Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil

Abstract

The spatial and genetic unit of bacterial population structure is the clone. Surprisingly, very little is known about the spread of a clone (spatial distance between clonally related bacteria) and the relationship between spatial distance and genetic distance, especially at very short scale (microhabitat scale), where cell division takes place. Agrobacterium spp. Biovar 1 was chosen because it is a soil bacterial taxon easy to isolate. A total of 865 microsamples 500 microm in diameter were sampled with spatial coordinates in 1 cm(3) of undisturbed soil. The 55 isolates obtained yielded 42 ribotypes, covering three genomic species based on amplified ribosomal DNA restriction analysis (ARDRA) of the intergenic spacer 16S-23S, seven of which contained two to six isolates. These clonemates (identical ARDRA patterns) could be found in the same microsample or 1 cm apart. The genetic diversity did not change with distance, indicating the same habitat variability across the cube. The mixing of ribotypes, as assessed by the spatial position of clonemates, corresponded to an overlapping of clones. Although the population probably was in a recession stage in the cube (10(3) agrobacteria g(-1)), a high genetic diversity was maintained. In two independent microsamples (500 microm in diameter) at the invasion stage, the average genetic diversity was at the same level as in the cube. Quantification of the microdiversity landscape will help to estimate the probability of encounter between bacteria under realistic natural conditions and to set appropriate sampling strategies for population genetic analysis.

FIG. 1.

Spatial distribution of positive VUs in the 1-cm³ cube. The names of each subcube and the numbers of isolates obtained in the subcube are given as “name-number” at the top of each cube. The spatial spread of the clones (identical ribotype) is also indicated. Stars represent the positions of clonemates found in a single VU. The dashed subcubes contained clonemates. Otherwise, identical ribotypes are joined by arrows.

FIG. 2.

Dendrogram of genetic distances between ribotypes. Isolates with the letter “B” or “C” belong to VU B or VU C, respectively. Isolates from the cube are indicated by the letter “J.” G1 to G9 indicate representative strains of genomic species as determined by Popoff et al. (25) in biovar 1.