STRATEGIES FOR PHYLOGENETIC CHARACTERIZATION OF SUBSURFACE BACTERIA

The purpose of this study was to evaluate approaches for phylogenetic characterization of bacteria from terrestrial subsurface environments by analysis of 16S ribosomal RNA gene (16S rDNA) nucleotide sequences. Three methods for detecting identical or very closely related strains among large groups of isolates (to reduce the number of strains that must be fully sequenced) were examined: (i) analysis of existing morph ological and physiological data, (ii) restriction endonuclease analysi s of genomic DNA, and (iii) analysis of short (ca. 350-base) 16S rDNA sequences. These three methods were applied to a test group of 20 subs urface bacteria and evaluated by comparing their results to those obta ined by analysis of relatively long 16S rDNA sequences. Short sequence analysis yielded the most useful predictive information and, thus, ap peared to be the best method for 'prescreening' large numbers of isola tes (so that representative strains can be selected for full sequencin g). The analysis of longer sequences placed 12 test-group strains in t hree subdivisions of the Proteobacteria (Purple Bacteria) and 8 strain s in the high-G+C Gram-positive bacteria. Seven of the former were rel ated to Pseudomonas aeruginosa or other members of the fluorescent pse udomonad group, while six of the latter were tentatively identified as Arthrobacter globiformis (based on 97-99% sequence similarity).