A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community

Clones from the same marine bacterioplankton community were sequenced, 100 clones based on DNA (16S rRNA genes) and 100 clones based on RNA (16S rRNA). This bacterioplankton community was dominated by alpha-Proteobacteria in terms of repetitive DNA clones (52%), but gamma-Proteobacteria dominated in terms of repetitive RNA clones (44%). The combined analysis led to a characterization of phylotypes otherwise uncharacterized if only the DNA or RNA libraries would have been analyzed alone. Of the DNA clones, 25.5% were found only in this library and no close relatives were detected in the RNA library. For clones from the RNA library, 21.5% of RNA clones did not indicate close relatives in the DNA library. Based on the comparisons between DNA and RNA libraries, our data indicate that the characterization of the bacterial community based on RNA has the potential to characterize distinct phylotypes from the marine environment, which remain undetected on the DNA level.     

基于线粒体12S和16S rRNA基因部分序列探讨蚱科12种的系统发育关系

用ABI377自动测序仪测定了蚱科5属11个种的12s和16S rRNA基因部分序列,并从GenBank获得1属1种的同源序列;用Clustal X1．81比较其同源性,用Mega2．1计算序列变异性和遗传距离。在获得的736bp序列中,A T含量为71．2％～77．5％,平均为73．9％;G C含量为22．5％～28．8％,平均为26．1％。经Clustal X1．81软件比对,共得到755个位点,其中简约信息位点185个。以Cylindraustralia kochii为外群,构建NJ、MP和ML分子系统树,结果表明：(1)蚱属并非一个单系群,而是一个并系群;(2)环江柯蚱Coptltettix huanjiangensis和贡山柯蚱C.gongshanensis为同一个种,即贡山柯蚱,而环江柯蚱是贡山柯蚱的同物异名。     

耐热嗜盐菌的分离及16S rRNA基因序列分析

从位于西藏自治区澜沧江边一个47℃的盐井中分离筛选到一株耐热嗜盐菌菌株 YJ0238.对其进行了生理生化特性研究,采用PCR方法扩增其16S rRNA基因序列,并进行了测定.基于生理生化特性和16S rRNA基因序列的同源性比较,以及系统发育分析,发现菌株YJ0238是Idiomarina属中成员zobellii的一个亚种,其16S rRNA基因序列已被GenBank数据库收录,序列号为EF693953.迄今为止,国内极少有关高温、高盐环境中微生物研究的报道,本研究可为今后研究同类极端环境中新的物种资源以及微生物多样性提供素材和参考.     

耐热嗜盐菌的分离及16S rRNA基因序列分析

从位于西藏自治区澜沧江边一个47℃的盐井中分离筛选到一株耐热嗜盐菌菌株YJ0238, 对其进行了生理生化特性研究, 采用PCR方法扩增其16S rRNA基因序列, 并进行了测定。基于生理生化特性和16S rRNA基因序列的同源性比较, 以及系统发育分析, 发现菌株YJ0238是Idiomarina属中成员zobellii的一个亚种, 其16S rRNA基因序列已被GenBank数据库收录, 序列号为EF693953。迄今为止, 国内极少有关高温、高盐环境中微生物研究的报道, 本研究可为今后研究同类极端环境中新的物种资源以及微生物多样性提供素材和参考。     

Characterization of halotolerant rhizobia isolated from root nodules of Canavalia rosea from seaside areas

Twelve nodule isolates from Canavalia rosea, an indigenous leguminous halophyte growing in the seaside areas of southern Taiwan, were effective symbionts for the original host and able to grow at NaCl concentrations up to 3-3.5% (w/v). The taxonomy of these isolates was investigated using a polyphasic approach, including phenotypic characteristics, banding patterns of total proteins from sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), genomic fingerprint patterns from random amplified polymorphic DNA (RAPD) analysis, pulsed-field gel electrophoresis (PFGE) analysis, amplified 16S rDNA restriction analysis (ARDRA), 16S rRNA gene sequencing, and nifH gene sequencing. Based on the SDS-PAGE, RAPD, PFGE and ARDRA results, the 12 isolates are highly diverse. The 16S rRNA and nifH gene sequences were determined for isolates with distinct ARDRA patterns and compared with other members of the rhizobial species. We propose these isolates should be classified into the genus Sinorhizobium and distinguished from the current species of this genus.     

嗜盐古细菌的系统发育分析

用“Clustalw”和“PHYLIP”程序包分析嗜盐古细菌16S rRNA序列,建立了嗜盐古细菌的系统发育树。比较分析的结果进一步支持了以前的结论,即嗜盐古细菌在自然系统分类上应被分成嗜盐菌科的6个属。此系统发育分析方法不仅体现了在嗜盐古细菌属一级分类上的优势,而且还可能被用作一种相应于以《伯杰氏细菌系统分类手册》(第三卷)为基础的嗜盐古细菌种一级分类上的代换方法。实际上,这种系统发育分析方法比其他建立在表型特性基础上的分类系统更真实地反映了嗜盐古细菌内的亲缘关系。该方法的其他运算细节在本文中也进行了讨论。     

斑鳠烂鳃病病原菌的研究

从池塘患烂鳃病的斑鳠(Mystus guttatus)亲鱼病灶中分离出一株毒力较强的致病菌-Mg2,经形态学观察、生理生化特性和16S rRNA基因序列分析鉴定,其主要特征为：菌体细长,无鞭毛和荚膜,革兰氏阴性,大小0.5×(6.5－11)μm,菌落黄色,边缘不整齐呈假树根状。氧化酶、过氧化氢酶阳性,分解酪素和明胶,硝酸盐还原阳性;不分解纤维素、几丁质、酪氨酸、七叶灵和淀粉,吲哚和葡萄糖产气阴性。对恩诺沙星、诺氟沙星、萘啶酸、红霉素、洁霉素敏感,菌株的16S rRNA基因序列分析结果表明：Mg2菌株与柱状黄杆菌聚类,基因序列的同源性在97.5%以上,综合生理生化、分子生物学两方面的分类鉴定结果,Mg2菌株应归类鉴定为柱状黄杆菌（Flavobacterium Columnare）。     

Genetic interrelationships of saccharolytic Clostridium botulinum types B, E and F and related clostridia as revealed by small-subunit rRNA gene sequences

Abstract The phylogenetic interrelationships of saccharolytic C. botulinum types B, E and F together with eleven other saccharolytic clostridia were examined by 16S rRNA gene sequencing. Comparative analysis of the sequence data revealed that the saccharolytic C. botulinum types B, E and F were highly related and represents a single genetic group. Strains of C. barati and C. butyricum that produce botulinal neurotoxin revealed almost 100% 16S rRNA sequence identity with their respective non-toxigenic counterparts and were phylogenetically distinct from saccharolytic C. botulinum (types B, E and F). Proteolytic C. botulinum type F was shown to be phylogenetically remote from the saccharolytic C. botulinum group. The implications of the sequence data for the taxonomy of the C. botulinum complex are discussed.