Phylogenetic relationships between rice dwarf phytoreovirus isolates from five countries

Rice dwarf virus isolates were collected from several locations in Japan, the Philippines, China, Nepal and Korea. Genomic dsRNA segment profiles in polyacrylamide gel electrophoresis differed among the isolates. There were less differences in the profiles between isolates from Japan and Korea than in those between these two Countries and others. Nucleic acid hybridization was used to examine the extent of genomic variation. Full-length cDNAs to all genomic segments encoding non-structural proteins (S4, S6, S9, S10, S11 and S12) were synthesized from two Japanese isolates, and were used for dot-blot hybridization. Hybridizations using probes generated from the full-length cDNA clones failed to differentiate isolates from different geographical areas. However, cDNA probes covering a variable region of S12 were able to distinguish Japanese and Korean isolates from those of other countries. Phylogenetic tree analysis based on the amino acid sequence of P12 encoded by S12 grouped Japanese and Korean isolates together. The Chinese isolates from two different locations (Yunnan and Fujian) were closely related to each other, and were the most distantly related to Japanese and Korean isolates.     

稻瘟菌双分病毒MoPV2特性研究

稻瘟病是稻瘟菌引起的一种世界性病害,每年造成水稻大幅减产。真菌病毒是指能够在真菌体内进行复制和繁殖的病毒,可以作为生物防治的资源。本实验从发病的水稻叶片上采用单孢分离的方法获得纯化培养的稻瘟菌菌株YC13。菌株YC13携带多条dsRNA片段,其中片段F1与Magnaporthe oryzae virus 2(MoV2)的Coat Protein(CP)和RNA-dependent RNA polymerase(RdRp)的氨基酸序列均具有99%的同源性,确定为MoV2的基因组;片段F4、F5序列与双分病毒Penicillium stoloniferum virus F(Ps V-F)的RdRp和CP的氨基酸序列分别具有69%和63%的同源性,命名为Magnaporthe oryzae partitivirus virus 2(MoPV2)。MoPV2的基因组含有2条dsRNA:dsRNA 1编码RdRp,dsRNA 2编码CP。根据MoPV2的RdRp编码的氨基酸序列将MoPV2归属于双分病毒科(Partitiviridae)G ammapartitivirus属,是一种新的真菌病毒。通过病毒粒子转染,将MoPV2转到稻瘟菌菌株RB11。与菌株RB11相比,带毒菌株RB11T25的分生孢子产生量显著减少,并且对大麦活体的致病性也有所降低,但其他生物学特征均无明显的影响。本研究在稻瘟菌中发现了一种新的真菌病毒,该病毒能够使稻瘟菌致病力下降,为稻瘟病的防治提供了潜在的病毒资源。     

进境加拿大豌豆中豌豆细菌性疫病菌的检测

 利用MT选择性培养基从进境加拿大豌豆样品上分离到一株细菌分离物(编号1314),对该分离物进行PCR检测、16S和23S rRNA序列扩增、多位点序列分析、Biolog测定、烟草过敏性反应和致病性测试。豌豆细菌性疫病菌(Pseudomonas syringae pv. pisi, Ppi)特异引物AN7F/AN7R扩增分离物1314和Ppi菌株ATCC 11043得到预期272 bp的条带,二者的PCR产物序列一致,与GenBank中Ppi (X97405)的序列相似性为99.57%。分离物1314的部分16S rRNA、23S rRNA序列以及16S-23S序列均与Ppi菌株ATCC 11043一致。选择gap1、gltA、gyrB和ropD 4个看家基因进行多位点序列分析,系统发育树显示分离物1314与Ppi菌株聚在同一组内。Biolog鉴定结果表明:分离物1314为Ppi,PROB值为0.898,SIM为0.72。该分离物人工接种豌豆茎秆能引起水渍状症斑,接种烟草叶片产生过敏性反应。基于上述试验结果,将分离物1314鉴定为豌豆细菌性疫病菌。     

Isolation and characterization of a novel simazine-degrading beta-proteobacterium and detection of genes encoding s-triazine-degrading enzymes

A moderately persistent herbicide, simazine, has been used globally and detected as a contaminant in soil and water. The authors have isolated a simazine-degrading bacterium from a simazine-degrading bacterial consortium that was enriched using charcoal as a microhabitat. The isolate, strain CDB21, was gram-negative, rod-shaped (0.5-0.6 microm x 1.0-1.2 microm) and motile by means of a single polar flagellum. Based on 16S rRNA sequence analysis, strain CDB21 was identified as a novel beta-proteobacterium exhibiting 100% sequence identity with the uncultured bacterium HOClCi25 (GenBank accession number AY328574). PCR using primers that were specific for the genes of the atrazine-degrading enzymes (atzABCDEF) of Pseudomonas sp. strain ADP showed that strain CDB21 also possessed the entire set of genes of these enzymes. Nucleotide sequences of the atzCDEF genes of strain CDB21 were 100% identical to those of Pseudomonas sp. strain ADP. Sequence identity of the atzA genes between these bacteria was 99.7%. The 398-nucleotide upstream fragment of the atzB gene of strain CDB21 was 100% identical to ORF30 of Pseudomonas sp. strain ADP, and the 1526-nucleotide downstream fragment showed 99.8% sequence similarity to the atzB gene of the pseudomonad.     

GA1-2菌株的分离鉴定及其对香蕉尖孢镰刀菌的抑菌效果

为了从土壤中分离筛选对香蕉尖孢镰刀菌具有良好拮抗作用的放线菌,采用平板稀释涂布法从四川省会理县干热河谷小麦根际土壤中进行放线菌分离,并采用平板对峙法和孢子萌发法进行筛选,通过形态特征、培养特征、生理生化特征以及16S r DNA序列分析对筛选菌株进行鉴定。结果表明,从四川省会理县干热河谷小麦根际土壤筛选获得一株对香蕉尖孢镰刀菌4号生理小种Fusarium oxysporum f.sp.cubense race 4(FOC4)菌丝和孢子萌发都有很强抑制作用的菌株GA1-2,对FOC4菌丝和孢子萌发抑制率分别为36.34%和94.81%。菌株GA1-2与薰衣草灰链轮丝菌Streptoverticillium lavenduligriseum的亲缘关系最近,相似率达99.85%,且其形态特征、培养特征、生理生化特征也与薰衣草灰链轮丝菌基本相符,因此将菌株GA1-2初步鉴定为薰衣草灰链轮丝菌。     

来源于桃和苹果的苹果褪绿叶斑病毒的部分分子生物学特性和cp基因的原核表达

 从桃和苹果上分离得到苹果褪绿叶斑病毒ACLSV-HBP和ACLSV-C2个分离物,采用RT-PCR法进行扩增,所获扩增片段经序列测定,其全长分别为1768nt(ACLSV-HBP)和1751nt(ACLSV-C)。这2个分离物扩增片段全长的同源性为83%,mp基因片段核苷酸和推导编码氨基酸序列同源性分别为82.6%和87.1%;cp基因均由582nt组成,其核苷酸和推导编码氨基酸序列同源性分别为87.8%和95.9%。将2个分离物的cp基因与已报道ACLSV分离物进行序列同源性比较,结果显示ACLSV-HBP与SX/2的cp基因核苷酸序列及推导编码氨基酸序列同源性最高,分别为94.0%和96.4%。将ACLSV-HBP分离物的cp基因克隆到原核表达载体pGEX-KG,在大肠杆菌BL21(DE3)中诱导表达,SDS-PAGE分析表明,融合蛋白大小约为46kDa。Western-blot分析表明,该基因在大肠杆菌内得到高效表达,融合蛋白具有抗原性。     

蝴蝶兰软腐病中一种新致病菌的分离与鉴定

 Soft rot disease often affects Phalaenopsis amabilis during the growing season. However, the pathogen of the disease is remaining poorly studied. In this study, bacterial strain R1 was isolated from soft rot tissues in Wuhan. The pathogenic, morphological, physiological, biochemical tests and 16S rDNA sequence analysis were carried out. The homology of 16S rDNA sequence between strain R1 and Pseudomonas grimontii was 99.72%, and its physiological and biochemical properties were also similar to those of Pseudomonas grimontiis. All these evidences indicated that strain R1 could be identified as a novel strain of Pseudomonas grimontii. The pathogenicity of the novel isolate was proved according to the Koch's postulates. This is the first report that Pseudomonas grimontii can cause soft rot disease of Phalaenopsis amabilis.     

生防细菌L5生防相关因子的初步分析及其种类鉴定

从扬州郊区土壤中分离到细菌菌株L5,该菌株抑菌谱广,对多种病原真菌都有明显的拮抗能力,离体叶片生物测定结果表明菌株L5对番茄灰霉病防效达72%.对该菌株的生防相关性状进行分析,结果表明菌株L5可产生硝吡咯菌素(Pyrrolnitrin)和嗜铁素等抗菌物质.经过16S rDNA序列、16S-23S rDNA间区序列同源性分析和生理生化性状的测定,将该菌株鉴定为气味沙雷氏菌(Serratia odorifera).细菌菌株L5包含2个16S-23S rDNA的间区(IGSs),其中IGS1内含tRNA Glu基因,间区类型属于IGSG;IGS2内含tRNA lle和tRNA Aia基因,间区类型属于IGS LA.     

辽中地区西瓜花叶病病原的分子鉴定

 利用ELISA和RT-PCR方法对采自我国辽中地区的西瓜花叶病样品进行检测,表明其病原为黄瓜绿斑驳花叶病毒(Cucumber green mottle mosaic virus,CGMMV)。将此分离物(CGMMV-Wcn)的外壳蛋白基因克隆后进行序列分析,结果表明其cp基因由486个碱基组成,编码161个氨基酸,与已报道的其它分离物一致;CGMMV-Wcn所致症状与西瓜株系(CGMMV-W)相同,且二者cp基因的氨基酸序列完全一致,因此该分离物应为CGMMV-W。     

Sequence and evolutionary analysis of ribosomal DNA from Huanglongbing (HLB) isolates of Western India

Citrus greening (Huanglongbing, HLB) is a widespread and economically important citrus disease all over the world. The disease is caused by a phloem-limited fastidious gram negative bacterium, “Candidatus Liberibacter spp.” which belongs to the alpha-proteobacteria group classified on the basis of its 16SrDNA sequence. Although the pathogen has been classified under three distinct groups, viz. Asian, African and American isolates, nothing is known about the status and the molecular variabilities among the Indian HLB isolates collected from different citrus cultivars grown in India. Five different HLB isolates showing variable symptoms based on their severity of infection on different citrus, viz. Mosambi, Rangpur lime, Cleopatra mandarin, acid lime and rough lemon, were studied by PCR amplification, sequence and evolutionary analysis of their 16S and 16S/23S rDNA intergenic regions. Analysis of the 16S/23S rDNA intergenic region separated all five Indian isolates from existing African isolates but failed to differentiate among Asian, American and Indian isolates. However, further analysis of complete 16S rDNA clearly indicated that Indian isolates fall within the Asian HLB group. Overall, our results suggest that all the five Indian HLB isolates taken for the current analysis belong to the Candidatus Liberibacter asiaticus strain, which showed distinct sequence variabilities and produced noticeable symptoms on the citrus trees. These results provide a robust framework for understanding how differences in pathogenicity among various HLB isolates may be related to evolutionary history.     

安徽桑黄花型萎缩病植原体16S rDNA序列分析及分子检测

 Mulberry yellow dwarf(MYD)disease is an quarantine disease and the causal agent is a phytoplasma.Two pairs of published universal primer, P1/P7 and Rm16F2/Rm16R1, based on the 16S-23S rDNA sequence of phytoplasma and total DNA extracted from infected mulberry tissues were employed for PCR and nested-PCR detection.The results revealed that a phytoplasma-specific 1 830 bp fragment with a G+C content of 46.01% was sequenced(GenBank accession No.GQ249410).The sequence shared 99.7% and 99.8% identity with aster yellows, the representatiive phytoplasma in 16SrI group, and mulberry dwarf phytoplasma classified into subgroup B in 16SrI group and named as the MYD phytoplasma strain Anhui(MYD-Anh).A phylogenetic tree based on 16S rDNA sequences was constructed and showed that MYD-Anh was clustered into 16SrI group.Identity of 16S rDNA sequence between MYD-Anh and mulberry yellow dwarf phytoplasma strain Zhenjiang(MD-zj) was nearly 100%, and they might belong to the same strain.Nested-PCR was used to detect the pathogenic phytoplasma from the differential tissues of mulberry infected with MYD-Anh.The results showed that a phytoplasma-specific 1.4 kb fragment was amplified with total DNA extracted from bark and vein.Nested-PCR was more sensitive than PCR for detecting MYD phytoplasma.     

河南省地黄病毒病初步鉴定

 利用血清学、RT-PCR并结合核苷酸序列测定等方法,对河南省地黄病毒病进行了初步鉴定。结果表明,烟草花叶病毒(TMV)为侵染地黄的主要病毒;对TMV地黄分离物(TMV-RH) CP基因的序列分析结果表明,TMV-RH与TMV-U1株系CP基因的核苷酸同源性为86.5%,氨基酸同源性为94.3%;与已发表的TMV其它株系CP基因的核苷酸同源性在76.3%~88.5%之间,氨基酸同源性在79.3%~95.0%之间,同源性较低。根据不同株系CP的氨基酸序列进化树分析,推测该分离物可能为TMV的一个新株系。     

Phylogenetic Analysis of 16S rRNA Genes and PCR Analysis of the nec1 Gene from Streptomyces spp. Causing Common Scab, Pitted Scab, and Netted Scab in Finland

ABSTRACT The sequences of the 16S rRNA genes (nucleotides 29 to 1,521) from various Streptomyces strains pathogenic to potato were compared. These included 10 pathogenic Streptomyces strains isolated from potato scab lesions in Finland, the type strains of S. aureofaciens NRRL 2209(T) and S. lydicus ATCC 25470(T), 'S. griseus subsp. scabies' ATCC 10246, and two S. griseus strains that were originally deposited to the collection as pathogens. The nucleotide sequence (>94.5% sequence identity [SI]) and length (1,469 to 1,481 nucleotides) of the analyzed region varied. Phylogenetic analysis of 16S rRNA genes placed Finnish strains into three species, supported by previously characterized morphological and physiological traits. Six Finnish strains, including two strains that deviated from the others in one trait (no spiral sporophores or D-xylose utilization), had identical 16S rRNA genes and were identified as S. scabies (99.9% SI to S. scabies ATCC 49173). Three Finnish strains were identified as S. turgidiscabies, a species previously described only in Japan (99.9% SI to S. turgidiscabies ATCC 700248). Finnish strain 317 and S. aureofaciens NRRL 2209 (99.8% SI) were placed in a distinct phylogenetic cluster together with Kitosatospora spp., which suggests that S. aureofaciens may belong to the recently revived genus Kitosatospora. In pathogenicity tests, S. scabies caused characteristic symptoms of common scab, S. turgidiscabies caused mainly pitted scab, and S. aureofaciens caused netted scab and necrotic lesions on stolons of potato cultivars Bintje and Matilda in the greenhouse. The nec1 gene and the intergenic region between nec1 and the 5' transposase pseudogene ORFtnp were successfully amplified by polymerase chain reaction from S. scabies ATCC 49173 and the pathogenic Finnish strains of S. scabies, but not from a nonpathogenic strain of S. scabies, three pathogenic and two nonpathogenic strains of S. turgidiscabies, and S. aureofaciens.     

12种寄主来源的茄科雷尔氏菌16S-23SrDNA间隔区序列比较

应用PCR方法,获得了分离自广东番茄、茄子、辣椒、烟草、空心菜、沙姜、姜、马铃薯、花生、菊花、桑树和藿香等12种作物21个茄科雷尔氏菌菌株的16S 23S rDNA 间隔区序列（ITS）。序列分析结果表明,除HZ 1菌株外,其余20个茄科雷尔氏菌菌株ITS序列长均为503 bp,序列间相似性99.2%~100%,序列间差异仅1~4 bp;而HZ 1菌株的ITS序列长为498 bp,与其他菌株的ITS序列相似性为95.4%~95.6%。这些结果说明,这21株来源于12种不同寄主的茄科雷尔氏菌菌株的16S 23S rDNA ITS序列比较保守。系统进化分析显示,仅菌株HZ 1聚类于茄科雷尔氏菌区组2中,其余20个菌株均聚类于茄科雷尔氏菌区组1中。     

Differential detection and genetic relatedness of phytoplasmas in papaya

The genetic relatedness of phytoplasmas associated with dieback (PDB), yellow crinkle (PYC) and mosaic (PM) diseases in papaya was studied by restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene and 16S rRNA/23S rRNA spacer region (SR). RFLP and SR sequence comparisons indicated that PYC and PM phytoplasmas were identical and most closely related to members of the faba bean phyllody strain cluster. By comparison the PDB phytoplasma was most closely related to Phormium yellow leaf (PYL) phytoplasma from New Zealand and the Australian grapevine yellows (AGY) phytoplasma from Australia. These three phytoplasmas cluster with the stolbur and German grapevine yellows (VK) phytoplasmas within the aster yellows strain cluster. Primers based on the phytoplasma tuf gene, which amplify gene products from members of the AY strain cluster, also amplified a DNA product from the PDB phytoplasma but not from either the PYC or PM phytoplasmas. Primers deduced from the 16S rRNA/SR selectively amplified rDNA sequences from the PDB and AGY phytoplasmas but not from other members of the stolbur strain cluster. Similarly, primers designed from 16S rRNA/SR amplified rDNA from the PYC and PM phytoplasmas but not from the PDB phytoplasma. These primers may provide for more specific detection of these pathogens in epidemiological studies.     

Identification, Phylogenetic Analysis, and Biological Characterization of Serratia marcescens Strains Causing Cucurbit Yellow Vine Disease

ABSTRACT A serious vine decline of cucurbits known as cucurbit yellow vine disease (CYVD) is caused by rod-shaped bacteria that colonize the phloem elements. Sequence analysis of a CYVD-specific polymerase chain reaction (PCR)-amplified 16S rDNA product showed the microbe to be a gamma-proteobacterium related to the genus Serratia. To identify and characterize the bacteria, one strain each from watermelon and zucchini and several noncucurbit-derived reference strains were subjected to sequence analysis and biological function assays. Taxonomic and phylogenetic placement was investigated by analysis of the groE and 16S rDNA regions, which were amplified by PCR and directly sequenced. For comparison, eight other bacterial strains identified by others as Serratia spp. also were sequenced. These sequences clearly identified the CYVD strains as Serratia marcescens. However, evaluation of metabolic and biochemical features revealed that cucurbit-derived strains of S. marcescens differ substantially from strains of the same species isolated from other environmental niches. Cucurbit strains formed a distinct cluster, separate from other strains, when their fatty acid methyl ester profiles were analyzed. In substrate utilization assays (BIOLOG, Vitek, and API 20E), the CYVD strains lacked a number of metabolic functions characteristic for S. marcescens, failing to catabolize 25 to 30 compounds that were utilized by S. marcescens reference strains. These biological differences may reflect gene loss or repression that occurred as the bacterium adapted to life as an intracellular parasite and plant pathogen.