'Agricultural Waste to Treasure' - Biochar and eggshell to impede soil antibiotics/antibiotic resistant bacteria (genes) from accumulating in Solanum tuberosum L

Biochar-derived dissolved organic matter enhanced the release of residual ciprofloxacin from the soil solid phase

Biochar has been utilized to reduce ciprofloxacin (CIP) residues in soil. However, little is known about the effect of biochar-derived dissolved organic matter (DOM) on residual CIP transformation. Thus, we analyzed the residual soil CIP as influenced by biochar generated from rice straw (RS3 and RS6), pig manure (PM3 and PM6), and cockroach shell (CS3 and CS6) at 300 °C and 600 °C. The three-dimensional excitation-emission matrix (3D-EEM), parallel factor analysis (PARAFAC) and two-dimensional correlation spectral analysis (2D-COS) were used to describe the potential variation in the DOM-CIP interaction. Compared with CK, biochar amendment increased the water-soluble CIP content by 160.7% (RS3), 55.2% (RS6), 534.1% (PM3), 277.5% (PM6), 1160.6% (CS3) and 703.9% (CS6), indicating that the biochar feedstock controlled the soil CIP release. The content of water-soluble CIP was positively correlated with the content of dissolved organic carbon (r = 0.922, p < 0.01) and dissolved organic nitrogen (r = 0.898, p < 0.01), suggesting that the major influence of the water-soluble CIP increase was DOM. The fluorescence quenching experiment showed that the interaction between DOM and CIP triggered static quenching and the creation of a DOM complex. The mean log K of protein-like material (4.977) was higher than that of terrestrial humus-like material (3.491), suggesting that the protein-like material complexed CIP was more stable than the humus-like material. Compared with pyrolysis at 300 °C, pyrolysis at 600 °C decreased the stability of the complex of protein-like material and CIP by 0.44 (RS), 1.689 (PM) and 0.548 (CS). This result suggested that the influence of temperature change was more profound on PM biochar-derived DOM than on RS and CS. These insights are essential for understanding CIP transportation in soil and controlling CIP contamination with biochar.

Development of a 3-step sequential extraction method to investigate the fraction and affecting factors of 21 antibiotics in soils

Antibiotic exist in various states after entering agricultural soil through the application of manure, including the aqueous state (I), which can be directly absorbed by plants, and the auxiliary organic extraction state (III), which is closely associated with the pseudo-permanence of antibiotics. However, effective analytical methods for extracting and affecting factors on fractions of different antibiotic states remain unclear. In this study, KCl, acetonitrile/Na2EDTA-McIlvaine buffer, and acetonitrile/water were successively used to extract states I, II, and III of 21 antibiotics in soil, and the recovery efficiency met the quantitative requirements. Random forest classification and variance partitioning analysis revealed that dissolved organic matter, pH, and organic matter were important factors affecting the recovery efficiency of antibiotic in states I, II, and III, respectively. Additionally, 65-day spiked soil experiments combined with Mantel test analysis suggested that pH, organic acids, heavy metals, and noncrystalline minerals differentially affected antibiotic type and state. Importantly, a structural equation model indicated that organic acids play a crucial role in the fraction of antibiotic states. Overall, this study reveals the factors influencing the fraction of different antibiotic states in soil, which is helpful for accurately assessing their ecological risk.

Characteristics of microplastics in the atmosphere of Anyang City

In order to clarify the characteristics of microplastics in the atmosphere of Anyang city, TSP, PM10, and PM2.5 samples are collected when the ambient air quality is good, slightly polluted, and severely polluted. After pretreatment, the physical and chemical characteristics are observed and identified by using stereomicroscope and micro-infrared spectrometer. The results show that the average abundance of microplastics is 0.19 items/m3, 0.26 items/m3, and 0.42 items/m3, respectively, when the ambient air quality is good, light pollution, and heavy pollution in Anyang City. It can be seen that with the decline of ambient air quality, the average abundance of microplastics in TSP, PM2.5, and PM10 gradually increases. The black fiber strip microplastics account for about 80% of the total TSP, PM2.5, and PM10 in the ambient air of Anyang City, followed by yellow flake and black granular microplastics and a small amount of green, red, and blue fiber strip microplastics. AQI has a good correlation with the abundance of microplastics in TSP, PM10, and PM2.5, and the maximum microplastic trapping effect could be obtained according to the sampling method of PM2.5 in the ambient air. The main components of microplastics are cellophane, followed by PET and EVA. The explorations of human respiratory exposure risk assessment show that with the increase of AQI, the daily intake of microplastics in adults also increased. At high levels of pollution, the human body breathes an average of 222 ± 5 microplastics per day.

Calcium-enriched biochar shifts negative effects of fluoride on the properties of arid sandy soil

This study sheds light on the influence of fluoride on the changes in the properties of alkaline sandy soils and the efficiency of calcium-enriched biochar application. The investigation involved an incubation experiment with soil contaminated with varying NaF concentrations (0, 400, 800, and 1200 mg NaF kg-1 soil) and biochar (1% w/w). The data revealed that adding NaF to the soil resulted in significant increases in soil pH and decreases in total nitrogen (TN) content. Short-term fluoride pollution did not affect the microbial abundance due to certain factors such as increased soil pH and decreased microbial metabolism promoting the survival of cells under fluoride stress. However, a shift from bacterial to fungal-dominated microbial communities was observed at the highest NaF concentration. The nitrogen functional gene amoA was found to be highly sensitive to fluoride toxicity. The decrease in the abundance of amoA gene and the increase in soil pH can explain reduced nitrogen concentration. On the other hand, our findings indicated a significant decrease in enzyme activity in soil contaminated with mild to severe levels of NaF. This reduction in enzyme activity can be attributed to increased soil pH, decreased TN content, and the inhibition of microbial metabolism due to fluoride toxicity. Furthermore, the addition of calcium-rich biochar reduced fluoride solubility and adjusted pH, mitigating the negative effects of fluoride toxicity on soil properties. The use of biochar was also found to inhibit the accumulation of soil fluoride-resistant microbial genes.

Mechanism for combined application of biochar and Bacillus cereus to reduce antibiotic resistance genes in copper contaminated soil and lettuce

The remediation of agricultural soil contaminated by antibiotic resistance genes (ARGs) is of great significance for protecting food safety and human health. Reducing the availability of copper in soil may control coresistance to ARGs. However, the feasibility of applying nano-biochar and Bacillus cereus to mitigate the spread of ARGs in Cu contaminated soil remains unclear. Therefore, this study investigated the use of biochar with different particle sizes (2 % apple branch biochar and 0.5 % nano-biochar) and 3 g m-2B. cereus in a 60-day pot experiment with growing lettuce. The effects of single and combined application on the abundances of ARGs in Cu-contaminated soil (Cu = 200 mg kg-1) were compared, and the related mechanisms were explored. Studies have shown that the addition of biochar alone is detrimental to mitigating ARGs in soil-lettuce systems. The combined application of 3 g m-2B. cereus and 0.5 % nano-biochar effectively inhibited the proliferation of ARGs in Cu-contaminated soil, and 3 g m-2B. cereus effectively inhibited the proliferation of ARGs in lettuce. Partial least squares-path modeling and network analysis showed that bacterial communities and mobile genetic elements were the key factors that affected the abundances of ARGs in rhizosphere soil, and Cu resistance genes and bioavailable copper (acid extractable state Cu (F1) + reducing state Cu (F2)) had less direct impacts. The bacterial community was the key factor that affected the abundances of ARGs in lettuce. Rhodobacter (Proteobacteria), Corynebacterium (Actinobacteria), and Methylobacterium (Proteobacteria) may have been hosts of ARGs in lettuce plants. B. cereus and nano-biochar affected the abundances of ARGs by improving the soil properties and reducing the soil bioavailability of Cu, as well as directly or indirectly changing the bacterial community composition in soil and lettuce, thereby impeding the transport of ARGs to aboveground plant parts.

Change of tetracycline speciation and its impacts on tetracycline removal efficiency in vermicomposting with epigeic and endogeic earthworms

Tetracycline pollution is common in Chinese arable soils, and vermicomposting is an effective approach to accelerate tetracycline bioremediation. However, current studies mainly focus on the impacts of soil physicochemical properties, microbial degraders and responsive degradation/resistance genes on tetracycline degradation efficiencies, and limited information is known about tetracycline speciation in vermicomposting. This study explored the roles of epigeic E. fetida and endogeic A. robustus in altering tetracycline speciation and accelerating tetracycline degradation in a laterite soil. Both earthworms significantly affected tetracycline profiles in soils by decreasing exchangeable and bound tetracycline but increasing water soluble tetracycline, thereby facilitating tetracycline degradation efficiencies. Although earthworms increased soil cation exchange capacity and enhanced tetracycline adsorption on soil particles, the significantly elevated soil pH and dissolved organic carbon benefited faster tetracycline degradation, attributing to the consumption of soil organic matter and humus by earthworms. Different from endogeic A. robustus which promoted both abiotic and biotic degradation of tetracycline, epigeic E. foetida preferently accelerated abiotic tetracyline degradation. Our findings described the change of tetracycline speciation during vermicompsiting process, unraveled the mechanisms of different earthworm types in tetracycline speciation and metabolisms, and offered clues for effective vermiremediation application at tetracycline contaminated sites.

Manure and biochar have limited effect on lettuce leaf endophyte resistome

Soil amendment with manure compost and biochar is widely adopted to improve soil fertility and promote plant growth, and their effects on soil microbial communities and resistome have been well documented. However, there is sparse information regarding their effects on vegetable endophytes, which represent a major source of human exposure to pathogens and antibiotic resistance genes (ARGs) when eaten raw. Here, we investigated the impacts of manure compost or biochar addition on the bacterial community compositions and ARGs in the soil-lettuce continuum including soil, seed, leaf, and root samples. A total of 137 ARGs and 31 mobile genetic elements (MGEs) were detected in all the samples after 60 days of cultivation. The relative abundance of ARGs and the diversity of bacteria communities presented a consistent decreasing trend from soil to root endophytes, then leaf endophytes. Manure compost addition increased the diversity and abundance of ARGs in soil, while significant changes in the ARG profiles and bacterial communities were not observed in leaf endophytes after manure compost or biochar addition, or both. Bipartite networks analysis suggested that seed microbiome was one of the major sources of plant endophytes and ARGs. Twenty potential human pathogens were isolated from lettuce, indicating potential exposure risk to pathogens via the consumption of raw lettuce. These results suggest limited impacts of manure compost and biochar addition on lettuce endophytes and highlight the contribution of seed microbiome to endophyte ARG profiles.

Effect of ofloxacin levels on growth, photosynthesis and chlorophyll fluorescence kinetics in tomato

Antibiotic pollution has become a global environmental pollution problem. Chlorophyll fluorescence is one of the most important indicators reflecting the degree to which plants are influenced by the environment. Ofloxacin (OFL) is a highly toxic antibiotic pollutant, and there are few reports on the effects of changes in OFL levels on tomato chlorophyll fluorescence parameters. In this study, we investigated the responses of tomato growth, photosynthetic activity and chlorophyll fluorescence kinetics to exogenous OFL exposure (as the concentrations of 0, 2.5, 5, 10 and 20 mg L^-1). The results showed that lower concentrations of OFL (2.5 mg L^-1) had little impact on tomato growth, while plant growth was inhibited with the OFL concentration increasing. At higher OFL concentrations (5, 10 and 20 mg L^-1), chloroplasts ruptured, and chlorophyll became degraded, resulting in leaf etiolation. Furthermore, the photosynthetic and photochemical efficiency and electron transfer rate were significantly inhibited by OFL. Moreover, damage to the oxygen-evolving complex on the donor side of PSⅡ prevented electron transfer from QA to QB and led to photoinhibition. In conclusion, higher OFL concentration reduced photosynthesis by destroying the photosynthetic mechanism in tomato, resulting in tomato leaf etiolation and plant growth inhibition.

The effects of biochar on antibiotic resistance genes (ARGs) removal during different environmental governance processes: A review

Antibiotic resistance genes (ARGs) pollution has been considered as one of the most significant emerging environmental and health challenges in the 21st century, many efforts have been paid to control the proliferation and dissemination of ARGs in the environment. Among them, the biochar performs a positive effect in reducing the abundance of ARGs during different environmental governance processes and has shown great application prospects in controlling the ARGs. Although there are increasing studies on employing biochar to control ARGs, there is still a lack of review paper on this hotspot. In this review, firstly, the applications of biochar to control ARGs in different environmental governance processes were summarized. Secondly, the processes and mechanisms of ARGs removal promoted by biochar were proposed and discussed. Then, the effects of biochar properties on ARGs removal were highlighted. Finally, the future prospects and challenges of using biochar to control ARGs were proposed. It is hoped that this review could provide some new guidance for the further research of this field.

Impact of biochar on persistence and diffusion of antibiotic resistance genes in sediment from an aquaculture pond

Aquaculture sediments are a purported sizable pool of antibiotic resistance genes (ARGs). However, the pathways for transmission of ARGs from sediments to animals and humans remain unclear. We conducted an ARG survey in sediments from a bullfrog production facility located in Guangdong, China, and simulated zebrafish breeding systems were constructed, with or without biochar addition in sediments, to explore the effects of biochar on ARGs and their precursors of the sediment and zebrafish gut. After 60 days, 6 subtypes of ARGs and intI1 were detected, with sediments harboring more ARGs than zebrafish gut. The addition of biochar reduced the abundance of ARGs in the sediment and zebrafish gut, as well as suppressed the horizontal transmission of ARGs from sediment to zebrafish gut. Network analysis and partial least squares path modeling revealed that ARG enrichment was mainly affected by bacterial groups dominated by Nitrospirae, Gemmatimonades, Chloroflexi, and Cyanobacteria and intI1. Our findings provide insights into the transmission of ARGs from sediment to animals and highlight the efficacy of biochar amendments to aquaculture sediments to reduce the transmission of ARGs.

Accumulation of antibiotic resistance genes in pakchoi (Brassica chinensis L.) grown in chicken manure-fertilized soil amended with fresh and aged biochars

Biochar has been used to alleviate the contamination of antibiotic resistance genes (ARGs) in soil and to inhibit ARGs transfer from soil to plants. However, the effect of aged biochar on ARGs abundance in soil and ARGs enrichment in plants are scarcely investigated. In this study, a pot experiment was conducted to compare the effects of fresh and aged biochars on the accumulation of five typical ARGs including tetX, tetW, sul2, ermB, and intI1 in a chicken manure-fertilized soil and in pakchoi (Brassica chinensis L.). Results showed that both biochars significantly decreased the abundance of tetW, sul2, and ermB and increased the abundance of tetX and intI1 in soil. However, the accumulation of all tested ARGs in pakchoi were significantly decreased by both biochars. At the lower addition rate (1%), the fresh biochar was superior to the aged biochar in decreasing the accumulation of some genes (tetW, tetX, and sul2) in pakchoi, whereas an opposite tendency was observed for other genes (ermB and intI1). As the addition rate increased to 2%, the difference between the two biochars diminished, and a similar capacity of decreasing ARGs transfer was observed. The reduction in ARGs accumulation in pakchoi was highly related to the type of ARGs, the biochar addition level, and the aging of biochar. Our results provide insights into the naturally aged biochar on the fate of ARGs in a soil-plant system.

Silicon enhanced the resistance of Chinese cabbage (Brassica rapa L. ssp. pekinensis) to ofloxacin on the growth, photosynthetic characteristics and antioxidant system

The negative impact of the misuse of antibiotics on agriculture and human health has become a popular research topic with the increasing usage of antibiotics; however, little information is available about the mechanisms of OFL (ofloxacin) and Si (silicon). In this experiment, we applied 7 OFL concentrations to two Chinese cabbage cultivars (Qinghua and Biyu) to screen proper OFL concentrations. OFL concentrations of 0, 1, 2.5 and 5 mg L-1 were selected for the subsequent test and 1.2 mmol L-1 Si was used as mitigation. The results showed that Biyu suffered more damage than Qinghua and the injury degree increased in a concentration-dependent manner. With increasing OFL concentrations, the photosynthetic fluorescence was weakened significantly; under 1, 2.5 and 5 mg L-1 OFL, the Pn reduced by 5.35%, 35.92% and 43.62% in Qinghua and 33.98%, 41.94% and 64.66% in Biyu, respectively. The production rate of O2-, H2O2 and the MDA content were increased and Biyu appeared higher increase rates. In addition, the antioxidant enzymes contents first increased and then decreased and that of Qinghua increased more than Biyu. Si ensured the growth under OFL and protected its photosynthetic ability. Under the OFL1+Si, OFL2.5 + Si and OFL5+Si treatments, Pn increased by 3.91%, 15.95 and 15.69% in Qinghua and 28.82%, 20.40% and 39.01% in Biyu. Si also maintained the structural integrity of leaf organelles and improved the scavenging ability of ROS by increasing the activity and relative gene expression of antioxidant enzymes. Moreover, varietal differences may play a more important role than Si.

Optimizing magnetic functionalization conditions for efficient preparation of magnetic biochar and adsorption of Pb(II) from aqueous solution

Recoverable magnetic biochar has great potential for treating wastewater contaminants such as Pb(II). However, whether magnetic modification could enhance metal adsorption efficiency is currently contradictory in the literature mainly due to the differences in selecting various magnetic functionalization conditions. Considering this gap in knowledge, the effects of magnetic functionalization method (impregnation and precipitation), concentration of precursor iron solution (0.01-1 M), and pyrolysis temperature (300-700 °C) on the characteristics and Pb(II) adsorption capacity of biochar were systematically investigated in this paper. Results indicated that Fe₃O₄ was the main product for magnetic biochars synthesized using the impregnation (denoted as FWFe(3)) and precipitation methods (denoted as FWFe(2)). Magnetic functionalization resulted in remarkably increased pH and more negative zeta potential for FWFe(2) samples, whereas FWFe(3) samples showed the opposite trends. The adsorption of Pb(II) on different biochars fitted the pseudo-second order model and the Langmuir model. The maximum adsorption capacity was 817.64 mg/g for FWFe(2)1M700C (precipitation by 1 M of Fe(II)/Fe(III), pyrolysis at 700 °C), outperforming FWFe(3) and pristine biochar samples by around 5-13 times. Mechanism study indicated that the adsorption mainly involved electrostatic attraction, ion exchange, co-precipitation, and complexation. Pb(II) adsorption capacity was strongly dependent on the alkali pH of biochar. However, this efficiency was less affected by biochar surface area and its morphology. The higher pH of FWFe(2) samples not only led to an increased surface charge for stronger electrostatic attraction and ion exchange but also favored the formation of co-precipitates. By contrast, FWFe(3) samples showed a decreased adsorption capacity for Pb(II) with increased concentration of embedded iron. Overall, magnetic biochar, prepared using precipitation followed by high-temperature pyrolysis (such as, FWFe(2)1M700C), can be a promising adsorbent for Pb(II) adsorption from wastewater.

Field aging alters biochar's effect on antibiotic resistome in manured soil

Current understanding of biochar's effect on antibiotic resistance genes (ARGs) in soil is limited, and whether the effect could change after long-term field aging remains largely unknown. In this study, we employed high-throughput quantitative PCR to assess the effect of biochar amendment on soil resistome as affected by three years of field aging. Application of fresh biochar significantly elevated the number and abundance of ARGs in the manured soil, but did not show such effect under pakchoi cultivation. The presence of aged biochar caused a marked reduction of ARGs only in the planted manured soil. Results of principal coordinate analysis and structural equation modeling indicate that biochar's effect on soil ARG profile was changed by field aging through altering soil microbial composition. These results highlight the necessity of considering aging effect of biochar during its on-farm application to mitigate soil antibiotic resistance.

Grafting resulting in alleviating tomato plant oxidative damage caused by high levels of ofloxacin

Antibiotic pollution has become a global problem threatening human health. Ofloxacin is one of the more widely used antibiotics, but reports on the reaction of plant to ofloxacin pollution are limited. In this study, using adversity-resistant (R), adversity-sensitive (S) and grafted plant S/R as models, we investigated the biological response of tomato to exogenous ofloxacin residues. The results showed that lower levels of ofloxacin treatment (5 mg L^-1 and 10 mg L^-1) promoted tomato growth, and 10 mg L^-1 ofloxacin was the critical dose to stimulate growth among the different treatments. In addition, the photosynthetic and fluorescence parameters, antioxidant enzyme activities and transcription-level expression of the enzymes were stimulated by low ofloxacin treatment. However, high ofloxacin treatment (20 mg L^-1 and 40 mg L^-1) exhibited a significantly negative effect on plant growth, photosynthesis, fluorescence parameters, antioxidant enzyme activities and transcript levels expression. Reactive oxygen species (ROS) and malondialdehyde (MDA) levels increased with increasing ofloxacin concentrations, indicating that the oxidative damage of plants was severe with increasing doses. In contrast, the role of antioxidant enzymes in the antibiotic response was limited at high ofloxacin concentrations. The grafting experiment demonstrated that grafted plants had the ability to alleviate ofloxacin stress. In conclusion, ofloxacin can damage the photosynthetic machinery by promoting ROS accumulation, which results in the etiolation of tomato leaves and inhibits plant growth, but grafting can reduce its.

Effects of Partial Organic Substitution for Chemical Fertilizer on Antibiotic Residues in Peri-Urban Agricultural Soil in China

Recycling of organic wastes in agricultural ecosystems to partially substitute chemical fertilizer is recommended to improve soil productivity and alleviate environmental degradation. However, livestock manure- and sewage sludge-derived amendments are widely known to potentially carry antibiotic residues. The aim of this study is to investigate how substituting organic fertilizer for chemical fertilizer affects soil quality and antibiotic residues in agricultural soil, as well as their tradeoffs. A field experiment was conducted with the different treatments of pig manure and sewage sludge as typical organic fertilizers at equal total nitrogen application rates. The analysis of variance showed that the increments on the levels of residual antibiotics in the agricultural soils due to organic substitution for chemical fertilizer by pig manure and sewage sludge were observed. The antibiotic residues ranged from 13.73 to 76.83 ng/g for all treatments. Partial organic substitution significantly increased the sequestration of antibiotics in agricultural soil by 138.1~332.5%. Organic substitution will also significantly improve soil quality, especially for nutrient availability. Based on principal component analysis, organic substitution will strongly affected soil quality and antibiotic contamination. Pearson's correlation showed that soil physicochemical properties had significant correlations with concentrations of antibiotics in soil, indicating organic fertilizers can promote the persistence of antibiotics in soil by modifying soil quality. To balance the benefits and risks, appropriate management practices of organic fertilizers should be adopted.

A critical review on the occurrence of resistomes in the environment and their removal from wastewater using apposite treatment technologies: Limitations, successes and future improvement

Recent reports are pointing towards the potential increasing risks of resistomes in human host. With no permissible limit in sight, resistomes are continually multiplying at an alarming rate in the ecosystem, with a disturbing level in drinking water source. The morphology and chemical constituent of resistomes afford them to resist degradation, elude membrane and counter ionic charge, thereby, rendering both conventional and advanced water and wastewater treatment inefficient. Water and wastewater matrix may govern the propagation of individual resistomes sub-type, co-selection and specific interaction towards precise condition may have enhanced the current challenge. This review covers recent reports (2011-2019) on the occurrence of ARB/ARGs and ease of spread of resistance genes in the aquatic ecosystem. The contributions of water matrix to the spread and mitigation, treatment options, via bulk removal or capture, and intracellular and extracellular DNA lysis were discussed. A complete summary of recent occurrences of ARB/ARGs, fate after disinfection and optimum conditions of individual treatment technology or in tandem, including process limitations, with a brief assessment of removal or degradation mechanism were highlighted.

Effects of biochar amendments on antibiotic resistome of the soil and collembolan gut

A diverse array of ARGs has been detected in the guts of soil fauna residing in farmland soil. Biochar has been widely used in farmland for soil remediation and improvement of soil quality; however, the effects of biochar amendment on the gut-associated ARGs of soil fauna remain unclear. In the present study, collembolans were cultivated in soils amended with 6 types of biochars. High-throughput qPCR was used to establish ARG profiles of the collembolan guts as well as the surrounding soils. A total of 73 and 162 subtypes of ARGs were detected in the collembolan guts and soils, respectively. Biochar amendment significantly altered the ARG compositions of the collembolan guts and soils, in a biochar quality-dependent manner. However, only manure-derived biochar, which contained elevated concentrations of heavy metals, increased the relative abundance of gut-associated ARGs. Changes in the gut microbial community, MGEs and biochar properties explained 84% of the total ARG variations in the collembolan guts. The findings of this study suggested that biochar properties should receive more attention, as high doses of heavy metals in biochar could increase the abundance of ARGs in collembolan guts, thereby contributing to the spread of ARGs in the environment through collembolan movement.

A review of bacteriophage therapy for pathogenic bacteria inactivation in the soil environment

The emerging contamination of pathogenic bacteria in the soil has caused a serious threat to public health and environmental security. Therefore, effective methods to inactivate pathogenic bacteria and decrease the environmental risks are urgently required. As a century-old technique, bacteriophage (phage) therapy has a high efficiency in targeting and inactivating pathogenic bacteria in different environmental systems. This review provides an update on the status of bacteriophage therapy for the inactivation of pathogenic bacteria in the soil environment. Specifically, the applications of phage therapy in soil-plant and soil-groundwater systems are summarized. In addition, the impact of phage therapy on soil functioning is described, including soil function gene transmission, soil microbial community stability, and soil nutrient cycling. Soil factors, such as soil temperature, pH, clay mineral, water content, and nutrient components, influence the survival and activity of phages in the soil. Finally, the future research prospects of phage therapy in soil environments are described.

Effect of antibiotic use and composting on antibiotic resistance gene abundance and resistome risks of soils receiving manure-derived amendments

Manure-derived amendments are commonly applied to soil, raising questions about whether antibiotic use in livestock could influence the soil resistome (collective antibiotic resistance genes (ARGs)) and ultimately contribute to the spread of antibiotic resistance to humans during food production. Here, we examined the metagenomes of soils amended with raw or composted manure generated from dairy cows administered pirlimycin and cephapirin (antibiotic) or no antibiotics (control) relative to unamended soils. Initial amendment (Day 1) with manure or compost significantly increased the diversity (richness) of ARGs in soils (p < 0.01) and resulted in distinct abundances of individual ARG types. Notably, initial amendment with antibiotic-manure significantly increased the total ARG relative abundances (per 16S rRNA gene) in the soils (2.21 × unamended soils, p < 0.001). After incubating 120 days, to simulate a wait period before crop harvest, 282 ARGs reduced 4.33-fold (median) up to 307-fold while 210 ARGs increased 2.89-fold (median) up to 76-fold in the antibiotic-manure-amended soils, resulting in reduced total ARG relative abundances equivalent to those of the unamended soils. We further assembled the metagenomic data and calculated resistome risk scores, which was recently defined as a relative index comparing co-occurrence of sequences corresponding to ARGs, mobile genetic elements, and putative pathogens on the same scaffold. Initial amendment of manure significantly increased the soil resistome risk scores, especially when generated by cows administered antibiotics, while composting reduced the effects and resulted in soil resistomes more similar to the background. The risk scores of manure-amended soils reduced to levels comparable to the unamended soils after 120 days. Overall, this study provides an integrated, high-resolution examination of the effects of prior antibiotic use, composting, and a 120-day wait period on soil resistomes following manure-derived amendment, demonstrating that all three management practices have measurable effects and should be taken into consideration in the development of policy and practice for mitigating the spread of antibiotic resistance.

Reducing water use by alternate-furrow irrigation with livestock wastewater reduces antibiotic resistance gene abundance in the rhizosphere but not in the non-rhizosphere

Livestock wastewater is rich in nutrients but may contain antibiotics and antibiotic resistance genes (ARGs). Their discharge to watercourses or soil may result in proliferation of ARGs. Irrigation with wastewater appears to be the most feasible option of disposing of it. One efficient irrigation technology used in arid regions is alternate-furrow irrigation (AFI) by alternately drying part of the plant roots for a prolonged period to physiologically reduce transpiration without compromising yield. However, the extent to which AFI with wastewater influences the concentration of antibiotics and spread of ARGs in soil is poorly understood. The purpose of this paper is to investigate how AFI using swine wastewater alters antibiotic kinetics and ARGs abundance under different irrigation rates, using pepper as the model plant. We examined three AFI treatments using 50%, 65% and 80% of the amount of water employed in sufficient conventional furrow irrigation. Each treatment had a groundwater irrigation control. The results showed that antibiotic concentrations and relative ARGs abundance in the top 20 cm of soil did not increase with the irrigation amount, although they were higher than those in the groundwater-irrigated soils. The relative ARGs abundance in the soil was modulated by irrigation amount and reducing the irrigation amount in AFI reduced ARGs dispersion only in rhizosphere. When the soil moisture was close to field capacity, ARGs were more abundant in rhizosphere than in non-rhizosphere, possibly because the rhizosphere is rich in microbes and increasing antibiotic concentrations due to an increase in irrigation rate favors antibiotic-resistant microbiome in competing for substrates. These, however, were not mirrored in the relative ARGs abundance in the roots. These results have important implications as it revealed that reducing the input of antibiotics and ARGs into soil with AFI does not necessarily reduce ARGs proliferation.