Geographical diversity of genomic lineages in Bacillus subtilis (Ehrenberg) Cohn sensu lato

Prior genetic studies of wild isolates of Bacillus subtilis (Ehrenberg) Cohn from a single site in Arizona, USA, revealed four deeply separated lineages within this bacterial species traditionally defined through its physiological traits. The present study examines isolates from eight sites at varying degrees of geographical separation to assess the global genomic variation of B. subtilis, Sites are located in Arizona, California, and Utah in the USA, and in Mexico, Chile, Chad, Tunisia, and China. Using a random 10-bp PCR primer, RAPD DNA fingerprints were obtained for 106 isolates. From these data a UPGMA dendrogram was constructed. Six major genomic lineages separating at 9-18% similarity were found. Tree topology was virtually identical with an independently derived phylogeny using distinctly different data. Three lineages were the same as previously observed in Arizona, two were new, and one involved association of a small cluster of Tunisian isolates with the single member of a distinctive fourth lineage from Arizona, though this association was ambiguous. Four of the lineages were found on three or four continents; the others were found only on one or two continents depending on the interpretation of the ambiguous association. Within each major lineage there were cascades of sublineages. Some sublineages exhibited geographically local genomic differentiation; others mingled similar genomes from geographically distant locations, The major lineages separated at levels of genomic similarity only slightly different from those observed with random permutations of the data.