Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain.
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain.
Syst Appl Microbiol. 2014 May;37(3):216-28. doi: 10.1016/j.syapm.2013.11.005. Epub 2014 Jan 23.
Microbial isolates are useful models for physiological and ecological studies and can also be used to reassemble genomes from metagenomic analyses. However, the phylogenetic diversity that can be found among cultured marine bacteria may vary significantly depending on the isolation. Therefore, this study describes a set of 136 bacterial isolates obtained by traditional isolation techniques from the Blanes Bay Microbial Observatory, of which seven strains have had the whole genome sequenced. The complete set was compared to a series of environmental sequences obtained by culture-independent techniques (60 DGGE sequences and 303 clone library sequences) previously obtained by molecular methods. In this way, each isolate was placed in both its "ecological" (time of year, nutrient limitation, chlorophyll and temperature values) context or setting, and its "phylogenetic" landscape (i.e. similar organisms that were found by culture-independent techniques, when they were relevant, and when they appeared). Nearly all isolates belonged to the Gammaproteobacteria, Alphaproteobacteria, or the Bacteroidetes (70, 40 and 20 isolates, respectively). Rarefaction analyses showed similar diversity patterns for sequences from isolates and molecular approaches, except for Alphaproteobacteria where cultivation retrieved a higher diversity per unit effort. Approximately 30% of the environmental clones and isolates formed microdiversity clusters constrained at 99% 16S rRNA gene sequence identity, but the pattern was different in Bacteroidetes (less microdiversity) than in the other main groups. Seventeen cases (12.5%) of nearly complete (98-100%) rRNA sequence identity between isolates and environmental sequences were found: nine in the Alphaproteobacteria, five in the Gammaproteobacteria, and three in the Bacteroidetes, indicating that cultivation could be used to obtain at least some organisms representative of the various taxa detected by molecular methods. Collectively, these results illustrated the largely unexplored potential of culturing on standard media for complementing the study of microbial diversity by culture-independent techniques and for obtaining phylogenetically distinct model organisms from natural seawater.
微生物分离物是生理和生态研究的有用模型，也可用于从宏基因组分析中重新组装基因组。然而，从培养的海洋细菌中发现的系统发育多样性可能因分离方法而异。因此，本研究描述了一组 136 个细菌分离物，这些分离物是通过传统的分离技术从布兰斯湾微生物观测站获得的，其中 7 个菌株已经完成了全基因组测序。对完整数据集与一系列通过非培养技术（60 个 DGGE 序列和 303 个克隆文库序列）获得的环境序列进行了比较，这些序列是之前通过分子方法获得的。通过这种方式，每个分离物都被置于其“生态”（一年中的时间、营养限制、叶绿素和温度值）背景或环境中，以及其“系统发育”景观（即通过非培养技术发现的相似生物体，在相关时和出现时）。几乎所有的分离物都属于γ变形菌纲、α变形菌纲或拟杆菌门（分别为 70、40 和 20 个分离物）。稀疏分析显示，分离物和分子方法的序列具有相似的多样性模式，除了α变形菌纲，其单位努力的多样性更高。大约 30%的环境克隆和分离物形成了微多样性簇，限制在 16S rRNA 基因序列同一性的 99%，但在拟杆菌门中的模式与其他主要群体不同（微多样性较少）。在分离物和环境序列之间发现了 17 个几乎完全（98-100%）rRNA 序列同一性的情况（12.5%）：9 个在α变形菌纲，5 个在γ变形菌纲，3 个在拟杆菌门，表明培养可以用于获得至少一些代表通过分子方法检测到的不同分类群的生物。总的来说，这些结果说明了在标准培养基上进行培养的巨大潜力，可以补充非培养技术对微生物多样性的研究，并从天然海水中获得系统发育不同的模式生物。
