RNA- and DNA-based profiling of soil fungal communities in a native Australian eucalypt forest and adjacent Pinus elliotti plantation     

Brigitte A. Bastias  Zhihong Xu 《Soil biology & biochemistry》2007,39(12):3108-3114

Total and active soil fungal communities in a native eucalypt forest and first rotation Pinus elliotti plantation were investigated by direct extraction of DNA and RNA from soil. Terminal restriction fragment length polymorphism (T-RFLP) analysis of internal transcribed spacer (ITS) and 18S rRNA profiles indicated that total and active fungal communities differed significantly in both forest types. This was supported by DGGE profile analysis on an individual plot basis for both forest types and when groups in the canonical analysis were redefined to allow comparison between forest types. Analyses of both ITS and 18S T-RFLP profiles indicated that conversion from native eucalypt forest to P. elliottii plantation may significantly alter total and active soil fungal communities. ITS DGGE (DNA) and 18S (RNA) profiles also suggested differences in fungal communities in the two forest types. No significant separation of the fungal communities in the two forest types was observed, however, when ITS DGGE (RNA) profiles were compared. Overall, the data suggest that conversion from native eucalypt forest to P. elliottii plantation at the Beerburrum State Forest in subtropical Australia has significantly altered soil fungal communities.  相似文献   

Influence of repeated prescribed burning on the soil fungal community in an eastern Australian wet sclerophyll forest     

Brigitte A. Bastias  Tim Blumfield  John W.G. Cairney 《Soil biology & biochemistry》2006,38(12):3492-3501

A long-term prescribed burning experiment, incorporating replicated plots that receive burning biennially (2 yr burn) or quadrennially (4 yr burn) and unburned controls, has been maintained in a wet sclerophyll forest at Peachester, Queensland, Australia since 1972. In 2003 we extracted DNA from soil collected from the experimental plots and investigated the influence of the burning on the soil fungal community by comparing denaturing gradient gel electrophoresis (DGGE) profiles of PCR-amplified partial rDNA internal transcribed spacer regions (ITS1). Canonical analysis of principal coordinates (CAP) of the DGGE profiles of the upper 10 cm of the soil profile grouped the data strongly according to treatment, indicating that both burning regimes significantly altered fungal community structure compared to the unburned controls. In contrast, no obvious trend was observed for soil from a depth of 10-20 cm of the profile. Sequencing of selected DGGE bands found no obvious patterns of presence/absence of taxonomic groups between the treatments. Analysis of soil nitrogen and carbon by mass spectrometry indicated that total soil C and N, along with both gross and net N mineralisation, were significantly lower in 2 yr plots compared to control and 4 yr plots.  相似文献   

Molecular phylogeny of Chinese vegetable mustard (<Emphasis Type="Italic">Brassica juncea</Emphasis>) based on the internal transcribed spacers (ITS) of nuclear ribosomal DNA     

Xiao-Hua Qi  Ming-Fang Zhang  Jing-Hua Yang 《Genetic Resources and Crop Evolution》2007,54(8):1709-1716

Sequence variation of nuclear internal transcribed spacer regions of ribosomal DNA (ITS1, 5.8S rRNA and ITS2) from Chinese vegetable mustards (AB-genome) and its putative parents Brassica rapa (the A-genome) and Brassica nigra (the B-genome) were used to investigate the molecular phylogeny and the probable evolutional pattern of this amphidiploid species that uniquely formed in China. Totally, 16 accessions of Chinese vegetable mustard those covering nearly all the diverse variations were included in this study, and together with three accessions of B. rapa and one accession of B. nigra. The results disclosed two strongly supported clades, one containing four accessions of vegetable mustard which have closer relationship with B-genome species “B.nigra” lineage and the other containing 12 accessions of B. juncea and three A-genome accessions. This classification was in disagreement with the evidence from chloroplast DNA, mitochondrial DNA, nuclear DNA restriction fragment length polymorphism (RFLP), which suggested that B. juncea was closely related to the A-genome type. For the incongruence, we speculated that the B. juncea crops derived from Chinese have evolved through different recombined events of the diploid morphutypes and evolved unidirectional concerted evolution. The traditional phenotypic classification of B. juncea was not wholly supported by ITS results, and hence the phylogenetic relationships among these subspecies need to be reconsidered on molecular level.  相似文献   

一株具有抗菌活性有丝真菌092902的鉴定     

张志华 《安徽农业科学》2015,(35):229-230

[目的]对一株具有抗菌活性的有丝真菌092902进行鉴定.[方法]采用典型形态特征、生理生化碳源同化及ITS序列3种鉴定方法.[结果]从形态方面,菌株092902与标准菌株黑曲霉As3.40菌落形态和显微形态观察极为相似,初步判断菌株092902属于黑曲霉;从Biolog微生物鉴定仪碳源同化方面,鉴定结果是黑曲霉;从菌株ITS序列进一步确认菌株092902与NCBI数据库中黑曲霉相似率达到100％.[结论]从这3个方面共同对菌株092902作出鉴定,该菌属于黑曲霉.  相似文献   

Phoma–Didymella complex on hybrid arctic bramble with wilting symptoms     

H. Lindqvist-Kreuze  S. Hellqvist  H. Koponen  J. P. T. Valkonen † 《Plant pathology》2003,52(5):567-578

Pycnidia containing conidia characteristic of Phoma spp. and pseudothecia containing ascospores characteristic of Didymella applanata were isolated from edges of expanding stem lesions and dead stems of wilted cultivated hybrid arctic bramble plants ( Rubus arcticus nothossp. stellarcticus ) in Sweden in 1998 and 1999. The fungi were morphologically similar when grown on culture media, but some differences in growth rate were observed. They were also similar to the reference isolates of D. applanata (anamorph Phoma argillacea ). However, they were different from an isolate of Phoma sp. (HPP 38) isolated from cultivated arctic bramble ( R. arcticus ssp. arcticus ) in Finland in 1980, and from reference isolates of Phoma glomerata isolated from other hosts. Multivariate analysis of growth rate data and conidial dimensions measured in vitro indicated that the fungi isolated from hybrid arctic bramble in Sweden were not distinguishable from D. applanata , but were clearly distinct from P. glomerata and P. exigua. Furthermore, they had identical ITS1 and ITS2 sequences, and were placed in a phylogenetic clade very closely related to the clade that contained isolates of D. applanata isolated from raspberry ( Rubus idaeus ). In contrast, isolate HPP 38 from Finland was placed in a clade with P. exigua. These data indicate that the Swedish isolates infecting arctic bramble belong to a strain of D. applanata that differs from the isolate infecting raspberry only by two common nucleotide substitutions in ITS2. Fungi of the Phoma–Didymella complex on wild and cultivated arctic bramble (a total of 291 plants showing symptoms sampled from 37 sites) were detected by a PCR-based assay and found to be common in northern Sweden, but rare, albeit widely distributed, in Finland.  相似文献   

Development of specific PCR primers for identification and detection of <Emphasis Type="Italic">Phytophthora capsici</Emphasis> Leon     

C.?Silvar  J.?M.?Duncan  D.?E.?L.?Cooke  N.?A.?Williams  J.?Díaz  F.?MerinoEmail author 《European journal of plant pathology / European Foundation for Plant Pathology》2005,112(1):43-52

A PCR-based method was developed for the identification and detection of Phytophthora capsici in pepper plants. Three PCR primers (CAPFW, CAPRV1 and CAPRV2) specific for P. capsiciwere designed based on the sequence of its internal transcribed spacer regions. CAPFW/CAPRV1 amplify a 452 bp product from P. capsici DNA whereas CAPFW/CAPRV2 a 595 bp fragment; neither set amplifies DNA from pepper or several fungi pathogenic to pepper. In conventional (single-round) PCR, the limit of detection was 5 pg DNA for both primer sets, whereas in nested PCR the detection limit for both was of 0.5 fg. However, when the dilution series of target DNA were spiked with plant DNA, amplification declined two-fold in both conventional and nested PCR. The CAPFW/CAPRV2 set in conventional PCR was used to detect P. capsici DNA in inoculated plants. Detection occurred as soon as 8h post-inoculation in stem samples from infected but still symptomless plants. The method was also tested to detect fungal DNA in infected soils.  相似文献   

Development and validation of species-specific primers that provide a molecular diagnostic for virus-vector longidorid nematodes and related species in German viticulture     

Judith Hübschen  Lilo Kling  Ulrike Ipach  Volker Zinkernagel  Derek Brown  Roy Neilson 《European journal of plant pathology / European Foundation for Plant Pathology》2004,110(9):883-891

The nematode species Longidorus attenuatus, L. elongatus, L. macrosoma and Paralongidorus maximusare economically important pests to the viticulture industry due to their ability to vector two nepoviruses (Raspberry Ringspot Virus and Tomato Black Ring Virus) to grapevines. In Germany, these species occur in vineyard soil with other non-vector but morphologically similar longidorid species, L. helveticus, L.profundorum and L. sturhani. Species-specific primers were designed from ribosomal DNA for all seven species to facilitate taxonomic identification for non-specialists. Primers were assessed for their reliability by screening, where possible, a number of populations of each species. Furthermore, their selectivity and sensitivity were determined when challenged with closely related longidorid species and general nematode communities typical of vineyard soil. A multiplex approach using a common forward primer combined with species-specific reverse primers enabled three target nematode species to be detected in the same PCR reaction. All primers were highly specific, detecting all nematode developmental forms from disparate populations and were sufficiently sensitive to detect a single target nematode within a whole nematode community typical of a vineyard soil comprising of a range of non-target species. Given their specificity, sensitivity and reliability, these diagnostic primers should be of great benefit to both phytosanitary/quarantine services related to the viticulture industry and also as a decision management tool for growers.  相似文献   

Detection of genomic DNA of the crayfish plague fungus Aphanomyces astaci (Oomycete) in clinical samples by PCR     

Oidtmann B  Schaefers N  Cerenius L  Söderhäll K  Hoffmann RW 《Veterinary microbiology》2004,100(3-4):269-282

A diagnostic procedure, based on a polymerase chain reaction method (PCR) was developed to detect infection of crayfish with the Oomycete Aphanomyces astaci. A set of oligonucleotide primers was designed to specifically amplify A. astaci DNA in the ITS region surrounding the 5.8S rDNA gene. The PCR amplifies a 115 bp amplicon. The specificity of the primers was demonstrated by testing on 27 A. astaci strains and against 20 non-A. astaci Oomycetes and 5 fungal species. Most of the non-A. astaci Oomycete or fungal species included in the study are either known parasites of freshwater crayfish cuticle or can be found in their natural environment. Specificity was also tested against crayfish tissue and some known parasites and bacteria infecting crayfish.

A protocol for the extraction of A. astaci DNA from infected crayfish tissue was developed. The optimised method allows the detection of two genome equivalents of purified A. astaci genomic DNA.

The method was tested on noble crayfish (Astacus astacus), artificially infected with A. astaci. Detection of A. astaci was possible at the very first time of sampling, which was 2 days after the beginning of spore exposure.  相似文献   

芦笋茎枯病菌的鉴定及区域差异性分析   总被引：4，自引：3，他引：1  

杨迎青  李湘民  孟凡  兰波  张洁 《植物保护学报》2012,39(4):315-320

芦笋茎枯病是一种世界性分布的毁灭性病害,为准确鉴定其致病菌和探明不同区域菌株的分化程度,通过形态学观察和核糖体DNA内转录间区(rDNA ITS)序列比对进行形态学和分子生物学鉴定,比较五省份菌株的生物学特性和ITS序列上的差异,并进行系统发育分析。结果表明,芦笋茎枯病的致病菌为天门冬拟茎点霉Phomopsis asparagi。海南省菌株的菌丝生长较快,培养5天后的平均直径为8.5 cm;培养14天后,江西省菌株由白色变为淡绿色,其它各省菌株由白色变为灰白色,海南省菌株的菌落呈现同心轮纹状;福建省菌株产生的分生孢子器较多,平均60个/皿;五省菌株在1～238 bp和298～591 bp的ITS区段存在差异性碱基,其中河北省菌株的差异性碱基数最多;五省菌株大致聚为2个组群,河北省菌株单独聚为1个组群,其它省份菌株聚为1个组群,天门冬拟茎点霉P.asparagi与叶下珠生拟茎点霉P.phyllanthicola亲缘关系较近。  相似文献   

中国鹤虱属(Lappula Moench)分子系统学研究     

黄建峰  张明理 《干旱区研究》2012,29(5):811-815

以黄花软紫草(Arnebia guttata Bunge)和双柱紫草(Coldenia procumbens L.)为外类群,用PAUP*4.0 对鹤虱属(Lappula Moench)13个代表种的核糖体ITS和叶绿体rpS16序列进行分子系统发育分析。采用最大简约法和最大似然法对获得的序列矩阵进行分析,得到一致性进化树。拓扑结构显示,Lappula为单系类群,前人对该属属下阶元的划分带有一定的人为主观性,不能完全真实反映其系统发育关系。结合形态学特征,得出该属植物大致沿着花由小型到大型,果实由同型到异型,小坚果边缘有瘤或刺到具翅这样的路线演化的。  相似文献