鳜源致病性荧光假单菌的分离与鉴定

为确定导致鳜（Siniperca chuatsi）细菌性感染死亡的病原,从患病濒死的鳜肝中分离出一株优势菌B01,经人工回感实验确定其分离菌的致病性,并利用VITEK-2全自动微生物鉴定仪及16S rRNA序列分析对纯培养细菌进行鉴定。此外,对分离的菌株进行药敏实验。研究结果表明,菌株B01对鳜鱼具有致病性。经VITEK-2全自动微生物鉴定仪鉴定菌株B01为荧光假单胞菌（Pseudomonas fluorescens）（表1）,并在紫外灯可以产生荧光（图1）。进一步的16S rRNA基因序列和系统发育树分析表明,该菌与荧光假单胞菌同源性达到了97%以上,并和（图2）。药物敏感性实验结果显示,该分离株对恩诺沙星、诺氟沙星、链霉素和四环素药物等6种药物高度敏感（表2）。     

铜绿假单胞菌氨基糖苷16SrRNA甲基化酶基因分析

目的调查215株湖州地区临床分离铜绿假单胞菌对氨基糖苷类抗生素的耐药性和16S rRNA甲基化酶基因分布情况。方法收集2011年1月至2012年12月湖州地区临床分离铜绿假单胞菌215株,琼脂稀释法测定5种氨基糖苷类抗菌药物（庆大霉素、阿米卡星、妥布霉素、伊帕米星、奈替米星）的MIC值;PCR检测armA、rmtA、rmtB、rmtC、rmtD和npmA六种氨基糖苷类16S rRN甲基化酶基因,序列分析明确基因型。测定产16S rRNA甲基化酶菌株对常见抗菌的敏感性,并检测碳青霉烯耐药株产碳青霉烯酶情况。结果铜绿假单胞菌对异帕米星敏感率最高为81.4%,对5种氨基糖苷类抗生素全部耐药的22株菌株中,17株检出armA基因;未发现其他16S rRNA甲基化酶基因阳性菌株。17株armA阳性菌株对碳青霉烯类抗生素耐药5株（耐药率为29.4%）,对头孢他啶、头孢吡肟、哌拉西林/他唑巴坦、环丙沙星耐药率均超过40%。5株碳青霉烯耐药菌株中检测到2株产VIM-2型金属碳青霉烯酶。结论铜绿假单胞菌对氨基糖苷类抗生素耐药率高,检测到16S rRNA甲基化酶基因armA。产16S rRNA甲基化酶铜绿假单胞菌耐药性强,部分菌株同时产金属碳青霉烯酶,给临床抗感染治疗及院内感染控制带来挑战。     

转录调节因子σ~(38)介导铜绿假单胞菌绿脓菌素合成代谢调控

【目的】为了进一步鉴定铜绿假单胞菌转录调控因子σ~(38)对2个拷贝吩嗪合成基因簇(phz A1-G1和phz A2-G2)的具体调控方式并推定介导绿脓菌素合成代谢的可能调控机制。【方法】根据铜绿假单胞菌基因组信息,利用同源重组原理构建rpo S基因缺失突变株Δrpo S以及克隆全长rpo S基因作互补分析;再以单一吩嗪基因簇缺失突变株Δphz1和Δphz2为出发菌株,分别构建rpo S缺失突变株Δrpo Sphz1和rpo S插入突变株Δrpo Sphz2,测定并比较野生株及相关突变株的绿脓菌素合成量,初步推定σ~(38)因子对2个不同吩嗪基因簇表达的调控方式。【结果】在GA培养基中,突变株Δrpo S的绿脓菌素合成量比野生株显著增加;互补分析证实,σ~(38)可使突变株Δrpo S的绿脓菌素降低并接近野生株PAO1水平;与对照株Δphz1相比,突变株Δrpo Sphz1的绿脓菌素合成量因σ~(38)因子缺失而显著减少;而与对照株Δphz2相比,突变株Δrpo Sphz2的绿脓菌素合成量因σ~(38)因子缺失显著增加。【结论】转录调控因子σ~(38)对铜绿假单胞菌绿脓菌素的合成代谢的确具一定的负调控作用;结合已报道的研究结果,初步推定:σ~(38)因子通过负调控吩嗪基因簇phz1,正调控吩嗪基因簇phz2的表达实现对绿脓菌素合成代谢的调控。     

rpoS基因缺失突变对荧光假单胞菌胁迫耐受性、群体感应及腐败活性的影响

【目的】微生物活动是引起食品腐败的主要原因,研究食品腐败菌的腐败作用调控机制对于保证食品的质量和安全具有重要意义。荧光假单胞菌是一种代表性的食品腐败菌,本文旨在研究RNA聚合酶的选择性sigma因子Rpo S在荧光假单胞菌致腐败过程中的作用。【方法】运用同源重组的方法构建荧光假单胞菌冷藏鱼分离株的rpo S基因缺失突变株,比较野生型和突变株暴露于不同胁迫条件下的存活率;通过液相色谱-串联质谱(LC-MS/MS)分析野生型和突变株产生高丝氨酸内酯类(AHLs)群体感应信号分子的种类和含量;检测野生型和突变株接种于灭菌三文鱼汁后4°C贮存过程中的菌落总数和挥发性盐基氮的生成量。【结果】成功构建了荧光假单胞菌rpo S基因缺失突变株。rpo S基因的缺失导致荧光假单胞菌对10 mmol/L H2O2和15%乙醇的耐受性显著降低,对150μg/m L结晶紫和175 mmol/L醋酸的耐受性有一定程度增强,不影响其对47°C和20%Na Cl的耐受性。荧光假单胞菌在rpo S基因缺失突变后长链信号分子C_(10)-HSL、C_(12)-HSL和C_(14)-HSL的含量增加。在灭菌三文鱼汁中的腐败活性检测表明rpo S基因缺失可导致荧光假单胞菌挥发性盐基氮的生成量显著降低。【结论】荧光假单胞菌的Rpo S不仅调节细菌对多种胁迫条件的耐受性,还影响AHL群体感应和腐败活性。     

一株产海藻糖合成酶极地细菌的鉴定

从来源于极地的微生物中筛选得到一株产海藻糖合成酶的耐冷细菌S1,通过形态特征、培养特征、生理生化特征及16S rRNA基因序列分析,初步鉴定该菌为恶臭假单胞菌(Pseudomonas putida)。     

携带armA基因的铜绿假单胞菌耐药性及基因周边环境

目的了解多重耐药(MDR)铜绿假单胞菌armA基因与可移动遗传元件的携带情况及其相关性;分析armA基因的周边环境,探讨armA基因转移的可能机制。方法收集MDR铜绿假单胞菌98株,琼脂稀释法测定MIC,PCR方法检测16S rRNA甲基化酶基因armA、I型整合子、可移动元件IS26及重要耐药基因侧翼基因环境,测序并拼接PCR产物明确耐药基因座位排列,并对armA基因进行周边序列分析。结果 98株MDR铜绿假单胞菌检出5株armA基因PCR扩增阳性,携带armA基因的菌株对庆大霉素和阿米卡星全耐药;检出20株携带I型整合子,17株携带可移动元件IS26;armA基因扩增阳性的菌株均携带I型整合子和IS26;序列测序显示armA定位于Tn1548相关区域,位于插入序列ISCR1的下游,该序列含多种移动元件。结论大连市氨基糖苷类高水平耐药基因armA广泛分布在MDR铜绿假单胞菌中,均对庆大霉素和阿米卡星高度耐药;该基因定位在转座子Tn1548的质粒上,提示16S rRNA甲基化酶基因armA的广泛播散可能是可移动元件ISCR1-armA-IS26结构参与其中。     

基于核糖体基因序列快速鉴定产脂肪酶微生物

利用含罗丹明B的橄榄油检测平板从中国各省市油污土壤中分离、筛选产脂肪酶微生物菌株,扩增细菌的核糖体基因16S rDNA序列和真菌的ITS2序列,分析核糖体基因簇DNA,并结合形态学特征从而对产脂肪酶菌株进行分子生物学鉴定.核糖体基因16S rDNA序列分析及系统发育分析表明,分离得到的产脂肪酶细菌分别属于枯草芽孢杆菌(Bacillus subtilis)、产碱假单胞菌(Pseudomonas alcaligenes)、洋葱伯克霍尔德氏(Burkholderia cepacia)、琼氏不动杆菌(Acinetobater jurii)、嗜麦芽窄食单孢菌(Stenotrophomonas maltophilia)和荧光假单胞菌(Pseudomonas sp.);真菌核糖体基因转录间隔区(ITS2)序列及同源性分析表明产脂肪酶真菌分别属于黑曲酶(Aspergillus niger)、白地酶(Galactomyces geotrichum)、解脂耶氏酵母(Yarrowia lipolytica)、丝孢酵母(Trichosporon guehoae)和假丝酵母(Candida sp.).研究结果表明,核糖体基因簇的DNA分析技术为从自然界分离、鉴定产脂肪酶菌种提供了一种快速有效的手段,为产脂肪酶微生物资源开发利用奠定了技术基础.     

利用16S rRNA基因同源性分析鉴定两株明串珠菌

从酸马奶中分离出2株明串珠菌KLDS 5.0301和KLDS 5.0302,对2株菌的16S rRNA基因经PCR扩增测序,将测序结果同该属内菌株的16S rRNA序列作多序列比较,并建立明串珠菌属的系统发育树.结果表明,KLDS 5.0301的16S rRNA序列同L. garlicum的同源性百分比为100%.KLDS 5.0302的16S rRNA序列同L.mesenteroides LM2菌株的16S rRNA序列的同源性百分比为99.9%.根据系统发育树的结果,将KLDS5.0301鉴定为L.garlicum,KLDS 5.0302鉴定为L.mesenteroides.菌株KLDS 5.0301和KLDS 5.0302的16SrRNA序列已经在GeneBank申请国际序列注册号,分别为DQ239691和DQ297412.     

塔河天然胡杨林地可培养细菌的生态分布研究

目的：研究塔里木河天然胡杨林部分地区可培养细菌的生态分布。方法：通过塔里木河胡杨林采样,可培养菌分离及16S rDNA序列鉴定。结果：从3种不同样品（水样、土样和胡杨树杆分泌物）中分离筛选了22株细菌,其中17株菌为革兰氏阳性菌,5株为革兰氏阴性菌。根据生理生化特征与16S rDNA序列分析结果表明,其中15株菌属于芽孢杆菌属,4株属于不动杆菌属、假单胞菌属、动性球菌属和Agrococcus属各含有1个分离株。结论：塔里木河胡杨林可培养微生物中芽孢杆菌比较丰富,其中有3个可能的新种。     

番茄根内生假单胞菌的分离与鉴定

[目的]通过对番茄根内生假单胞菌的分离和纯化,为研究番茄根内生假单胞菌生态学及其与植物生长之间的关系,筛选潜在的植物病害生防菌株奠定基础。[方法]以福州闽侯蔬菜大棚种植的番茄为研究对象,采用传统微生物培养技术分离纯化根内生细菌。通过16S rDNA序列同源比对与分析,鉴定和统计番茄根内生菌中可培养假单胞菌的种类和数量。[结果]在分离纯化得到的21株番茄根内生菌中,经分子鉴定其中12株为假单胞菌(Pseudomonas),序列对比和系统发育分析表明12株假单胞属可分为4个不同的类群。从统计结果来看,假单胞菌属占所培养的番茄根内生菌总数的52.1%。[结论]假单胞属细菌占番茄根可培养内生菌总数的52.1%,为优势菌,并具有较高的种类多样性。     

Aeromonas piscicola sp. nov., isolated from diseased fish

Four Aeromonas strains (S1.2^T, EO-0505, TC1 and TI 1.1) isolated from moribund fish in Spain showed a restriction fragment length polymorphism (RFLP) pattern related to strains of Aeromonas salmonicida and Aeromonas bestiarum but their specific taxonomic position was unclear. Multilocus sequence analysis (MLSA) of housekeeping genes rpoD, gyrB, recA and dnaJ confirmed the allocation of these isolates to an unknown genetic lineage within the genus Aeromonas with A. salmonicida, A. bestiarum and Aeromonas popoffii as the phylogenetically nearest neighbours. Furthermore, a strain biochemically labelled as Aeromonas hydrophila (AH-3), showing a pattern of A. bestiarum based on 16S rDNA-RFLP, also clustered with the unknown genetic lineage. The genes rpoD and gyrB proved to be the best phylogenetic markers for differentiating these isolates from their neighbouring species. Useful phenotypic features for differentiating the novel species from other known Aeromonas species included their ability to hydrolyze elastin, produce acid from l-arabinose and salicin, and their inability to produce acid from lactose and use l-lactate as a sole carbon source. A polyphasic approach using phenotypic characterization, phylogenetic analysis of the 16S rRNA gene and of four housekeeping genes, as well as DNA–DNA hybridization studies and an analysis of the protein profiles by MALDI-TOF-MS, showed that these strains represented a novel species for which the name Aeromonas piscicola sp. nov. is proposed with isolate S1.2^T (=CECT 7443^T, =LMG 24783^T) as the type strain.     

Evaluation of biosorption potency of <Emphasis Type="Italic">Acinetobacter</Emphasis> sp. for removal of hexavalent chromium from tannery effluent

Two bacterial consortia were developed by continuous enrichment of microbial population of tannery and pulp and paper mill effluent contained Serratia mercascens, Pseudomonas fluorescence, Escherichia coli, Pseudomonas aeruginosa and Acinetobacter sp. identified by 16S rDNA method. The consortia evaluated for removal of chromate [(Cr(VI)] in shake flask culture indicated pulp and paper mill consortium had more potential for removal of chromate. Acinetobacter sp. isolated from pulp and paper mill consortium removed higher amount of chromate [Cr(VI)] under aerobic conditions. Parameters optimized in different carbon, nitrogen sources, and pH, indicated maximum removal of chromate in sodium acetate (0.2%), sodium nitrate (0.1%) and pH 7 by Acinetobacter sp. Bacteria was applied in 2-l bioreactor significantly removed chromate after 3 days. The results of the study indicated removal of more than 75% chromium by Acinetobacter sp. determined by diphenylcarbazide colorimetric assay and atomic absorption spectrophotometer after 7 days. Study of microbial [Cr(VI)] removal and identification of reduction intermediates has been hindered by the lack of analytical techniques. Therefore, removal of chromium was further substantiated by transmission electron microscopy (TEM), scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX) which indicated bioaccumulation of chromium in the bacterial cells.     

Isolation and characterization ofAcinetobacter sp. mutants defective in exopolysaccharide biosynthesis

Nitrosoguanidine-induced mutants ofAcinetobacter sp. defective in exopolysaccharide biosynthesis did not differ from the parent strain in distinguishing physiological and biochemical properties, such as requirements for growth factors, utilization of mono- and disaccharides, and resistance to antibiotics. The genetic relation of parent and mutant strains was shown by 16S rRNA PCR analysis. The comparative study of parent and mutant strains with respect to resistance to unfavorable environmental factors confirmed our hypothesis thatAcinetobacter sp. exopolysaccharides perform protective functions. Hybridization experiments revealed the conjugal transfer of plasmid R68.45 fromPseudomonas putida BS228 (R68.45) to mutant but not to the parentAcinetobacter sp. strains. The role of theAcinetobacter sp. exopolysaccharides in providing the genetic stability of this bacterium is discussed.     

Use of rpoB gene sequence analysis for phylogenetic identification of Cronobacter species

Here, we report the RNA polymerase beta-subunit gene (rpoB) as a new molecular marker for the identification of the Cronobacter species. The results indicated that members of the Cronobacter genus are more easily discriminated by rpoB sequencing than 16S rRNA sequencing, and reliable identification could be achieved by rpoB gene sequence comparison.     

Species-level identification of <Emphasis Type="Italic">Bacillus</Emphasis> strains isolates from marine sediments by conventional biochemical, 16S rRNA gene sequencing and inter-tRNA gene sequence lengths analysis

The aim of this study was to compare the ability of commonly used conventional biochemical tests, sequencing analysis of 16S rRNA genes and tDNA-intergenic spacer length polymorphism (tDNA-PCR) to identify species of the genus Bacillus recovered from marine sediments. While biochemical tests were not sufficiently sensitive to distinguish between the 23 marine strains analyzed, partial 16S rRNA gene sequences allowed a correct identification, clustering them into four species belonging to Bacillus licheniformis (n = 6), Bacillus cereus (n = 9), Bacillus subtilis (n = 7) and Bacillus pumilus (n = 1). The identification results obtained with 16S rRNA sequencing were validated by tDNA-PCR analysis of 23 marine isolates that were identified by the similarities of their fingerprints to those of reference strains. tDNA-PCR fingerprinting was as discriminatory as 16S rRNA sequencing analysis. Although it was not able to distinguish among the species of the B. cereus and B. subtilis groups, it should be considered a rapid and easy approach for the reliable identification of unknown Bacillus isolates or at least for the primary differentiation of Bacillus groups.     

Phylogenetic characterization of the purple sulfur bacterium Thiocapsa sp. BBS by analysis of the 16S rRNA, cbbL, and nifH genes and its description as Thiocapsa bogorovii sp. nov., a new species

Strain BBS, the purple sulfur bacterium assigned initially to the species Thiocapsa roseopersicina, is the best studied representative of this species. However, no molecular phylogenetic analysis has been performed to confirm its systematic position. Based on the results of analysis of the sequences of 16S rRNA, cbbL, and nifH genes, DNA-DNA hybridization with the T. roseopersicina type strain, and comparative analysis of the phenotypic characteristics of various species belonging to the genus Thiocapsa, we suggest that strain BBS should be assigned to a new species of the genus Thiocapsa, Thiocapsa bogorovii sp. nov. Original Russian Text ? T.P. Tourova, O.I. Keppen, O.L. Kovaleva, N.V. Slobodova, I.A. Berg, R.N. Ivanovsky, 2009, published in Mikrobiologiya, 2009, Vol. 78, No. 3, pp. 381–392.     

Speciation of <Emphasis Type="Italic">Bacillus</Emphasis> spp. in honey produced in Northern Ireland by employment of 16S rDNA PCR and automated DNA sequencing techniques

Phenotypic speciation of foodborne Bacillus spp. remains problematic in terms of obtaining a reliable identification. In this study, we wished to identify several bacterial isolates from honey produced in Northern Ireland, and which belonged to the genus Bacillus, through employment of a molecular identification scheme based on PCR amplification of universal regions of the 16S rRNA operon in combination with direct automated sequencing of the resulting amplicons. Seven samples of honey and related materials (propolis) were examined microbiologically and were demonstrated to have total viable counts (TVC) ranging from <100 to 1700 colony-forming units/g. No yeasts or filamentous fungi were isolated from the honey materials. Several bacterial isolates were identified using this method, yielding two different genera (Paenibacillus and Bacillus), as well as four Bacillus species, namely Bacillus pumilus, B. licheniformis, B. subtilis and B. fusiformis, with B. pumilus the most frequently identified species present. When the use of molecular identification methods is justified, employment of partial 16S rDNA PCR and sequencing provides a valuable and reliable method of identification of Bacillus spp. from foodstuffs and negates associated problems of conventional laboratory and phenotypic identification.     

Detection of Microcystis in Lake Sediment using Molecular Genetic Techniques

Summary Microcystis, which are toxic microcystin-producing cyanobacteria, normally bloom in summer and drop in numbers during the winter season in Senba Lake, Japan. Recently, this lake has been treated by ultrasonic radiation and jet circulation which were integrated with flushing with river water. This treatment was most likely sufficient for the destruction of cyanobacterial gas vacuoles. In order to confirm whether Microcystis viridis was still present, a molecular genetic monitoring technique on the basis of DNA direct extraction from the sediment was applied. Three primer sets were used for polymerase chain reaction (PCR) based on rRNA intergenic spacer analysis (RISA), the DNA dependent RNA polymerase (rpoC1) and a Microcystis sp.-specific rpoC1 fragment. The results from each primer were demonstrated on the basis of single strand conformation polymorphisms (SSCP). Using the RISA primer showed different results from the rpoC1 and Microcystis sp.-specific rpoC1 fragment; meanwhile, the rpoC1 Microcystis sp.-specific fragment was more specific than the RISA primer. Therefore, the Microcystis sp.-specific rpoC1 fragment was further analysed by denaturing gradient gel electrophoresis (DGGE). The DNA pattern representing M. viridis could not be detected in any of the sediment samples. However, the results were confirmed with another technique, terminal restriction fragment length polymorphisms (T-RFLP). Although T-RFLP patterns of 16S rDNA in sediment at 91 bp and 477 bp lengths were matched with the T-RFLP of M. viridis (HhaI and MspI endonuclease digestion, respectively), the T-RFLP pattern of 75 bp length was not matched with M. viridis (both of HhaI and MspI endonuclease digestion) which were the major T-RFLP pattern of M. viridis. Therefore, the results most likely indicated that M. viridis seems to have disappeared because of the addition of the ultrasonic radiation and jet circulation to the flushing treatment.     

Isolation and characterization of arsenite-oxidizing bacteria from arsenic-contaminated soils in Thailand

Two hundred and eighty-eight arsenic-resistant bacteria were isolated by an enrichment culture method from a total of 69 arsenic-contaminated soil-samples collected from Dantchaeng district in Suphanburi province (47 samples), and from Ron Phiboon district in Nakhon Sri Thammarat province (22 samples), in Central and Southern Thailand, respectively. Twenty-four of the 288 isolated arsenic-resistant bacteria were found to be arsenite-oxidizing bacteria. On the basis of their morphological, cultural, physiological, biochemical and chemotaxonomic characteristics, and supported by phylogenetic analysis based upon their 16S rRNA gene sequences, they were divided into five groups, within the genera Acinetobacter, Flavobacterium, Pseudomonas, Sinorhizobium and Sphingomonas, respectively. Within genera, phylogenetic analysis using the 16S rRNA gene sequences suggested that they were comprised of at least ten species, five isolates being closely related to known bacteria (Acinetobacter calcoaceticus NCCB 22016^T, Pseudomonas plecoglossicida FPC951^T, Ps. knackmussii B13^T, Sinorhizobium morelense Lc04^T, and Sphingomonas subterranea IFO16086^T). The other five proposed species are likely to be new species closely related to Flavobacterium johnsoniae, Sinorhizobium morelense, Acinetobacter calcoaceticus and Pseudomonas plecoglossicida, but this awaits further characterization for confirmation of the taxonomic status. No overlap in isolated species or strains was observed between the two sites. The strain distribution and characterization are described.     

Detailed identification of desert-originated bacteria carried by Asian dust storms to Japan

Several halotolerant bacteria were isolated from dust allowed to settle passively on saline medium in Higashi-Hiroshima, Japan during Asia dust events in 2005–2006. The primary identification, based on the sequence similarity of the 16S rRNA gene, revealed that these isolates were strains of Bacillus subtilis, B. licheniformis, Staphylococcus epidermidis, Gracillibacillus sp., and Halomonas venusta. A parallel investigation carried out on desert sand collected directly from sand dunes in Dunhuang, Gobi Desert, China resulted in the revivification of seven bacterial strains that were highly identical to the B. subtilis and B. licheniformis strains obtained in Higashi-Hiroshima (99.7 and 100% of 16S rDNA sequence similarity, respectively). A subsequent genetic analysis on the group of B. licheniformis isolates based on the universally house-keeping genes, gyrB and parE, revealed high sequence similarities in both genes among the strains of both locations (99.0–99.4%), which clustered them in a monophyletic line. Phenotype characterized by numerical taxonomy for 150 physiological tests confirmed the close relatedness between strains (similarity coefficient S _SM = 96.0%). The remarkable agreement between phenotype and genotype of the bacterial isolates allows us to conclude that there may have been an aerosolized dispersion of a Gobi Desert B. licheniformis by dust storms to Japan. This study provides evidence of microbial transport by yellow dust events in North-East Asia.