A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis
A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis
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DOI：
10.1186/1471-2164-16-s5-s10
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发表时间：
2015-05-26
期刊：
影响因子：
4.4
通讯作者：
Hungria, Mariangela
中科院分区：
文献类型：
--
作者：
Azevedo, Helton;Lopes, Fabricio Martins;Hungria, Mariangela
背景：以豆科植物-根瘤菌共生为重点的生物固氮是农业和环境的关键过程，可以替代氮肥，减少硝酸盐对水的污染以及温室气体的排放。土壤中含有许多属于慢生根瘤菌属的菌株，它们与各种豆类植物建立了共生关系。然而，由于缓慢根瘤菌16S rRNA基因的高度保守性-被认为是原核生物分类学的支柱-很少有物种被描述出来。多位点序列分析(MLSA)方法，包括看家基因的分析，已被证明是确定细菌种类的有效方法，在本研究中，它被应用于慢生根瘤菌，增加了我们对固氮菌多样性的了解。描述：具有重要农学意义的细菌的分类与生物多样性有关，也与提高农业生产力的生物技术操作有关。我们建议建立一个在线数据库，利用MLSA提供信息和工具，改善慢生根瘤菌的系统发育和分类特征，使基因组序列与每个物种的模式菌株和代表性菌株的基因组序列进行比较。结论：利用MLSA建立慢生根瘤菌属分类和系统发育鉴定数据库，将有助于使用通过直观的网络界面获得的生物学数据。通过将多种比对算法和计算程序集成到数据库中，可以将存储在在线数据库中的序列与其他菌株的多个序列进行简单和灵活的比较。拟议的数据库和软件工具可在http://mlsa.cnpso.embrapa.br，上获得，世界各地的研究人员可以免费使用它们来对慢生根瘤菌菌株进行分类；该数据库和软件可用于复制本研究中提出的实验以及产生新的实验。下一步将是扩大数据库，以包括其他根瘤菌物种。
Background: Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of housekeeping genes, has been shown to be promising and powerful for defining bacterial species, and, in this study, it was applied to Bradyrhizobium, species, increasing our understanding of the diversity of nitrogen-fixing bacteria.Description: Classification of bacteria of agronomic importance is relevant to biodiversity, as well as to biotechnological manipulation to improve agricultural productivity. We propose the construction of an online database that will provide information and tools using MLSA to improve phylogenetic and taxonomic characterization of Bradyrhizobium, allowing the comparison of genomic sequences with those of type and representative strains of each species.Conclusion: A database for the taxonomic and phylogenetic identification of the Bradyrhizobium, genus, using MLSA, will facilitate the use of biological data available through an intuitive web interface. Sequences stored in the on-line database can be compared with multiple sequences of other strains with simplicity and agility through multiple alignment algorithms and computational routines integrated into the database. The proposed database and software tools are available at http://mlsa.cnpso.embrapa.br, and can be used, free of charge, by researchers worldwide to classify Bradyrhizobium, strains; the database and software can be applied to replicate the experiments presented in this study as well as to generate new experiments. The next step will be expansion of the database to include other rhizobial species.