Goregues C M, Michotey V D, Bonin P C
Laboratoire de Microbiologie, de Géochimie et d'Ecologie Marines, CNRS-UMR 6117, Centre d'Océanologie de Marseille, Campus de Luminy, Case 90l, 13288, Marseille cedex 9, France.
Microb Ecol. 2005 Feb;49(2):198-208. doi: 10.1007/s00248-004-0256-7. Epub 2005 Feb 24.
One of the major challenges in microbial ecology for the future is to establish links between structural and functional biodiversity. This is particularly difficult when one is interested in a phylogenetically diversified function such as denitrification. The data banks are very rich in functional gene sequences (nirS in this study), but most of them were obtained from not yet cultivated bacteria, and thus must be supplemented by sequences of organisms from the environment for which we could associate a taxonomic position and physiological characteristics. Combined analysis including molecular (16S-rRNA or nirS genes), physiological, and biochemical approaches was carried out on a bacterial set of 89 strains isolated from marine sediment. The denaturing gradient gel electrophoresis (DGGE) technique was successfully applied on unclamped polymerase chain reaction (PCR) products of nirS genes to compare the picture of the biodiversity obtained with 16S rRNA and nirS genes. The diversity of nirS genes and denitrifier characteristics were found within several of the 16S rDNA phylotypes. In contrast, the nirS phylotypes were no diverse both with respect to 16S rDNA and to physiology and biochemistry of denitrification. Sequences of the nirS PCR products were very close to marine environmental clones and were analyzed within the same phylogenetic tree.
未来微生物生态学面临的主要挑战之一是建立结构生物多样性与功能生物多样性之间的联系。当人们对诸如反硝化作用这样具有系统发育多样性的功能感兴趣时，这一挑战尤为艰巨。数据库中功能基因序列（本研究中的nirS）非常丰富，但其中大多数来自尚未培养的细菌，因此必须用来自环境的生物序列进行补充，对于这些生物我们能够确定其分类地位和生理特征。对从海洋沉积物中分离出的89株细菌进行了包括分子（16S - rRNA或nirS基因）、生理和生化方法在内的综合分析。变性梯度凝胶电泳（DGGE）技术成功应用于nirS基因的非夹钳式聚合酶链反应（PCR）产物，以比较通过16S rRNA和nirS基因获得的生物多样性情况。在几个16S rDNA系统发育型中发现了nirS基因的多样性和反硝化细菌的特征。相比之下，nirS系统发育型在16S rDNA以及反硝化作用的生理和生化方面均无多样性。nirS PCR产物的序列与海洋环境克隆非常接近，并在同一系统发育树中进行了分析。
