Effect of sulfadiazine-contaminated pig manure on the abundances of genes and transcripts involved in nitrogen transformation in the root-rhizosphere complexes of maize and clover

Recycling nitrogen from liquid digestate via novel reactive struvite and zeolite minerals to mitigate agricultural pollution

Recycling nutrients is of paramount importance. For this reason, struvite and nitrogen enriched zeolite fertilizers produced from wastewater treatments are receiving growing attention in European markets. However, their effects on agricultural soils are far from certain, especially struvite, which only recently was implemented in EU Fertilizing Product Regulations. In this paper, we investigate the effects of these materials in acid sandy arable soil, particularly focusing on N dynamics, evaluating potential losses, transformation pathways, and the effects of struvite and zeolitic tuffs on main soil biogeochemical parameters, in comparison to traditional fertilization with digestate. Liming effect (pH alkalinization) was observed in all treatments with varying intensities, affecting most of the soil processes. The struvite was quickly solubilized due to soil acidity, and the release of nutrients stimulated nitrifying and denitrifying microorganisms. Zeolitic tuff amendments decreased the NO_x gas emissions, which are precursors to the powerful climate altering N₂O gas, and the N enriched chabazite tuff also recorded smaller NH₃ emissions compared to the digestate. However, a high dosage of zeolites in soil increased NH₃ emissions after fertilization, due to pronounced pH shifts. Contrasting effects were observed between the two zeolitic tuffs when applied as soil amendments; while the chabazite tuff had a strong positive effect - increasing up to ∼90% the soil microbial N immobilization - the employed clinoptilolite tuff had immediate negative effects on the microbial biomass, likely due to the large quantities of sulphur released. However, when applied at lower dosages, the N enriched clinoptilolite also contributed to the increase of microbial N. From these outcomes, we confirm the potential of struvite and zeolites to mitigate the outfluxes of nutrients from agricultural systems. To gain the best results and significantly lower environmental impacts, extension practitioners could give recommendations based on the soils that are planned for zeolite application.

Microbially mediated Fe-N coupled cycling at different hydrological regimes in riparian wetland

Although the significance of the coupled Fe- and N- cycling processes on biogeochemical transformation in riparian wetlands is well-known, the regulation associated with the changes on the microbiotas during different hydrological regimes remains unclear. This study performed field investigations on the bacterial community compositions (BCC) and specific genera associated to Fe- and N- cycling in the rhizosphere soil and sediments in a riparian wetland in Poyang lake, China. The predominant phyla Proteobacteria, Acidobacteria, and Nitrospirae from all the samples remarkably decreased after long-term continuous flooding, while Actinobacteria, Firmicutes and Bacteroidetes were enriched. For the family level, the relative abundances of iron-oxidizing bacteria (FeOB) Gallionellaceae, and N fixing bacteria Nitrospiraceae and Bradyrhizobiaceae significantly declined upon the long-term flooding and then increased with dewatering, which were consistent with the functional genes sequencing analysis. In which, the Bradyrhizobiaceae (RA 2.0 %-34.6 %) was the dominant nirS denitrifier and potential iron-reducing bacteria (FeRB), Sideroxydans lithotrophicus was one of the dominant FeOB (RA 1.7 %-23 %), which was also identified to be the nirS dentrifier (RA 0.2 %-4.3 %). The absolute quantification of the functional genes levels including nirS, nirK, FeRB (Geobacter spp.) showed their significant increases by 3-7 times upon desiccation compared to that under post-CF. The PCA and RDA results indicated the linkage between redox changes of N and Fe during inundation mediated by FeRB, NOB, and FeOB, which were closely related to hydrochemical indices NO₃^-, Fe²⁺ and SO₄^2-. These evidences all implied the likely occurrence of nitrate reduction coupled to Fe(II) oxidation (NRFeOx) under oligotrophic conditions, which was potentially facilitated by metabolizers consisting of highly correlated Bradyrhizobiaceae and Sideroxydans (rho = 0.86, p < 0.01). These findings provide an interpretation of the biological reactions in the microbially mediated NRFeOx processes driven by hydrological change, which could assist the mechanistic understanding of the global biogeochemical cycles of iron and nitrogen in riparian wetlands.

Sulfonamide antibiotics alter gaseous nitrogen emissions in the soil-plant system: A mesocosm experiment and meta-analysis

Veterinary antibiotics are widely used in many countries worldwide to treat diseases and protect the health of animals. However, the effects of sulfonamide antibiotics introduced via manure and wastewater irrigation on nitrogen (N) loss in the soil-plant system remain poorly understood. Here, we conducted a pot experiment to assess the effects of sulfamethazine (SMZ) and its degradation product (2-amino-4,6-dimethylpyrimidine, ADPD) at four concentration gradients (i.e., 0, 1, 10, 100 mg kg^-1) on nitrous oxide (N₂O) and ammonia (NH₃) emissions, and the abundances of N-cycling functional genes and sulfonamide resistance genes. We also collated 350 observations from 62 published papers and performed a meta-analysis of antibiotic addition effects on N₂O emission and soil net nitrification and denitrification. Antibiotics additions showed an inhibitory effect on N₂O emissions, which accords with the trend of our meta-analysis showing a significant decrease of 32%. The decreased N₂O emissions were attributed to the significant reduction in the abundances of total bacterial communities, ammonia oxidizers, and nir-type denitrifiers and to the resultant changes in soil inorganic N. N₂O emissions did not differ between non-environmentally relevant concentrations for SMZ but lowered with increasing ADPD concentrations. This discrepancy can be explained by differential responses of the gene abundances of ammonia oxidizers and nirK-type denitrifiers and the development of antibiotic resistance genes in the highest concentration following antibiotic additions. Antibiotic additions increased soil NH₃ volatilization but did not affect vegetable yield. Therefore, these findings provide insight into how the prevalence of antibiotics in soils could alter the N-cycling process and associated gas emissions, with implications for understanding the ecological risks of antibiotics in agriculture.

Oxytetracycline Degrading Potential of Lysinibacillus sp. Strain 3+I Isolated from Poultry Manure

Oxytetracycline (OTC) which is a broad-spectrum veterinary tetracycline antibiotic is extensively used in poultry farms as a prophylactic, therapeutic, and growth stimulator. Upon administration, unmetabolized OTC is excreted from the animal body through droppings and accumulated in litter in the poultry industry. This study aimed at investigating the OTC degradation potential of an-OTC tolerant bacterial strain, isolated from poultry manure. The isolated strain's morphology, biochemical properties, and 16S ribosomal RNA (rRNA) gene sequence confirmed that it belonged to the Lysinibacillus genus. To measure the residual OTC concentration, a high-performance liquid chromatography method was used. OTC degradation rates were 2.579 mg L-1d-1 with Lysinibacillus strain 3+I and 1.149 mg L-1d-1 without Lysinibacillus strain 3+I. In the presence of strain 3+I, the half-life significantly reduced to 2.68 days, compared to 6.03 days without strain 3+I. The strain demonstrated 85% removal with the OTC concentration of 10 μg/ml. The influence of pH, temperature, carbon sources, and nitrogen source, which influence degradation, were also investigated. The optimum condition favouring degradation was pH 6 at a temperature of 30°C. In addition, Lysinibacillus sp. strain 3+I's ability to degrade OTC in poultry litter offers a promising approach to treat poultry manure and effluent containing OTC, preventing its contamination in the environment.

Effect of pig manure-derived sulfadiazine on species distribution and bioactivities of soil ammonia-oxidizing microorganisms after fertilization

To evaluate the effect of pig manure-derived sulfadiazine (SDZ) on the species distribution and bioactivities of ammonia-oxidizing microorganisms (AOMs), ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox) within the soil were investigated pre- and post-fertilization. Kinetic modeling and linear regression results demonstrated that the DT₅₀ value of different SDZ fractions under initial SDZ concentrations of 50 and 100 mg·kg^-1 exhibited the following trend: total SDZ>CaCl₂-extractable SDZ>MeOH-extractable SDZ, whereas their inhibiting effect on AOMs showed an opposite trend. qPCR analysis suggested that comammox was the predominant ammonia oxidizer in soils regardless of SDZ addition, accounting for as much as 77.2-94.7% of the total amoA, followed by AOA (5.3-22.5%), whereas AOB (<0.5%) was the lowest. The SDZ exhibited a significant effect on the AOM abundance. Specifically, SDZ exerted the highest inhibitory effect on comammox growth, followed by AOA, whereas negligible for AOB. The community diversity of AOMs within the pig manure-fertilized soils was affected by SDZ, and AOA Nitrososphaera cluster 3 played a key role in potential ammonia oxidation capacity (PAO) maintenance. This study provides new insights into the inhibition mechanisms of pig manure-derived antibiotics on AOMs within the fertilized soil.

Oxytetracycline and Ciprofloxacin Exposure Altered the Composition of Protistan Consumers in an Agricultural Soil

Protists, an integral component of soil microbiome, are one of the main predators of bacteria. Bacteria can produce toxic secondary metabolites, e.g., antibiotics to fight stress under the predation pressure of protists; however, impacts of antibiotics on the profile of protists in soils remain unclear. Here, we constructed a microcosm incubation to investigate the effects of two common antibiotics, oxytetracycline and ciprofloxacin, on the protistan and bacterial communities in an arable soil. Rhizaria were the most abundant protist supergroup, followed by Amoebozoa, Stramenopiles, and Aveolata. Among trophic functional groups, consumers were predominant within the protistan community. The protistan alpha-diversity was not significantly changed, while the bacterial alpha-diversity was decreased under the pressure of antibiotics. Nevertheless, the antibiotic exposure considerably reduced the relative abundance of protistan lineages in Rhizaria and Amoebozoa, which were the dominant supergroups of protistan consumers, while increased the relative abundance of other consumer and phototrophic protists. Altogether, we provide novel experimental evidence that the bacterivorous consumers, an important functional group of protists, were more sensitive to antibiotics than other functional groups. Our findings have potential implications for the induced alterations of protistan community and their ecological functions under the scenarios of projected increasing global antibiotic usage.

Differential responses of encoding-amoA nitrifiers and nir denitrifiers in activated sludge to anatase and rutile TiO2 nanoparticles: What is active functional guild in rate limiting step of nitrogen cycle?

The long-terms effects of different crystal-composition TiO₂ nanoparticles (NPs) on nitrogen-cycle-related functional guilds in activated sludge remain unclear, especially under natural light irradiation. Accordingly, activated sludge was exposed to anatase TiO₂-NPs (TiO₂-A) and rutile TiO₂-NPs (TiO₂-R) for up to 45 days. With markedly (p < 0.05) reducing nitrification-/denitrification-enzymatic-activities and abundances of ammonia-oxidizing-microorganisms (AOMs) and nitrite-reducing-bacteria (NRB), TiO₂-NPs triggered bacteria and archaea UPGMA clustering and a deep modification of N-cycling functional diversity guided by crystal structure. in situ¹³C-DNA-SIP confirmed ammonia-oxidizing-bacteria (AOB) (Nitrosomonas and Nitrosospira) in original sludge as main active AOMs with 75.4 times more abundance than ammonia-oxidizing-archaea (AOA), while AOA within Nitrosopumilus and Nitrososphaera genera were the main active AOMs and tended to aggregate inside sludge after 10-mg/L TiO₂-NPs exposure. Encoding-nirK NRB were more sensitive, while encoding-nirS Zoogloea with a total share of 4.97% to 14.93%, etc. were the main active NRB. AOB was more sensitive to TiO₂-A, while TiO₂-R showed the stronger toxicity to AOA and NRB resulting from differences in water environmental behaviors and crystal characteristics of two TiO₂-NPs. This work expands understanding of the ecological risks of titanium-dioxide-crystal-NPs in aquatic environment and may help devise better methods to alleviate environmental stress caused by NPs at wastewater treatment plants.

Fate and behaviour of veterinary sulphonamides under denitrifying conditions

Antibiotics are among the most widely administered drugs in the growing animal food industry. Of all the antibiotics approved for agriculture, sulphonamides are of particular interest. Their spectrum of activity is broad, affecting gram-positive, gram-negative, and many protozoal organisms, and they have been used for the treatment of a wide variety of animals. Animal manure is one of primary sources of soil contamination by sulphonamides. As they have a low soil sorption potential and are therefore highly mobile in soil, they can be transported to groundwater. In the present study, papers dealing with the fate and behaviour of veterinary sulphonamides under denitrifying conditions often arising in the subsurface are reviewed. Veterinary sulphonamide-exposed conditions can result in either inhibition or stimulation of the denitrification process owing to their toxicity or stress for denitrifiers. The effect of sulphonamides on individual denitrification steps is unbalanced, which can cause accumulation of process intermediates (dinitrogen oxide, nitrites). Although research results related to veterinary sulphonamide biodegradation in a nitratereducing environment show great variety, they indicate that these compounds are biodegradable under denitrifying conditions, that their biodegradation fits the first-order kinetics model, and that microbial action is the main mechanism of their dissipation. Regarding biodegradation pathways, research to date has only focused on sulfamethoxazole. Its degradation is driven by the presence of nitrous acid, which is formed from nitrites generated by the denitrification process as an intermediate product. Nevertheless, sulfamethoxazole degradation is abiotic, meaning that it does not participate in the denitrifying metabolism. For the formation of sulfamethoxazole transformation products, including its nitro, nitroso and desamino derivatives, the presence of the primary aromatic amine group is key. As this functional group is common for all sulphonamides, it can be assumed that these transformation products are also involved in the degradation pathways of other sulphonamides.

Insight into the nitrification kinetics and microbial response of an enriched nitrifying sludge in the biodegradation of sulfadiazine

The intensive use of antibiotics results in the continuous release of antibiotics into wastewater treatment systems, leading to the spread of antibiotic resistance. Nitrifying system is reported to be capable of degrading antibiotics, yet few studies have systematically investigated the inherent correlation among ammonium oxidation rate, antibiotic degradation and genetic expression of nitrifying bacteria along the process. This study selected a widely used sulfonamide antibiotic, sulfadiazine (SDZ), to investigate its biodegradation potential by an enriched nitrifying culture and the response of nitrifying bacteria against antibiotic exposure. Our results demonstrated that SDZ degradation was mainly contributed by cometabolism of ammonia-oxidizing bacteria (AOB), rather than biomass adsorption. The quantitative reverse transcription PCR (RT-qPCR) analysis revealed that the expression level of amoA gene was down-regulated due to the SDZ exposure. In addition, the degradation products of SDZ did not exhibit inhibitory effect on Escherichia coli K12, indicating the biotoxicity of SDZ could be mitigated after biodegradation. The findings offer insights regarding the biodegradation process of sulfonamide antibiotics via cometabolism by AOB.

Separate and joint eco-toxicological effects of sulfadimidine and copper on soil microbial biomasses and ammoxidation microorganisms abundances

Heavy metals and antibiotics residues in agricultural soils are attracting more and more attention. A laboratory study was conducted to evaluate the single and combined effects of sulfadimidine (SM2) (0.05, 0.20, 0.80 mmol/kg) and copper (Cu) (1.60 mmol/kg) on soil microbial biomasses and ammoxidation microorganisms abundances after 7, 14, 21 and 28 days. The results demonstrated that the single and combined contaminations had a significant and persistent inhibitory effect on soil bacteria, fungi and actinomycetes populations and amoA gene copies of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) (Except SM2 0.05 and 0.20 mmol/kg on 7 and 14 d and SM2 0.05 mmol/kg on 21 d led to a stimulatory effect on fungi and AOA-amoA gene, respectively). With higher dosage and longer exposure time, the toxic effect of single and combined contaminants on soil bacteria, fungi and actinomycetes as well as on the amoA gene of AOA and AOB was greatly reinforced. Combined contaminants produced more toxicity than the chemicals were used alone. Overall, the interaction effects of SM2 and Cu on bacteria (on 14, 21 and 28 d), fungi and AOA-amoA were mainly synergism, in contrast, on actinomycetes (on 14, 21 and 28 d) and AOB-amoA were mainly antagonism. The order of the toxic effects of the single Cu and combined contaminants on microbial activity was: bacteria > actinomycetes > fungi. Furthermore, AOB-amoA was more sensitive to both contaminants toxicity than AOA-amoA, while AOA-amoA gene copies were greater than AOB-amoA gene copies about one order of magnitude.

Symbiotic Nitrogen Fixation in Soil Contaminated with the Veterinary Antibiotics Oxytetracycline and Sulfamethazine

Veterinary and growth-promoting antibiotics are widely used in animal husbandry and accumulate in manure-fertilized soils. However, the impact of these antibiotics on symbiotic nitrogen fixation is poorly understood. We investigated the effect of the veterinary antibiotics oxytetracycline and sulfamethazine, and a combination of both, on nitrogen fixation in alfalfa ( L.) inoculated with . In a pot experiment, was grown in soils fertilized with fresh manure that contained environmentally relevant antibiotic concentrations (0.2, 2, and 200 mg kg). Nodulation, nitrogen fixation, and nutrient concentrations were determined in the alfalfa plants and soils after 12 wk. Compared with the antibiotic-free control, symbiotic nitrogen fixation increased significantly in soils mixed with manure containing 2 and 200 mg kg oxytetracycline (20.1 and 20.8% increase, respectively) and a mixture of 200 mg kg oxytetracycline and sulfamethazine (12.4% increase). The measured plant- and soil-related parameters failed to explain the observed increase in nitrogen fixation. However, using concentration levels that accurately reflect common agricultural practices, we obtained results that directly contradict other experiments conducted under unrealistically high antibiotic concentrations.

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

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

Potential of Wheat Straw, Spruce Sawdust, and Lignin as High Organic Carbon Soil Amendments to Improve Agricultural Nitrogen Retention Capacity: An Incubation Study

Plants like winter wheat are known for their insufficient N uptake between sowing and the following growing season. Especially after N-rich crops like oilseed rape or field bean, nitrogen retention of the available soil N can be poor, and the risk of contamination of the hydrosphere with nitrate (NO3-) and the atmosphere with nitrous oxide (N2O) is high. Therefore, novel strategies are needed to preserve these unused N resources for subsequent agricultural production. High organic carbon soil amendments (HCA) like wheat straw promote microbial N immobilization by stimulating microbes to take up N from soil. In order to test the suitability of different HCA for immobilization of excess N, we conducted a laboratory incubation experiment with soil columns, each containing 8 kg of sandy loam of an agricultural Ap horizon. We created a scenario with high soil mineral N content by adding 150 kg NH4+-N ha-1 to soil that received either wheat straw, spruce sawdust or lignin at a rate of 4.5 t C ha-1, or no HCA as control. Wheat straw turned out to be suitable for fast immobilization of excess N in the form of microbial biomass N (up to 42 kg N ha-1), followed by sawdust. However, under the experimental conditions this effect weakened over a few weeks, finally ranging between 8 and 15 kg N ha-1 immobilized in microbial biomass in the spruce sawdust and wheat straw treatment, respectively. Pure lignin did not stimulate microbial N immobilization. We also revealed that N immobilization by the remaining straw and sawdust HCA material in the soil had a greater importance for storage of excess N (on average 24 kg N ha-1) than microbial N immobilization over the 4 months. N fertilization and HCA influenced the abundance of ammonia oxidizing bacteria and archaea as the key players for nitrification, as well as the abundance of denitrifiers. Soil with spruce sawdust emitted more N2O compared to soil with wheat straw, which in relation released more CO2, resulting in a comparable overall global warming potential. However, this was counterbalanced by advantages like N immobilization and mitigation of potential NO3- losses.

Toxic effects of oxytetracycline and copper, separately or combined, on soil microbial biomasses

The production of commercial livestock and poultry often involves using with antibiotics and feed additives, such as oxytetracycline (OTC) and copper (Cu). These are often excreted into the soil by animal feces; hence, combined pollutants may contaminate the soil. To evaluate single and combined toxic effects of OTC and Cu on the soil ecology, changes in quantities of bacteria, fungi, and actinomycetes in the soil were studied over a 28-d incubation period by a plate count method, microbes numbers counted on days 7, 14, 21, and 28. Abundances of ammonia monooxygenase (amoA) gene expression by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in soil samples also were tested by real-time polymerase chain reactions (RT-PCRs) on day 21. The results revealed that the numbers of bacteria, fungi and actinomycetes and amoA genes copies of AOA and AOB were reduced seriously by exposure to Cu (1.60 mmol/kg). Similarly, the combined pollution treatments (mole ratios of OTC: Cu was 1:2, 1:8, and 1:32) also had inhibitory effect on bacteria, fungi, and actinomycetes numbers and amoA gene copies of AOA and AOB; the inhibitory rate was on obvious growth trend with the increasing mole ratios. Effects from single OTC pollution were found on bacteria (days 7 and 14), fungi (days 7, 14, 21, and 28), and AOA-amoA gene copies (day 21), with promotion at a low concentration (0.05 mmol/kg) and suppression at higher concentrations (0.2 and 0.8 mmol/kg). Also, numbers of bacteria, fungi, and actinomycetes decreased with longer culture times. Combining OTC and Cu led to a higher inhibition of soil microbes than when either chemical was used alone. However, there was no significant relationship between single and combined toxic chemicals because of their complicated interactions, either antagonistic or synergistic. The results also indicated the sensitivity of bacteria, fungi, actinomycetes on toxic chemicals existed difference and that the AOA were more tolerant than the AOB to these chemicals.

Aquatic toxicity of ivermectin in cattle dung assessed using microcosms

Ivermectin (IVM) is a parasiticide widely used for livestock. It is a semisynthetic derivative of avermectin, a macrocyclic lactone produced by Streptomyces avermitilis. This drug is only partly metabolized by livestock; considerable amounts of parent drug are excreted mostly via feces. To simulate exposure of aquatic invertebrates and macrophytes to direct excretion of cattle dung into surface waters, a microcosm experiment with IVM spiked in cattle dung was conducted. The objectives of this study were to characterize accumulation of IVM in water, sediment+dung, roots of the floating fern Salvinia and the zooplankton Ceriodaphnia dubia, the amphipod Hyalella and the apple snail Pomacea; to determine the effect of this drug spiked in cattle dung on life-history traits of these invertebrates; and to evaluate the influence of IVM on aquatic nutrient cycling. Dung was spiked with IVM to attain concentrations of 1150, 458, 50 and 22µgkg^-1dung fresh weight, approximating those found in cattle dung at days 3, 7, 16 and 29 following subcutaneous injection. Concentrations found in dung during the first week of excretion were lethally toxic to Ceriodaphnia dubia and Hyalella, whereas no mortality was observed in Pomacea. Concentrations of IVM in roots, sediment + dung and Pomacea increased significantly from the lowest to the highest treatment level. The effect of this drug on decomposition and release of nutrients from dung would have negative consequences for nutrient cycling in water. Increasing concentrations in sediment + dung with days of the experiment suggested that toxic concentrations would persist for an extended period in the water-sediment system. IVM represents an ecological risk for aquatic ecosystems, underscoring the need for livestock management strategies to limit its entry into water bodies.

Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities

Maize inoculation by Azospirillum stimulates root growth, along with soil nitrogen (N) uptake and root carbon (C) exudation, thus increasing N use efficiency. However, inoculation effects on soil N-cycling microbial communities have been overlooked. We hypothesized that inoculation would (i) increase roots-nitrifiers competition for ammonium, and thus decrease nitrifier abundance; and (ii) increase roots-denitrifiers competition for nitrate and C supply to denitrifiers by root exudation, and thus limit or benefit denitrifiers depending on the resource (N or C) mostly limiting these microorganisms. We quantified (de)nitrifiers abundance and activity in the rhizosphere of inoculated and non-inoculated maize on 4 sites over 2 years, and ancillary soil variables. Inoculation effects on nitrification and nitrifiers (AOA, AOB) were not consistent between the three sampling dates. Inoculation influenced denitrifiers abundance (nirK, nirS) differently among sites. In sites with high C limitation for denitrifiers (i.e. limitation of denitrification by C > 66%), inoculation increased nirS-denitrifier abundance (up to 56%) and gross N2O production (up to 84%), likely due to increased root C exudation. Conversely, in sites with low C limitation (<47%), inoculation decreased nirS-denitrifier abundance (down to -23%) and gross N2O production (down to -18%) likely due to an increased roots-denitrifiers competition for nitrate.

4-nitroso-sulfamethoxazole generation in soil under denitrifying conditions: Field observations versus laboratory results

The formation of 4-nitroso-sulfamethoxazole and 4-nitro-SMX, two transformation products (TPs) of sulfamethoxazole (SMX) was investigated under batch soil slurry experiments and in a field study. Due to their low occurrence levels (ng/L) in environmental waters, a suitable analytical method based on liquid chromatography - high resolution - mass spectrometry was developed. Consequently, field observations revealed, for the first time, the occurrence of 4-nitroso-SMX in groundwater at concentrations as high as 18ng/L.Nitric oxide (NO) steady-state concentrations were determined in soil slurry experiments because this reactive specie accounted for the formation of 4-nitroso-SMX and 4-nitro-SMX. Measurements revealed that environmental SMX concentrations (0.2-2μg/L) at neutral pH induced the accumulation of nitric oxide. Under acidic conditions (pH<6), nitrous acid (HONO) was the major source of nitric oxide while under neutral/basic conditions nitric oxide release was related to the inhibition of denitrification processes. Under laboratory experiments, SMX nitration reaction appeared to be an irreversible transformation pathway, while 4-nitroso-SMX was slowly transformed over time. The occurrence of 4-nitroso-SMX conditions was therefore unexpected in the field study but could be due to its continuous input from soil and/or its relative persistence under anoxic conditions. A mechanism for 4-nitroso-SMX formation was proposed involving a nitrosative desamination pathway through a phenyl radical.

Impact of Veterinary Pharmaceuticals on the Agricultural Environment: A Re-inspection

The use of veterinary pharmaceuticals (VPs) is a result of growing animal production. Manure, a great crop fertilizer, contains a significant amount of VPs. The investigation of VPs in manure is prevalent, because of the potential risk for environmental organisms, as well as human health. A re-evaluation of the impact of veterinary pharmaceuticals on the agricultural environment is needed, even though several publications appear every year. The aim of this review was to collate the data from fields investigated for the presence of VPs as an inevitable component of manure. Data on VP concentrations in manure, soils, groundwater and plants were collected from the literature. All of this was connected with biotic and abiotic degradation, leaching and plant uptake. The data showed that the sorption of VPs into soil particles is a process which decreases the negative impact of VPs on the microbial community, the pollution of groundwater, and plant uptake. What was evident was that most of the data came from experiments conducted under conditions different from those in the environment, resulting in an overestimation of data (especially in the case of leaching). The general conclusion is that the application of manure on crop fields leads to a negligible risk for plants, bacteria, and finally humans, but in future every group of compounds needs to be investigated separately, because of the high divergence of properties.

Improvement of the soil nitrogen content and maize growth by earthworms and arbuscular mycorrhizal fungi in soils polluted by oxytetracycline

Interactions between earthworms (Eisenia fetida) and arbuscular mycorrhizal fungi (Rhizophagus intraradices, AM fungi) have been suggested to improve the maize nitrogen (N) content and biomass and were studied in soils polluted by oxytetracycline (OTC). Maize was planted and amended with AMF and/or earthworms (E) in the soil with low (1mgkg(-1) soil DM) or high (100mgkg(-1) soil DM) amounts of OTC pollution in comparison to soil without OTC. The root colonization, shoot and root biomass, shoot and root N contents, soil nitrogen forms, ammonia-oxidizing bacteria (AOB) and archaea (AOA) were measured at harvest. The results indicated that OTC decreased maize shoot and root biomass (p<0.05) by mediating the soil urease activity and AOB and AOA abundance, which resulted in a lower N availability for maize roots and shoots. There was a significant interaction between earthworms and AM fungi on the urease activity in soil polluted by OTC (p<0.05). Adding earthworms or AM fungi could increase the maize biomass and N content (p<0.05) in OTC polluted soil by increasing the urease activity and relieving the stress from OTC on the soil N cycle. AM fungi and earthworms interactively increased maize shoot and root biomass (p<0.05) in the OTC polluted soils through their regulation of the urease activity and the abundance of ammonia oxidizers, resulting in different soil NH4(+)-N and NO3(-)-N contents, which may contribute to the N content of maize shoots and roots. Earthworms and AM fungi could be used as an efficient method to relieve the OTC stress in agro-ecosystems.

Prophylactic Bacteriophage Administration More Effective than Post-infection Administration in Reducing Salmonella enterica serovar Enteritidis Shedding in Quail

Infections caused by Salmonella bacteria, often through poultry products, are a serious public health issue. Because of drawbacks associated with antibiotic prophylaxis, alternative treatments are sought. Bacterial viruses (bacteriophages) may provide an effective alternative, but concerns remain with respect to bacteriophage stability and effectiveness. To this end, we assessed the stability of a novel bacteriophage isolated from poultry excreta, siphovirus PSE, and its effectiveness in reducing Salmonella enterica serovar Enteritidis colonization in vitro and in vivo. Moreover, we sought to determine how the timing (prophylactic or therapeutic) and route (oral gavage or vent lip) of PSE administration impacted its effectiveness. Here we report that significant quantities of viable PSE bacteriophages were recovered following exposure to high and low pH, high temperatures, and bile salts, testifying to its ability to survive extreme conditions. In addition, we found that ileal lactic acid bacteria and Streptococcus spp. counts increased, but colibacilli and total aerobe counts decreased, in quail receiving phage PSE through both oral gavage and vent lip routes. In other experiments, we assessed the efficiency of PSE administration, in both prophylactic and therapeutic contexts, via either oral gavage or vent lip administration, on S. Enteritidis colonization of quail cecal tonsils. Our results demonstrate that administration of PSE as a preventive agent could reduce the S. Enteritidis colonization more effectively than post-challenge administration. Furthermore, oral administration of PSE phage is a more effective prophylactic tool for reduction of S. Enteritidis shedding in poultry than is vent lip administration.

Variations in the fate and biological effects of sulfamethoxazole, norfloxacin and doxycycline in different vegetable-soil systems following manure application

The fate of sulfamethoxazole (SMZ), norfloxacin (NOR) and doxycycline (DOX) and their biological effects in radish and pakchoi culture systems were investigated. DOX dissipated more rapidly than SMZ and NOR, while radish and pakchoi cultivation increased the removal of residual DOX in soils. Dissipation of NOR was accelerated in radish soils but was slowed down slightly in pakchoi soils. Vegetable cultivation exerted an insignificant effect on SMZ removal. Investigation of antibiotic bioaccumulation showed that the uptake of DOX by radish and pakchoi was undetectable, but the radish accumulated more SMZ and NOR than pakchoi. Among the three antibiotics, only SMZ use exhibited an apparent suspension of plant seed germination, up-ground plant growth and soil microbial diversity. Pakchoi responded more sensitively to SMZ than did the radish. Principal component analysis (PCA) based on MicroRESP™ indicated that the sampling time and antibiotic treatments could influence the soil microbial community. Only in the pakchoi soils did antibiotic application exert a more robust effect on the microbial community than the sampling time; SMZ treatments and DOX treatments could be clearly discriminated from the control treatments. These results are crucial for an assessment of the potential risks of antibiotics to culture system practices and suggest that good agricultural practices help to limit or even reduce antibiotic pollution.

Interspecific differences in growth response and tolerance to the antibiotic sulfadiazine in ten clonal wetland plants in South China

Pollution caused by residual antibiotics is a worldwide environmental issue. Antibiotic residues often occur in aquatic ecosystems, posing threats to the health of aquatic organisms. The effects of antibiotic residues on the growth of crop plants and on human health are reasonably well known. However, less is known about antibiotic effects on wetland plants. Therefore, we studied the response and tolerance of ten clonal wetland plants grown in soil spiked with sulfadiazine at 10 mg kg(-1) (an environmentally relevant concentration) and 100 mg kg(-1). At 10 mg kg(-1), ramet number was the least affected trait, while root number was the most affected among plant species. Plant shoot and total biomass were reduced in all species except in Cyperus malaccensis var. brevifolius and Panicum repens. Chlorophyll content was reduced in Alocasia macrorrhiza, Saururus chinensis, and Commelina diffusa. In general, Panicum paludosum and C. malaccensis var. brevifolius showed the least reduction of growth parameters, whereas growth of both A. macrorrhiza and S. chinensis was severely reduced. At 100 mg kg(-1), negative responses occurred in all species. Comprehensive tolerance analysis revealed that P. paludosum and C. malaccensis var. brevifolius were the species most resistant to sulfadiazine. These species are potential candidates for sulfadiazine polluted wetland restoration. A. macrorrhiza and S. chinensis were the most susceptible species and they should be protected from sulfadiazine pollution. Relative plant shoot biomass and height were the most useful indicators for evaluating plant tolerance to sulfadiazine. Plant tolerance to sulfadiazine was associated with the differences of plants in height and shoot biomass.

Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms

Antibiotics play a pivotal role in the management of infectious disease in humans, companion animals, livestock, and aquaculture operations at a global scale. Antibiotics are produced, consumed, and released into the environment at an unprecedented scale causing concern that the presence of antibiotic residues may adversely impact aquatic and terrestrial ecosystems. Here we critically review the ecotoxicological assessment of antibiotics as related to environmental risk assessment (ERA). We initially discuss the need for more specific protection goals based on the ecosystem service concept, and suggest that the ERA of antibiotics, through the application of a mode of toxic action approach, should make more use of ecotoxicological endpoints targeting microorganisms (especially bacteria) and microbial communities. Key ecosystem services provided by microorganisms and associated ecosystem service-providing units (e.g. taxa or functional groups) are identified. Approaches currently available for elucidating ecotoxicological effects on microorganisms are reviewed in detail and we conclude that microbial community-based tests should be used to complement single-species tests to offer more targeted protection of key ecosystem services. Specifically, we propose that ecotoxicological tests should not only assess microbial community function, but also microbial diversity (‘species’ richness) and antibiotic susceptibility. Promising areas for future basic and applied research of relevance to ERA are highlighted throughout the text. In this regard, the most fundamental knowledge gaps probably relate to our rudimentary understanding of the ecological roles of antibiotics in nature and possible adverse effects of environmental pollution with subinhibitory levels of antibiotics.

Exposure to vancomycin causes a shift in the microbial community structure without affecting nitrate reduction rates in river sediments

Antibiotics and antibiotic resistance genes have shown to be omnipresent in the environment. In this study, we investigated the effect of vancomycin (VA) on denitrifying bacteria in river sediments of a Waste Water Treatment Plant, receiving both domestic and hospital waste. We exposed these sediments continuously in flow-through reactors to different VA concentrations under denitrifying conditions (nitrate addition and anoxia) in order to determine potential nitrate reduction rates and changes in sedimentary microbial community structures. The presence of VA had no effect on sedimentary nitrate reduction rates at environmental concentrations, whereas a change in bacterial (16S rDNA) and denitrifying (nosZ) community structures was observed (determined by polymerase chain reaction-denaturing gradient gel electrophoresis). The bacterial and denitrifying community structure within the sediment changed upon VA exposure indicating a selection of a non-susceptible VA population.

Sulfadiazine uptake and effects in common hazel (Corylus avellana L.)

Soil contamination by antibiotics is a possible consequence of animal husbandry waste, sewage sludge, and reclaimed water spreading in agriculture. In this study, 1-year-old hazel plants (Corylus avellana L.) were grown in pots for 64 days in soil spiked with sulfadiazine (SDZ) in the range 0.01-100 mg kg(-1) soil. Leaf gas exchanges, fluorescence parameters and plant growth were measured regularly during the experiment, whereas plant biomass, sulfonamide concentrations in soil and plant tissues, and the quantitative variation of culturable bacterial endophytes in leaf petiole were analyzed at the end of the trial. During the experiment, photosynthesis and leaf transpiration as well as fluorescence parameters were progressively reduced by the antibiotic. Effects were more evident for leaf transpiration and for the highest SDZ spiking concentrations, whereas growth analyses did not reveal negative effects of the antibiotic. At the end of the trial, a high number of culturable endophytic bacteria in the leaf petiole of plants treated with 0.1 and 0.01 mg kg(-1) were observed, and SDZ was extractable from soil and plant roots for spiking concentrations ≥1 mg kg(-1). Inside plants, the antibiotic was mainly stored at the root level with bioconcentration factors increasing with the spiking dose, and the hydroxylated derivate 4-OH-SDZ was the only metabolite detected. Overall results show that 1-year-old hazel plants can contribute to the reduction of sulfonamide concentrations in the environment, however, sensitive reactions to SDZ can be expected at the highest contamination levels.

Nitrogen removal capacity of the river network in a high nitrogen loading region

Denitrification is the primary process that regulates the removal of bioavailable nitrogen (N) from aquatic ecosystems. Quantifying the capacity of N removal from aquatic systems can provide a scientific basis for establishing the relationship between N reduction and water quality objectives, quantifying pollution contributions from different sources, as well as recommending control measures. The Lake Taihu region in China has a dense river network and heavy N pollution; however, the capacity for permanent N removal by the river network is unknown. Here, we concurrently examined environmental factors and net N2 flux from sediments of two rivers in the Lake Taihu region between July 2012 and May 2013, using membrane inlet mass spectrometry, and then established a regression model incorporating the highly correlated factors to predict the N removal capacity of the river network in the region. To test the applicability of the regression model, 21 additional rivers surrounding Lake Taihu were sampled between July and December 2013. The results suggested that water nitrate concentrations are still the primary controlling factor for net denitrification even in this high N loading river network, probably due to multicollinearity of other relevant factors, and thus can be used to predict N removal from aquatic systems. Our established model accounted for 78% of the variability in the measured net N2 flux in these 21 rivers, and the total N removed through N2 production by the river network was estimated at 4 × 10(4) t yr(-1), accounting for about 43% of the total aquatic N load to the river system. Our results indicate that the average total N content in the river water discharged into Lake Taihu would be around 5.9 mg of N L(-1) in the current situation, far higher than the target concentration of 2 mg of N L(-1), given the total N load and the N removal capacity. Therefore, a much stronger effort is required to control the N pollution of the surface water in the region.

Soil microbial systems respond differentially to tetracycline, sulfamonomethoxine, and ciprofloxacin entering soil under pot experimental conditions alone and in combination

This study investigated soil microbial responses to the application of tetracycline (TC), sulfamonomethoxine (SMM), and ciprofloxacin (CIP) alone and in combination in a soil culture pot experiment conducted at Hangzhou, China. Multiple approaches were applied for a better and complete depiction. Among the three antibiotics, SMM has a lowest dissipation and shows a most dramatic inhibition on microbial community and metabolism diversity. The combined application (AM) of SMM, CIP, and TC improved the dissipation of each antibiotic; similarly, SMM- and CIP-resistant bacteria showed larger populations in the AM than all single applications. Soils accumulated a large content of NO3-N at day 20 after multi-antibiotics perturbation. All antibiotics stimulated soil basal respirations and inhibited soil metabolism diversity, whereas the interruption exerted by SMM and AM lasted for a longer time. Six nitrogen-cycling genes including chiA, amoA, nifH, nirK, nirS, and narG were quantified and found to decrease owing to both single- and multi-antibiotics perturbation. Overall, AM was most interruptive for soils, followed by SMM perturbation, while other antibiotics could be less interruptive. These results provide systematic insights into how soil microbial systems would shift under each single- or multi-antibiotics perturbation.

Soil microbial community responses to antibiotic-contaminated manure under different soil moisture regimes

Sulfadiazine (SDZ) is an antibiotic frequently administered to livestock, and it alters microbial communities when entering soils with animal manure, but understanding the interactions of these effects to the prevailing climatic regime has eluded researchers. A climatic factor that strongly controls microbial activity is soil moisture. Here, we hypothesized that the effects of SDZ on soil microbial communities will be modulated depending on the soil moisture conditions. To test this hypothesis, we performed a 49-day fully controlled climate chamber pot experiments with soil grown with Dactylis glomerata (L.). Manure-amended pots without or with SDZ contamination were incubated under a dynamic moisture regime (DMR) with repeated drying and rewetting changes of >20 % maximum water holding capacity (WHCmax) in comparison to a control moisture regime (CMR) at an average soil moisture of 38 % WHCmax. We then monitored changes in SDZ concentration as well as in the phenotypic phospholipid fatty acid and genotypic 16S rRNA gene fragment patterns of the microbial community after 7, 20, 27, 34, and 49 days of incubation. The results showed that strongly changing water supply made SDZ accessible to mild extraction in the short term. As a result, and despite rather small SDZ effects on community structures, the PLFA-derived microbial biomass was suppressed in the SDZ-contaminated DMR soils relative to the CMR ones, indicating that dynamic moisture changes accelerate the susceptibility of the soil microbial community to antibiotics.

Chronic exposure of river sediments to environmentally relevant levels of tetracycline affects bacterial communities but not denitrification rates

The effects of tetracycline (TC) at chronic sub-inhibitory exposure concentrations on benthic denitrification rates and bacterial communities were explored. River sediments were continuously exposed to different TC concentrations (0.5, 20 and 10,000 μg L(-1)) for 2 weeks in flow-through reactors allowing denitrification and bacterial growth conditions. Bacterial communities were fingerprinted by Denaturing Gradient Gel Electrophoresis of 16S rRNA gene amplification products. Cultivable denitrifiers enriched from the sediment were tested for TC resistance (2-128 mg L(-1)). Denitrification rates were unaffected by exposure to TC, regardless of concentration. In contrast, the bacterial community composition changed significantly from sub-inhibitory (ng-μg L(-1)) to therapeutic (mg L(-1)) exposure concentrations. Furthermore the cultivable denitrifiers showed a high TC sensitivity (<4 mg L(-1)). Maintenance of efficient benthic denitrification rates, even at the highest level of TC exposure most likely originated from an adaptation of the autochthonous bacterial community where dominant species become those that acquire, or already have resistance to antibiotics.

Effects of roxithromycin on ammonia-oxidizing bacteria and nitrite-oxidizing bacteria in the rhizosphere of wheat

In a pot-cultural experiment, the impact of the antibiotic roxithromycin (ROX) addition was assessed on the diversities of microbial structure and function communities, especially involved in ammonia and nitrite oxidation in wheat rhizosphere soil with and without the addition of earthworms. The abundances of ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), and total bacteria were surveyed by the quantitative PCR. The quantities of total bacteria, AOB, and NOB with earthworms were higher than those without earthworms because of the synergistic effect. ROX inhibited the growth of AOB in all treatments, although the quantities of AOB were in a light increase in medium and heavy polluted treatments compared with that in the light polluted treatments. Different from AOB, the quantities of NOB were lowest in light polluted treatments, but the quantities of NOB were rapidly increased in medium and heavy polluted treatments compared with that in the control. These results indicated that the application of ROX principally had a negative effect on nitrification performance by affecting the abundances and relative ratios of both AOB and NOB in soil communities, which affected the N cycle in an agricultural ecosystem. According to the metabolic diversities evaluated by the biologic assay, the tendency of metabolic diversities was quite contrary to the quantities of NOB in all treatments and showed the contrast growing relation of autotrophic and heterotrophic bacteria under ROX pollution pressure in agricultural ecosystems.

Effects of repeated application of sulfadiazine-contaminated pig manure on the abundance and diversity of ammonia and nitrite oxidizers in the root-rhizosphere complex of pasture plants under field conditions

In a field experiment, the impact of repeated application of the antibiotic sulfadiazine (SDZ)-contaminated pig manure was assessed on functional microbial communities involved in ammonia and nitrite oxidation in the root-rhizosphere complexes (RRCs) of diverse plants composing a pasture. We surveyed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) as well as Nitrobacter- and Nitrospira-like nitrite-oxidizing bacteria (NOB) by quantitative PCR (qPCR), and the diversity of amoA AOA and Nitrobacter-like nxrA amplicons using a cloning-sequencing approach. Whereas the first SDZ-contaminated manure application caused only slight effects on the investigated microbial communities and did not change the diversity and abundance pattern significantly, the second application of SDZ-contaminated manure induced an up to 15-fold increased ratio of AOA:AOB and a reduction of nrxA genes. The diversity of AOA amoA increased after the second application of SDZ-contaminated manure compared to the control treatment whereas a clear reduction of nrxA OTUs was visible in the same samples. The results indicate that the application of SDZ may principally affect nitrite oxidation by NOB and alternative pathways like nitrite reduction might be favored under these conditions.

Biodegradation of ciprofloxacin in water and soil and its effects on the microbial communities

While antibiotics are frequently found in the environment, their biodegradability and ecotoxicological effects are not well understood. Ciprofloxacin inhibits active and growing microorganisms and therefore can represent an important risk for the environment, especially for soil microbial ecology and microbial ecosystem services. We investigated the biodegradation of (14)C-ciprofloxacin in water and soil following OECD tests (301B, 307) to compare its fate in both systems. Ciprofloxacin is recalcitrant to biodegradation and transformation in the aqueous system. However, some mineralisation was observed in soil. The lower bioavailability of ciprofloxacin seems to reduce the compound's toxicity against microorganisms and allows its biodegradation. Moreover, ciprofloxacin strongly inhibits the microbial activities in both systems. Higher inhibition was observed in water than in soil and although its antimicrobial potency is reduced by sorption and aging in soil, ciprofloxacin remains biologically active over time. Therefore sorption does not completely eliminate the effects of this compound.