Bacterial community variations in paddy soils induced by application of veterinary antibiotics in plant-soil systems

Response characteristics and functional predictions of soil microorganisms to heavy metals, antibiotics, and their resistance genes originating from different animal farms amended with Herbaspirillum huttiense

Current understanding is limited regarding technologies that use biochar and microorganisms to simultaneously treat soils contaminated with both veterinary antibiotics (VAs) and heavy metals (HMs) from different animal farms. The contributions of the keystone taxa and their similarities from different animal farms under VA and HM stresses before and after soil remediation should be further investigated as well. An innovative treatment of Herbaspirillum huttiense (HHS1) inoculated waste fungus chaff-based (WFCB) biochar was designed for immobilization of copper (Cu) and zinc (Zn), and the removal of oxytetracycline (OTC), enrofloxacin (ENR), and a subsequent reduction in their resistance genes in soils from pig, cow, and chicken farms. Roles of indigenous microorganisms which can treat soils contaminated with VAs and HMs were summarized. Results showed that available Cu and Zn were reduced by 19.5% and 28.1%, respectively, while 49.8% of OTC and 85.1% of ENR were removed by WFCB-HHS1. The decrease in ENR improved overall microbial community diversity, and the increases in genera HHS1, Pedobacter, Flavobacterium and Aequorivita, along with the decreases of genera Bacillus, Methylobacter, and Fermentimonas were indirectly favorable to treat HMs and VAs in soils from different animal farms. Bacterial communities in different animal farm soils were predominantly influenced by stochastic processes. The regulations of functional genes associated with metabolism and environmental information processing, which contribute to HM and VA defense, were altered when using WFCB-HHS1. Furthermore, the spread of their antibiotic resistance genes was restricted.

Ecotoxicity of five veterinary antibiotics on indicator organisms and water and soil communities

This study explores the environmental effects of five common veterinary antibiotics widely detected in the environment, (chlortetracycline,CTC; oxytetracycline,OTC; florfenicol,FF; neomycin, NMC; and sulfadiazine, SDZ) on four bioindicators: Daphnia magna, Vibrio fischeri, Eisenia fetida, and Allium cepa, representing aquatic and soil environments. Additionally, microbial communities characterized through 16 S rRNA gene sequencing from a river and natural soil were exposed to the antibiotics to assess changes in population growth and metabolic profiles using Biolog EcoPlates™. Tetracyclines are harmful to Vibrio fisheri (LC50 ranges of 15-25 µg/mL), and the other three antibiotics seem to only affect D. magna, especially, SDZ. None of the antibiotics produced mortality in E. fetida at concentrations below 1000 mg/kg. NMC and CTC had the highest phytotoxicities in A. cepa (LC50 = 97-174 µg/mL, respectively). Antibiotics significantly reduced bacterial metabolism at 0.1-10 µg/mL. From the highest to the lowest toxicity on aquatic communities: OTC > FF > SDZ ≈ CTC > NMC and on edaphic communities: CTC ≈ OTC > FF > SDZ > NMC. In river communities, OTC and FF caused substantial decreases in bacterial metabolism at low concentrations (0.1 µg/mL), impacting carbohydrates, amino acids (OTC), and polymers (FF). At 10 µg/mL and above, OTC, CTC, and FF significantly decreased metabolizing all tested metabolites. In soil communities, a more pronounced decrease in metabolizing ability, detectable at 0.1 µg/mL, particularly affected amines/amides and carboxylic and ketonic acids (p < 0.05). These new ecotoxicity findings underscore that the concentrations of these antibiotics in the environment can significantly impact both aquatic and terrestrial ecosystems.

Root-associated bacteria strengthen their community stability against disturbance of antibiotics on structure and functions

Antibiotics affect bacterial community structure and functions in soil. However, the response and adaptation of root-associated bacterial communities to antibiotic stress remains poorly understood. Here, rhizobox experiments were conducted with maize (Zea mays L.) upon exposure to antibiotics ciprofloxacin or tetracycline. High-throughput sequencing analysis of bacterial community and quantitative PCR analysis of nitrogen cycling genes show that ciprofloxacin and tetracycline significantly shift bacterial community structure in bulk soil, whereas plant host may mitigate the disturbances of antibiotics on bacterial communities in root-associated niches (i.e., rhizosphere and rhizoplane) through the community stabilization. Deterministic assembly, microbial interaction, and keystone species (e.g., Rhizobium and Massilia) of root-associated bacterial communities benefit the community stability compared with those in bulk soil. Meanwhile, the rhizosphere increases antibiotic dissipation, potentially reducing the impacts of antibiotics on root-associated bacterial communities. Furthermore, rhizospheric effects deriving from root exudates alleviate the impacts of antibiotics on the nitrogen cycle (i.e., nitrification, organic nitrogen conversion and denitrification) as confirmed by functional gene quantification, which is largely attributed to the bacterial community stability in rhizosphere. The present study enhances the understanding on the response and adaptation of root-associated bacterial community to antibiotic pollution.

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization

BACKGROUND

Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the success of the AM symbiosis.

RESULTS

Using partitioned microcosms containing field soil, we discovered that AM hyphae and roots selectively assemble their own microbiome from the surrounding soil. In two independent experiments, we identified several bacterial genera, including Devosia, that are consistently enriched on AM hyphae. Subsequently, we isolated 144 pure bacterial isolates from a mycorrhiza-rich sample of extraradical hyphae and isolated Devosia sp. ZB163 as root and hyphal colonizer. We show that this AM-associated bacterium synergistically acts with mycorrhiza on the plant root to strongly promote plant growth, nitrogen uptake, and mycorrhization.

CONCLUSIONS

Our results highlight that AM fungi do not function in  isolation and that the plant-mycorrhiza symbiont can recruit beneficial bacteria that support the symbiosis. Video Abstract.

The effect of manure-borne doxycycline combined with different types of oversized microplastic contamination layers on carbon and nitrogen metabolism in sandy loam

The different forms and properties of microplastics (MPs) have different effects on the elemental cycles in soil ecosystems, and this is further complicated when the soil contains antibiotics; meanwhile, oversized microplastic (OMP) in soil is always ignored in studies of environmental behavior. In the context of antibiotic action, the effects of OMP on soil carbon (C) and nitrogen (N) cycling have rarely been explored. In this study, we created four types of oversized microplastic (thick fibers, thin fibers, large debris, and small debris) composite doxycycline (DOX) contamination layers (5-10 cm) in sandy loam, hoping to reveal the effects on soil C and N cycling and potential microbial mechanisms when exposed to the combination of manure-borne DOX and different types of OMP from the perspective of metagenomics in the longitudinal soil layer (0-30 cm). The results showed that all different forms of OMP, when combined with DOX, reduced the soil C content in each layer, but only reduced the soil N content in the upper layer of the OMP contamination layer. The microbial structure of the surface soil (0-10 cm) was more noteworthy than that of the deeper soil (10-30 cm). The genera Chryseolinea and Ohtaekwangia were key microbes involved in C and N cycling in the surface layer and regulated carbon fixation in photosynthetic organisms (K00134), carbon fixation pathways in prokaryotes (K00031), methane metabolism (K11212 and K14941), assimilatory nitrate reduction (K00367), and denitrification (K00376 and K04561). The present study is the first to reveal the potential microbial mechanism of C and N cycling under OMP combined with DOX in different layers, mainly the OMP contamination layer and its upper layer, and the OMP shape plays an important role in this process.

Aerobic granular sludge formation and stability in enhanced biological phosphorus removal system under antibiotics pressure: Performance, granulation mechanism, and microbial successions

Wastewater containing antibiotics can pose a significant threat to biological wastewater treatment processes. This study investigated the establishment and stable operation of enhanced biological phosphorus removal (EBPR) by aerobic granular sludge (AGS) under mixed stress conditions induced by tetracycline (TC), sulfamethoxazole (SMX), ofloxacin (OFL), and roxithromycin (ROX). The results show that the AGS system was efficient in removing TP (98.0%), COD (96.1%), and NH₄⁺-N (99.6%). The average removal efficiencies of the four antibiotics were 79.17% (TC), 70.86% (SMX), 25.73% (OFL), and 88.93% (ROX), respectively. The microorganisms in the AGS system secreted more polysaccharides, which contributed to the reactor's tolerance to antibiotics and facilitated granulation by enhancing the production of protein, particularly loosely bound protein. Illumina MiSeq sequencing revealed that putative phosphate accumulating organisms (PAOs)-related genera (Pseudomonas and Flavobacterium) were enormously beneficial to the mature AGS for TP removal. Based on the analysis of extracellular polymeric substances, extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory, and microbial community, a three-stage granulation mechanism was proposed including adaption to the stress environment, formation of early aggregates and maturation of PAOs enriched microbial granules. Overall, the study demonstrated the stability of EBPR-AGS under mixed antibiotics pressure, providing insight into the granulation mechanism and the potential use of AGS for wastewater treatment containing antibiotics.

Occurrence profiling and environmental risk assessment of veterinary antibiotics in vegetable soils at Chongqing region, China

Veterinary antibiotics (VAs) are emerging contaminants in soils as they may pose high risks to the ecosystem and human health. Identifying VAs accumulation in soils is essential for assessing their potential risks. Therefore, we investigated the distribution of VAs in soils from vegetable fields and evaluated their potential ecological and antimicrobial resistance risks in the Chongqing region of the Three Gorges Reservoir area, China. Results indicated that twenty-six species of VAs, including nine sulfonamides (SAs), seven quinolones (QNs), four tetracyclines (TCs), four macrolides (MLs), and two other species of VAs were detected in soils, with their accumulative levels ranging from 1.4 to 3145.7 μg kg^-1. TCs and QNs were the dominant VAs species in soils with high detection frequencies (100% TCs and 80.6% for QNs) and accumulative concentration (up to 1195 μg kg^-1 for TCs and up to 485 μg kg^-1 for QNs). Risk assessment indices showed that VAs (specifically SAs, TCs, and QNs) in most vegetable soils would pose a medium to high risk to the ecosystem and antimicrobial resistance. Mixture of VAs posed a higher risk to soil organisms, antimicrobial resistance, and plants than to aquatic organisms. Modeling analysis indicated that socioeconomic conditions, farmers' education levels, agricultural practices, and soil properties were the main factors governing VAs accumulation and environmental risks. Farmers with a high educational level owned large-scale farms and were more willing to use organic fertilizers for vegetable production, which eventually led to high VAs accumulation in vegetable soil. These findings would provide a reference for sustainable agricultural and environmental production under the current scenario of chemical fertilizer substitution by organic products and green agricultural development.

Effect of long-term application of bioorganic fertilizer on the soil property and bacteria in rice paddy

The application of novel bioorganic fertilizer (BIO) has been established as a weed biocontrol strategy, and reduce herbicides pollution and negatively effects on agricultural ecosystems. However, its long-term influences on soil bacterial communities are unknown. Here, 16 S rRNA sequencing to identify the changes that occur in soil bacterial community and enzyme under BIO treatments after five years in a field experiment. BIO application effectively controlled weeds, however no obvious differences between treatments were observed under BIO-50, BIO-100, BIO-200 and BIO-400 treatment. Anaeromyxobacter and Clostridium_ sensu_ stricto_1 were the two dominant genera among BIO-treated soil samples. The BIO-800 treatment had a slight influence on the species diversity index, which was more remarkable after five years. The seven significantly-different genera between BIO-800 treatment and untreated soils included C._sensu_stricto_1, Syntrophorhabdus, Candidatus_Koribacter, Rhodanobacter, Bryobacter, Haliangium, Anaeromyxobacter. In addition, BIO application had different effects on soil enzymatic activities and chemical properties. The extractable P and pH saliency correlated with Haliangium and C._Koribacter, and C._sensu_stricto_1 observably correlated with exchangeable K, hydrolytic N and organic matter. Taken together, our data suggest that BIO application effectively controlled weeds and a slight influence on soil bacterial communities and enzymes. These findings expand our knowledge of the application of BIO as widely used as a sustainable weed control in rice paddy.

Responses of soil microbial communities to concentration gradients of antibiotic residues in typical greenhouse vegetable soils

To explore the responses of soil microbial communities to concentration gradients of antibiotic residues in soil, 32 soil samples were collected from a typical greenhouse vegetable production base in Northern China in 2019. The total concentrations of 26 antibiotic residues in these soil samples was 83.24-4237.93 μg·kg^-1, of which metabolites of tetracyclines were 23.34-1798.80 μg·kg^-1. The total concentrations in 32 samples were clustered into three levels (L: <100 μg·kg^-1, M: 100-300 μg·kg^-1, H: >300 μg·kg^-1) to elucidate the impacts of antibiotic residues on the diversity, structure, composition, function and antibiotic resistome of soil microbial community. Results showed that higher concentration of antibiotic residues in soil was prone to decrease the diversity and shift the structure and composition of soil microbial community. Antibiotic resistome occurred in soils with antibiotic residues exceeding 300 μg·kg^-1. Interactions among soil bacteria followed the order of H > L > M, consistent with the relative abundances of mobile genetic elements. Bacteroidetes and Firmicutes were the top attributors impacting the profile of antibiotics in soil. According to weighted comprehensive pollution index of risk quotient, in 28.1 % of soil samples the residual antibiotics presented high ecological risk, whereas in the rest of soil samples the ecological risk is medium. The results will enrich the database and provide references for antibiotic contamination control in soils of the region and alike.

Distribution characteristics of soil microbial communities and their responses to environmental factors in the sea buckthorn forest in the water-wind erosion crisscross region

Soil microorganisms are an important part of forest ecosystems, and their community structure and ecological adaptations are important for explaining soil material cycles in the fragile ecological areas. We used high-throughput sequencing technology to examine the species composition and diversity of soil bacterial and fungal communities in sea buckthorn forests at five sites in the water-wind erosion crisscross in northern Shaanxi (about 400 km long). The results are described as follows: (1) The soil bacterial community of the sea buckthorn forest in the study region was mainly dominated by Actinobacteria, Proteobacteria, and Acidobacteria, and the fungi community was mainly dominated by Ascomycota. (2) The coefficient of variation of alpha diversity of microbial communities was higher in the 0-10 cm soil layer than in the 10-20 cm soil layer. (3) Soil electrical conductivity (36.1%), available phosphorous (AP) (21.0%), available potassium (16.2%), total nitrogen (12.7%), and the meteorological factors average annual maximum temperature (33.3%) and average annual temperature (27.1%) were identified as the main drivers of structural changes in the bacterial community. Available potassium (39.4%), soil organic carbon (21.4%), available nitrogen (AN) (13.8%), and the meteorological factors average annual maximum wind speed (38.0%) and average annual temperature (26.8%) were identified as the main drivers of structural changes in the fungal community. The explanation rate of soil factors on changes in bacterial and fungal communities was 26.6 and 12.0%, respectively, whereas that of meteorological factors on changes in bacterial and fungal communities was 1.22 and 1.17%, respectively. The combined explanation rate of environmental factors (soil and meteorological factors) on bacterial and fungal communities was 72.2 and 86.6%, respectively. The results of the study offer valuable insights into the diversity of soil microbial communities in the water-wind erosion crisscross region and the mechanisms underlying their interaction with environmental factors.

Genetically engineered microorganisms for environmental remediation

In the recent era, the increasing persistence of hazardous contaminants is badly affecting the globe in many ways. Due to high environmental contamination, almost every second species on earth facing the worst issue in their survival. Advances in newer remediation approaches may help enhance bioremediation's quality, while conventional procedures have failed to remove hazardous compounds from the environment. Chemical and physical waste cleanup approaches have been used in current circumstances; however, these methods are costly and harmful to the environment. Thus, there has been a rise in the use of bioremediation due to an increase in environmental contamination, which led to the development of genetically engineered microbes (GEMs). It is safer and more cost-effective to use engineered microorganisms rather than alternative methods. GEMs are created by introducing a stronger protein into bacteria through biotechnology or genetic engineering to enhance the desired trait. Biodegradation of oil spills, halobenzoates naphthalenes, toluenes, trichloroethylene, octanes, xylenes etc. has been accomplished using GEMs such bacteria, fungus, and algae. Biotechnologically induced microorganisms are more powerful than naturally occurring ones and may degrade contaminants faster because they can quickly adapt to new pollutants they encounter or co-metabolize. Genetic engineering is a worthy process that will benefit the environment and ultimately the health of our people.

Ecological life strategies of microbes in response to antibiotics as a driving factor in soils

Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.

Removal of sulfamethoxazole and antibiotic resistance genes in paddy soil by earthworms (Pheretima guillelmi): Intestinal detoxification and stimulation of indigenous soil bacteria

Vermiremediation, which use earthworms to remove contaminants from soil, has been proven to be an alternative, low-cost technology. However, the effects of earthworm activity, especially the degraders in earthworm intestines, on the fate of sulfamethoxazole (SMX), and the effects of intestinal bacteria on degrading bacteria in soil are unclear. In this study, the effects of earthworms on the fate of SMX and related antibiotic resistance genes (ARGs) were investigated. Special attention was paid to the impact of earthworms on SMX degradation efficiency, degradation products, related ARGs, and degraders in both soil and earthworm intestines; the effect of intestinal bacteria on soil bacteria associated with SMX was also studied. Earthworms significantly accelerated SMX degradation by both intestinal detoxification and the stimulation of indigenous soil bacteria. Compared with the treatment without earthworms, the treatment with earthworms reduced SMX residues by 25.1 %, 49.2 %, 35.7 %, 34.2 %, and 35.7 % on the 10th, 20th, 30th, 60th, and 90th days, respectively. Compared with those in soil (treated with earthworms), the SMX residues in wormcasts were further reduced by 12.2-29.0 % from the 2nd to the 20th day, producing some unique anaerobic degradation products that were distinct from those in the soil. In earthworm intestines, SMX degradation was enhanced by bacteria of the genera Microvirga, Sphingomonas, Methylobacterium, Bacillus, and Tumebacillus. All of these bacteria (except Bacillus spp.) entered and colonised the soil with wormcasts, further promoting SMX degradation. Additionally, earthworms removed a significant number of ARGs by increasing the fraction of potential SMX degraders and inhibiting the potential hosts of ARGs and int1. This study demonstrated that earthworms could remediate SMX-contaminated soil by enhancing the removal of SMX and ARGs.

Effects of tetracycline, sulfonamide, fluoroquinolone, and lincosamide load in pig slurry on lettuce: Agricultural and human health implications

The application of pig slurry as fertilizer in agriculture provides nutrients, but it can also contain veterinary medicines, including antibiotic residues (ABs), which can have an ecotoxicological impact on agroecosystems. Furthermore, uptake, translocation, and accumulation of ABs in crops can mobilize them throughout the food chain. This greenhouse study aims to assess AB uptake from soil fertilized with pig slurry and its phenotypical effects on Lactuca sativa L. The plants were cropped in loamy clay soil dosed at 140 kg total N/ha and containing antibiotics (lincomycin, sulfadiazine, oxytetracycline, and enrofloxacin) at different concentration levels (0, 0.05, 0.5, 5, 50, and 500 mg/kg fresh weight, fw). Whereas sulfadiazine (11.8 ng/g fw) was detected in lettuce leaves at the intermediate doses (0.5 mg/kg), lincomycin and its transformation products (hydroxy/sulfate) were only detected at the 50 mg/kg fw dose. In addition, increased AB doses in the pig slurry resulted in decreased lettuce fresh weight and lipid and carbohydrate content and became lethal to lettuce at the highest AB concentrations (500 mg/kg fw). Nevertheless, even at higher doses, the AB content in lettuce following pig-slurry fertilization did not pose any direct significant human health risk (total hazard quotient<0.01). However, the promotion of antimicrobial resistance in humans due to the intake of these vegetables cannot be ruled out.

Partial nitrification in free nitrous acid-treated sediment planting Myriophyllum aquaticum constructed wetland strengthens the treatment of black-odor water

Black-odor water pollution in rural areas, especially swine wastewater, can lead to the deterioration of water quality and thus seriously affect the daily life of people in the area. However, there is a lack of effective treatment measures with simultaneous attention to carbon, nitrogen and sulfur pollution in rural black-odor water bodies. This study evaluated the feasibility of an in-situ pilot-scale constructed wetland (CW) for the synchronous removal of COD, ammonium, and sulfur compounds in the swine wastewater. In this study, the operation strategy of CW sediment pretreated with free nitrous acid (FNA) and Myriophyllum aquaticum plantation was established. Throughout the 114-day operation, the total removal efficiencies of COD and ammonium nitrogen in experimental groups were 81.2 ± 4.2 % and 72.8 ± 1.8 %, respectively, which were significantly higher than CW without any treatment. Removal efficiencies of Sulfur compounds, i.e. sulfide, sulfate, thiosulfate, and sulfite, were 92.3 ± 1.9 % (61.2 % higher than the no-treatment group), 42.1 ± 3.8 %, 97.9 ± 1.7 %, and 42.7 ± 4.5 % respectively. High-throughput sequencing and qPCR revealed that experimental group significantly increased denitrification genes (nirK, nosZ) and sulfur oxidation genes (soxB, fccAB) and enriched the corresponding microbial taxa (Bacillus, Conexibacter and Clostridium sensu stricto). Moreover, metabolic pathways related to nitrogen and sulfur and the degradation of organic matter were up-regulated. These results indicated that partial nitrification in CW planted with M. aquaticum promoted sulfur oxidation denitrification and heterotrophic denitrification. Overall, the in-situ pilot-scale study revealed that the cultivation of M. aquaticum in FNA-treated CW can be a sustainable approach to treat black-odor water bodies.

Adsorption-desorption and degradation of colistin in soils under aerobic conditions

Colistin has broad-spectrum activity against Gram-negative bacteria and has been considered as the last-resort treatment for multiantibiotic-resistant Gram-negative bacteria infections in human. And it is also world widely utilized as a veterinary medicine for the promotion of growth, prevention and control of diseases in livestock and poultry. Extensive use of colistin in husbandry results in the introduction of large amounts of colistin to the surrounding environment via animals' urine and feces, potentially inducing the prevalence of colistin resistance bacteria and the impact of the ecological environment. The study investigated the adsorption, desorption and degradation of colistin in soils using high sensitivity UPLC-MS/MS assays. An MS based assay was established to directly determine colistin in the soil. It was observed that the moderate adsorption affinity of colistin to the three soils with adsorption strength (1/n) ranging from 0.6897 to 1.3333. Colistin exhibited the highest adsorption affinity to the sandy loam, followed by the sand and loam. Despite of different characteristics of three soils, the adsorption capacity of the three soils was comparable. The adsorption of colistin to the three types of soils analyzed was irreversible. The degradation experiments showed that the degradation of colistin in the sandy loam was relatively slow with a degradation half-life in a range of 13.2-29.7 days when colistin was applied to the sandy loam at a level of 10 ~ 40 µg/g. The degradation of colistin occurred in the mixture of the sandy loam and feces recovered from the colistin treated broiler as well. 25% of colistin remained in the mixture under environmental conditions after 14 days. Composting the sandy loam by directly covering the soil surface with colistin treated broilers' feces resulted in the introduction of colistin to the sandy loam. Colistin was observed in both the topsoil from the contact surface and sandy loam samples collected 20 cm below the contact surface. The understanding of adsorption-desorption behaviors, degradation and mobility of colistin in soils might offer insights into the potential impact of colistin on the emergence and prevalence of resistant bacteria and the ecological environment.

Fate and impact of wastewater-borne micropollutants in lettuce and the root-associated bacteria

The reuse of water for agricultural practices becomes progressively more important due to increasing demands for a transition to a circular economy. Treated wastewater can be an alternative option of blue water used for the irrigation of crops but its risks need to be evaluated. This study assesses the uptake and metabolization of pharmaceuticals and personal care products (PPCPs) derived from treated wastewater into lettuce as well as the impact on root-associated bacteria under a realistic and worst-case scenario. Lettuce was grown in a controlled greenhouse and irrigated with water or treated wastewater spiked with and without a mixture of fourteen different PPCPs at 10 μg/L or 100 μg/L. After harvesting the plants, the same soil was reused for a consecutive cultivation campaign to test for the accumulation of PPCPs. Twelve out of fourteen spiked PPCPs were detected in lettuce roots, and thirteen in leaves. In roots, highest concentrations were measured for sucralose, sulfamethoxazole and citalopram, while sucralose, acesulfame and carbamazepine were the highest in leaves. Higher PPCP concentrations were found in lettuce roots irrigated with spiked treated wastewater than in those irrigated with spiked water. The absolute bacterial abundance remained stable over both cultivation campaigns and was not affected by any of the treatments (type of irrigation water (water vs. wastewater) nor concentration of PPCPs). However, the irrigation of lettuce with treated wastewater had a significant effect on the microbial α-diversity indices at the end of the second cultivation campaign, and modified the structure and community composition of root-associated bacteria at the end of both campaigns. Five and fourteen bacterial families were shown to be responsible for the observed changes at the end of the first and second cultivation campaign, respectively. Relative abundance of Haliangium and the clade Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium was significantly affected in response to PCPPs exposure. Caulobacter, Cellvibrio, Hydrogenophaga and Rhizobacter were significantly affected in microcosms irrigated with wastewater.

The Deterioration of Agronomical Traits of the Continuous Cropping of Stevia Is Associated With the Dynamics of Soil Bacterial Community

Stevia rebaudiana Bertoni is grown worldwide as an important, natural sweetener resource plant. The yield of steviol glycosides (SVglys) is greatly influenced by continuous cropping. In this study, we collected the roots, rhizosphere soils, and bulk soils from 2 years of continuous cropping (Y2) and 8 years of continuous cropping (Y8). A high-throughput sequencing technology based on Illumina Hiseq 2500 platform was used to study the structure and diversity of bacterial communities in the roots and soils of stevia with different years of continuous cropping. The results demonstrated that although the content of a group of SVglys was significantly increased in stevia of long-term continuous cropping, it inhibited the growth of plants and lowered the leaf dry weight; as a result, the total amount of SVglys was significantly decreased. Meanwhile, continuous cropping changed the physicochemical properties and the bacterial composition communities of soil. The different sampling sources of the root, rhizosphere soil, and bulk soil had no impact on the richness of bacterial communities, while it exhibited obvious effects on the diversity of bacterial communities. Continuous cropping had a stronger effect on the bacterial community composition in rhizosphere soil than in root and bulk soil. Based on linear discriminant analysis effect size (LEfSe), in the rhizosphere soil of Y8, the relative abundance of some beneficial bacterial genera of Sphingomonas, Devosia, Streptomyces, and Flavobacterium decreased significantly, while the relative abundance of Polycyclovorans, Haliangium, and Nitrospira greatly increased. Moreover, the soil pH and nutrient content, especially the soil organic matter, were correlated with the relative abundance of predominant bacteria at the genus level. This study provides a theoretical basis for uncovering the mechanism of obstacles in continuous stevia cropping and provides guidance for the sustainable development of stevia.

An Overview of Antibiotic Resistance and Abiotic Stresses Affecting Antimicrobial Resistance in Agricultural Soils

Excessive use of antibiotics in the healthcare sector and livestock farming has amplified antimicrobial resistance (AMR) as a major environmental threat in recent years. Abiotic stresses, including soil salinity and water pollutants, can affect AMR in soils, which in turn reduces the yield and quality of agricultural products. The objective of this study was to investigate the effects of antibiotic resistance and abiotic stresses on antimicrobial resistance in agricultural soils. A systematic review of the peer-reviewed published literature showed that soil contaminants derived from organic and chemical fertilizers, heavy metals, hydrocarbons, and untreated sewage sludge can significantly develop AMR through increasing the abundance of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in agricultural soils. Among effective technologies developed to minimize AMR's negative effects, salinity and heat were found to be more influential in lowering ARGs and subsequently AMR. Several strategies to mitigate AMR in agricultural soils and future directions for research on AMR have been discussed, including integrated control of antibiotic usage and primary sources of ARGs. Knowledge of the factors affecting AMR has the potential to develop effective policies and technologies to minimize its adverse impacts.

Effect of g-C3N4 on biodiversity and structure of bacterial community in sediment of Xiangjiang River under tetracycline pressure

Photocatalysts have been widely prepared and used in wastewater treatment. Although the influence of photocatalyst application on survival and activity of organisms has been examined, its impact on composition and diversity of microbial community is not fully understood. In this study, the impact of photocatalyst g-C₃N₄ (Graphitic carbon nitride) on microbial communities in riverbed sediments polluted by antibiotic tetracycline (TC) was investigated. The sediment samples collected from the Xiangjiang River of China were exposed to different concentrations of TC, g-C₃N₄ and TC/g-C₃N₄ and the bacterial community were analyzed by Illumina sequencing. The results showed that the dominant bacterial phyla were Acidobacteriota, Proteobacteria, Actinobacteriota, and Chloroflexi in the study site. When compared to the control treatments, the application of TC, g-C₃N₄ and TC/g-C₃N₄ exhibited distinguishable effects on bacterial community structure in sediments. The presence of TC had greater influence on bacterial composition, while g-C₃N₄ and TC/g-C₃N₄ had less influence on bacteria. The diversity and richness of microorganisms in sediment increased under g-C₃N₄ application and reached the highest values when g-C₃N₄ was 75 mg/kg. The photocatalyst g-C₃N₄ restored bacterial community diversity affected by TC, reduced the TC residues in aquatic environment, and eliminated the side effects of TC application in sediments. Our study indicated that g-C₃N₄ was an environmentally friendly photocatalyst with lightly negative effects on microbial community in riverbed sediments, and could be used for effective remediation of TC-contaminated environments.

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.

How anammox process resists the multi-antibiotic stress: Resistance gene accumulation and microbial community evolution

The effects of multiple antibiotics on the anaerobic ammonia oxidation (anammox) process were investigated. The resistance of the anammox system to high-concentration antibiotics was also demonstrated through gradual acclimation experiments. Inhibition of the anammox process (R₁) occurred when the concentrations of erythromycin (ERY), sulfamethoxazole (SMX) and tetracycline (TC) were 0.1, 5.0 and 0.1 mg L^-1, respectively. The nitrogen removal efficiency (NRE) of R₁ was reduced from 97.2% to 60.7% within 12 days and then recovered to 88.9 ± 9.5% when the nitrogen loading declined from 4.52 ± 0.69 to 2.11 ± 0.58 kg N m^-3 d^-1. Even when the concentrations of ERY, SMX and TC were as high as 1.0, 15.0 and 1.0 mg L^-1, respectively, R₁ maintained stable operation. The increases in the abundance of antibiotic resistance genes (ARGs) and in extracellular polymeric substances (EPS) content showed that the anammox process alleviated stress from multiple antibiotics mainly by producing ARGs and secreting EPS. The molecular docking simulation results illustrated the potential binding sites between ammonium transporter and different antibiotics. The upregulation of functional gene expression and the stable abundance of Candidatus Kuenenia in R₁ compared with that in the control suggested that the R₁ reactor generally maintained more stable long-term operation. This work provides a new understanding of the application of the anammox process to treat wastewater containing multiple antibiotics.

Comparative characterization of microbial communities that inhabit PFAS-rich contaminated sites: A case-control study

The historic usage and discharge of per- and polyfluoroalkyl substances (PFAS) containing chemicals have produced many contaminated sites and PFAS contamination has become a global concern due to their persistence, widespread distribution, and potential adverse impacts for human and environmental health. However, there have been limited investigations on the specific behavior of bacterial communities in PFAS contaminated soils. In this study, a quantitative PCR assay and Illumina MiSeq sequencing were used to investigate the variations of bacterial communities in a regional Australian airport contaminated with PFAS. The dominate PFAS detected in soil samples was Perfluorooctanesulfonic acid (PFOS), which accounted for 82% of total PFAS and the maximum PFOS level was noted (20,947±1824 ng.PFOS/mg.Soil) at the top soil. Irrespective of the degree of PFAS contamination at different depths, the comparable percentile contribution of each PFAS was observed in soil samples. Significantly higher bacteria amplicon sequence variant (ASV) and diversity were noted in uncontaminated soil than PFAS contaminated soil. Bacterial genera Rhodanobacter and Chujaibacter were dominant in the PFAS contaminated soil. Three different bacterial genera of Alphaproteobacteria, Ambiguous taxa of Acidobacteriia, and genus Chujaibacter of Gammaproteobacteria showed a significant positive correlation and RB41, Gaiella showed a significant negative correlation with 11 different PFAS concentrations. Overall, the results presented in this study suggest that the counts and species diversity of soil microorganisms are adversely influenced by PFAS contamination.

A Literature Review of Wetland Treatment Systems Used to Treat Runoff Mixtures Containing Antibiotics and Pesticides from Urban and Agricultural Landscapes

Wetland treatment systems are used extensively across the world to mitigate surface runoff. While wetland treatment for nitrogen mitigation has been comprehensively reviewed, the implications of common-use pesticides and antibiotics on nitrogen reduction remain relatively unreviewed. Therefore, this review seeks to comprehensively assess the removal of commonly used pesticides and antibiotics and their implications for nitrogen removal in wetland treatment systems receiving non-point source runoff from urban and agricultural landscapes. A total of 181 primary studies were identified spanning 37 countries. Most of the reviewed publications studied pesticides (n = 153) entering wetlands systems, while antibiotics (n = 29) had fewer publications. Even fewer publications reviewed the impact of influent mixtures on nitrogen removal processes in wetlands (n = 16). Removal efficiencies for antibiotics (35–100%), pesticides (−619–100%), and nitrate-nitrogen (−113–100%) varied widely across the studies, with pesticides and antibiotics impacting microbial communities, the presence and type of vegetation, timing, and hydrology in wetland ecosystems. However, implications for the nitrogen cycle were dependent on the specific emerging contaminant present. A significant knowledge gap remains in how wetland treatment systems are used to treat non-point source mixtures that contain nutrients, pesticides, and antibiotics, resulting in an unknown regarding nitrogen removal efficiency as runoff contaminant mixtures evolve.

Strategies to Control Human Health Risks Arising from Antibiotics in the Environment: Molecular Modification of QNs for Enhanced Plant-Microbial Synergistic Degradation

In the present work, a comprehensive screening and evaluation system was established to improve the plant-microbial synergistic degradation effects of QNs. The study included the construction of a 3D-QSAR model, the molecular modification, environmental friendliness and functional evaluation of drugs, degradation pathway simulation, and human health risk assessment. Molecular dynamics was applied to quantify the binding capacity of QNs toward the plant degradation enzyme (peroxidase) and microbial degradation enzymes (manganese peroxidase, lignin peroxidase, and laccase). The fuzzy comprehensive evaluation method was used in combination with the weighted average method for normalization and assigning equal weights to the plant and microbial degradation effect values of the QNs. Considering the synergistic degradation effect value as the dependent variable and the molecular information of the QNs as the independent variable, a 3D-QSAR model was constructed for the plant-microbial synergistic degradation effect of QNs. The constructed model was then employed to conduct the molecular modification, environmental friendliness and functional evaluation, degradation pathway simulation, and human health risk assessment of transformation products using pharmacokinetics and toxicokinetics. The results revealed that the synergistic degradation effect 3D-QSAR (CoMSIA) model exhibited good internal and external prediction ability, fitting ability, stability, and no overfitting phenomenon. Norfloxacin (NOR) was used as the target molecule in the molecular modification. A total of 35 NOR derivatives with enhanced plant-microbial synergistic degradation effect (1.32-21.51%) were designed by introducing small-volume, strongly electronegative, and hydrophobic hydrogen bond receptor groups into the active group of the norfloxacin structure. The environment-friendliness and the functionality of NOR were evaluated prior to and after the modification, which revealed seven environment-friendly FQs derivatives exhibiting moderate improvement in stability and bactericidal efficacy. The simulation of the NOR plant and microbial degradation pathways prior to and after the modification and the calculation of the reaction energy barrier revealed Pathway A (D-17 to D-17-2) and Pathway B (D-17 to D-17-4) as the most prone degradation pathways in plants and Pathway A (D-17 to D-17-1) and Pathway B (D-17 to D-17-4) as the most prone degradation pathways in microorganisms. This demonstrated that the degradation of the modified NOR derivatives was significantly enhanced, with the hydroxylation and piperazine ring substitution reaction playing an important role in the degradation process. Finally, the parameters, including hepatotoxicity, mutagenicity, and rodent carcinogenicity, among others, predicted using the pharmacokinetics and toxicokinetics analyses revealed a significant reduction in the human health risk associated with the modified NOR, along with a considerable reduction in the toxicity of its transformation products, implying that the human health risk associated with the transformation products was reduced remarkably. The present study provides a theoretical basis for novel ideas and evaluation programs for improving the plant-microbial synergistic degradation of the QNs antibiotics for source control and drug design, thereby reducing the residues of these antibiotics and the associated hazard in the complex plant-soil environment, ultimately decreasing the potential risks to human health.

Ecological improvement of antimony and cadmium contaminated soil by earthworm Eisenia fetida: Soil enzyme and microorganism diversity

Vermiremediation on improvement of antimony (Sb) and cadmium (Cd) contaminated soil was less reported. In this study, earthworm Eisenia fetida was exposed into soil spiked with Sb and Cd and their mixture for 30 days, and then we measured multiple soil enzyme activities and bacteria communities via enzymatic reaction and high-throughput sequencing of 16 S rRNA genes. The results showed that Sb and Cd at high treatment levels inhibited the activities of urease, neutral phosphatase and protease significantly, but earthworm could promote the activities of urease and neutral phosphatase by 17.75%-121.91% and 1.46%-118.97%, respectively. However, earthworms inhibited catalase and had no effect on protease. The Geometric Mean Index suggested that earthworms led to a higher soil biochemistry function. According to a taxonomic analysis, bacterial community structure predominantly consisted of phylum Proteobacteria, Actinobacteria, Firmicutes, etc. and class Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, etc.; furthermore, Pielou index and Shannon index (Alpha diversity in the habitat) indicated that bacteria diversity and evenness increased in the presence of earthworms. The heating map revealed that earthworms made genus Sphingomonas, Flavobacterium, etc. and species Sphingomonas jaspsi, Conexibacter, etc. dominate. Overall, earthworm is a suitable remediation species to improve the ecological function of heavy metal polluted soil. However, the specific mechanism and causal relationship of how earthworm to control enzyme activity and bacteria community remained to be explored.

Temporal and spatial variability of antibiotics in agricultural soils from Huang-Huai-Hai Plain, northern China

The objective of this study was to investigate the temporal and spatial distribution of antibiotics in agricultural soils of Huang-Huai-Hai Plain, which is a major agricultural producing area and economically developed region in China. In this study, 105 soil samples including 13 groups of soil profile samples (0-20, 20-40 and 40-60 cm) and 23 paired surface soil samples of greenhouse and open-field were collected from four provinces/municipality in 2018. The occurrence of 20 antibiotics, including four tetracyclines (TCs), seven quinolones (QNs), six sulfonamides (SAs) and three macrolides (MLs) were measured. The concentrations of total antibiotics fell in the range of 1.62-575 μg kg^-1, with the mean value of 68.8 μg kg^-1. TCs and QNs were dominant antibiotics in soil, accounting for 99.6% of the total concentration. Regional differences of antibiotic residues in soil were found among the four regions as well as between different cropping systems. The levels of antibiotics in greenhouse soils (3.52-575 μg kg^-1) were higher than those in open-field soils (1.62-142 μg kg^-1). In soils of greenhouse of 1-6 years old, the levels of antibiotics were higher than those with longer history (7-30 years). Antibiotics were mainly distributed in the depth of 0-20 cm. The total concentrations of antibiotics/QNs followed the order of 0-20 cm > 40-60 cm > 20-40 cm, due to probably their interactions with total organic carbon and associated bacterial communities. The results in the study will provide data supports for the formulation of soil antibiotic contamination prevention and control measures.

Impacts of biochars on bacterial community shifts and biodegradation of antibiotics in an agricultural soil during short-term incubation

This study investigated the effects of applying different biochars to soil on shifts in the bacterial community, the biodegradation of antibiotics, and their relationships. In total, nine biochars were applied to agricultural soil contaminated with 16 antibiotics. Clustering analysis showed that the responses of bacteria at the genus level to biochars were highly dependent on the biochar feedstock rather than the pyrolysis temperature. Among the antibiotics tested in the study, the biodegradation percentage was lower for tetracyclines (TCs, 6-14%) than sulfonamides (SAs, 8-26%) and quinolones (QLs, 8-24%). For specific individual antibiotics from the same class with similar structures, the high adsorption affinity of soil particles for antibiotics due to hydrophobic interactions (logK_ow) and electrostatic interactions (pK_a) resulted in low biodegradation percentages for antibiotics in the soil. The biodegradation of TCs was affected more by the biochar type (effect size: -10% to 42%) than those of QLs (-26% to 14%) and SAs (-24% to 22%). According to the relationships determined between the bacterial taxonomic composition and biodegradation of antibiotics, Steroidobacter from the phylum Proteobacteria has significant positive correlations with the biodegradation of all SAs (p < 0.01), thereby indicating that Steroidobacter had a high capacity for biodegrading SAs. Significant positive correlations were also detected (p < 0.05) between specific genera (Iamia, Parviterribacter, and Gaiella) from the phylum Actinobacteria and the biodegradation of SAs. No significant positive correlations were found between bacterial genera and the biodegradation percentages for QLs and TCs, possibly due to the specific microorganisms involved in these biodegradation processes. The results in this study provide insights into the biodegradation mechanisms of antibiotics in soil and they may facilitate the development of strategies for the bioremediation of antibiotic-contaminated soil.

Effects of novel bioorganic fertilizer application on soil enzymes and bacterial community in multi-site rice paddies in China

Application of a novel bioorganic fertilizer (BIO) has been effectively used to inhibit weeds in rice paddies. To identify changes in soil bacterial community and enzymes in response to BIO treatments, field experiments were carried out in five major rice-growing areas in China. The dominant phylogenetic groups recorded included Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Acidobacteria. Anaeromyxobacter, Bacteroides, Bifidobacterium, Escherichia- Shigella, Geobacter and Haliangium were significantly different between BIO-treatment and untreated control and aided in general function (R), amino acid transport, metabolism (E) and transcription (K) clusters. The soil chemical properties and enzyme activities were less affected by BIO at these study sites. RDA analysis showed that soil bacterial community had a significant positive correlations among northern latitude, eastern longitude, exchangeable K, total K, total P, soil pH, and total N, except for organic matter, hydrolytic N and extractable P. Overall, our work showed that application of BIO does not alter the main community structure and functional diversity of soil bacteria in rice paddies and should be encouraged for use as a sustainable weed management strategy.

Effect of Organic Fertilizer on Soil Bacteria in Maize Fields

Soil microorganisms play an important role in agricultural ecosystems, but their response to organic fertilizer application has not been thoroughly elucidated. Thus, high-throughput sequencing was used to investigate the responses of soil bacterial to organic fertilizer amendment (composted from pig manure) in the field during the entire growth cycle of maize plants. Four treatments were studied: treatment with 2 kg·m−2 organic fertilizer application (OF_2), treatment with 4 kg·m−2 organic fertilizer application (OF_4), treatment with 6 kg·m−2 organic fertilizer application (OF_6), and a controlled treatment (CK) without fertilization. The results revealed that the bacterial richness in OF_2 was significantly lower than that of CK (p < 0.05). Soil eutrophication bacteria Bacteroidetes increased effectively in all fertilized soils, relative abundance in OF_2, OF_4, and OF_6 for the entire maize growth cycle was 68.00%, 71.40%, and 77.93% higher than that in CK, respectively. In addition, soil nitrobacteria (Nitrospirae, Nitrospira), were markedly decreased (p < 0.05) with fertilization amount. The relative abundance of the nitrogen-fixing genus Adhaeribacter in OF_6 was 209.28%, 72.8% and 35.66% higher than that in CK, OF_2 and OF_4 at mature stage. The pathogenic genus Flavolibacterium was significantly increased (p < 0.05) in fertilized soil at the seeding stage. The driving factor governing the variations of bacterial community in CK, OF_2, OF_4 and OF_6 were pH value, available phosphorus, available phosphorus, and chromium, respectively. The findings highlight that part of the soil functional or pathogenic bacteria population was susceptible to organic fertilizer application; and the driving factor of bacterial composition change was associated with the rate of fertilization. More targeted experiments are needed to enhance the understanding of functional bacteria and the synergistic effect of soil physicochemical property physical on soil bacteria.

Effect of antibiotic type and vegetable species on antibiotic accumulation in soil-vegetable system, soil microbiota, and resistance genes

Antibiotic accumulation in soil and plants is an escalating problem in agriculture and is receiving increasing attention. However, the effect of plant species on the fate of different types of antibiotics in a soil-vegetable system and soil resistome has not been adequately explored. To this end, greenhouse pot experiments were conducted to simulate contamination by ciprofloxacin (CIP), oxytetracycline (OTC), sulfamethoxazole (SMZ), and tylosin (TY) at 1 mg kg^-1 in the soils in which cabbage, endive, and spinach were grown. We investigated antibiotic persistence in soils and accumulation in vegetables (i.e., spinach, endive, and cabbage), microbial community profiles, and the abundance of 17 antibiotic resistance genes (ARGs) in contaminated soils. After 40 days, the residues of CIP and OTC in soil and their accumulation in vegetables were significantly higher than those of SMZ and TY. Of all vegetables, spinach had the highest antibiotic accumulation. Further, antibiotic contamination had no significant effect on soil microbial abundance; however, soil microbial diversity significantly decreased in soils amended with TY. The antibiotic type more significantly affected microbial composition than the kind of vegetable species. The relative abundances of some ARGs significantly increased in contaminated soils. Particularly, in endive soil, quinolone-associated cmlA, cmlA2, and qnrS1 increased with CIP contamination, OTC contamination increased tetG2 and otrA, SMZ increased sul1, and TY increased macrolide-related carB and msrc-01 relative abundance. However, some individual ARGs declined upon antibiotic contamination. Our results indicated that antibiotic type and vegetable species jointly shape the profiles of soil microorganisms and ARGs.

Petroleum Contaminated Seawater Detoxification in Microcosm by Halotolerant Consortium Isolated from Persian Gulf

Bioremediation of a petroleum contaminated seawater from Persian Gulf was investigated and efficiency of natural attenuation by native halotolerant bacterial consortium, biostimulation by addition of macro nutrients (nitrogen and phosphorus) and surfactant and bioaugmentation by application of halotolerant hydrocarbon degrading strains were evaluated. Biodegradation rates in defined conditions were studied for 30 days. Four pure isolates including Bacillus sp. PG-1, Pseudomonas aeruginosa PG-2, Paenibacillus lautus PG-3, and Pseudomonas putida PG-4 were used to preparation of bacterial consortium. Results indicated that the bioaugmentation yielded the best TPH removal efficiency of 56.24%, followed by biostimulation with surfactant addition (removal of 31.52%). The most bacterial density was also observed for bioaugmentation bioreactor. Toxicity of reaction medium was evaluated by oxygen consumption rate inhibition, dehydrogenase activity inhibition and growth rate inhibition methods in which, the least toxicity rates of 27%, 25% and 31% were observed for bioaugmentation based bioreactor, respectively. Simultaneous bioaugmentation and biostimulation can efficiently reduce the crude oil content in the surface of seawater using halotolerant strains.

Sulfamethoxazole affects the microbial composition and antibiotic resistance gene abundance in soil and accumulates in lettuce

Pot experiments were set up to simulate the soil contamination by three initial concentrations of sulfamethoxazole (SMX) (S1, 100 mg/kg; S2, 200 mg/kg; S3, 300 mg/kg). The content of SMX in soil and its accumulation in lettuce were analysed. Additionally, the effects of SMX on soil microorganisms and antibiotic resistance genes were studied by Illumina high-throughput sequencing and droplet digital polymerase chain reaction (ddPCR). The results demonstrated that the SMX content in soil reduced by 97%, 86% and 75% in the S1, S2 and S3 treatment groups after 120 days, respectively. The accumulated SMX in lettuce was positively correlated with the initial concentration of SMX in soil. SMX contamination significantly reduced the bacterial diversity and altered the composition of bacterial and fungal communities in soil. The dominant bacterial and fungal genera in the SMX-contaminated soil were obviously different from those in the control soil. The relative abundance of sul1 (sulfonamide resistance gene) remarkably increased in the SMX-contaminated soil, while that of other ARGs, such as sul2 and tetracycline and quinolone resistance genes, showed no significant change.

Insight into dynamics and bioavailability of antibiotics in paddy soils by in situ soil moisture sampler

Plant-soil systems have complex regulatory mechanisms for xenobiotics uptake by plant, and these chemicals in soil pore water (SPW) are regarded as the bioavailable fraction. To date, little is known about the role of SPW in regard to the bioavailability of antibiotics for plant. In this study, in situ soil moisture sampler (SMS) was adopted to collect SPW from four paddy soils without disrupting the rhizosphere zone to evaluate antibiotic uptake in rice. The results show that SMS is applicable for antibiotics that have small molecular sizes and Log K_ow values, e.g., sulfadiazine (SDZ), sulfamethoxazole (SMZ), trimethoprim (TRM), and florfenicol (FLR). However, SMS performance was not feasible for large size and medium hydrophobic clarithromycin (CLR). Antibiotics in SPW demonstrated differences among chemicals and soils. Relatively higher levels of SDZ, SMZ, and FLR were observed in SPW than TRM, and neutral Panjin soil had the highest levels of antibiotics in SPW among four soils. The levels of antibiotics in SPW were negatively correlated with their soil partition parameter, K_d. Rapid decreases of SMZ, FLR, and SDZ in the SPW were consistent with their low residues in the final soils. All antibiotics were detectable in rice roots, followed by low detection levels in a few shoot samples, while no antibiotics were detectable in the grains of four soils. Relatively higher levels of SDZ, SMZ and FLR were observed in the roots of Panjin soil, consistent with their levels in SPW and K_d values. Furthermore, CLR and TRM were observed to have higher levels in roots, which was regarded as a consequence of their relatively longer persistence. Our study indicates that SMS is an applicable technique for in situ sampling of SPW, and level of antibiotics in SPW can work as a useful indicator to explore their bioavailability to plants.

Effects of antibiotics on microbial community structure and microbial functions in constructed wetlands treated with artificial root exudates

In the rhizosphere, plant root exudates can mediate the toxicity of antibiotics on microorganisms, yet the mechanisms are poorly understood. To simulate the antibiotic contamination of global rivers and lakes, the current study investigated the effects of two antibiotics (ofloxacin at 8.69 × 10⁴ ng L^-1 and tetracycline at 8.62 × 10⁴ ng L^-1) and their binary combination (8.24 × 10⁴ ng L^-1 ofloxacin and 7.11 × 10⁴ ng L^-1 tetracycline) on bacterial communities in micro-polluted constructed wetlands with and without artificial root exudates. The two antibiotics had no significant effects on the removal of excess carbon and nitrogen from the microcosms treated with and without exudates. Furthermore, with regard to bacterial community structure, antibiotic exposure increased the bacterial richness of bulk and exudate treated microcosms (P < 0.05). However, a significant increase (P < 0.05) in bacterial diversity elicited by ofloxacin and antibiotic mixture exposure was only observed in microcosms with exudates. In exudate treated microcosms, ofloxacin promoted the relative abundance of Arthrobacter spp., which are ofloxacin-resistant bacterial species, which significantly varied from what was observed in microcosms free of exudates. Moreover, tetracycline, ofloxacin and their combination all significantly increased the relative abundance of nitrogen cycling bacteria Rhizobacter spp. and Rhizobium spp., and decreased the relative abundance of antibiotic-resistant bacteria Pseudomonas spp. Simultaneously, with regard to bacterial community functions, the functional profiles (Kyoto Encyclopedia of Genes and Genomes) showed that the pathways of amino acid and carbohydrate metabolism were enhanced by antibiotics in microcosms with exudates. The findings illustrate that antibiotics not only alter the bacterial structure and composition but also change their functional properties in constructed wetlands, and these interruption effects could be affected by root exudates of plants, which may further reveal the ecological implication of plants in constructed wetlands.

Microbial action and mechanisms for Cr(VI) removal performance by layered double hydroxide modified zeolite and quartz sand in constructed wetlands

This study was conducted to evaluate the performance underlying the removal of hexavalent chromium Cr(VI) associated with Zn-layered double hydroxides (Zn-LDHs)-modified substrates utilized in simulated constructed wetlands (CWs) from a microbial perspective. To accomplish this, Zn-LDHs-modified substrates (zeolite and quartz sand (QS)) were synthesized at various Zn²⁺/Al³⁺ and Fe³⁺ molar ratios by co-precipitation under alkaline conditions. The experimental group was then compared with a control group to determine the microbial action responsible for Cr(VI) removal during the Cr(VI) removal experiments. The removal experiment revealed that the average Cr(VI) removal rates of the Zn-LDHs-modified substrates were superior to those of natural substrates. Subsequent evaluation of the microbial structure by Illumina high-throughput sequencing revealed that the relative abundance of Novosphingobium, Brevundimonas, Methylophilus, and Acidovorax related to Cr(VI) removal was relatively high in Zn-LDHs-modified substrates. Moreover, the extracellular polymeric substance (EPS) content was significantly influenced by the Zn-LDHs coating according to the relative microbial experiments. Similar trends were observed in enzyme activity. Taken together, these findings illustrated that the Zn-LDHs coating had a significant impact on microbial action, and the Cr(VI) removal efficiency of the Zn-LDHs-modified QS (zeolite) substrate was better than that of the natural substrate because of intracellular and extracellular removal mechanisms. Briefly, the microbial action of Zn-LDHs-modified QS played an important role in Cr(VI) removal, since the EPS content possessed the appropriate concentrations. Moreover, the microbial activity of ZnAl-LDHs-modified QS (zeolite) may have been higher than that of ZnFe-LDHs-modified QS (zeolite) because Al had a stronger promoting effect on Cr(VI) bio-removal than Fe. Therefore, the microbial Cr(VI) removal supported by ZnAl-LDHs-modified QS is a better choice for CWs.

Removal of veterinary antibiotics in constructed wetland microcosms - Response of bacterial communities

This study aimed to evaluate the response of bacteria, in terms of microbial community structure, from constructed wetland (CW) microcosms exposed to two veterinary antibiotics, enrofloxacin (ENR) and ceftiofur (CEF), alone or in a mixture, identifying which bacterial groups were dominant in CWs substrate during livestock wastewater treatment. Wastewater, not-doped or doped with ENR and/or CEF (100 µg/L each), was treated during 18 one-week cycles. Systems showed removal percentages > 85% for the added antibiotics, showing also high removal percentages for nutrients and organic matter and confirming CWs systems were working properly. However, both time of exposure and presence of antibiotics influenced significantly CWs substrate bacterial community structure. Pyrosequencing results showed bacterial communities were dominated by phyla Proteobacteria (38-48%), Firmicutes (20-27%), Bacteroidetes (12-15%) and Actinobacteria (4-9%), and that their relative abundance was clearly affected by the presence of the antibiotics. Results suggest the applicability of CWs for the removal of veterinary antibiotics from livestock wastewaters and provide new knowledge about the bacteria within the system, which can potentially be involved in removal processes. This information could in the future be used to improve CWs removal rates of pharmaceuticals from livestock wastewaters.