Center for Microbial Ecology, Michigan State University, 48824, East Lansing, Michigan, USA.
Microb Ecol. 1995 Jul;30(1):3-24. doi: 10.1007/BF00184510.
To develop a better understanding of the ecological aspects of microbial biodegradation, it is important to assess the phenotypic and biochemical diversity of xenobiotic degrading organisms. Forty-six bacterial isolates capable of degrading 2,4-dichlorophenoxyacetic acid (2,4-D) and representing several geographically distinct locations were characterized and placed into taxonomic groups based on the results of several independent analyses. The isolates were characterized based on Gram's reaction, colony morphology, cell morphology, fatty acid methyl ester (FAME) fingerprints, carbon substrate oxidation patterns (BIOLOG), DNA homology to whole-plasmid probes and repetitive extragenic palindromic (REP) fingerprints. Attempts to group organisms taxonomically based on colony morphology and cell morphology were largely unsuccessful. Both FAME and BIOLOG analyses were generally unable to provide reliable genus or species identifications of these environmental isolates by comparison of fingerprints or substrate use patterns to existing data bases. Modification of the standard protocols for these analyses, however, allowed taxonomic grouping of the isolates and the construction of new data bases, comprised solely of 2,4-D-degrading organisms, against which future novel isolates can be compared. Independent cluster analysis of the FAME and BIOLOG data shows that the isolates can be segregated into five taxonomic classes. The collection of 2,4-D-degrading isolates was also separated into five classes based on DNA homology to whole-plasmid probes obtained from individual isolates. REP analysis allowed isolates that likely represent the same (or very similar) organism(s) to be identified and grouped. Each of the analyses used represents a mechanistically different means of classifying organisms, yet the taxonomic groupings obtained by several of the methods (FAME, BIOLOG, DNA homology, and to some degree, REP analysis) were in good agreement. This indicates that the features discriminated by these different methods represent fundamental characteristics that determine phylogenetic groups of bacteria.
为了更好地了解微生物生物降解的生态方面，评估外来化合物降解生物的表型和生化多样性非常重要。对 46 株能够降解 2,4-二氯苯氧乙酸（2,4-D）的细菌分离株进行了表征，并根据几项独立分析的结果将其归入分类群。这些分离株的特征基于革兰氏反应、菌落形态、细胞形态、脂肪酸甲酯（FAME）指纹图谱、碳底物氧化模式（BIOLOG）、与全质粒探针的 DNA 同源性和重复外回文（REP）指纹图谱。根据菌落形态和细胞形态对生物体进行分类学分组的尝试在很大程度上没有成功。FAME 和 BIOLOG 分析通常无法通过比较指纹图谱或底物使用模式与现有数据库来提供这些环境分离株的可靠属或种鉴定。然而，对这些分析的标准方案进行修改，允许对分离株进行分类分组，并构建仅由 2,4-D 降解生物组成的新数据库，以便将来可以对新的分离株进行比较。FAME 和 BIOLOG 数据的独立聚类分析表明，这些分离株可以分为五个分类类群。根据从单个分离株获得的全质粒探针的 DNA 同源性，2,4-D 降解分离株也分为五个类群。REP 分析允许鉴定和分组可能代表相同（或非常相似）生物的分离株。使用的每种分析方法都代表了一种机制上不同的分类生物体的方法，但几种方法（FAME、BIOLOG、DNA 同源性，在某种程度上，REP 分析）获得的分类分组非常一致。这表明这些不同方法区分的特征代表了决定细菌系统发育群的基本特征。
