Agriculture Reference
In-Depth Information
group and the same or similar vegetation, and hence population differences
would be more likely to be due to distance. Soil samples were collected
from two ecosystem types (Mediterranean and Boreal Forest) that exist in
widely separated global regions (southwest Australia, southwest South
Africa, central Chile and central California for the former, and northern
Saskatchewan and northwest Russia for the latter) (Fulthorpe et al ., 1996).
We used a hierarchical geographic sampling strategy scaling from samples
5 m apart in 200-m transects, to multiple sites in the same continental
region (100-850 km apart), to sites on different continents. The sites either
were in parks or nature preserves, or otherwise unimpacted by human
activity. Importantly, all soil samples were collected from below the soil
surface (5-10 cm) using a soil core sterilized between each sampling. By
sampling below the soil surface, we hoped to improve the probability of
sampling long-term resident soil bacteria not influenced by human activity.
The 3-CBA-degrading isolates obtained from this global sampling showed
an endemic pattern; no genotype determined by rep-polymerase chain
reaction (PCR) (a rapid measure of chromosome structure) was found on
more than one of the six continental regions and most genotypes were
not found at multiple sites within the region, although they were found
repeatedly in samples from the same 200-m transect (Fulthorpe et al .,
1998). The chlorobenzoate-degrading trait, however, is often borne on
transmissible plasmids which could mean that the isolate collection
contains organisms from multiple phylogenies. Hence, we also examined a
readily isolated soil colonizer, the fluorescent Pseudomonas , from the same
soil collection. In this case, we explored three levels of genetic difference
ranging from coarse to fine resolution: (i) amplified ribosomal DNA
restriction analysis (ARDRA); (ii) 16S-23S rDNA intergenic transcribed
spacer fragment length polymorphism (ITS-RFLP) and rep-PCR genomic
fingerprinting (Rademaker et al ., 1998). As expected, no endemicity was
seen at the coarse level of resolution (ARDRA method) since the rRNA
operon is highly conserved. The ITS-RFLP analysis, however, showed a
weak level of endemicity. This species to sub-species level of resolution
also analyses a more conserved part of the genome. At the finest level
of resolution (rep-PCR), however, we observed strong endemicity. No
genotypes were found in more than one continental region, nor in more
than one site of the same continental region; however, seven genotypes
were found repeatedly along particular 200-m transects. Hence, this sec-
ond biological example supports the hypothesis that soil heterotrophic pop-
ulations are endemic, but only at a rather fine scale of resolution. This scale,
however, is significant to many ecologically important properties such as
pathogenesis, rates of reaction and biotechnological value.
We calculated the relationship between the genetic distance based
on the rep-PCR fingerprinting and the corresponding geographic distance
(Fig. 6.4). We used one genotype from our reference site in Australia as the
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