Using a modified Eckhardt method, we visualized replicons larger than 1,000 kb in Rhizobium tropici strains belonging to both subgroup A and subgroup B. The megaplasmid of R. tropici CFN299 was characterized. This megaplasmid is different from a cointegrate of various plasmids and from the chromosome. Hybridization of Eckhardt blots of 15 R. tropici strains with fragments derived from the megaplasmids of the type strains of subgroups A and B revealed that the megaplasmids are subgroup specific.Rhizobium spp. form nitrogen-fixing nodules on the roots of leguminous plants. In Rhizobium strains plasmids constitute an important part of the genome (11,18,28). Megaplasmids larger than 1,000 kb have been found in Rhizobium meliloti (32), Rhizobium fredii (20), and Rhizobium galegae strains (24). In Rhizobium species, genes essential for nodule formation and nitrogen fixation are located on plasmids called symbiotic plasmids (pSym) (12,25), and these genes have been shown to be located on megaplasmids in R. meliloti (11,32).Rhizobium tropici strains nodulate Phaseolus vulgaris L. beans and other tropical legumes, including Leucaena sp. trees. Two subgroups, corresponding to type A and type B strains, have been described for this species on the basis of differences in rRNA genes and differences in several other phenotypic characteristics, including resistance to metals and antibiotics and the ability to metabolize certain carbon sources (19). We analyzed 15 previously described (19) R. tropici strains, including members of both subgroups, for their plasmids by using a modification (37) of the Eckhardt procedure (4) in which horizontal agarose gels are used (Fig. 1A). A replicon larger than 1,000 kb that has not been observed previously was found in all of the R. tropici strains, as well as in R. ji-edii USDA 191 (13) and R. meliloti RCR 2011, but not in Rhizobium loti NZP2037 (3), Rhizobium leguminosarum bv. viciae VF39 (29), R. leguminosarum bv. trifolii USDA 2152, or Rhizobium etli CFN42 (30) (Fig. 2). The nature of the replicon was determined in type A strain CFN299. To verify that this replicon was not a cointegrate of smaller plasmids, the homology between the megaplasmid and smaller plasmids was examined. Each of the smaller plasmids used (185,225, and 410 kb) was transferred to an Agrobacterium tumefaciens plasmidless strain (16; this study), purified from it, and used as a probe for the CFN299 plasmid. We observed no homology with any of the plasmids (Fig. 3, lanes 1 to 4). In order to distinguish between a chromosome and a megaplasmid, an Eckhardt blot was hybridized to a 300-bp fragment of the R. etli 16s rRNA genes (34). No hybridization was detected (Fig. 3, lane 5), indicating that the replicon was different from the chromosome.When R. tropici CFN299 was cross-mated with Escherichia coli S17 pSup 5011 (35), the CFN299 mutants (which were resistant to 60 mg of kanamycin per liter) were analyzed to locate Tn5. Hybridization between pSup 5011 and blotted plasmid patterns revealed that the frequencies of Tn5 ins...