Isolation of a new vahlkampfiid amoeba from soil: Paravahlkampfia lenta n. sp.

When the genus Paravahlkampfia was distinguished from the genus Vahlkampfia on the basis of significant differences in small subunit ribosomal DNA sequences, Paravahlkampfia ustiana was the only described species of this new genus. More recently, a vahlkampfiid strain has been isolated (from soil from an upland farm in Scotland) which has trophozoite and cyst morphology more similar to P. ustiana than to other non-flagellating vahlkampfiid species. Also, it clusters with P. ustiana in phylogenetic trees derived from 5.8S ribosomal DNA sequences. However, it is significantly different from P. ustiana in both phenotype and internal transcribed spacer sequence. Consequently, a new species, Paravahlkampfia lenta, is proposed.     

适冷溶菌酶产生菌的分子鉴定及其酶学性质的研究

采用比浊法对本试验室保存的126株南极微生物产适冷溶菌酶进行测定,发现7株菌产溶菌酶.并对其中的菌株NJ147进行ITS-5.8 S rDNA基因序列的同源性和系统发育分析,结果表明:菌株NJ147属于Debaryomyces hansenii属.该菌株所分泌溶菌酶的最适作用温度为30 ℃,在0 ℃时酶活性是最高活性的...     

橡树岭军团菌的分离及用16S rDNA测序法的鉴定

军团菌属（Ｌｅｇｉｏｎｅｌａ）自１９７１年确定以来,现已有３９个成员。军团菌属主要分布于供水系统中,如空调冷却塔水和浴池淋浴水中。我们曾于１９９４年从北京某宾馆冷却塔水中分离出一株可疑军团菌,但因缺乏标准抗血清而未能定种。由于核酸分析技术和细菌鉴定观念上进步,使我们能根据１６ＳｒＤＮＡ序列比较推测细菌间进化关系,并进而对未知细菌进行鉴定和检测。我们用以１６ＳｒＤＮＡ为靶序列的ＰＣＲ和测定鉴定,确定了该分离株为橡树岭军团菌（Ｌ．ｏａｋｒｉｄｇｅｎｓｉｓ）。     

Distribution and identification of red yeasts in deep-sea environments around the northwest Pacific Ocean

We isolated 99 yeast strains, including 40 red yeasts, from benthic animals and sediments collected from the deep-sea floor in various areas in the northwest Pacific Ocean. Comparing the yeast isolates from animals and sediments collected from shallow locations, the proportion of red yeasts differed considerably, comprising 81.5% and 10.6% of the isolates from animals and sediments, respectively. All of the red yeast isolates belonged to the genera Rhodotorula and Sporobolomyces. On the basis of morphological and physiological characteristics, the isolates were identified as R. aurantiaca, R. glutinis, R. minuta and R. mucilaginosa of the genus Rhodotorula, and S. salmonicolor and S. shibatanus of the genus Sporobolomyces. Only R. glutinis and R. mucilaginosa were isolated from sediments. All of the others were isolated from animal sources. Phylogenetic analyses based on internal transcribed spacer (ITS) regions and 5.8S rRNA gene sequences allowed us to establish the precise taxonomic placement of each of the isolates and thereby investigate the intraspecific relationships among the isolates. Twenty-two strains identified as members of R. glutinis, which showed a wide distribution in the deep-sea, and five isolates identified as R. minuta, which were isolated only from benthic animals, showed substantial heterogeneity within the species. The isolates phenotypically identified as Sporobolomyces species and R. mucilaginosa phylogenetically occupied the placements corresponding to these species. Some strains assigned to known species on the basis of phenotypic features should be regarded as new species as suggested by the results of molecular analysis.     

Shiraia sp．SUPER—H168 ITS-5．8S rDNA序列分析及产竹红菌素条件初步优化

对产竹红菌素的菌株SUPER-H168的ITS-5．8S rDNA进行了序列测定和进化树聚类分析,表明其属于竹黄属;对该菌株固态发酵产竹红菌素的条件进行了初步优化,得到的初步优化条件为玉米渣25g,麸皮5g,葡萄糖1．5g,NaNO3 0．15g,ZnSO4·7H2O 0．03g,起始含水量为50％,起始pH为7．0,培养温度为30℃。在该条件下发酵18d,竹红菌素的产量为9．37mg／g干基。     

基于18S rDNA与ITS-5.8S rDNA对 重庆地区网状车轮虫的种内分化研究

本研究基于形态和分子数据对采自重庆地区5个地理株系的网状车轮虫(Trichodina reticulata)进行了比较研究及重描述。研究结果表明,网状车轮虫不同株系表现出不同的表型分化,含形态略有不同的齿体及有或无中央颗粒,因而具有明显的种内形态多样性。不同地理株系网状车轮虫的18S rDNA序列相似度在99.0%~100%之间,遗传距离为0.000~0.008,并在三大变异区(V4、V5与V7)均具一致的二级结构,表明不同株系的18Sr DNA相似度与遗传距离均属种内水平。综合18SrDNA和ITS-5.8S rDNA的变异位点和系统发育对种内分歧的研究分析显示,来自不同地理分布和宿主的网状车轮虫株系皆因相同的变异位点而聚为一枝,以此推断网状车轮虫的种内分化主要受其基因的影响,地理分布与宿主差异等环境影响在目前的种群分化阶段暂未突显。此外,本研究进一步验证了中央颗粒不能作为网状车轮虫的主要鉴别性特征的观点。     

黄颡单尾虫(粘体门,双壳目)的重描述及基于28S rDNA和ITS-5.8S序列的系统地位分析

采用形态分类学方法与以28S rDNA和ITS-5.8S序列为基础的分子系统学研究方法,对采自嘉陵江重庆市磁器口江段的黄颡单尾虫Unicauda pelteobagrusMa,1998进行了形态学和分子生物学的研究。基于28S rDNA数据探讨了黄颡单尾虫以及单尾虫属与相邻种属粘孢子虫间的系统地位;基于5.8S rDNA数据比较分析了粘孢子虫的系统地位。补充了黄颡单尾虫重庆种群形态学信息和28S rDNA、ITS-5.8S rDNA序列的分子信息。     

Two new records of ascomycetes from Japan,Pyrenopeziza protrusa and P. nervicola (Helotiales,Dermateaceae sensu lato)

Two Pyrenopeziza species, P. protrusa and P. nervicola known to have similar morphology, were newly reported from Japan. This study clarified that P. protrusa morphologically differs from P. nervicola in (1) more protruded outermost cells in ectal excipulum, (2) smaller ascospores, and (3) longer and thinner asci. Pyrenopeziza protrusa produces chlamydospore-like brown cells under culture while P. nervicola forms more complex, brown bulbils. These species formed distinct clades based on ITS-5.8S rDNA in the phylogenetic analysis. The two species did not share the same host.     

大叶醉鱼草内生真菌LL3026菌株杀虫活性及ITS-5.8S rDNA序列分析

从大叶醉鱼草的叶子中分离得到一株内生真菌LL3026,以卤虫模型测稀释后发酵液的杀虫活性,结果表明LL3026发酵液杀虫活性较强,且温度、光照及紫外照射对LL3026发酵液杀虫活性影响不显著;采用分子生物学方法对LL3026菌株rDNA的ITS基因(ITS-5.8S rDNA)进行PCR扩增、测序,构建系统发育树。ITS基因显示其属于刺盘孢属真菌。     

There are high levels of functional and genetic diversity in Oxyrrhis marina

Oxyrrhis marina, a widely distributed marine protist, is used to model heterotrophic flagellate responses in microbial food webs. Although clonal variability occurs in protists, assessments of intraspecific diversity are rare; such assessments are critical, particularly where species are used as models in ecological studies. To address the extent of intraspecific variation within O. marina, we assessed diversity among 11 strains using 5.8S rDNA and ITS sequences. The 5.8S rDNA and ITS regions revealed high divergence between strains: 63.1% between the most diverse. To compare O. marina diversity relative to other alveolates, 18S rDNA sequences for five strains were analysed with sequences from representatives of the major alveolate groups. 18S rDNA also revealed high divergence in O. marina. Additionally, consistent with phylogenies based on protein coding genes, maximum likelihood analysis indicated that O. marina was monophyletic and ancestral to the dinoflagellates. To assess ecophysiological differences, growth rates of seven O. marina strains were measured at 10 salinities (10-55 per thousand). Two salinity responses occurred: one group achieved highest growth rates at high salinities; the other grew best at low salinities. There was no clear correlation between molecular, ecophysiological, or geographical differences. However, salinity tolerance was associated with habitat type: intertidal strains grew best at high salinities; open-water strains grew best at low salinities. These data indicate the need to examine many strains of a species in both phylogenetic and ecological studies, especially where key-species are used to model ecological processes.     

Molecular definition and the ubiquity of species in the genus Naegleria

To investigate the variability within species of the genus Naegleria, the ITS1,5.8S and ITS2 rDNA were sequenced of several strains of N. lovaniensis and its Western Australian variants, N. australiensis, N. fowleri, N. andersoni, N. jamiesoni, N. tihangensis, N. pringsheimi, N. pagei, N. gruberi sensu lato and a Naegleria lineage that lost a group I intron from the SSUrDNA twintron. As a result, it is possible to define a molecular species within the Naegleria genus. In addition, one strain of each different allozyme cluster was sequenced to investigate whether they belong to described species or should be treated as distinct new species. This leads to the proposal of eleven new species. The sequencing results from those Naegleria spp. of which several strains are available indicate that these species are ubiquitous. The only exception might be the species represented by the WA variants. However, there are still many Naegleria spp. for which only one strain has been isolated, hence, it is important that the search for more isolates should be continued worldwide.     

一株携带质粒的人两歧双歧杆菌的分离与鉴定

目的:分离携带天然质粒的人双歧杆菌.方法:用自制的改良型Blb双歧杆菌选择培养基,从人新鲜粪便分离双歧杆菌,对初步质粒检测阳性的单菌落通过糖发酵试验、(G C)mol%测定和16S rDNA序列分析,进行菌株鉴定.结果:筛选到一株携带天然质粒的人双歧杆菌,编号B200304,在1.0%琼脂糖凝胶上,测得质粒的相对分子质量约为22 kb.通过对该菌株的形态学观察和糖发酵试验等生理生化特征研究,证明该菌株为两歧双歧杆菌(Bifidobacterium bifidum);HPLC法测得其(G C)mol%为55.6,16SrDNA序列分析进一步证实该菌株为两歧双歧杆菌.结论:分离得到一株携带天然质粒的人两歧双歧杆菌新菌株.     

中间偃麦草(Thinopyrum intermedium)18S-5.8S-26S rDNA位点在染色体上的分布及对其核ITS序列异质性的分析

中间偃麦草(Thinopyrum intermedium(Host)Barkworth et Dewey)是禾本科小麦族植物中的一个异源六倍体物种,是重要的牧草植物,在小麦的抗病育种中发挥了重要作用.利用荧光原位杂交(FISH)技术,在体细胞中期染色体上,对18S-5.8S-26S rDNA位点进行了物理定位,发现该物种有3～4对染色体携带18S-5.8S-26S rDNA主位点.结合基因组原位杂交(GISH)分析,证明中间偃麦草的St基因组中有一对同源染色体短臂末端携带一个主位点,其余2～3对主位点位于E基因组染色体上.对不同来源的材料研究表明:18S-5.8S-26S rDNA位点的数目(包括主位点和小位点)、位置、拷贝数在不同收集材料之间的差异较大,甚至在同一个体的不同细胞中也存在差异.讨论了rDNA物理作图数据在分析系统发育问题中的局限性.结合中间偃麦草的三个可能的二倍体基因组供体(Th.bessarabicum、Th.elongatum和Pseudoroegneria stipifolia)rDNA位点分析的结果,对中间偃麦草进化过程中rDNA位点的变化进行了分析,同时,对其中一份材料的核ITS序列进行了克隆、测序和系统发育分析,发现在中间偃麦草中,ITS序列具有很高的异质性.     

苔藓动物主要类群28S rDNA多变区的分子形态分析及其系统学意义

测定了苔藓动物主要代表类群3种苔虫的28S rDNA全序列(3 459～3 613 bp),结合已公布的相关类群的28S rDNA全序列数据,分析了其一级结构特征,并分别绘制了D2、D3和D8区段的二级结构.比较分析结果显示:各类群的全序列总长均超过3 300 bp,GC含量为41.8%～57.7%;D3和D8区段的二级结构保守性较高,D2区差异显著;各区段的长度变化较大,但是,大多都具有相似的主干结构.基于二级结构多变区分子形态学特征的比较基本和基于一级结构的分子系统学结论相吻合,提示它们同样包含着重要的系统发育信息.     

应用5.8S rDNA及ITS区序列分析链格孢种级分类*

对9个链格孢小孢子种和3个大孢子种共20个链格孢菌株的5.8S rDNA及其两侧的ITS1区和ITS2区进行了序列分析。聚类分析结果表明形态差异大的种可以明确加以区分,而供试的9个小孢子种之间差异很小,不能根据对所选区段的序列分析加以区分。传统分类上的滨菊链格孢不属于Alternaria, 其分类地位需进一步研究。     

Phylogenetic relationships of the genus Secale based on the characterisation of rDNA ITS sequences

 Sequence analysis of the internal transcribed spacer of the 18S-5.8S-26S rDNA (ITS-1) region was performed in order to analyse the phylogenetic relationships of eleven taxa of cultivated and wild rye species. The ITS regions were amplified using designed primers. At least ten positive clones of each taxonomic unit were sequenced and compared. Two different ITS sequences were found in three taxa: Secale sylvestre Host, Secale strictum ssp. kuprijanovii Grossh. and Secale strictum ssp. africanum Stapf. Secale sylvestre Host was the species that showed the greatest number of comparative differences in the sequences, and was the most distant of all the taxonomic units analysed. A certain degree of variation was found among all four subspecies of S. strictum analysed. S. strictum Presl ssp. strictum was most closely related to S. strictum ssp. africanum Stapf and S. strictum ssp. kuprijanovii Grossh to S. strictum ssp. anatolicum (Boiss.) Hammer. S. vavilovii showed similarities with this group of subspecies and with the S. cereale group. No differences were found between the weed forms of S. cereale and cultivated rye. Received March 8, 2002; accepted May 31, 2002 Published online: November 20, 2002 Address of the authors: Alfredo De Bustos, Nicolás Jouve (e-mail: nicolas.jouve@uah.es), Department of Cell Biology and Genetics, University of Alcalá, E-28871 Alcalá de Henares (Madrid), Spain.     

Nucleotide sequence of the 17S–25S spacer region from rice rDNA

Summary The nucleotide sequence of a spacer region between rice 17S and 25S rRNA genes (rDNAs) has been determined. The coding regions for the mature 17S, 5.8S and 25S rRNAs were identified by sequencing terminal regions of these rRNAs. The first internal transcribed spacer (ITS1), between 17S and 5.8S rDNAs, is 194–195 bp long. The second internal transcribed spacer (ITS2), between 5.8S and 25S rDNAs, is 233 bp long. Both spacers are very rich in G+C, 72.7% for ITS1 and 77.3% for ITS2. The 5.8S rDNA is 163–164 bp long and similar in primary and secondary structures to other eukaryotic 5.8S rDNAs. The 5.8S rDNA is capable of interacting with the 5′ terminal region of 25S rDNA.     

Molecular characterization of Serratia marcescens strains by RFLP and sequencing of PCR-amplified 16S rDNA and 16S-23S rDNA intergenic spacer

AIMS: To establish the specific DNA patterns in 16S rDNA and 16S-23S rDNA intergenic spacer (IGS) regions from different kinds of Serratia marcescens strains using polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP) and sequences analysis. METHODS AND RESULTS: Two pairs of primers based on the 16S rDNA and 16S-23S rDNA IGS were applied to amplify the rrn operons of two kinds of S. marcescens strains. About 1500 bp for 16S rDNA and four fragments of different sizes for 16S-23S rDNA IGS were obtained. PCR-amplified fragments were analysed by RFLP and sequence analysis. Two distinct restriction patterns revealing three to five bands between two kinds of strains were detected with each specific enzyme. According to the sequence analysis, two kinds of strains showed approximately 97% sequence homology of 16S rDNA. However, there was much difference in the sequences of IGS between the two kinds of strains. Intercistronic tRNA of strains H3010 and A3 demonstrated an order of tRNA of 5'-16S-tRNA(Ala)-tRNA(Ile)-23S-3', but strain B17 harboured the tRNA of 5'-16S-tRNA(Glu)-tRNA(Ile)-23S-3'. CONCLUSIONS: The method was specific, sensitive and accurate, providing a new technique for differentiating different strains from the same species. SIGNIFICANCE AND IMPACT OF THE STUDY: This paper provided the first molecular characterization of 16S rDNA and 16S-23S rDNA IGS from S. marcescens strains.