Genotyping of Serratia marcescens Strains Associated with Cucurbit Yellow Vine Disease by Repetitive Elements-Based Polymerase Chain Reaction and DNA-DNA Hybridization

ABSTRACT The bacterium that causes cucurbit yellow vine disease (CYVD) has been placed in the species Serratia marcescens based on 16S rDNA and groE sequence analysis. However, phenotypic comparison of the organism with S. marcescens strains isolated from a variety of ecological niches showed significant heterogeneity. In this study, we compared the genomic DNA of S. marcescens strains from different niches as well as type strains of other Serratia spp. through repetitive elements-based polymerase chain reaction (rep-PCR) and DNA-DNA hybridization. With the former, CYVD strains showed identical banding patterns despite the fact that they were from different cucurbit hosts, geographic locations, and years of isolation. In the phylogenetic trees generated from rep-PCR banding patterns, CYVD strains clearly were differentiated from other strains but formed a loosely related group with S. marcescens strains from other niches. The homogeneity of CYVD strains was supported further by the DNA relatedness study, in that labeled DNA from the cantaloupe isolate, C01-A, showed an average relative binding ratio (RBR) of 99%, and 0.33% divergence to other CYVD strains. Used as a representative strain of CYVD, the labeled C01-A had a RBR of 76%, and a 4.5% divergence to the S. marcescens type strain. These data confirm the previous placement of CYVD strains in S. marcescens. Our investigations, including rep-PCR, DNA-DNA hybridization, and previous phenotyping experiments, have demonstrated that CYVD-associated strains of S. marcescens cluster together in a group significantly different from other strains of the species.     

Brenneria quercina and Serratia spp. isolated from Spanish oak trees: molecular characterization and development of PCR primers

Brenneria quercina has been reported as one of the causal agents of oak decline in Spain. To investigate the bacterial variability of this pathogen from different Spanish oak forests, a collection of 38 bacterial isolates from seven geographic locations and from different oak species was analysed by sequencing 16S rDNA and rep-PCR fingerprinting. All Spanish isolates of B. quercina were grouped by rep-PCR into a homogenous cluster that differed significantly from B. quercina reference strains from California. 16S rDNA analysis revealed that 34 out of 38 isolates were Brenneria . However, four isolates belonged to the genus Serratia , suggesting that this bacterium could cause cankers in oak trees. The information obtained by rep-PCR fingerprint analysis was used to develop PCR primers for the sensitive and specific detection of B. quercina from infected plant tissues. Pathogenicity tests performed with Brenneria and Serratia isolates showed that both were able to grow and cause cankers in oak trees.     

Pseudomonas syringae pv. coryli, the Causal Agent of Bacterial Twig Dieback of Corylus avellana

ABSTRACT Thirty-eight bacterial strains isolated from hazelnut (Corylus avellana) cv. Tonda Gentile delle Langhe showing a twig dieback in Piedmont and Sardinia, Italy, were studied by a polyphasic approach. All strains were assessed by fatty acids analysis and repetitive sequence-based polymerase chain reaction (PCR) fingerprinting using BOX and ERIC primer sets. Representative strains also were assessed by sequencing the 16S rDNA and hrpL genes, determining the presence of the syrB gene, testing their biochemical and nutritional characteristics, and determining their pathogenicity to hazelnut and other plants species or plant organs. Moreover, they were compared with reference strains of other phytopathogenic pseudomonads. The strains from hazelnut belong to Pseudomonas syringae (sensu latu), LOPAT group Ia. Both fatty acids and repetitive-sequence-based PCR clearly discriminate such strains from other Pseudomonas spp., including P. avellanae and other P. syringae pathovars as well as P. syringae pv. syringae strains from hazelnut. Also, the sequencing of 16S rDNA and hrpL genes differentiated them from P. avellanae and from P. syringae pv. syringae. They did not possess the syrB gene. Some nutritional tests also differentiated them from related P. syringae pathovars. Upon artificial inoculation, these strains incited severe twig diebacks only on hazelnut. Our results justify the creation of a new pathovar because the strains from hazelnut constitute a homogeneous group and a discrete phenon. The name of P. syringae pv. coryli is proposed and criteria for routine identification are presented.     

西瓜细菌性果斑病菌的16S rDNA序列分析及特异性引物的设计

 利用细菌16S rDNA基因的通用引物对16个供试菌株进行PCR扩增,把扩增产物进行核苷酸序列测定。将获得的序列与GenBank中相关菌株的16S rDNA序列进行同源性分析。以此设计出检测A.a.c的特异性引物,并利用最大简约法构建了16S rDNA系统演化树。系统演化关系分析表明,6~9号供试菌株的16S rDNA序列与A.a.c标准菌株仅有3个位点的差异,其同源性均在99.8%以上,在构建的系统演化树上,它们聚为同一个族群。利用设计的一对特异性引物(BFB64/65),对各供试菌株进行PCR检测,结果只有A.a.c相关菌株产生扩增条带,产物大小与预期一致。     

进境韩国大花蕙兰上唐菖蒲伯克氏菌的分离鉴定及生物学研究

 大花蕙兰（Cymbidium hybridum）,又名虎头兰、喜姆比兰,兰科、兰属多年生草本植物,是近几年我国花卉市场上流行的高档室内盆栽花卉。大花蕙兰的杂交育种已有一百多年的历史,每年新增加的品种有几十种之多。近年来,我国检验检疫部门分别从各入境口岸的进境大花蕙兰中多次发现携带有菊基腐病菌（Erwinia chrysanthemi）、兰花细菌性褐腐病菌（Erwinia cypripedii）、建兰花叶病毒（Cymbidium mosaic virus）等多种病原生物,均有潜伏期长、发病率高等特点。入境大花蕙兰种苗携带植物病原细菌、病毒等有害生物隐蔽性强、风险较高。     

轮纹病菌拮抗性大豆根瘤内生菌的筛选、抗性和促生作用

从河南部分地区采集的大豆根瘤中分离276株内生细菌,采用平板对峙法进行初筛、复筛和内生菌发酵滤液抑菌活性测定,对拮抗性代表菌株进行大豆轮纹病菌菌丝抑制效果显微观察、菌体生理生化特性测试、16SrDNA测序、系统发育分析及抗盐碱性试验和接种试验。结果表明,17株初筛内生菌经复筛和发酵滤液抑菌活性测定,其中8株抑菌率达50%以上;受作用菌丝发生扭结、缠绕成环状,菌丝末端分枝增多、变细、透明,部分菌丝末端膨大、原生质浓缩、断裂,一些菌丝被内生菌形成生物薄膜包埋、逐渐消融。8株内生菌中5株(DD013、DD123、DD156、DD159、DD287)初步鉴定为芽孢杆菌属Bacillus,DD150为赖氨酸芽孢杆菌属Lysinibacillu、DD267为肠杆菌属Enterobacter,菌株DD303为苍白杆菌属Ochrobactrum。抗盐碱性生长曲线表明,菌株DD287对3%NaCl盐浓度具有一定抗性,在碱性环境(pH8)下能正常生长,随pH(9~11)增大,菌体生长量受影响。部分拮抗性菌株对大豆生长有促进作用。筛选拮抗性菌株对丰富生物防治菌种资源具有重要意义。     

小麦赤霉病菌拮抗菌筛选及最适培养条件初步研究

<正>小麦赤霉病(Fusarium head blight)是我国小麦生产上最重要的真菌病害之一。已有的研究表明,在我国其致病菌的优势种主要为Fusarium graminearum和F. asiaticum。此病害具有爆发速度快、流行范围广等特点[1,2],而且其致病菌还可产生脱氧雪腐镰刀菌烯醇(deoxynivalenol, DON)和玉米赤霉烯酮(zearalenone, ZEN)等毒素,人畜吃过会产生不同程度的中毒反应[3]。目前小麦     

小麦赤霉病菌拮抗菌筛选及最适培养条件初步研究

Fusarium head blight is one of the most important diseases in the world and is a major disease on wheat in China. Therefore, this study aimed to isolate antagonistic bacteria with strong inhibitory effects on F. graminearum, and to provide theoretical basis for biological control of FHB. Endophytic strains were screened by plate confrontation and were identified by 16S rDNA sequence analysis. Among seven isolated antagonistic strains, WJ-2 was the best one with 15.4 mm bacteriostatic circle in diameter. Through analysis on 16S rDNA sequence and physiological and biochemical characteristics, strain WJ-2 was preliminarily identified as Bacillus subtilis.     

西北地区马铃薯疮痂病病原菌鉴定及其生物学特性

为明确西北地区马铃薯疮痂病病原菌的种类和生物学特性,分别采用常规组织分离法和土壤混悬液分离法从宁夏、陕西和甘肃3个省区采集的29份疮痂病发病薯块和8份发病地块土壤中进行病原菌分离,并利用形态特征、生理生化特性和16S rDNA序列分析对病原菌进行鉴定。结果表明,从发病薯块和发病土壤中共分离到50株链霉菌Streptomyces spp.,通过回接法验证获得6株马铃薯疮痂病致病菌株。6株致病菌株的培养特性和形态特征差别较大;其中菌株G4-1、G9和SYN13不能以果糖和木糖为单一碳源,菌株SYNT3不能以棉子糖为单一碳源;除菌株NLG4-1外,其余5株菌株均能在络氨酸琼脂培养基上产生黑色素。经16S rDNA序列分析,菌株G4-1、G9与疮痂病链霉菌S. scabiei的相似率分别达99.47%和99.34%,菌株NLG4-1、SYNT3与S. enissocaesilis的相似率分别达97.90%和98.18%,菌株GBH2与加利利链霉菌S. galilaeus的相似率达99.93%,菌株SYN13与S. turgidiscabies的相似率达97.56%,表明西北地区马铃薯疮痂病病原菌至少存在4个种。     

巨大芽胞杆菌YB-3的筛选、鉴定及其对生姜青枯病的生防效果研究

青枯病（bacterial wilt）是生姜上的一种细菌土传毁灭性病害,化学防治易污染环境且常规化学药剂很难在土壤中起到持续控病的作用,生物防治是其理想的防治方法。为开发对生姜青枯病有效的生防措施,对从生姜根际土壤中分离的一株生防细菌YB-3进行了鉴定,并对其生物学特性及生防效果进行了研究,以丰富生防菌株资源库。采用抑菌圈法筛选拮抗细菌,对效果最好的拮抗菌株做盆栽试验,测定其对生姜青枯病的防治效果,根据形态特征、生理生化特性以及16S rDNA序列对筛选得到的优良菌株进行鉴定。试验结果表明,该拮抗菌在平皿上对青枯菌的抑菌率为50.67%,盆栽试验对青枯病的防治效果为60.86%;经16S rDNA序列分析,并结合形态学和生理生化特征,将菌株YB-3鉴定为巨大芽胞杆菌Bacillus megaterium。YB-3是一株具有开发利用价值的姜青枯病生防菌株。     

Biological Control of Late Leaf Spot of Peanut (Arachis hypogaea) with Chitinolytic Bacteria

ABSTRACT Late leaf spot (LLS), caused by Phaeoisariopsis personata, is a foliar disease of groundnut or peanut (Arachis hypogaea) with high economic and global importance. Antifungal and chitinolytic Bacillus circulans GRS 243 and Serratia marcescens GPS 5, selected among a collection of 393 peanut-associated bacteria, were applied as a prophylactic foliar spray and tested for control of LLS. Chitin-supplemented application of B. circulans GRS 243 and S. marcescens GPS 5 resulted in improved biological control of LLS disease. Supplementation of bacterial cells with 1% (wt/vol) colloidal chitin reduced lesion frequency by 60% compared with application of bacterial cells alone, in the greenhouse. Chitinsupplemented application of GRS 243 and GPS 5 also resulted in improved and stable control of LLS in a repeated field experiment and increased the pod yields by 62 and 75%, respectively, compared with the control. Chitin-supplemented application of GPS 5 was tested in six onfarm trials, and the increase in pod yields was up to 48% in kharif (rainy season). A 55-kDa chitinase was purified from the cell-free culture filtrate of GPS 5 by affinity chromatography and gel filtration. Purified chitinase of S. marcescens GPS 5 (specific activity 120 units) inhibited the in vitro germination of P. personata conidia, lysed the conidia, and effectively controlled LLS in greenhouse tests, indicating the importance of chitinolysis in biological control of LLS disease by GPS 5.     

小麦苗枯病菌的ITS分析及PCR检测

 小麦苗枯病菌(Clavibacter fangii,Cf)是引起小麦细菌性苗枯病的病原,本研究用16S~23S rDNA间的内源转录间隔区(internally transcribed spacer,ITS)序列通用引物L1(5'-AGTCGTAACAAGGTAGCCGT-3')和L2(5'-GTGCCAAGGCATCCACC-3')扩增Cf和其它相关细菌的基因组DNA;并对其PCR产物进行回收、克隆和测序,将所获序列和其它已报道的细菌ITS序列进行多重比较后设计出Cf的特异性引物I1(5'-TGCCAAGTCACACTGAGACGA-3')和I2(5'-CAATGATCTACCACCCTCCGA-3')。此引物可以从Cf中扩增出351bp的特异性片段,而其余参试的21个细菌PCR反应结果均为阴性。该方法可以应用于小麦苗枯病菌的快速、可靠检测。此外,本研究对多种植物病原棒形杆菌的ITS序列进行比较研究,发现其具有一定的分类意义。     

Molecular characterization of a phytoplasma causing Phyllody in Clover and other herbaceous hosts in Northern Italy

Red clover (Trifolium pratense) and Ladino clover (Trifolium repens) plants showing phytoplasma-associated symptoms (yellowing/reddening, virescence and phyllody) have been recovered in Friuli-Venezia Giulia, Italy. Using AluI RFLP analysis of PCR amplified 16S rDNA we showed that the disease can be caused independently by two phylogenetically distinct phytoplasmas. One of them showed the very typical 16S rDNA RFLP pattern of the agent of Clover Phyllody in Canada (CCPh). The 16S rDNA of the other phytoplasma (Italian Clover Phyllody phytoplasma, ICPhp) has been PCR amplified, cloned and sequenced. The sequence revealed high similarity (>98%) with phytoplasmas belonging to the X disease cluster, which includes organisms not reported to cause phyllody on their hosts. The analysis by AluI RFLP of the PCR amplified pathogen 16S rDNA from other herbaceous plants (Crepis biennis, Taraxacum officinale, Leucanthemum vulgare) collected nearby with phytoplasma-associated symptoms showed similar patterns. Southern blot hybridization of their EcoRI digested total DNA revealed identical RFLP patterns, suggesting that the causative agent may be the same organism.Abbreviations PCR Polymerase Chain Reaction - rDNA gene for the small subunit ribosomal RNA - RFLP Restriction Fragment Length Polymorphism     

棉花枯萎病拮抗短小芽胞杆菌筛选鉴定及生防研究

为获得对棉花枯萎病有较好生防效果的拮抗细菌,从健康海岛棉植株根围土壤中分离筛选棉花枯萎病拮抗细菌,探索研究拮抗菌株的抑菌作用,为其生物防治提供潜在资源菌。采用平板对峙法,以海岛棉枯萎病尖孢镰刀菌为靶标菌,从土壤中分离到的120株细菌菌株中筛选拮抗菌株。测定拮抗细菌发酵液抑菌活性,通过促芽和盆栽试验筛选生防效果最好的菌株,同时测定该菌株对棉花枯萎病的抑菌效果和耐盐碱性。基于形态特征、生理生化特性和16S rDNA序列分析鉴定菌株分类地位。从120株细菌中筛选到1株对棉花枯萎病拮抗作用很强的菌株,编号为KX-33。促芽分析和盆栽试验结果表明,菌株KX-33能明显缩短出芽时间,促进棉苗生长。对病原菌DD64、DD89、DD11和DD22防效分别为75.32%、72.77%、69.48%和68.81%,均显著高于对照药剂处理（P<0.05）。耐盐碱分析表明,菌株KX-33具一定的耐盐碱性。菌株KX-33镜检为革兰氏阳性菌、呈杆状、有芽胞,16S rDNA和序列与Bacillus pumilus（FJ763643.1）同源性最高。海岛棉根围土壤微生物中含有棉花枯萎病拮抗细菌,经鉴定菌株KX-33为短小芽胞杆菌Bacillus pumilus,促生和抑菌作用显著,在海岛棉枯萎病生物防治中具有潜在的应用价值。     

杏褪绿卷叶植原体新疆分离物16S rDNA基因克隆与序列分析

利用植原体16S rDNA基因通用引物对新疆轮台县疑似杏褪绿卷叶病植株总DNA进行巢氏PCR检测,扩增出大小约1.2 kb的特异性条带。对扩增产物克隆和测序,确定特异片段大小为1248 bp。序列同源性比较和系统进化分析表明,新疆杏褪绿卷叶植原体不同分离株16S rDNA基因序列同源性极高,达到99.8%~100%。与16SrⅤ组成员的同源性达到98.2%以上,其中与16SrⅤ-B亚组的枣疯病植原体山东宝山分离株,甜樱桃绿化植原体山东分离株同源性最高,达到99.4%~99.6%。进一步虚拟RFLP分析,结果表明该植原体属于榆树黄化组(16SrⅤ)的一个新的亚组,与其相似性最高的是16SrⅤ-B亚组,相似系数为0.94。本研究首次报道了新疆杏褪绿卷叶植原体16S rDNA的序列,确定了其分类地位,为杏褪绿卷叶病的早期诊断和检测提供了基础。     

Characterization and differentiation of soft rot causing Pectobacterium carotovorum of Indian origin

Twenty different strains of Pectobacterium carotovorum (Pcc) were recovered from vegetable-growing fields of Vadodara, Gujarat (India) using a plant host enrichment approach during the years 2006–9. The isolated strains, based on differences in physiological and biochemical features, were classified into five different biovars, and then identified as Pectobacterium carotovorum (Pcc) by species-specific PCR and 16S rDNA sequences. Moreover, these Pcc strains were also differentiated based on virulence traits, plant cell wall degrading enzymes production and phylogenetic analysis of 16S rDNA sequence and Repetitive extragenic palindromic—PCR (rep-PCR). High genetic variability, independent of their pathogenicity, was revealed among these Pcc strains by rep-PCR typing using four different primer sets . Factors other than the plant host specificity seem to correlate with genetic variability of these economically important Pcc strains. Significantly, polyphasic characterization of the Pcc strains clearly reveals the heterogeneity among them. The present studies can be considered as useful epidemiological surveillance (or distribution) of soft rot causing Pcc in the semi arid region of India.     

Identification and sensitive endophytic detection of the fire blight pathogen Erwinia amylovora with 23S ribosomal DNA sequences and the polymerase chain reaction

Two short sequences, situated in the bacterial 23S rDNA gene, were used as primers for the PCR detection of Erwinia amylovora bacteria. All 34 E. amylovora strains tested, coming from different geographical and host plant origins and of different virulence, produced a 565-bp PCR fragment. The E. amylovora bacteria could be discriminated from all other phytobacteria with which no PCR product was observed. Only Escherichia coli bacteria were cross-recognized by the production of a weaker PCR band of similar size to E. amylovora . In a fast PCR protocol, where two temperatures were cycled, E. amylovora in pure culture could be detected on gel at concentrations as low as 3 × 10² cfu mL^–1. This corresponds to a detection limit of 1.5 bacteria per PCR. However, reliable PCR detection in woody host plant tissue was only obtained with PVP/PVPP-treated sample extracts. Using E. amylovora -spiked plant extracts and extracts of fruit tree shoots artificially infected with E. amylovora , the PCR detection sensitivity was determined to be 6.6 × 10² cfu mL^–1 of extract. Starting from the plant samples, the PCR detection results were visualized on gels within 5 h.     

Detection and molecular characterization of phytoplasma associated with chickpea phyllody disease in south India

Chickpea (Cicer arietinum L.) plants showing typical symptoms of infection by a phytoplasma that causes phyllody disease have been commonly observed in recent years in parts of south India. The symptoms included pale green leaves, bushy appearance due to excessive stunting of shoots, reduced internodal length and excessive axillary proliferation. The causal agent of the phyllody disease was identified based on symptoms, amplification of 16S rDNA of the phytoplasma by polymerase chain reaction (PCR) from infected samples, as well as by sequencing and phylogenetic analysis. First round PCR and nested-PCR protocols were standardized for improved efficiency and reliability of the diagnostic protocols. Using the primers P1/P7 and R16F2n/R16R2, 1,800?bp and 1,200?bp size products were amplified in first round PCR and nested-PCR protocols, respectively. The PCR product was cloned and sequenced and compared with the reference phytoplasma sequences from the database (NCBI). The Indian chickpea phyllody phytoplasma 16S rDNA sequences shared the highest nucleotide identity (>98%) with the 16S rII group phytoplasma candidates, also infecting chickpea from Australia and Pakistan. This is the first report of a phytoplasma of the 16SrII-group infecting chickpea from India. The genetic similarities and the potential threat of this new disease to chickpea cultivation in India are discussed.     

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。     

Phylogenetic Relationships of Xylella fastidiosa Strains Isolated from Landscape Ornamentals in Southern California

ABSTRACT Xylella fastidiosa is an insect-borne, xylem-limited pathogenic bacterium that has been associated with a rise in incidence of diseased landscape ornamentals in southern California. The objective of this study was to genetically characterize strains isolated from ornamental hosts to understand their distribution and identity. Strains of X. fastidiosa isolated from ornamentals were characterized using a multiprimer polymerase chain reaction (PCR) system, random amplified polymorphic DNA (RAPD)-PCR, and sequence analysis of the 16S-23S rDNA intergenic spacer region (ISR). Based on RAPD-PCR and 16S-23S rDNA ISR, strains isolated from daylily, jacaranda, and magnolia clustered with members of X. fastidiosa subsp. sandyi and caused oleander leaf scorch but not Pierce's disease symptoms in glasshouse assays on oleander and grape, respectively. This demonstrated both that our groupings based on genetic characterization were valid and that strains of X. fastidiosa subsp. sandyi are present in hosts other than oleander. Strains isolated from Spanish broom, cherry, and one strain isolated from western redbud clustered with X. fastidiosa subsp. fastidiosa members. Strains isolated from purple-leafed plum, olive, peach, plum, sweetgum, maidenhair tree, crape myrtle, and another western redbud strain clustered with members of X. fastidiosa subsp. multiplex. All strains isolated from mulberry and one from heavenly bamboo formed a separate cluster that has not yet been defined as a subspecies.