Characterization of Nitrate-Reducing and Amino Acid–Using Bacteria Prominent in Nitrotoxin-Enriched Equine Cecal Populations

Horses can be at risk for nitropoisoning by consuming plants containing 3-nitro-1-propionic acid or 3-nitro-1-propanol and to a lesser extent by plants containing nitrate. Populations of equine cecal microbes enriched for enhanced rates of 3-nitro-1-propionic acid (NPA) or nitrate metabolism were cultured for NPA- or nitrate-metabolizing bacteria on basal enrichment medium or tryptose soy agar supplemented with either 5-mM NPA or nitrate and under H₂:CO₂ (20:80) as the energy source. After 72 hours, separated colonies picked from plates, or roll tubes were cultured in fresh broth medium for 72 hours and then identified by 16S rRNA gene sequencing. Isolates from the NPA-enriched populations were identified as Streptococcus lutetiensis (five strains), Escherichia coli (two strains), and Sporanaerobacter acetigens (one strain). Strains isolated from nitrate-enriched populations were identified as Escherichia coli (one strain) and Wolinella succinogenes (three strains). None of these strains degraded NPA. Enriched populations of equine cecal microbes, the isolated pure strains and the type strain of Denitrobacterium detoxificans, a competent NPA-metabolizing microbe, were examined using denaturing gradient gel electrophoresis (DGGE). The DGGE analysis indicated that none of the strains in the enriched population of equine cecal microbes were similar to D. detoxificans. However, we report for the first time the isolation of the anaerobic amino acid–using Sporanaerobacter acetigenes from the equine cecum.     

Establishment of macro-aggregates and organic matter turnover by microbial communities in long-term incubated artificial soils

The study of interactions between minerals, organic matter (OM) and microorganisms is essential for the understanding of soil functions such as OM turnover. Here, we present an interdisciplinary approach using artificial soils to study the establishment of the microbial community and the formation of macro-aggregates as a function of the mineral composition by using artificial soils. The defined composition of a model system enables to directly relate the development of microbial communities and soil structure to the presence of specific constituents. Five different artificial soil compositions were produced with two types of clay minerals (illite, montmorillonite), metal oxides (ferrihydrite, boehmite) and charcoal incubated with sterile manure and a microbial community derived from a natural soil. We used the artificial soils to analyse the response of these model soil systems to additional sterile manure supply (after 562 days). The artificial soils were subjected to a prolonged incubation period of more than two years (842 days) in order to take temporally dynamic processes into account. In our model systems with varying mineralogy, we expected a changing microbial community composition and an effect on macro-aggregation after OM addition, as the input of fresh substrate will re-activate the artificial soils. The abundance and structure of 16S rRNA gene and internal transcribed spacer (ITS) fragments amplified from total community DNA were studied by quantitative real-time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The formation of macro-aggregates (>2 mm), the total organic carbon (OC) and nitrogen (N) contents, the OC and N contents in particle size fractions and the CO₂ respiration were determined. The second manure input resulted in higher CO₂ respiration rates, 16S rRNA gene and ITS copy numbers, indicating a stronger response of the microbial community in the matured soil-like system. The type of clay minerals was identified as the most important factor determining the composition of the bacterial communities established. The additional OM and longer incubation time led to a re-formation of macro-aggregates which was significantly higher when montmorillonite was present. Thus, the type of clay mineral was decisive for both microbial community composition as well as macro-aggregation, whereas the addition of other components had a minor effect. Even though different bacterial communities were established depending on the artificial soil composition, the amount and quality of the OM did not show significant differences supporting the concept of functional redundancy.     

The effect of lactic acid bacterial starter culture and chemical additives on wilted rice straw silage

Lactic acid bacteria (LAB) are suitable for rice straw silage fermentation, but have been studied rarely, and rice straw as raw material for ensiling is difficult because of its disadvantages, such as low nutrition for microbial activities and low abundances of natural populations of LAB. So we investigated the effect of application of LAB and chemical additives on the fermentation quality and microbial community of wilted rice straw silage. Treatment with chemical additives increased the concentrations of crude protein (CP), water soluble carbohydrate (WSC), acetic acid and lactic acid, reduced the concentrations of acid detergent fiber (ADF) and neutral detergent fiber (NDF), but did not effectively inhibit the growth of spoilage organisms. Inoculation with LABs did not improve the nutritional value of the silage because of poor growth of LABs in wilted rice straw. Inoculation with LAB and addition of chemical materials improved the quality of silage similar to the effects of addition of chemical materials alone. Growth of aerobic and facultatively anaerobic bacteria was inhibited by this mixed treatment and the LAB gradually dominated the microbial community. In summary, the fermentation quality of wilted rice straw silage had improved by addition of LAB and chemical materials.     

Potato brown rot incidence and severity under different management and amendment regimes in different soil types

Ralstonia solanacearum race 3 biovar 2, the causative agent of potato brown rot (bacterial wilt), is an economically important disease in tropical, subtropical and temperate regions of the world. In view of previous reports on suppression of the disease by organic amendments, and the expansion of organic agriculture, it was timely to compare the effects of organic and conventional management and various amendments on brown rot development in different soils (type: sand or clay; origin: Egypt or the Netherlands). Brown rot infection was only slightly reduced in organically compared to conventionally managed sandy soils from Egypt, but organic management significantly increased disease incidence and pathogen survival in Dutch sandy and clay soils, which correlated with high DOC contents in the organic Dutch soils. There was no correlation between disease incidence or severity and bacterial diversity in the potato rhizosphere in differently managed soils (as determined by 16S DGGE). NPK fertilization reduced bacterial wilt in conventional Egyptian soils but not in Dutch soils. Cow manure amendment significantly reduced disease incidence in organic Dutch sandy soils, but did not affect the bacterial population. However, cow manure did reduce densities of R. solanacearum in Egyptian sandy soils, most probably by microbial competition as a clear shift in populations was detected with DGGE in these and Dutch sandy soils after manure amendment. Amendment with compost did not have a suppressive effect in any soil type. The absence of a disease suppressive effect of mineral and organic fertilization in Dutch clay soils may be related to the already high availability of inorganic and organic nutrients in these soils. This study shows that the mechanism of disease suppression of soil-borne plant pathogens may vary strongly according to the soil type, especially if quite different types of soil are used.     

Succession and phylogenetic profile of eukaryotic communities in rice straw incorporated into a rice field: Estimation by PCR-DGGE and sequence analyses

Abstract

Succession and the phylogenetic profile of eukaryotic communities associated with rice straw decomposition in a rice field were studied using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 18S rDNA sequencing. Nylon mesh bags containing leaf sheaths or blades were buried in the plow layer of a rice field under flooded conditions after transplanting (Experiment 1) and under drained conditions during the off-crop season (Experiment 2). In addition, rice straw samples in Experiment 2 were taken out before plowing in spring and re-placed in the rice field under flooded conditions at transplanting. Statistical analyses based on DGGE patterns showed that eukaryotic communities were divided into two groups, namely group A before the placement in soil, after the mid-season drainage in Experiment 1 and under the drained conditions in Experiment 2 and group B before the mid-season drainage in Experiment 1 and under the flooded conditions in Experiment 2. Based on the sequence analysis of DGGE bands, which characterized the eukaryotic communities, succession of the communities was revealed, that is, most of the bands in group A were closely related to fungi, whereas the bands in group B were closely related to protozoa. These results indicated that eukaryotic communities associated with rice straw decomposition in the rice field are mainly affected by soil conditions, such as oxic or reduced conditions, irrespective of rice straw parts (leaf sheaths and blades).     

土壤微生物多样性的分子生态学研究方法

传统的平板培养法分离培养和鉴定土壤微生物只能反映极少数微生物的信息,种类只占土壤微生物种类总数的0.1%～1%,分子生态学方法应用于土壤微生物的鉴定显示出极大的优越性.着重阐述了土壤微生物多样性的研究内容、意义及目前的采用分子生态学的方法研究土壤微生物多样性,尤其以DGGE（denaturing gradient gel electrophoresis）分子生物学技术以及RAPD（Random amplified polymorphic DNA ）随机扩增的多态性分析方法更为精确和快速,为土壤微生物多样性研究提供了一个更加广阔的前景.     

免疫增强剂党参对仿刺参肠道菌群结构的影响

采用平板计数法和聚合酶链式反应( PCR)-变性梯度凝胶电泳( DGGE)技术分析免疫增强剂党参对仿刺参( Apostichopus japonicas)肠道菌群结构的影响。将初始体重为(18.00±2.00) g的仿刺参随机分为2组(对照组、试验组),每组6个重复,每个重复12只。对照组投喂海泥、鼠尾藻粉按照1∶1的质量比配制的饵料,试验组饵料中以鼠尾藻粉质量的2%添加党参,连续投喂28 d。结果表明：应用免疫增强剂党参不仅能够显著提高仿刺参的特定生长率( P<0.05),降低其饵料系数(P<0.05),而且能够显著增加仿刺参肠道内容物中异养菌的数量(P<0.05);序列统计分析显示投喂党参后仿刺参肠道细菌优质序列比例显著增加( P<0.05),试验组达97.57%,对照组仅为80.22%;Beta多样性分析反映投喂党参后仿刺参肠道微生态环境发生了变化,其多样性系数范围在14.91%~15.47%、15.47%~16.21%、14.91%~16.21%;丰度分析显示投喂党参后仿刺参肠道内容物中变形菌门( Proteobacteria)和拟杆菌门( Bacteroidetes)丰度提高,疣微菌门( Verrucomicrobia)、放线菌门( Actinobacteria)和厚壁菌门( Firmiaites)丰度降低;聚类分析显示试验组与对照组肠道菌群结构相似性系数为0.97。由此可见,免疫增强剂党参可提高仿刺参的特定生长率,降低饵料系数,增加肠道异养菌数量和优势菌群丰度,优化肠道微生态环境。     

混合益生菌对仔猪生长及肠道菌群的影响

选用50头体重相近的三元杂交断奶健康仔猪,随机分为5组:对照组全程饲喂玉米-豆粕型基础日粮;试验1、2、3、4组在试验第1天到第28天分别饲喂基础日粮+蜡样芽孢杆菌、鼠李糖乳杆菌和戊糖乳杆菌(质量比为1∶1∶1、1∶2∶1、2∶1∶2、1∶1∶2)的混合益生菌制剂,在第29天到第42天饲喂基础日粮。饲喂28 d后计算各组仔猪日增重、料重比、腹泻率。结果表明:4个试验组仔猪的日增重均高于对照组,料重比均低于对照组,腹泻率均显著低于对照组;试验1、3组仔猪的日增重显著高于对照组,且试验1组仔猪的日增重又稍高于试验3组;试验1、3组仔猪的料重比显著低于对照组,而试验1组仔猪的料重比又稍低于试验3组;试验1组和3组仔猪的腹泻率相同,且低于试验2组和4组,表明4种比例混合的益生菌制剂均能促进仔猪生长,且以质量比1∶1∶1、2∶1∶2混合的益生菌制剂促进仔猪生长的效果较好;对试验1组和对照组仔猪在试验0、7、14、21、28、42 d肠道内菌群的定量PCR结果表明,试验1组仔猪肠道内蜡样芽孢杆菌、鼠李糖乳杆菌数量在饲喂益生菌制剂期间呈现一致的变化趋势,即先上升后下降,再上升,而对照组3种菌的变化趋势不一致;在停喂益生菌制剂2周后,3种益生菌仍呈规律变化,表明饲喂益生菌制剂能够调节仔猪肠道相应菌群的生长;对仔猪肠道粪样菌群的16SrDNA的特异序列的进行变性梯度凝胶电泳及抠胶测序的结果表明,仔猪在饲喂益生菌制剂7 d后,肠道蜡样芽孢杆菌、肠球菌、链球菌、双歧杆菌、戊糖乳杆菌、大肠杆菌、鼠李糖乳杆菌菌群数量均下降,到第28天时,各种菌群数量均上升,表明饲喂益生菌制剂不仅能调节仔猪肠道相应益生菌的生长,还能调节肠道肠球菌、链球菌、大肠杆菌与双歧杆菌的生长。     

呼伦贝尔沙地不同植被恢复模式土壤氨氧化细菌群落结构及多样性

采用PCR-DGGE技术和克隆测序分析方法,对不同植被恢复模式下呼伦贝尔沙地土壤氨氧化细菌群落结构、多样性及与土壤理化因子的相关性进行探讨。结果表明,5种植被恢复模式土壤氨氧化细菌16S rRNA基因Shannon指数均显著高于对照(裸地),其中柠条(Caragana korshinskii)+冰草(Agropyron cristatum)(AC)模式下Shannon指数最高,其他依次为单播柠条(UC)、单播冰草(UA)、柠条+羊柴(Hedysarum fruticosum)+冰草+披碱草(Elymus nutans)(ACHE)和单播羊柴(UH),各植被恢复模式不同程度地提高了土壤氨氧化细菌的多样性。系统发育分析结果表明,对照(裸地)土壤氨氧化细菌群落由亚硝化螺菌属的Cluster 2和Cluster 3组成,而5种植被恢复模式土壤氨氧化细菌群落由亚硝化螺菌属的Cluster 3和亚硝化单胞菌属的Cluster 6组成,植被恢复改变了土壤氨氧化细菌群落结构组成。土壤理化性质测定结果表明,5种植被恢复模式在不同程度上提高了土壤各项理化指标。典范对应分析结果表明,pH值、有机质(OM)、全氮(TN)、全磷(TP)和土壤含水量(SM)对氨氧化细菌群落结构组成的影响均达到显著水平(P0.05),相关性分析发现pH值、OM、TN、TP和SM各指标之间均具有极显著相关性(P0.01),说明植被恢复过程中土壤氨氧化细菌群落结构组成的变化是土壤各项理化因子相互关联、共同作用的结果。     

Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil

To explore long-term impact of organic and inorganic fertilizers on microbial communities, we targeted both the total bacterial community and the autotrophic ammonia oxidizing bacteria (AOB) in soil from six treatments at an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO₃)₂, (NH₄)₂SO₄, unfertilized and unfertilized without crops. All plots, except the bare fallows, were cropped with maize. Effects on activity were assessed by measuring the basal respiration and substrate induced respiration (SIR) rates, and the potential activity of the AOB. To determine the bacterial community composition, 16S rRNA genes were used to fingerprint total soil communities by terminal restriction fragment length polymorphism analysis and AOB communities by denaturing gradient gel electrophoresis. The fertilization regimes had clear effects on both activity and composition of the soil communities. Basal respiration and r, which was kinetically derived as the exponentially growing fraction of the SIR-response, correlated well with the soil organic C content (r=0.93 and 0.66, respectively). Soil pH ranged from 3.97 to 6.26 in the treatments and was found to be an important factor influencing all microbial activities. pH correlated negatively with the ratio between basal respiration and SIR (r=0.90), indicating a decreased efficiency of heterotrophic microorganisms to convert organic carbon into microbial biomass in the most acid soils with pH 3.97 and 4.68 ((NH₄)₂SO₄ and sewage sludge fertilized plots, respectively). The lowest SIR and ammonia oxidation rates were also found in these treatments. In addition, these treatments exhibited individually different community fingerprints, showing that pH affected the composition of AOB and total bacterial communities. The manure fertilized plots harbored the most diverse AOB community and the pattern was linked to a high potential ammonia oxidation activity. Thus, the AOB community composition appeared to be more strongly linked to the activity than the total bacterial communities were, likely explained by physiological differences in the populations present.