTC resistance genes in dual graphene modified bioelectrode microbial fuel cell (O-D-GM-BE MFC). In phylum level, Proteobacteria was accounted to 95.04% in O-GM-BA, Proteobacteria and Bacteroidetes were accounted to 59.13% and 20.52% in O-GM-BC, which were beneficial for extracellular electron transport (EET) process and OTC biodegradation. In genus level, the most dominant bacteria in O-GM-BA were Salmonella and Trabulsiella, accounting up to 83.04%, moreover, representative exoelectrogens (Geobacter) were enriched, which contributed to OTC biodegradation and electrochemical performances; abundant degrading bacteria (Moheibacter, Comamonas, Pseudomonas, Dechloromonas, Nitrospira, Methylomicrobium, Pseudorhodoferax, Thiobacillus, Mycobacterium) were enriched in O-GM-BC, which contributed to the maximum removal efficiency of OTC; coding resistance genes of efflux pump, ribosome protective protein and modifying or passivating were all found in O-GM-BE, and this explained the OTC removal mechanisms from gene level.

Biodegradation of oxytetracycline and electricity generation in microbial fuel cell with in situ dual graphene modified bioelectrode

A three-step method to prepare dual graphene modified bioelectrode (D-GM-BE) in microbial fuel cell (MFC) in previous studies. This study explored the biodegradation of oxytetracycline (OTC) and electricity generation in O-D-GM-BE MFC. The OTC removal efficiency of graphene modified biocathode and bioanode (O-GM-BC, O-GM-BA) was 95.0% and 91.8% in eight days. The maximum power density generated by O-D-GM-BE MFC was 86.6 ± 5.1 mW m^-2, which was 2.1 times of that in OTC control bioelectrode (O-C-BE) MFC. The Rct of O-GM-BA and O-GM-BC were decreased significantly by 78.3% and 76.3%. OTC was biodegraded to monocyclic benzene compounds by bacteria. O-GM-BA was affected strongly by OTC, and Salmonella and Trabulsiella were accounted for 83.0%, while typical exoelectrogens (Geobacter) were still enriched after the maturity of biofilm. In O-GM-BC, bacteria related with OTC biodegradation (Comamonas, Ensifer, Sphingopyxis, Pseudomonas, Dechloromonas, etc.) were enriched, which contributed to the high removal efficiency of OTC.

Evaluating biological plausibility in supporting evidence for action through systematic reviews in public health

OBJECTIVES

The objective of this research was to develop and test methods for accessing and evaluating information on the biological plausibility of observed associations between exposures or interventions and outcomes to generate scientific evidence for action consistent with practice in systematic reviews.

STUDY DESIGN

To undertake this research, we used the example of the observed associations between antimicrobial use in food animals and increased risks of human exposures to antimicrobial-resistant pathogens of zoonotic origin.

METHODS

We conducted a scoping search using terms related to biological plausibility or mechanism to identify key references. As recommended by these references, we also used expert consultation with researchers and a public health informationist. We used their recommendations, which included expert consultation, to identify mechanisms relevant to biological plausibility of the association we selected to test. We used the reviews conducted by the World Health Organization (WHO) Guidelines Development Group in support of reducing antimicrobial use in food animal production to populate our model for assessing biological plausibility.

RESULTS

We were able to develop a transparent model for biological plausibility based on the adverse outcome pathway used in toxicology and ecology. We were also able to populate this model using the WHO reviews.

CONCLUSIONS

This analysis of biological plausibility used transparent and validated methods to assess the evidence used in systematic reviews based on the observational studies accessed through searches of the scientific literature. Given the importance of this topic in systematic reviews and evidence-based decision-making, further research is needed to define and test the methodological approaches to access and properly evaluate information from the scientific literature.

Use of the PCR-DGGE Method for the Analysis of the Bacterial Community Structure in Soil Treated With the Cephalosporin Antibiotic Cefuroxime and/or Inoculated With a Multidrug-Resistant Pseudomonas putida Strain MC1

The widespread use of cefuroxime (XM) has resulted in the increase in its concentration in hospital and domestic wastewaters. Due to the limited removal of antibiotics and antibiotic-resistant genes in conventional systems, the drugs enter the surface water and soils. Moreover, the introduction of XM and/or XM-resistant bacteria into soil may cause a significant modification of the biodiversity of soil bacterial communities. Therefore, the goal of this research was to assess the genetic diversity of a bacterial community in the cefuroxime (XM1 – 1 mg/kg and XM10 – 10 mg/kg) and/or antibiotic-resistant Pseudomonas putida strain MC1 (Ps – 1.6 × 10⁷ cells/g)-treated soils as determined by the DGGE (denaturing gradient gel electrophoresis) method. The obtained data were also evaluated using a multivariate analysis and the resistance (RS)/resilience (RL) concept. Strain MC1 was isolated from raw sewage in the presence of XM and was resistant not only to this antibiotic but also to vancomycin, clindamycin and erythromycin. The DGGE patterns revealed that the XM10 and XM10+Ps treatments modified the composition of the bacterial community by the alteration of the DGGE profiles as well as a decline in the DGGE indices, in particular on days 30, 60, and 90. In turn, the XM1 and XM1+Ps or Ps treatments did not affect the values of richness and diversity of the soil bacteria members. A principal component analysis (PCA) also indicated that XM markedly changed the diversity of bacterial assemblages in the second part of the experiment. Moreover, there were differences in the RS/RL of the DGGE indices to the disturbances caused by XM and/or Ps. Considering the mean values of the RS index, the resistance was categorized in the following order: diversity (0.997) > evenness (0.993) > richness (0.970). The soil RL index was found to be negative, thus reflecting the progressing detrimental impact of XM on the genetic biodiversity of bacteria within the experiment. These results indicate that the introduction of XM at higher dosages into the soil environment may exert a potential risk for functioning of microorganism.

Long-Term Exposure of Agricultural Soil to Veterinary Antibiotics Changes the Population Structure of Symbiotic Nitrogen-Fixing Rhizobacteria Occupying Nodules of Soybeans (Glycine max)

Antibiotics are entrained in agricultural soil through the application of manures from medicated animals. In the present study, a series of small field plots was established in 1999 that receive annual spring applications of a mixture of tylosin, sulfamethazine, and chlortetracycline at concentrations ranging from 0.1 to 10 mg · kg-1 soil. These antibiotics are commonly used in commercial swine production. The field plots were cropped continuously for soybeans, and in 2012, after 14 annual antibiotic applications, the nodules from soybean roots were sampled and the occupying bradyrhizobia were characterized. Nodules and isolates were serotyped, and isolates were distinguished using 16S rRNA gene and 16S to 23S rRNA gene intergenic spacer region sequencing, multilocus sequence typing, and RSα fingerprinting. Treatment with the antibiotic mixture skewed the population of bradyrhizobia dominating the nodule occupancy, with a significantly larger proportion of Bradyrhizobium liaoningense organisms even at the lowest dose of 0.1 mg · kg-1 soil. Likewise, all doses of antibiotics altered the distribution of RSα fingerprint types. Bradyrhizobia were phenotypically evaluated for their sensitivity to the antibiotics, and there was no association between in situ treatment and a decreased sensitivity to the drugs. Overall, long-term exposure to the antibiotic mixture altered the composition of bradyrhizobial populations occupying nitrogen-fixing nodules, apparently through an indirect effect not associated with the sensitivity to the drugs. Further work evaluating agronomic impacts is warranted.IMPORTANCE Antibiotics are entrained in agricultural soil through the application of animal or human waste or by irrigation with reused wastewater. Soybeans obtain nitrogen through symbiotic nitrogen fixation. Here, we evaluated the impact of 14 annual exposures to antibiotics commonly used in swine production on the distribution of bradyrhizobia occupying nitrogen-fixing nodules on soybean roots in a long-term field experiment. By means of various sequencing and genomic fingerprinting techniques, the repeated exposure to a mixture of tylosin, sulfamethazine, and chlortetracycline each at a nominal soil concentration of 0.1 mg · kg-1 soil was found to modify the diversity and identity of bradyrhizobia occupying the nodules. Nodule occupancy was not associated with the level of sensitivity to the antibiotics, indicating that the observed effects were not due to the direct toxicity of the antibiotics on bradyrhizobia. Altogether, these results indicate the potential for long-term impacts of antibiotics on this agronomically important symbiosis.

Human dissemination of genes and microorganisms in Earth's Critical Zone

Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.

Effect of composting and soil type on dissipation of veterinary antibiotics in land-applied manures

The objective of this study was to determine the fate of commonly used veterinary antibiotics in their naturally excreted form when manure-based amendments are applied to soil. Beef cattle were administered sulfamethazine, tylosin, and chlortetracycline and dairy cows were treated with pirlimycin. The resulting manure was composted for 42 d under static or turned conditions and applied at agronomic N rates to sandy, silt, and silty clay loam soils and compared with amendment with corresponding raw manures in sacrificial microcosms over a 120-day period. Antibiotic dissipation in the raw manure-amended soils followed bi-phasic first order kinetics. The first phase half-lives for sulfamethazine, tylosin, chlortetracycline, and pirlimycin ranged from 6.0 to 18, 2.7 to 3.7, 23 to 25, and 5.5-8.2 d, respectively. During the second phase, dissipation of sulfamethazine was negligible, while the half-lives for tylosin, chlortetracycline, and pirlimycin ranged from 41 to 44, 75 to 144, and 87-142 d, respectively. By contrast, antibiotic dissipation in the compost-amended soils followed single-phase first order kinetics with negligible dissipation of sulfamethazine and half-lives of tylosin and chlortetracycline ranging from 15 to 16 and 49-104 d, respectively. Pirlimycin was below the detection limit in the compost-amended soils. After incubating 120 d, antibiotics in compost-amended soils (up to 3.1 μg kg^-1) were significantly lower than in manure-amended soils (up to 19 μg kg^-1, p < .0001), with no major effect of soil type on the dissipation. Risk assessment suggested that composting can reduce antibiotic resistance selection potential in manure-amended soils.

Impact of sludge treatments on the extractability and fate of acetyl sulfamethoxazole residues in amended soils

Sludge recycled in agriculture may bring antibiotics into cropped soils. The nature, total amount, and availability of the antibiotics in soil partly depend on the sludge treatments. Our paper compares the fate of N-acetyl sulfamethoxazole (AC-SMX) residues between soils incubated with the same sludge but submitted to different processes before being added in soil. The fate of ¹⁴C-AC-SMX residues was studied in mixtures of soil and sludges at different treatment levels: 1) activated and 2) centrifuged sludges, both enriched with ¹⁴C-AC-SMX, and 3) limed and 4) heat-dried sludges obtained by treating the previously contaminated centrifuged sludge. The evolution of the extractability of ¹⁴C residues (CaCl₂, methanol) and their mineralization were followed during 119 days. More than 80% of the initial ¹⁴C-activity was no longer extractable after 14 days, except in soil with limed sludge. Liming and drying the centrifuged sludge decreased the mineralized ¹⁴C fraction from 5.7-6.4% to 1.2-1.8% and consequently, the corresponding soils contained more ¹⁴C residues after 119 days. Although ¹⁴C residues were more CaCl₂-extractable in soil with limed sludge, they seemed to be poorly bioavailable for biodegradation. For all solid sludges, the mineralization rate of ¹⁴C-AC-SMX residues was strongly correlated to that of sludge organic carbon, with a coefficient three times lower for the limed and dried sludges than for the centrifuged sludge after 14 days.

Novel Antibiotic Resistance Determinants from Agricultural Soil Exposed to Antibiotics Widely Used in Human Medicine and Animal Farming

Antibiotic resistance has emerged globally as one of the biggest threats to human and animal health. Although the excessive use of antibiotics is recognized as accelerating the selection for resistance, there is a growing body of evidence suggesting that natural environments are "hot spots" for the development of both ancient and contemporary resistance mechanisms. Given that pharmaceuticals can be entrained onto agricultural land through anthropogenic activities, this could be a potential driver for the emergence and dissemination of resistance in soil bacteria. Using functional metagenomics, we interrogated the "resistome" of bacterial communities found in a collection of Canadian agricultural soil, some of which had been receiving antibiotics widely used in human medicine (macrolides) or food animal production (sulfamethazine, chlortetracycline, and tylosin) for up to 16 years. Of the 34 new antibiotic resistance genes (ARGs) recovered, the majority were predicted to encode (multi)drug efflux systems, while a few share little to no homology with established resistance determinants. We characterized several novel gene products, including putative enzymes that can confer high-level resistance against aminoglycosides, sulfonamides, and broad range of beta-lactams, with respect to their resistance mechanisms and clinical significance. By coupling high-resolution proteomics analysis with functional metagenomics, we discovered an unusual peptide, PPP^{AZI 4}, encoded within an alternative open reading frame not predicted by bioinformatics tools. Expression of the proline-rich PPP^{AZI 4} can promote resistance against different macrolides but not other ribosome-targeting antibiotics, implicating a new macrolide-specific resistance mechanism that could be fundamentally linked to the evolutionary design of this peptide.IMPORTANCE Antibiotic resistance is a clinical phenomenon with an evolutionary link to the microbial pangenome. Genes and protogenes encoding specialized and potential resistance mechanisms are abundant in natural environments, but understanding of their identity and genomic context remains limited. Our discovery of several previously unknown antibiotic resistance genes from uncultured soil microorganisms indicates that soil is a significant reservoir of resistance determinants, which, once acquired and "repurposed" by pathogenic bacteria, can have serious impacts on therapeutic outcomes. This study provides valuable insights into the diversity and identity of resistance within the soil microbiome. The finding of a novel peptide-mediated resistance mechanism involving an unpredicted gene product also highlights the usefulness of integrating proteomics analysis into metagenomics-driven gene discovery.

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R² = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.

Effect of antibiotics on bacterial populations: a multi-hierachical selection process

Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.