5. Phylogenetic patterns among biodegraders and a strain database
To search for patterns of microbial degradation within a phylogenetic context, we have undertaken a study to establish the phylogenetic distribution of biodegrading bacteria. Described, degradative, bacterial strains were identified through a search of online nucleic acid sequence and culture collection databases and of the scientific literature and then compared to the 16S rRNA phylogeny. For purposes of manageability, we restricted our search to the bacteria and to aerobic processes. Catabolized compounds included BTEX compounds, halogenated aromatics, nitroaromatics, polycyclic aromatic hydrocarbons (PAHs), halosolvents and other toxic aliphatics and polyesters (biodegradable plastics). To date, we have identified 348 bacterial strains, representing 53 validly described genera, that catabolize at least one of 111 compounds. The vast majority of the strains (319 [91.7%]) and genera (47 [88.7%]) were distributed among only two 16S rRNA phylogenetic groups, the high G+C gram-positives and the proteobacteria. Distribution within the proteobacteria was limited to three of the five subgroups (alpha-, beta- and gamma-subgroups). Other phylogenetic groups represented in the collection were the low G+C Gram positives (3 genera, 6 strains), Cytophagales (1 genus, 3 strains) and the cyanobacteria (2 genus, 2 strains). These numbers do not reflect an additional 175 biodegrader citations (and an additional 27 substrates) for which we are still collecting data. We are also conducting a survey of nucleic acid elements (plasmids, transposons, etc.) capable of facilitating the lateral transfer of biodegradative genes.
The difficulty in comprehensively compiling strain data for this study has underscored the potential usefulness of an on-line database that would consolidate strain-level microbial data. To meet this need, we are developing an on-line database of information on described, biodegradative, microbial strains. This database is meant to complement and is being coordinated with the University of Minnesota Biocatalysis/Biodegradation Database. A prototype of the Biodegradative Strain Database (BSD) is available at http://bsd.cme.msu.edu/bsd/index.html. The website currently contains up-to-date data from this investigation (including detailed strain and substrate lists and a phylogenetic tree illustrating the distribution of biodegrading bacteria), our vision for future development of the database, and on-line user survey and data submission forms for input from the microbiological community and for the contribution of new and corrected data.
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