梭鱼和鲻鱼线粒体16S rRNA和COⅠ基因片段的比较分析     

程国宝  李三磊  徐冬冬  薛宝贵  耿智  楼宝 《浙江水产学院学报》2012,(2):103-106

运用PCR技术,扩增了梭鱼和鲻鱼线粒体16S rRNA和COⅠ基因片段,并比较分析了其种间的序列差异。获得16S rRNA基因的540～560 bp碱基序列,出现26个碱基的插入与缺失位点;获得COⅠ基因的602～604 bp碱基序列,出现2个插入缺失位点;16S rRNA和COⅠ基因的序列中G平均含量最低,且（A＋T）含量高于（G＋C）含量,与其他鱼类中的16S rRNA和COⅠ基因片段研究结果相一致。在16S rRNA基因片段中,梭鱼出现1种单倍型,鲻鱼为2种单倍型;在COⅠ基因片段中,梭鱼样品中检测到3个单倍型,鲻鱼样品中检测到5个单倍型。以Takifugu poecilonotus为外群,构建的NJ系统发育树,基于16S rRNA和COⅠ基因序列获得的NJ系统树基本一致,鲻鱼和梭鱼种内个体分别聚为一支,显示16S rRNA和COⅠ基因适合于梭鱼和鲻鱼的物种鉴定。  相似文献   

兔多杀性巴氏杆菌16S rRNA PCR检测方法的建立     

季权安  刘燕  庞安娜  肖琛闻  韦强  鲍国连 《中国预防兽医学报》2012,34(6):468-470

为建立一种快速准确检测兔多杀性巴氏杆菌(P.multocida)的PCR方法,本研究以P.multocida的高度保守的16S rRNA为靶基因,参考已公布的P.multocida的16S rRNA基因设计1对特异性引物,优化PCR反应条件,建立了P.multocida PCR快速检测方法。该PCR方法的敏感性达到60 cfu/mL,采用该PCR方法扩增P.multocida标准株和分离株均能扩增出643 bp的目的片段,扩增兔大肠杆菌、支气管败血波氏杆菌结果为阴性,证明本实验所建立的P.multocida PCR检测方法快速、敏感、特异、可靠,可用于P.multocida的快速鉴定与诊断。同时用建立的PCR方法对临床疑似病兔的脏器分离菌进行扩增,可扩增出目的条带,与细菌的分离结果相一致。  相似文献   

First report of Wolbachia from field populations of Culex mosquitoes in south-western Nigeria     

《African Zoology》2013,48(3):181-185

Recent reports on finding Wolbachia-strain infections in field mosquito species in some West African countries and the potential for developing these as disease vector biocontrol tools have prompted a search for Wolbachia in mosquitoes within the study area. Using a completely randomised design, mosquito traps were set at different locations in a rural and an urbanised community. One hundred and eighty (180) mosquitoes were trapped and pooled on the basis of genus, sex and site of collection, because there have been no earlier reports of Wolbachia isolated from Nigeria. Twenty pools, made up of not more than ten mosquitoes per pool, were homogenised and analysed for Wolbachia-specific DNA. Mosquitoes were trapped within Ede (urbanised community) and Akoda (rural community). Genomic DNA was extracted from trapped mosquito samples and used as a template in a PCR reaction. The Wolbachia sp. specific 16S rRNA gene was amplified, sequence analysis of PCR products was performed and a chromatogram of the sequence was subjected to Basic Local Alignment Search Tool analysis to identify the Wolbachia sp. This sequence was subsequently submitted to GenBank with accession number MK127541. The first evidence of the presence of the endosymbiont, Wolbachia in field-caught mosquitoes is hereby documented. The homology of this strain of Wolbachia bears similarities to those reported recently from other parts of West Africa and forms a single clade with a Wolbachia sp. from Mali, with a strong bootstrap support of 99%. This finding of a Wolbachia strain in mosquitoes at Ede could form the basis for more searches for diverse strains of Wolbachia in Nigeria.  相似文献   

Phylogeography of the African common toad,Amietophrynus regularis,based on mitochondrial DNA sequences: inferences regarding the Cape Verde population and biogeographical patterns     

《African Zoology》2013,48(2):291-298

The amphibian Amietophrynus regularis is distributed throughout equatorial Africa, with presumed introduced populations in the Cape Verde archipelago. Portions of the 12S and 16S rRNA mitochondrial regions of 30 specimens from Kenya, Uganda, Niger, Mali, Burkina-Faso, Ghana, Guinea-Bissau and Cape Verde were used to assess genetic diversity and to identify the most probable geographic origin for the introduction of this toad on the latter archipelago. Two lineages with 1.4% genetic divergence between them were identified in western and eastern Africa. All sequences from the different Cape Verde Islands were identical to each other and to the Guinea-Bissau samples, indicating, together with other historical evidences, that an anthropogenic introduction event probably occurred, possibly from Guinea-Bissau, but further work is needed to confirm this. As previously noted, several individuals from previous genetic studies seem to have been misidentified.  相似文献   

快速检测兔支气管败血波氏杆菌环介导等温扩增(LAMP)方法的建立及应用     

李科  刘燕  肖琛闻  韦强  鲍国连  季权安 《中国兽医学报》2013,33(7)

利用Primer ExplorerV4软件,针对兔波氏杆菌16S rRNA基因设计4条LAMP引物,优化反应条件,检测特异性、敏感性并对临床样品进行检测.结果显示,LAMP反应在62℃恒温扩增1h即可完成,操作简便,不需要PCR仪等复杂仪器,结果可经电泳检测及肉眼观察;具有良好的特异性;敏感性为普通PCR的100倍,最低可检测到1.65×10-6 mg/L的细菌基因组DNA.用建立LAMP检测方法对32份疑似兔支气管败血波氏杆菌(Bb)样品检测呈阳性,与PCR检测结果相符.该方法的建立为Bb的临床快速检测提供了新的思路.  相似文献   

长薄鳅恶臭假单胞菌的分离鉴定及其感染的病理损伤   总被引：1，自引：0，他引：1  

白明焕  耿毅  邓龙君  甘维熊  周剑  黄小丽  陈德芳  欧阳萍  赵若璇  谌冰洁 《浙江农业学报》2019,31(2):207

恶臭假单胞菌(Pseudomonas putida)是广泛分布于土壤、水体中的一种条件致病菌,可感染两栖类、鱼类和甲壳类等多种水生动物。2017年8月,四川省西昌市某养殖场的长薄鳅出现一种以体表溃烂、鳍条出血为主要特征的传染病。为探究其病因,本研究进行了病原菌分离、人工感染、分离菌表型特征测定、16S rRNA与gyrB基因序列分析。从病鱼肝、脾、肾中分离到优势菌株(BMH170820),人工感染试验证实了其病原性。根据其菌落形态、生理生化特性,结合16S rRNA与gyrB基因序列分析鉴定其为恶臭假单胞菌。组织病理学观察发现,其感染长薄鳅对鳃、肾、肝、心、脾与消化道等多处组织器官造成损伤,表现出明显的变性、坏死和炎症反应,致全身多器官功能障碍而死亡。药物敏感试验显示,该菌对新霉素、氧氟沙星以及强力霉素等敏感,而对阿莫西林、头孢氨苄与氟苯尼考等耐药。  相似文献   

Assessing the relationship between patch type and soil mites: A molecular approach     

Karen Gibb  Jennifer Beard  Peter O&#x;Reagain  Keith Christian  Valeria Torok  Kathy Ophel-Keller 《Pedobiologia》2008,51(5-6):445-461

An urgent need exists for indicators of soil health and patch functionality in extensive rangelands that can be measured efficiently and at low cost. Soil mites are candidate indicators, but their identification and handling is so specialised and time-consuming that their inclusion in routine monitoring is unlikely. The aim of this study was to measure the relationship between patch type and mite assemblages using a conventional approach. An additional aim was to determine if a molecular approach traditionally used for soil microbes could be adapted for soil mites to overcome some of the bottlenecks associated with soil fauna diversity assessment. Soil mite species abundance and diversity were measured using conventional ecological methods in soil from patches with perennial grass and litter cover (PGL), and compared to soil from bare patches with annual grasses and/or litter cover (BAL). Soil mite assemblages were also assessed using a molecular method called terminal-restriction fragment length polymorphism (T-RFLP) analysis. The conventional data showed a relationship between patch type and mite assemblage. The Prostigmata and Oribatida were well represented in the PGL sites, particularly the Aphelacaridae (Oribatida). For T-RFLP analysis, the mite community was represented by a series of DNA fragment lengths that reflected mite sequence diversity. The T-RFLP data showed a distinct difference in the mite assemblage between the patch types. Where possible, T-RFLP peaks were matched to mite families using a reference 18S rDNA database, and the Aphelacaridae prevalent in the conventional samples at PGL sites were identified, as were prostigmatids and oribatids. We identified limits to the T-RFLP approach and this included an inability to distinguish some species whose DNA sequences were similar. Despite these limitations, the data still showed a clear difference between sites, and the molecular taxonomic inferences also compared well with the conventional ecological data. The results from this study indicated that the T-RFLP approach was effective in measuring mite assemblages in this system. The power of this technique lies in the fact that species diversity and abundance data can be obtained quickly because of the time taken to process hundreds of samples, from soil DNA extraction to data output on the gene analyser, can be as little as 4 days.  相似文献   

Survival of bacterial DNA and culturable bacteria in archived soils from the Rothamsted Broadbalk experiment     

Ian M. Clark  Penny R. Hirsch 《Soil biology & biochemistry》2008,40(5):1090-1102

Dried soil samples from many sources have been stored in archives world-wide over the years, but there has been little research on their value for studying microbial populations. Samples collected since 1843 from the Broadbalk field experiment on crop nutrition at Rothamsted have been used to document changes in the structure and composition of soils as agricultural practices evolve, also offering an invaluable record of environmental changes from the pre- to post-industrial era in the UK. To date, the microbial communities of these soils have not been studied, in part due to the well-documented drop in bacterial culturability in dried soils. However, modern molecular methods based on PCR amplification of DNA extracted directly from soil do not require bacterial cells to be viable or intact and may allow investigations into the legacy of bacteria that were present at the time of sample collection.

In a preliminary study, to establish if dried soils can provide a historical record of bacterial communities, samples from the Broadbalk soil archive dating back to 1868 were investigated and plots treated with either farmyard manure (FYM) or inorganic fertilizer (NPK) were compared. As anticipated, the processes of air-drying and milling greatly reduced bacterial viability whilst DNA yields declined less and may be preserved by desiccation. A higher proportion of culturable bacteria survived the archiving process in the FYM soil, possibly protected by the increased soil organic matter. The majority of surviving bacteria were firmicutes, whether collected in 2003 or in 1914, but a wide range of genera was detected in DNA extracted from the samples using PCR and DGGE of 16S rRNA genes. Analysis of DGGE band profiles indicated that the two plots maintained divergent populations. Sequence analysis of bands excised from DGGE gels, from a sample collected in 1914, revealed DNA from - and β-proteobacteria as well as firmicutes. PCR using primers specific for ammonia oxidizing bacteria showed similar band profiles across the two treatments in recently collected samples, however older samples from the NPK plot showed greater divergence. Primers specific for the genus Pseudomonas were designed and used in real-time quantitative PCR to indicate that archived soil collected in 1868 contained 10-fold less pseudomonad DNA than fresh soil, representing around 10⁵ genomes g⁻¹ soil. Prior to milling, dramatically less pseudomonad DNA was extracted from recently collected air-dried soil from the NPK compared to the FYM plot; otherwise, the two plots followed similar trends. Overall bacterial abundance, diversity and survival during the archiving process differed in the two soils, possibly due to differences in clay and soil organic matter content. Nevertheless, the results demonstrate that air-dried soils can protect microbial DNA for more than 150 years and offer an invaluable resource for future research.  相似文献   

The influence of soil properties on the structure of bacterial and fungal communities across land-use types   总被引：4，自引：1，他引：3  

Christian L. Lauber  Michael S. Strickland  Mark A. Bradford  Noah Fierer   《Soil biology & biochemistry》2008,40(9):2407

Land-use change can have significant impacts on soil conditions and microbial communities are likely to respond to these changes. However, such responses are poorly characterized as few studies have examined how specific changes in edaphic characteristics do, or do not, influence the composition of soil bacterial and fungal communities across land-use types. Soil samples were collected from four replicated (n = 3) land-use types (hardwood and pine forests, cultivated and livestock pasture lands) in the southeastern US to assess the effects of land-use change on microbial community structure and distribution. We used quantitative PCR to estimate bacterial–fungal ratios and clone libraries targeting small-subunit rRNA genes to independently characterize the bacterial and fungal communities. Although some soil properties (soil texture and nutrient status) did significantly differ across land-use types, other edaphic factors (e.g., pH) did not vary consistently with land-use. Bacterial–fungal ratios were not significantly different across the land-uses and distinct land-use types did not necessarily harbor distinct soil fungal or bacterial communities. Rather, the composition of bacterial and fungal communities was most strongly correlated with specific soil properties. Soil pH was the best predictor of bacterial community composition across this landscape while fungal community composition was most closely associated with changes in soil nutrient status. Together these results suggest that specific changes in edaphic properties, not necessarily land-use type itself, may best predict shifts in microbial community composition across a given landscape. In addition, our results demonstrate the utility of using sequence-based approaches to concurrently analyze bacterial and fungal communities as such analyses provide detailed phylogenetic information on individual communities and permit the robust assessment of the biogeographical patterns exhibited by soil microbial communities.  相似文献   

菊花绿变病植原体在中国的发生及分子鉴定     

李正男  鞠明岫  马强  张磊  孙平平  相宁 《植物检疫》2020,(3):37-42

对内蒙古农业大学校园内表现花器绿变症状的菊花样品进行采集和DNA提取,应用植原体16S rRNA基因和rp基因的引物进行巢式PCR扩增,从感病样品中分别扩增得到了长度均约为1.2 kb的片段。序列一致性分析表明,菊花绿变植原体16S rRNA基因与翠菊黄化植原体匈牙利风信子株系(GenBank登录号MN080271)、印度玉米株系(KY565571)、印度繁缕株系(KC623537)和印度马铃薯株系(KC312703)的核酸一致性最高,为99.9%,rp基因序列与翠菊黄化植原体立陶宛洋葱株系(GU228514)的核酸一致性最高,为99.8%。基于16S rRNA基因和rp基因构建系统进化树时发现,菊花绿变植原体均与16SrI-B亚组成员聚为一起。16S rRNA基因相似性系数分析表明,菊花绿变植原体与洋葱黄化植原体(AP006628)的相似性系数最高为1.00,洋葱黄化植原体(AP006628)在分类上属于16SrI-B亚组。因此,我们可以确定该菊花绿变植原体属于16SrI-B亚组。这是我国首次报道菊花绿变病的发生。  相似文献