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.     

Enzyme activities and microbial community structure in semiarid agricultural soils

This study investigated the effect of management on -glucosidase, -glucosaminidase, alkaline phosphatase, and arylsulfatase activities and the microbial community structure in semiarid soils from West Texas, USA. Surface samples (0–5 cm) were taken from a fine sandy loam, sandy clay loam, and loam that were under continuous cotton ( Gossypium hirsutum L.) or in cotton rotated with peanut ( Arachis hypogaea L.), sorghum ( Sorghum bicolor L.), rye ( Secale cereale) or wheat ( Triticum aestivum L.), and had different water management (irrigated or dryland), and tillage (conservation or conventional). The enzyme activities were higher in the loam and sandy clay loam than in the fine sandy loam. Soil pH was not affected by management, but the soil organic C and total N contents were generally affected by the different crop rotations and tillage practices studied. The trends of the enzyme activities as affected by management depended on the soil, but in general crop rotations and conservation tillage increased the enzyme activities in comparison to continuous cotton and conventional tillage. The soil enzyme activities were significantly correlated with the soil organic C ( r -values up to 0.90, P< 0.001), and were correlated among each other ( r -values up to 0.90, P <0.001). There were differences in the fatty acid methyl ester profiles between the fine sandy loam and the sandy clay loam and loam, and they reflected the differences in the enzyme activities found among the soils. For example, a 15:0 ranged from 1.61±0.25% in cotton-peanut/irrigated/no-till in the fine sandy loam to 3.86±0.48% in cotton-sorghum/dryland/conservation tillage in the sandy clay loam. There were no differences due to management within the same soil.Trade names and company names are included for the benefit of the reader and do not infer any endorsement or preferential treatment of the product by USDA-ARS     

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.     

Influence of ciprofloxacin on microbial community structure and function in soils

Microcosm experiments were designed to investigate the effects of the widely used antibiotic ciprofloxacin (CIP) on soil microbial communities by using four different concentrations (0, 1, 5, and 50 mg kg^?1 of soil) and five sampling times (1, 3, 9, 22, and 40 days). Untreated controls only received water. The addition of CIP significantly decreased microbial biomass (p?<?0.05) but did not affect soil respiration at high doses. Potential nitrification rates were stimulated at low CIP concentrations (1 mg kg^?1) and inhibited at high CIP concentrations (50 mg kg^?1) after 9 days of incubation. The nitrate and ammonium contents of soil were not altered after CIP addition at any time. The structure of soil microbial communities was assessed by phospholipid fatty acid (PLFA) analysis. The addition of CIP decreased the ratio of bacteria to fungi and increased the ratio of Gram-positive to Gram-negative bacteria. Principal component analysis of the PLFA data clearly distinguished among the different CIP concentrations. Redundancy analysis indicated that the CIP concentration and incubation time explained 33.5 % of the total variance in the PLFA data. These results confirmed that a single addition of CIP can influence structure and function of microbial communities in soil.     

Impact of sulfadiazine and chlorotetracycline on soil bacterial community structure and respiratory activity

Veterinary medicines enter agricultural soils by the use of animal excrements as fertilizers. To study their impact on soil bacterial communities, microcosms containing orthic luvisol soil were spiked with the antimicrobial agents sulfadiazine (SDZ) and chlorotetracycline (CTC) at three different concentrations (1, 10, 50 mg kg⁻¹ soil) and incubated for 48 days at 20 °C. The impact on the microbial respiratory activity was measured continuously in a respirometer (Sapromat). Changes in bacterial community structure were visualized by means of PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA derived from soil samples after 1, 7, 11 and 48 days. Additionally, growth inhibitory effects of SDZ and CTC on bacteria previously isolated from the same soil were tested in agar diffusion tests. In microcosms with soil and antibiotics only, no effects could be observed, either on respiratory activity or on bacterial population structure. Therefore, further incubations were conducted in the presence of an additional assimilable carbon source (5 g glucose kg⁻¹ soil). In the presence of glucose, SDZ affected soil respiration as well as the bacterial community structure: Additional bands appeared and some bands already visible at the beginning of incubations increased in intensity. A clear relationship between SDZ concentrations and changes in DGGE patterns became visible. During 48 days of incubation, changes in DGGE patterns were minimal in microcosms with 50 mg SDZ kg⁻¹soil indicating an inhibition of strains, which were capable of growing on glucose in the presence of lower SDZ concentrations. Only a few soil bacterial isolates (5 out of 47 strains tested) were weakly inhibited by SDZ in agar diffusion disk tests. Contrastingly, CTC inhibited growth of 12 soil bacterial isolates significantly in disk tests, but no effects on soil respiration and bacterial community structure could be observed. In the presence of the soil matrix the growth inhibitory potential of CTC decreased due to adsorption or complexation. This was confirmed in growth inhibition experiments with soil suspensions and time-dependent sampling.     

Impact of fumigation with metam sodium upon soil microbial community structure in two Japanese soils

The effects of fumigation with sodium methyl dithiocarbamate (metam sodium) on the microbial community structure and function in 2 soils were investigated using a variety of techniques. In both soils ca. 50% and 90% of the populations of total and culturable bacteria, respectively, were killed by fumigation, with recovery to levels prevailing in control soils 26 d after cessation of fumigation. The size of the ammonium and nitrite oxidiser populations was reduced by up to 4 orders of magnitude by fumigation, with the latter showing a slight recovery 105 d later. There were substantial changes in the C-utilisation (Biolog GN) profiles in the fumigated soils even 105 d later. The number and pattern of amplified 16S ribosomal DNA restriction analysis (ARDRA) fragments was changed by fumigation, and there was a shift in the %G+C profile toward a greater proportion of lower %G+C classes in treated soils. It appeared that DNA released from killed cells remained for some time after fumigation, and masked the apparent community DNA profiles. This study demonstrates that the effects of fumigation on the soil microbial community structure and function were pronounced and for some parameters very persistent. However, the effects on broad-scale properties such as total or culturable bacterial numbers were less enduring.     

分层接种对猪粪厌氧干发酵产气性能及微生物群落结构的影响

为避免厌氧干发酵酸抑制,提高产气效率,以猪粪和玉米秸秆为发酵原料,采用中温批式试验,在总固体（Total Solid, TS）为20%、接种比为25%的条件下研究分层接种和混合接种对猪粪干发酵厌氧消化性能的影响。结果表明：2种接种方式下的发酵体系内挥发性脂肪酸（Volatile Fatty Acids, VFAs）均发生明显积累,其中,分层接种在第15天的TVFAs质量浓度达到33.0 mg/g,之后明显降低,至发酵结束时VFAs消耗殆尽。混合接种从第15天至发酵结束,TVFAs质量浓度维持在29.2～38.5 mg/g高水平范围内。分层接种的累积挥发性固体甲烷产率为211.5 mL/g。高通量测序结果显示,氢营养型产甲烷途径在2种接种方式下均占主导,但分层接种增加了发酵体系中微生物的丰富度和多样性,且群落结构更加稳定。进一步分析表明,乙酸和pH值是影响厌氧干发酵中微生态结构的主要环境因子。该研究结果为解除畜禽养殖废弃物酸抑制、提高产气效率提供理论依据与有益借鉴。     

水热预处理对猪粪厌氧消化系统中磺胺嘧啶降解的影响

为进一步了解水热预处理对猪粪连续厌氧消化过程中磺胺嘧啶（sulfadiazine, SDZ）降解机制的影响,以及对厌氧消化系统性能的影响效果。该研究以猪粪为对象,对比研究了水热预处理对厌氧发酵模式下SDZ的降解变化规律与途径及其对猪粪产气性能的影响。研究结果表明：水热预处理（150 ℃）使中温连续厌氧反应器中的SDZ的综合去除率显著提升（P <0.05）,由40.5%～58.5%提高到54.4%～75.2%;并且通过中间降解产物推测SDZ的生物降解途径主要包括SDZ水解、羟基化、硫脱氧、氨基氧化、嘧啶环裂解等;在厌氧消化性能方面,水热预处理使稳定运行后反应器的日产沼气量提高了约34.05%（P <0.05）。此外,对反应器中微生物群落分析后,发现Syntrophomonas、Sedimentibacter与SDZ的降解高度相关,并且经过水热预处理后Sedimentibacter的相对丰度较未水热预处理显著提升。因此,水热预处理耦合厌氧消化工艺具有同步提高SDZ降解和厌氧消化性能的作用,有助于进一步提高沼液的生态安全性。     

Microbial community structure and activity in agricultural soils under different management

For the development of management strategies in sustainable agriculture it is necessary to describe and predict the role of soil microbes in different management systems. The classical approach uses the microbial biomass as the key parameter for the entire system, but for ecological purposes the variability of biotic parameters in time and space has to be better described. Moreover, the biomass active in the total soil profile or its most active zones should be used as a basis for the assessment of soil activity. The sum of adenylates was found to be more closely related to the microbial biomass than was ATP, which however appeared to be a better indicator for the microbial activity. Fatty acids from phospholipids were highly correlated with the soil microbial biomass. The pattern of fatty acids from soils under different long-term management indicated a high potential to typify the microbial community in soils and special organism populations. To overcome the problem, that only a small portion of the soil inhabiting microbes can be cultivated, first steps to use serological and genetical methods to directly identify or localize specific populations in the rhizosphere are shown.     

土壤微生物群落结构与多样性对农田集约化管理程度降低的响应

Using a scheme of agricultural fields with progressively less intensive management （deintensification）, different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage （CT） or no-tillage （NT）, an organic farming system （OR）, an integrated cropping system with animals （IN）, a successional field （SU）, and a plantation woodlot （WO）. Microbial phospholipid fatty acid （PLFA） profiles and substrate utilization patterns （BIOLOG ECO plates） were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N （P 〈 0.05） were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system （P 〈 0.05）. There were also significant decreases （P 〈 0.05） along with agricultural deintensification for contributions of total bacterial and gram positive （G＋） bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.     

磺胺嘧啶对土壤氮矿化及相关微生物参数的影响

兽用抗生素进入土壤,已经带来了新的土壤污染生态学问题,并已引起广泛关注。本文研究了不同浓度磺胺嘧啶残留对土壤氮矿化量及相关微生物参数的影响。结果表明,磺胺嘧啶对土壤氮矿化产生抑制作用,且抑制作用在低浓度比高浓度更为敏感。通过主成分分析和多元回归分析可知,在各相关微生物参数中,土壤微生物群落功能多样性可作为预测磺胺嘧啶残留时土壤氮矿化强度变化的指标。     

Seasonal influence of climate manipulation on microbial community structure and function in mountain soils

Microbial communities drive soil organic matter (SOM) decomposition through the production of a variety of extracellular enzymes. Climate change impact on soil microbial communities and soil enzymatic activities can therefore strongly affect SOM turnover, and thereby determine the fate of ecosystems and their role as carbon sinks or sources.To simulate projected impacts of climate change on Swiss Jura subalpine grassland soils, an altitudinal soil transplantation experiment was set up in October 2009. On the fourth year of this experiment, we measured microbial biomass (MB), microbial community structure (MCS), and soil extracellular enzymatic activities (EEA) of nine hydrolytic and oxidative extracellular enzymes in the transplanted soils on a seasonal basis.We found a strong sampling date effect and a smaller but significant effect of the climate manipulation (soil transplantation) on EEA. Overall EEA was higher in winter and spring but enzymes linked to N and P cycles showed higher potential activities in autumn, suggesting that other factors than soil microclimate controlled their pool size, such as substrate availability. The climate warming manipulation decreased EEA in most cases, with oxidative enzymes more concerned than hydrolytic enzymes. In contrast to EEA, soil MB was more affected by the climate manipulation than by the seasons. Transplanting soils to lower altitudes caused a significant decrease in soil MB, but did not affect soil MCS. Conversely, a clear shift in soil MCS was observed between winter and summer. Mass-specific soil EEA (EEA normalized by MB) showed a systematic seasonal trend, with a higher ratio in winter than in summer, suggesting that the seasonal shift in MCS is accompanied by a change in their activities. Surprisingly, we observed a significant decrease in soil organic carbon (SOC) concentration after four years of soil transplantation, as compared to the control site, which could not be linked to any microbial data.We conclude that medium term (four years) warming and decreased precipitation strongly affected MB and EEA but not MCS in subalpine grassland soils, and that those shifts cannot be readily linked to the dynamics of soil carbon concentration under climate change.     

Functional activity and microbial community structure in soils amended with bimetallic sludges

Heavy metal availability, microbial biomass and respiration, bacterial diversity and enzyme activity were studied in soils from long-term field experiments contaminated with Mn-Zn- or Cd-Ni-rich sludge, incorporated into soils at two different rates. Soils that never received sludge were used as controls. Microbial biomass C content (B_C) and soil respiration (CO₂-C) were slightly reduced in soils amended with Mn-Zn at the higher incorporation rate whereas in soils receiving Cd-Ni-rich sludge B_C and respiration were unaffected. Metabolic quotient values (qCO₂) calculated by the B_C-to-CO₂-C ratio were not significantly different, regardless of the sludge type whereas the microbial biomass C-to-total organic C (B_C-to-TOC) ratios were significantly reduced in the soils receiving the higher rates of both sludge types. Phosphomonoesterase, β-glucosidase and arylsulfatase activities and hydrolase-to-B_C ratios, were significantly reduced in soils amended with Ni-Cd-sludge at both rates, whereas the Mn-Zn-sludge only reduced the arylsulfatase activity at the higher rate. Protease activity was generally higher in all the sludge-amended soils as compared to control soils whereas urease activity was unaffected by sludge amendments. The structure of the bacterial community, as determined by denaturing gradient gel electrophoresis (DGGE), was different in the sludge-amended soils as compared to the respective controls. The most important changes were observed in the soils amended with high-level Ni-Cd sludge. Because some of the adverse effects were observed at moderate contamination levels, our results indicate that the presence of certain heavy metal combinations can be a serious limitation for sludge disposal.     

Hydrolase activity, microbial biomass and community structure in long-term Cd-contaminated soils

Long-term effects of high Cd concentrations on enzyme activities, microbial biomass and respiration and bacterial community structure of soils were assessed in sandy soils where Cd was added between 1988 and 1990 as Cd(NO₃)₂ to reach concentrations ranging from 0 to 0.36 mmol Cd kg⁻¹ dry weight soil. Soils were mantained under maize and grass cultivation, or ‘set-aside’ regimes, for 1 year. Solubility of Cd and its bioavailability were measured by chemical extractions or by the BIOMET bacterial biosensor system. Cadmium solubility was very low, and Cd bioavailability was barely detectable even in soils polluted with 0.36 mmol Cd kg⁻¹. Soil microbial biomass carbon (B_C) was slightly decreased and respiration was increased significantly even at the lower Cd concentration and as a consequence the metabolic quotient (qCO₂) was increased, indicating a stressful condition for soil microflora. However, Cd-contaminated soils also had a lower total organic C (TOC) content and thus the microbial biomass C-to-TOC ratio was unaffected by Cd. Alkaline phosphomonoesterase, arylsulphatase and protease activities were significantly reduced in all Cd-contaminated soils whereas acid phosphomonoesterase, β-glucosidase and urease activites were unaffected by Cd. Neither changes in physiological groups of bacteria, nor of Cd resistant bacteria could be detected in numbers of the culturable bacterial community. Denaturing gradient gel electrophoresis analysis of the bacterial community showed slight changes in maize cropped soils containing 0.18 and 0.36 mmol Cd kg⁻¹ soil as compared to the control. It was concluded that high Cd concentrations induced mainly physiological adaptations rather than selection for metal-resistant culturable soil microflora, regardless of Cd concentration, and that some biochemical parameters were more sensitive to stress than others.     

Response of microbial community composition and activity in agricultural and grassland soils after a simulated rainfall

Rainfall in Mediterranean climates may affect soil microbial processes and communities differently in agricultural vs. grassland soils. We explored the hypothesis that land use intensification decreases the resistance of microbial community composition and activity to perturbation. Soil carbon (C) and nitrogen (N) dynamics and microbial responses to a simulated Spring rainfall were measured in grassland and agricultural ecosystems. The California ecosystems consisted of two paired sets: annual vegetable crops and annual grassland in Salinas Valley, and perennial grass agriculture and native perennial grassland in Carmel Valley. Soil types of the respective ecosystem pairs were derived from granitic parent material and had sandy loam textures. Intact cores (30 cm deep) were collected in March 1999. After equilibration, dry soil cores (approx. −1 to −2 MPa) were exposed to a simulated Spring rainfall of 2.4 cm, and then were measured at 0, 6, 24, and 120 h after rewetting. Microbial biomass C (MBC) and inorganic N did not respond to rewetting. N₂O and CO₂ efflux and respiration increased after rewetting in all soils, with larger responses in the grassland than in the agricultural soils. Phospholipid fatty acid (PLFA) profiles indicated that changes in microbial community composition after rewetting were most pronounced in intensive vegetable production, followed by the relict perennial grassland. Changes in specific PLFA markers were not consistent across all sites. There were more similarities among microbial groups associated with PLFA markers in agricultural ecosystems than grassland ecosystems. Differences in responses of microbial communities may be related to the different plant species composition of the grasslands. Agricultural intensification appeared to decrease microbial diversity, as estimated from numbers of individual PLFA identified for each ecosystem, and reduce resistance to change in microbial community composition after rewetting. In the agricultural systems, reductions in both the measures of microbial diversity and the resistance of the microbial community composition to change after a perturbation were associated with lower ecosystem function, i.e. lower microbial responses to increased moisture availability.     

Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils

A number of studies have reported species specific selection of microbial communities in the rhizosphere by plants. It is hypothesised that plants influence microbial community structure in the rhizosphere through rhizodeposition. We examined to what extent the structure of bacterial and fungal communities in the rhizosphere of grasses is determined by the plant species and different soil types. Three grass species were planted in soil from one site, to identify plant-specific influences on rhizosphere microbial communities. To quantify the soil-specific effects on rhizosphere microbial community structure, we planted one grass species (Lolium perenne L.) into soils from three contrasting sites. Rhizosphere, non-rhizosphere (bulk) and control (non-planted) soil samples were collected at regular intervals, to examine the temporal changes in soil microbial communities. Rhizosphere soil samples were collected from both root bases and root tips, to investigate root associated spatial influences. Both fungal and bacterial communities were analysed by terminal restriction fragment length polymorphism (TRFLP). Both bacterial and fungal communities were influenced by the plant growth but there was no evidence for plant species selection of the soil microbial communities in the rhizosphere of the different grass species. For both fungal and bacterial communities, the major determinant of community structure in rhizospheres was soil type. This observation was confirmed by cloning and sequencing analysis of bacterial communities. In control soils, bacterial composition was dominated by Firmicutes and Actinobacteria but in the rhizosphere samples, the majority of bacteria belonged to Proteobacteria and Acidobacteria. Bacterial community compositions of rhizosphere soils from different plants were similar, indicating only a weak influence of plant species on rhizosphere microbial community structure.     

Long-term cattle manure application in soil. II. Effect on soil microbial populations and community structure

Studies were conducted to evaluate microbial populations and community structures in soils under different management systems in a long-term continuous winter wheat experiment. These soils had been treated with cattle manure for over a century, and P, NP, NPK, or NPK plus lime for over 70 years. Cattle manure application promoted the growth of bacteria, but not fungi, when compared with the control soil. Application of chemical fertilizers enriched the K-strategist bacterial community, while application of manure enriched both r- and K-strategists. DNA recovered was most abundant in the manure-treated soil. Effects on bacterial species richness and evenness following long-term soil treatments were also demonstrated by analyzing bacterial community DNA using amplified ribosomal DNA restriction analysis and repetitive extragenic palindromic-polymerase chain reaction fingerprinting. The richness and evenness of the bacterial community were enhanced by manure treatment and treatments that included N and P, which were positively correlated with soil productivity.     

不同培肥模式对茶园土壤微生物活性和群落结构的影响

以闽东地区红黄壤茶园定位实验地为对象,通过测定6种不同施肥处理土壤微生物学特性,研究不同培肥对土壤微生物特性和生物化学过程的影响,阐明各指标间的相互关系.结果表明,除了单施无机肥处理外,半量化肥+半量有机肥、全量有机肥、全量化肥+豆科绿肥以及半量化肥+半量有机肥+豆科绿肥等的培肥方式均不同程度提高了土壤有机质,可培养微生物数量,微生物量碳、氮含量及土壤酶活性,尤以半量无机肥+半量有机肥+豆科牧草的培肥模式增幅更为明显,而单施无机肥不利于微生物的生长、酶活性的提高和维持生态系统的稳定性.微生物群落磷脂脂肪酸(PLFAs)标记主成分分析显示,各种不同施肥方式使微生物群落结构发生改变.相关分析表明,微生物量与可培养微生物数量、微生物磷脂脂肪酸含量之间的相关性明显高于微生物量与各种酶活性之间的相关性,说明微生物数量大小对微生物群落结构的影响大于对酶活性功能的影响.研究也表明土壤各微生物指标能从不同方面反映土壤肥力水平,所以采用各种不同的方法能更客观地评价闽东地区茶园红黄壤质量的优劣.