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 m 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 m 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.

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

“…Therefore, at the smallest scale sampled here, multiple clones co-occurred. Overlapping of clones at small spatial scales has been found for other soil microbes [25,58,69]. A recent study focusing on actinomycetes also revealed high diversity among isolates of closely related genera from a single soil sample [44].…”

“…To identify local factors that may influence the spatial distribution of diversity, including competitive interactions and resource availability, information on how phenotypes and genotypes are arrayed in space is crucial. There is a growing body of empirical studies examining the spatial distribution of genetic diversity in the soil at a range of spatial scales from micrometers to kilometers [3,8,20,25,48,56,69).…”

Scaling community structure: how bacteria, fungi, and ant taxocenes differentiate along a tropical forest floor

“…They vary orders of magnitude in size. Bacterial cells, colonies, and biofilms-measured in micrometers to centimeters (Vogel et al 2003, Grundmann 2004)-are consistently the smallest of the three. Litter fungi range from unicellular yeasts (tens of micrometers) to filamentous hyphal cells that occupy several square meters of the forest floor (Lodge andCantrell 1995, Redecker et al 2001).…”

R E V I E W: Species definition of procaryotes based on 16S rRNA and protein coding genes sequence

“…Analisis juga dapat mentarget hanya suatu klaster gen seperti ribotyping pada operon rrn (Khetawat et al, 1999), atau bahkan gen individual seperti ARDRA (Vogel et al, 2003) dan T-RFLP (Dunbar et al, 2001) pada gen penyandi 16S rRNA, intergenic spacer regions/ISR (Garcia-Martinez et al, 1999), serta elemen genetik mobile (Gordon et al, 1999;Papadopoulus et al, 1999).…”