Veterinary antibiotics at environmentally relevant concentrations inhibit soil iron reduction and nitrification

Veterinary antibiotics used in food animal production, subsequently entering the agroecosystem through land application of animal manure, constitute a growing concern. Previous studies have reported inhibitory effects of antibiotics on soil microbial activities, however, treatment concentrations in these studies were often many times greater than the ranges typically found in the environment. When spiked into manure and mixed with soil at environmentally relevant concentrations in a laboratory study, sulfadimethoxine and monensin blocked soil iron reduction over periods extending from a few days to the entire 50-Day experiment. Sulfadimethoxine also had an inhibitory effect on soil nitrification periodically over the course of the study. Respiration and community-level physiological profile parameters were not inhibited by sulfadimethoxine, monensin, or chlortetracycline. We conclude that antibiotics at environmentally relevant concentrations can disrupt soil microbial processes, although the detection of such impact may be antibiotic and/or process specific.     

Veterinary antibiotics at environmentally relevant concentrations inhibit soil iron reduction and nitrification

Veterinary antibiotics used in food animal production, subsequently entering the agroecosystem through land application of animal manure, constitute a growing concern. Previous studies have reported inhibitory effects of antibiotics on soil microbial activities, however, treatment concentrations in these studies were often many times greater than the ranges typically found in the environment. When spiked into manure and mixed with soil at environmentally relevant concentrations in a laboratory study, sulfadimethoxine and monensin blocked soil iron reduction over periods extending from a few days to the entire 50-Day experiment. Sulfadimethoxine also had an inhibitory effect on soil nitrification periodically over the course of the study. Respiration and community-level physiological profile parameters were not inhibited by sulfadimethoxine, monensin, or chlortetracycline. We conclude that antibiotics at environmentally relevant concentrations can disrupt soil microbial processes, although the detection of such impact may be antibiotic and/or process specific.     

Influence of difloxacin-contaminated manure on microbial community structure and function in soils

Difloxacin (DIF) belongs to the fluoroquinolones, a frequently detected group of antibiotics in the environment. It is excreted in pig manure to a large extent and may consequently reach soils in potentially effective concentrations via manuring. The aim of this study was to assess the effects of DIF-spiked manure on microbial communities and selected functions in soils in a microcosm experiment up to 1 month after application. To test a dose dependency of the effects, three different concentrations of DIF (1, 10 and 100 mg/kg of soil) were used. Microcosms with application of pure manure, as well as untreated microcosms served as control. The addition of pure manure resulted in an increase of microbial biomass and soil respiration as well as a reduced bacteria/fungi ratio. Due to the fast and strong immobilisation of DIF, effects of the antbiotic compound were only visible up to 8 days after application (microbial biomass; respiration; potential denitrification; ratio of bacteria/fungi). As expected these short-term effects resulted in reduced potential denitrification rates as well as a reduced bacteria/fungal ratio in the treatments were DIF has been applied. Surprisingly, microbial biomass values as well as respiration rates were increased by DIF application. Other parameters like nitrate and ammonium content in soil were not influenced by DIF application at any time point. Long-term effects (32 days after application) were only visible for the potential nitrification rates. For those parameters that were influenced by the DIF application a clear dose dependency could not be described.     

Effects of long-term manure applications on the occurrence of antibiotics and antibiotic resistance genes (ARGs) in paddy soils: Evidence from four field experiments in south of China

Most studies of the effects of manure amendment on the occurrence of antibiotics and antibiotic resistance genes (ARGs) in soil employ the investigation of grab samples or short-term laboratory studies. However, the effects of long-term manure applications on antibiotics, ARGs and their vertical distribution in paddy soil in field experiments are lacking. We assessed the concentrations of antibiotics, ARGs and their vertical distribution in paddy soil receiving long-term manure applications in four field experiments. High concentrations of tetracyclines were detected in most manured soils, while sulfonamides were not detectable. Long-term manure amendments generally increased the antibiotic concentrations and ARGs abundances in the paddy soil over decades. However, in some sites such significant trends of ARGs could not be observed. The abundance of ARGs was statistically correlated with antibiotics and soil properties including pH and soil organic matter (SOM), indicating their importance in the selection of resistance genes. Tetracyclines could be detected in soil at different depths and the concentrations of tetracyclines and abundance of ARGs generally decreased with increasing soil depths.     

Combined effects of the antibiotic sulfadiazine and liquid manure on the soil microbial‐community structure and functions

Sulfonamides are the second most used antibiotic class in veterinary medicine and applied to livestock to treat bacterial infections. Subsequently, they are spread onto agricultural soils together with the contaminated manure used as fertilizer. Both manure and antibiotics affect the soil microbial community. However, the influence of different liquid manure loads on effects of antibiotics to soil microorganisms is not well understood. Therefore, we performed a microcosm experiment for up to 32 d to clarify whether the function and structure of the soil microbial community is differently affected by interactions of manure and the antibiotic sulfadiazine (SDZ). To this end selected concentrations of pig liquid manure (0, 20, 40, 80 g kg^–1) and SDZ (0, 10, 100 mg kg^–1) were combined. We hypothesized that incremental manure amendment might reduce the effect of SDZ in soils, due to an increasing sorption capacity of SDZ to organic compounds. Clear dose‐dependent effects of SDZ on microbial biomass and PLFA pattern were determined, and SDZ effects interacted with the liquid manure application rate. Soil microbial biomass increased with incremental liquid manure addition, whereas this effect was absent in the presence of additional SDZ. However, activities of enzymes such as urease and protease were only slightly affected and basal respiration was not affected by SDZ application, while differences mostly depended on the concentration of liquid manure. These results illustrated that the microbial biomass and structural composition react more sensitive to SDZ contamination than functional processes. Furthermore, effects disproportionally increased with incremental liquid manure addition, although extractable amounts of SDZ declined with increasing liquid manure application.     

Fate of sulfadiazine administered to pigs and its quantitative effect on the dynamics of bacterial resistance genes in manure and manured soil

The veterinary antibiotic sulfadiazine (SDZ), labelled by ¹⁴C, was administered to pigs to follow the fate of the drug and its metabolites in manure and manure-amended soil, and to investigate the dynamics of drug effects on resistance genes and bacterial communities. In the manure sampled over 10 days, more than 96% of the drug was found as parent compound or metabolites N-acetyl-SDZ and 4-hydroxy-SDZ. While the manure was stored the concentration of SDZ increased by 42% due to deacetylation of the metabolite N-acetyl-SDZ, whereas the minor metabolite 4-hydroxy-SDZ kept constant. In the soil the extractable amounts of the compounds decreased exponentially to less than 1 mg kg^?1 within 11 days after manure amendment. The abundances of SDZ resistance genes sul1 and sul2 were determined by qPCR relative to 16S rRNA genes in total DNA from manure and manure-amended soil. In manure both genes increased exponentially in copy number during the first 60 days of storage, suggesting preferential growth of resistant populations. However, the abundance of sul1 and sul2 decreased below 10^?5 copies per 16S rRNA gene after 175 days. With manure high amounts of sul1 and sul2 were introduced into the soil which were reduced by more than 10 times within 24 days. Thereafter, sul1 was stably maintained in soil, while sul2 further decreased between day 60 and day 165. A mathematical model was developed that could well explain the time course of sul gene abundance by considering the cost of sul genes, horizontal gene transfer, and selection of the resistant populations in the presence of SDZ. Modelling revealed a selective effect of SDZ on sul2 even at low concentrations down to 0.15 mg kg^?1 soil. Bacterial community profiles of manure and manure-amended soil were distinct, indicating that bacteria introduced with manure do not become prominent in soil. The composition of the bacterial community in manure constantly changed during storage, but mainly during the first 10 days. Profiles of soil bacterial communities revealed only a transient perturbation by manure containing SDZ.     

外源四环素对菜田土壤微生物活性及数量的影响

通过向土壤中添加四环素溶液的方法研究了油菜种植条件下,不同浓度(0.3,0.6,0.9mg/kg)的外源四环素对土壤微生物活性及数量的影响,以评价其环境生态效应。结果表明,土壤中加入四环素后,不同浓度的四环素药物对微生物量碳的影响表现为抑制作用,在27d达到最低,为空白的6.25%～11.97%;而对土壤代谢商qCO2却表现出明显的激活作用,7d达到最高,为空白的550%～622%,且微生物活性的受抑制—激活程度及持续时间与处理浓度成负相关,50d后施药土壤和对照组土壤的代谢商qCO2基本趋于一致。土壤中加入四环素后,各浓度处理对土壤微生物数量有强烈的抑制作用。     

Soil enzyme activities,microbial community composition and function after 47 years of continuous green manuring

Green manuring practices can influence soil microbial community composition and function and there is a need to investigate the influence compared with other types of organic amendment. This study reports long-term effects of green manure amendments on soil microbial properties, based on a field experiment started in 1956. In the experiment, various organic amendments, including green manure, have been applied at a rate of 4 t C ha⁻¹ every second year. Phospholipid fatty acid analysis (PLFA) indicated that the biomass of bacteria, fungi and total microbial biomass, but not arbuscular mycorrhizal (AM) fungi, generally increased due to green manuring compared with soils receiving no organic amendments. Some differences in abundance of different microbial groups were also found compared with other organic amendments (farmyard manure and sawdust) such as a higher fungal biomass and consequently a higher fungal/bacterial ratio compared with amendment with farmyard manure. The microbial community composition (PLFA profile) in the green manure treatment differed from the other treatments, but there was no effect on microbial substrate-utilization potential, determined using the Biolog EcoPlate. Protease and arylsulphatase activities in the green manure treatment were comparable to a mineral fertilized treatment receiving no additional C, whereas acid phosphatase activity increased. It can be concluded that green manuring had a beneficial impact on soil microbial properties, but differed in some aspects to other organic amendments which might be attributed to differences in quality of the amendments.     

Bacterial communities are more dependent on soil type than fertilizer type, but the reverse is true for fungal communities

The soil microbial community is strongly influenced by a wide variety of factors, such as soil characteristics and field management systems. In order to use biological indicators based on microbial community structure, it is very important to know whether or not these factors can be controlled. The present study aimed to determine whether soil type or fertilization has a greater influence on the soil microbial community based on denaturing gradient gel electrophoresis (DGGE) analysis of 12 experimental field plots containing four different soil types, Cumulic Andosol, Low-humic Andosol, Yellow Soil and Gray Lowland Soil, kept under three different fertilizer management systems since 2001 (the application of chemical fertilizer, the application of rice husk and cow manure, and the application of pig manure). Bacterial DGGE analysis using 16S rRNA genes and fungal DGGE analysis using 18S rRNA genes revealed that the bacterial community was related to the soil type more than the fertilization; however, the fungal community was related to the fertilization more than the soil type. These results might suggest that the fungal community is easier to control by fertilization than the bacterial community. Thus, we propose that indicators based on the fungal community might be more suitable as microbial indicators for soil quality.     

鸡粪与化肥不同配比对杨树苗根际土壤酶和微生物量碳、氮变化的影响

为比较鸡粪有机肥与化肥以不同比例配施对杨树苗根际土壤环境的作用效果,通过盆栽试验,研究了N100（尿素提供100%的氮）、 M10N90（鸡粪和尿素分别提供10%和90%的氮)、 M30N70（鸡粪和尿素分别提供30%和70%的氮）和M50N50（鸡粪和尿素各提供50%的氮）等处理对一年生杨树苗根际土壤酶活性、 微生物量碳（SMBC）和微生物量氮（SMBN）的影响。结果表明, 同N100处理相比,M30N70处理的杨树苗根际土壤脲酶、 碱性磷酸酶、 过氧化氢酶和蔗糖酶活性分别提高14.41%~26.49%、 13.87%~27.93%、 12.07%~27.08%和29.17%~46.43%; 根际SMBC、 SMBN含量分别提高63.00%~76.62%、 40.01%~90.38%。在杨树苗的年生长过程中,根际土壤脲酶、 碱性磷酸酶、 过氧化氢酶和蔗糖酶活性均在施肥后120 d 最高; 而根际SMBC和SMBN含量分别在施肥后90 d和30 d达到最大值。随着杨树苗的生长发育,SMBN含量逐渐降低,而在落叶期有一定的回升。与M30N70处理相比,M10N90和M50N50处理对杨树苗根际土壤酶和微生物量碳、 氮的影响较小。综合分析认为,鸡粪有机肥与化肥以3∶7比例配施对杨树苗根际区域生态环境的改善效果最佳。     

Impact of the antibiotic sulfadiazine and pig manure on the microbial community structure in agricultural soils

Large amounts of veterinary antibiotics enter soil via manure of treated animals. The effects on soil microbial community structure are not well investigated. In particular, the impact of antibiotics in the presence of manure is poorly understood. In this study, two agricultural soils, a sandy Cambisol (KS) and a loamy Luvisol (ML), were spiked with manure and sulfadiazine (SDZ; 0, 10 and 100 μg g^?1) and incubated for 1, 4, 32 and 61 days. Untreated controls received only water. The microbial community structure was characterised by investigating phospholipid fatty acids (PLFA) and using PCR–denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. The total concentration of PLFA increased with addition of manure and was reduced by both SDZ concentrations at incubation times >4 days. The SDZ addition decreased the bacteria:fungi ratio. The largest stress level, measured as ratio of PLFA (cyc17:0 + cyc19:0)/(16:1ω7c + 18:1ω7c), was found for the controls, followed by the manure treatments and the SDZ treatments. A discriminant analysis of the PLFA clearly separated treatments and incubation times. Both soils differed in total PLFA concentrations and Gram^?:Gram⁺ ratios, but showed similar changes in PLFA pattern upon soil treatment. Effects of manure and SDZ on the bacterial community structure were also revealed by DGGE analysis. Effects on pseudomonads and β-proteobacteria were less pronounced. While community structure remained altered even after two months, the extractable concentrations of SDZ decreased exponentially and the remaining solution concentrations after 32 days were ≤27% of the spiking concentration. Our results demonstrate that a single addition of SDZ has prolonged effects on the microbial community structure in soils.     

Microbial composition and diversity of an upland red soil under long-term fertilization treatments as revealed by culture-dependent and culture-independent approaches

Background, aim, and scope  Fertilization is an important agricultural practice for increasing crop yields. In order to maintain the soil sustainability, it is important to monitor the effects of fertilizer applications on the shifts of soil microorganisms, which control the cycling of many nutrients in the soil. Here, culture-dependent and culture-independent approaches were used to analyze the soil bacterial and fungal quantities and community structure under seven fertilization treatments, including Control, Manure, Return (harvested peanut straw was returned to the plot), and chemical fertilizers of NPK, NP, NK, and PK. The objective of this study was to examine the effects on soil microbial composition and diversity of long-term organic and chemical fertilizer regimes in a Chinese upland red soil. Materials and methods  Soil samples were collected from a long-term experiment station at Yingtan (28°15′N, 116°55′E), Jiangxi Province of China. The soil samples (0–20 cm) from four individual plots per treatment were collected. The total numbers of culturable bacteria and fungi were determined as colony forming units (CFUs) and selected colonies were identified on agar plates by dilution plate methods. Moreover, soil DNAs were extracted and bacterial 16S rRNA genes and fungal 18S rRNA genes were polymerase chain reaction amplified, and then analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. Results  The organic fertilizers, especially manure, induced the least culturable bacterial CFUs, but the highest bacterial diversity ascertained by DGGE banding patterns. Chemical fertilizers, on the other hand, had less effect on the bacterial composition and diversity, with the NK treatment having the lowest CFUs. For the fungal community, the manure treatment had the largest CFUs but much fewer DGGE bands, also with the NK treatment having the lowest CFUs. The conventional identification of representative bacterial and fungal genera showed that long-term fertilization treatments resulted in differences in soil microbial composition and diversity. In particular, 42.4% of the identified bacterial isolates were classified into members of Arthrobacter. For fungi, Aspergillus, Penicillium, and Mucor were the most prevalent three genera, which accounted for 46.6% of the total identified fungi. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Discussion  It was evident that more representative fungal genera appeared in organic treatments than other treatments, indicating that culturable fungi were more sensitive to organic than to chemical fertilizers. A very notable finding was that fungal CFUs appeared maximal in organic manure treatments. This was quite different from the bacterial CFUs in the manure, indicating that bacteria and fungi responded differently to the fertilization. Similar to bacteria, the minimum fungal CFUs were also observed in the NK treatment. This result provided evidence that phosphorus could be a key factor for microorganisms in the soil. Thus, despite the fact that culture-dependent techniques are not ideal for studies of the composition of natural microbial communities when used alone, they provide one of the more useful means of understanding the growth habit, development, and potential function of microorganisms from soil habitats. A combination of culture-dependent and culture-independent approaches is likely to reveal more complete information regarding the composition of soil microbial communities. Conclusions  Long-term fertilization had great effects on the soil bacterial and fungal communities. Organic fertilizer applications induced the least culturable bacterial CFUs but the highest bacterial diversity, while chemical fertilizer applications had less impact on soil bacterial community. The largest fungal CFUs were obtained, but much lower diversity was detected in the manure treatment. The lowest bacterial and also fungal CFUs were observed in the NK treatment. The long-term fertilization treatments resulted in different bacterial and fungal compositions ascertained by the culture-dependent and also the culture-independent approaches. Phosphorus fertilizer could be considered as a key factor to control the microbial CFUs and diversity in this Chinese upland red soil. Recommendations and perspectives  Soil fungi seem to be a more sensitive indicator of soil fertility than soil bacteria. Since the major limitation of molecular methods in soil microbial studies is the lack of discrimination between the living and dead, or active and dormant microorganisms, both culture-dependent and culture-independent methods should be used to appropriately characterize soil microbial diversity.     

Effect of LDPE microplastics on chemical properties and microbial communities in soil

The accumulation of plastics in the soil ecosystem poses an increasing environmental concern worldwide. However, little is known about the effect of plastic concentrations on soil properties and soil biota. In this study, we investigated the effect of low-density polyethylene (LDPE) microplastics (MPs) on the chemical and microbial properties of agricultural soil using a set of microcosm experiments. The soil was incubated for 100 days with LDPE at concentrations of 0%, 0.1%, 1%, 3%, 5%, and 7% at 25°C with 70% water-holding capacity. Along with soil chemical analysis, we conducted an analysis of soil microbial properties on the first day and again after 100 days of incubation. LDPE concentrations of ≥1% significantly (p < .05) decreased the pH but increased the electrical conductivity of the soil in comparison with the control (0% LDPE at 100 days). Increasing the LDPE concentration did not affect the soil exchangeable cation content or the available Pb concentration. Firmicutes were the most abundant phyla in the soil on the first day, whereas Proteobacteria, Firmicutes and Actinobacteria became dominant in all treatments after 100 days. An increasing LDPE concentration increased the abundance of Actinobacteria and decreased Proteobacteria. Principal component analysis demonstrated that only 7% LDPE was positively correlated with Actinobacteria, indicating that higher concentrations of LDPE contributed to the growth of this phylum. The findings of this study imply that MP contamination could affect soil chemical properties and microbial activity and that these effects primarily depend on MP concentrations in soil.     

Manure contaminated with the antibiotic sulfadiazine impairs the abundance of nirK- and nirS-type denitrifiers in the gut of the earthworm Eisenia fetida

The antibiotic sulfadiazine (SDZ) can affect denitrifying bacteria in soil. However, effects on denitrifiers in the gut of earthworms have not been described so far. Therefore, the influence of SDZ-contaminated manure applied to soil on denitrifiers in the gut of the earthworm Eisenia fetida was assessed by quantitative polymerase chain reaction targeting genes coding for nirK- and nirS-type nitrite reductases of denitrifiers. Gut contents of Eisenia fetida contained 2.5 × 10⁶ and 5.1 × 10⁵ gene copies of nirK and nirS, respectively, after 2 weeks in soils amended with manure only. Copy numbers of nirK and nirS in gut contents from manure treatments with SDZ were up to ten times less. Overall, the data indicate a negative impact of SDZ on denitrifiers in the gut of earthworms.     

Long-term manure amendments enhance neutral sugar accumulation in bulk soil and particulate organic matter in a Mollisol

Manure application generally increases soil organic matter (SOM) and particulate organic matter (POM) content in soil. Free and occluded POM (fPOM and oPOM) can be quantified by combining density and ultrasonic dispersion approaches, but it remains unclear which fraction of POM is more responsive to manure application, and whether manure treated soils have a more pronounced effect on POM content than unmanured soils (no or chemical fertilizer treated soils). Because neutral sugars in POM can be attributed to either plant- or microbial-derived compounds, we analyzed the pattern and ratio of different neutral sugars to clarify effects of different fertilizations on quality of POM in a study over two decades. Soil samples (0–20 cm) were collected from six fertilization treatments in a 25-year long fertilization experiment including no fertilizer (CK), low manure (M1), high manure (M2), chemical nitrogen, phosphorus and potassium fertilizers (NPK), and combined manure and chemical fertilizers (M1NPK, M2NPK). Our results showed that manure application generally led to higher organic carbon concentrations in bulk soil (M2NPK > M2 > M1NPK > M1 > CK > NPK), fPOM (M2NPK > M2 > M1 > M1NPK > NPK > CK) and oPOM (M1 > M2 > M1NPK > M2NPK > NPK > CK), respectively. As compared with unmanured treatments, manure amendments induced 48, 21 and 107% greater increases on average in neutral sugar concentrations in bulk soil, fPOM and oPOM, respectively. More plant-derived organic compounds were enriched in fPOM than oPOM and bulk soil, and the enrichment was more pronounced in manure treated soils than the unmanured soils. This study suggests that long-term use of manure enhanced microbial routing of specific monosaccharides into different POM fractions. Clearly, manure amendments improved labile SOM content and SOM quality in the Mollisol thus maintaining soil productivity over decades.     

长期冬种绿肥改变红壤稻田土壤微生物生物量特性

以进行了31年的双季稻-冬绿肥长期定位试验的红壤性水稻土为对象,研究了长期冬种绿肥条件下土壤微生物生物量特性的季节变化,为阐释冬绿肥措施在稻田生态系统土壤碳氮转化中的作用机制提供理论基础。试验包括双季稻-紫云英(RRV)、双季稻-冬油菜(RRP)、双季稻-黑麦草(RRG)及双季稻-冬闲(RRF)4个处理,在典型时期(绿肥盛花期、绿肥翻压后、早稻成熟期、晚稻收获后)采集土壤样品,分析土壤微生物生物量碳氮及微生物商等方面的变化。结果表明,3种冬绿肥均提高了土壤微生物生物量碳(SMBC)、微生物生物量氮(SMBN)和微生物商,在土壤性质相对稳定的晚稻收获后均显著高于对照处理,全年平均值也多显著高于对照处理。豆科绿肥紫云英对SMBC和SMBN的提高作用最显著,晚稻收获后相对冬闲分别提高了21.12%和98.45%,全年平均值分别提高了15.92%和36.49%。取样时期对SMBC、SMBN和微生物商有较大的影响,但变化趋势基本一致,即绿肥翻压前后无明显变化,早稻成熟期降至最低,至晚稻收获后再次上升。SMBC/SMBN比值在不同绿肥处理间差异不大,但有明显的季节变化,早稻成熟期较高而晚稻收获后降低。因此,南方稻田冬种绿肥后土壤微生物特性明显改善,冬种绿肥是提升稻田土壤肥力的高效措施。     

Alterations in total microbial activity and nitrification rates in soil due to amoxicillin‐spiked pig manure

Most veterinary drugs enter the environment via manure application. However, ecotoxic effects of antibiotics are varying as a function of their physicochemical characteristics and for most antibiotics it is still unclear how these substances interact with soil biota. It was the aim of the present study to investigate effects of manure containing different concentrations of the antibiotic amoxicillin (AMX) on microbial‐community function in two different soils over an incubation time of 18 d. Therefore, soil respiration, potential nitrification, and the products of N turnover were measured. We could show that CaCl₂‐extractable amounts of AMX in soil are low, even shortly after the application of high doses together with manure. Thus, not surprisingly basal respiration in soil was not influenced by the addition of the antibiotic with manure. In contrast, mainly shortly after manure addition the kinetic of substrate‐induced respiration was clearly shifted by the treatments depending on the presence of AMX in the manure. Potential nitrification rates in the two different soils were not significantly affected when data were related to the overall incubation time by the application of AMX to the manure. However, shortly after the addition of the manure containing AMX, a tendency to lower turnover rates was visible compared to the application of pure manure.     

Combined effects of compost containing Sulfamethazine and zinc on pakchoi (Brassica chinensis L.) growth,soil sulfonamide resistance genes,and microbial communities

To understand the ecotoxicity of antibiotics and heavy metals in soil, 5% (w/w) composts containing different concentrations of sulfamethazine (SMZ) and/or zinc (Zn) were applied to soil to investigate their effects on pakchoi (Brassica chinensis L.) growth, soil sulfonamide resistance genes (SRGs: sul1, sul2, and dfrA7), and soil microbial communities. Composts containing less than 1.0 mg SMZ kg^–1 or less than 2.8 g Zn kg^–1 promoted pakchoi growth and the metabolic activity of soil microbial communities. Compared with the control, the absolute abundances (AAs) of soil SRGs significantly increased by 0.85–4.54 times with 50.6 μg kg^–1 SMZ treatment (P < 0.05), the AA of sul2 increased by 166% with 248.8 mg Zn kg^–1 treatment. The combination treatments with 19.8 μg SMZ kg^–1 and 179.9 mg Zn kg^–1 in soil had synergistic stimulatory effects on pakchoi growth, soil SRGs and microbial metabolism, whereas 53.5 μg SMZ kg^–1 and 262.1 mg Zn kg^–1 had an opposite effect. Pearson’s correlation analysis showed that carbon metabolism by soil microorganisms had significant positive correlations with shoot height of pakchoi (r = 0.84, P < 0.05) and AAs of SRGs (r > 0.80, P < 0.05).     

Soil microbial community responses to sulfadiazine-contaminated manure in different soil microhabitats

Veterinary antibiotics such as sulfadiazine (SDZ) are applied with manure to agricultural soil. Antimicrobial effects of SDZ on soil microbial community structures and functions were reported for homogenized bulk soils. In contrast, field soil is structured. The resulting microhabitats are often hot spots that account for most of the microbial activity and contain strains of different antibiotic sensitivity or resilience. We therefore hypothesize that effects of SDZ are different in diverse soil microhabitats. We combined the results of laboratory and field experiments that evaluated the fate of SDZ and the response of the microbial community in rhizosphere, earthworm burrow, and soil macroaggregate microhabitats. Microbial communities were characterized by phenotypic phospholipid fatty acid (PLFA) and genotypic 16S rRNA gene patterns (DGGE) and other methods. Data was evaluated by principle component analyses followed by two-way ANOVA with post-hoc tests. Extractable SDZ concentrations in rhizosphere soil were not clearly different and varied by a factor 0.7–1.2 from those in bulk soil. In contrast to bulk soil, the extractable SDZ content was two-fold larger in earthworm burrows, which are characterized by a more hydrophobic organic matter along the burrow surface. Also, extractable SDZ was larger by up to factor 2.6 in the macroaggregate surface soil. The rhizosphere effect clearly increased the microbial biomass. Nonetheless, in the 10 mg SDZ kg⁻¹ treatment, the biomass deceased by about 20% to the level of uncontaminated bulk soil. SDZ contamination lowered the total PLFA concentrations by 14% in the rhizosphere and 3% in bulk soil of the field experiment. Structural shifts represented by Pseudomonas DGGE data were larger in SDZ-contaminated earthworm burrows compared to bulk soils. In the laboratory experiment, a functional shift was indicated by a four-fold reduced acid phosphatase activity in SDZ-contaminated burrows compared to bulk soil. Structural and functional shifts after SDZ contamination were larger by a factor of 2.5 in the soil macroaggregate surface versus interior, but this relation reversed over the long-term under field conditions. Overall, the combined effects of soil microhabitat, microbial community composition, and exposure to SDZ influenced the microbial susceptibility towards antibiotics under laboratory and field conditions.     

Effects of cover crops,compost, and manure amendments on soil microbial community structure in tomato production systems

Soil microbial community structure and crop yield was investigated in field tomato production systems that compared black polyethylene mulch to hairy vetch mulch and inorganic N to organic N. The following hypotheses were tested: (1) hairy vetch cover cropping increases crop yield and significantly affects soil microbial community structure when compared to the standard plastic mulch and synthetic fertilizer-based system; (2) within plastic mulch systems, organic amendments will increase crop yield and significantly affect soil microbial community structure when compared to synthetic fertilizer; (3) crop yields and microbial community structure will be similar in the hairy vetch cover cropping and the organic amended plasticulture systems. Treatments consisted of ammonium nitrate (control), hairy vetch cover crop, hairy vetch cover crop and poultry manure compost (10 Mg/ha), three levels of poultry manure compost (5, 10, and 20 Mg/ha), and two levels of poultry manure (2.5 and 5 Mg/ha). Black polyethylene mulch was used in all treatments without hairy vetch. Fatty acid analysis was used to characterize the total soil microbial community structure, while two substrate utilization assays were used to investigate the community structure of culturable bacteria and fungi. Crop yield was not significantly increased by hairy vetch cover cropping when compared to black polyethylene mulch, although microbial community structure was significantly affected by cover cropping. Under black polyethylene mulch, crop yields were significantly increased by the highest levels of compost and manure when compared to inorganic fertilizer, but there was no detectable effect on soil microbial community structure. When cover cropping was compared to organic amended plasticulture systems, crop yields were similar one year but dissimilar the next. However, hairy vetch cover cropping and organic amendments under black plastic mulch produced significantly different soil microbial community structure.