Rhizobium leguminosarum bv. trifolii forms a natural, endophytic association with rice roots that can promote the growth of this important cereal plant, resulting in higher grain production with less N fertilizer inputs (Yanni et al. 1997; Prayitno et al. 1999; Biswas et al. 2000; Yanni et al. 2001). Earlier work with rice in gnotobiotic culture indicated that the rhizobia accumulate and penetrate sites where lateral roots emerge, multiply within dead cortical cells and intercellularly within the lateral rootlets, and can disseminate further inside of growing roots (Reddy et al. 1997; Yanni et al.

1997; Prayitno et al. 1999). Here, we acquired 140 georeferenced SEM images of rice roots

colonized by strain Ell, and used CMEIAS (Center for Microbial Ecology Image Analysis Software; Dazzo et al. 2001; Liu et al. 2001) to analyze the spatial distribution of ~100,000 cells in situ on the root surface.

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