Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing

In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.

Assessment of prey overlap between a native (Polistes humilis) and an introduced (Vespula germanica) social wasp using morphology and phylogenetic analyses of 16S rDNA

In newly invaded communities, interspecific competition is thought to play an important role in determining the success of the invader and its impact on the native community. In southern Australia, the native Polistes humilis was the predominant social wasp prior to the arrival of the exotic Vespula germanica (Hymenoptera: Vespidae). Both species forage for similar resources (water, pulp, carbohydrate and protein prey), and concerns have arisen about potential competition between them. The aim of this study was to identify the protein foods that these wasps feed on. As many prey items are masticated by these wasps to the degree that they cannot be identified using conventional means, morphological identification was complemented by sequencing fragments of the mitochondrial 16S rRNA gene. GenBank searches using blast and phylogenetic analyses were used to identify prey items to at least order level. The results were used to construct complete prey inventories for the two species. These indicate that while P. humilis is restricted to feeding on lepidopteran larvae, V. germanica collects a variety of prey of invertebrate and vertebrate origin. Calculated values of prey overlap between the two species are used to discuss the implications of V. germanica impacting on P. humilis. Results obtained are compared to those gained by solely 'conventional' methods, and the advantages of using DNA-based taxonomy in ecological studies are emphasized.

Identification of Sarcocystis hominis-like (Protozoa : Sarcocystidae) cyst in water buffalo (Bubalus bubalis) based on 18S rRNA gene sequences

DNA templates were extracted from isolates of Sarcocystis hominis-like cysts collected from cattle and water buffalo, as well as from Sarcocystis fusiformis cysts and Sarcocystis suihominis cysts. The 18S rRNA genes were amplified using DNA from a single

Characterization of Sarcocystis species in domestic animals using a PCR-RFLP analysis of variation in the 18S rRNA gene: a cost-effective and simple technique for routine species identification

Thirteen restriction endonucleases were used to investigate nucleotide sequence variation in the 18S rRNA DNA of 88 individuals from ten Sarcocystis taxa collected as cysts from their intermediate hosts, swine, cattle and water buffalo. A DNA sequence of

Analysis of 18S rRNA gene of Octostigma sinensis (Projapygoidea : Octostigmatidae) supports the monophyly of Diplura

The phylogenetic position of Diplura within Hexapoda has been controversial. There are three major lineages in Diplura: Campodeoidea, Projapygoidea, and Japygoidea. However, most of the previous studies were restricted to Campodeoidea and Japygoidea. Unti

Molecular dynamics simulation on the complex of the tobramycin and 16S rRNA a site

A 3. 6 ns molecular dynamics simulation was carried out on the complex system of tobramycin and 16S rRNA in order to understand the speciality recognition mechanism between tobramycin and 16S rRNA at the molecular level. The results demonstrate that two l

Generic allocation of Indian and Sri Lankan Philautus (Anura: Rhacophoridae) inferred from 12S and 16S rRNA genes

The generic allocation of Indian and Sri Lankan Philautus needs further examination. In this study, a comprehensive understanding of the phylogeny of Indian and Sri Lankan Philautus is obtained based on 125 and 16S rRNA genes. All phylogenetic analyses indicate that Indian-Sri Lankan Philautus, Philautus menglaensis, Philautus longchuanensis, and Philautus gryllus form a well supported clade, separate from Philautus of Sunda Islands that form another well supported clade representing true Philautus. This result supports the designation of the genus Pseudophilautus to accommodate the Indian and Sri Lankan species. Pseudophilautus consists of two major lineages, one comprises the majority of Indian species, Chinese species, and Southeast Asian species, and one comprises all Sri Lankan species and a few Indian species. Pseudophilautus may have originated in South Asia and dispersed into Southeast Asia and China. Based on the results, we further suggest that Philautus cf. gryllus (MNHN1997.5460) belongs to the genus Kurixalus. (C) 2010 Published by Elsevier Ltd.

Tobramycin与16S rRNA A位点复合物的分子动力学模拟

采用分子动力学方法(Molecular dynamics,MD)对托普霉素(Tobramycin)与16S rRNA的A位点复合物的特异性识别机制进行了理论模拟研究,模拟时间为3.6 ns. 结果表明,A位点中波动最大的部位是两个环外碱基A1492和A1493;tobramycin的环Ⅰ和环Ⅱ是其最保守的结构单元,可能参与了Tobramycin与16S rRNA的A位点之间的特异性识别. 另外,发现一个残存时间为3.6 ns的"结构化"水分子,它桥接了Tobramycin环Ⅱ的N3与环Ⅰ的N6′之间的氢键,稳定了Tobramycin的结构;Tobramycin周围水合密度较高的位点出现在环Ⅰ和环Ⅱ附近,这也正是晶体结构中形成较多水媒介氢键及动力学模拟中结构化水分子出现的位置. 动力学模拟证实Tobramycin与16S rRNA间的结合是大量氢键及水分子相互作用的结果,这有助于设计和开发以Tobramycin为基础,具有高亲和力及特异性的16S rRNA抑制剂.

Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

洱海鱼腥藻优势种的形态鉴定与16S rRNA基因序列分析

分别在2004年、2005年和2006年洱海鱼腥藻水华暴发时期,分离优势种,获得藻株EH-A、EH-B和EH-C,通过形态学特征和16S rRNA基因序列分析鉴定了藻株的种类。选用藻丝的形态、气囊的存在与否、异形胞和孢子的位置、各种细胞的形状以及营养细胞、异形胞和孢子的大小等传统的分类特征描述藻株的形态。依据形态特征,初步判断这3个藻株可能为卷曲鱼腥藻(Anabaena circinalis)或A.crassa株系成员。利用16S rRNA基因序列构建邻接树分析了藻株间的系统进化关系,分析表明:藻株EH-

利用mtDNA 16S rRNA序列差异鉴定江西青岚湖的河蚌物种

对从青岚湖采集的 10属 14种河蚌的 19个样本进行了 16SrRNA的序列测定 ,并同GenBank中鄱阳湖流域相同物种河蚌的序列比较 ,分析了基于Kimura 2 parameter模型参数得到的遗传距离 ,并构建了它们的UPGMA树。结果显示 ,所有用于比较的河蚌种间遗传距离变化范围在 0 .0 2 74— 0 .2 2 90 ,平均为 0 .132 5 ,种内遗传距离在0 .0 0 34— 0 .0 0 6 8之间 ,平均为 0 .0 0 4 5 ,种间遗传距离远大于种内距离。表明以 16SrR

16S rRNA基因序列变异与中国鮡科鱼类系统发育

采用PCR技术获得了中国鮡科鱼类10属9种鰋鮡鱼类和6种非鰋鮡鱼类线粒体DNA 16S rRNA基因部分序列. 序列分析表明, 16S rRNA序列非配对区有A碱基偏倚性, 配对区有G碱基偏倚性. 在非配对区, 主要由于A→G转换引起转换大于颠换的偏倚, 且平均替代率几乎是配对区的2倍. 配对区和非配对区均没有替代饱和现象. 采用最大似然法(ML)和Bayesian方法构建分子系统树, 结果表明, 鮡科是一个单系群, 由(黑鮡属(魾属, 纹胸鮡属))与(褶鮡属+ 鰋鮡鱼类)两支构成. 鰋鮡鱼类可能不是一个

中国蚌科线粒体16S rRNA序列变异及系统发育

首次测定了中国淡水贝类———蚌科 (Unionidae) 1 3个属代表种类的线粒体 1 6SrRNA部分序列。用Clustal X排序软件进行 1 6SrRNA序列的对位排列 ,序列总长度为 30 5— 32 0bp。通过Mega 2 0软件对所得线粒体 1 6SrRNA片段序列进行比较 ,共发现 1 0 8个碱基存在变异 ,其中包括 77个简约信息位点 ,并用“Pairwisedistance”计算了各属间的相对遗传距离。以贻贝为外类群 ,采用Mega 2 0软件中的“Neighbore Joinin