Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris

Abstract

The biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris on a local scale was investigated. Thirty clones of phototrophic bacteria were isolated from each of five unevenly spaced sampling locations in freshwater marsh sediments along a linear 10-m transect, and a total of 150 clones were characterized by BOX-PCR genomic DNA fingerprinting. Cluster analysis of 150 genomic fingerprints yielded 26 distinct genotypes, and 106 clones constituted four major genotypes that were repeatedly isolated. Representatives of these four major genotypes were tentatively identified as R. palustris based on phylogentic analyses of 16S rRNA gene sequences. The differences in the genomic fingerprint patterns among the four major genotypes were accompanied by differences in phenotypic characteristics. These phenotypic differences included differences in the kinetics of carbon source use, suggesting that there may be functional differences with possible ecological significance among these clonal linages. Morisita-Horn similarity coefficients (C(MH)), which were used to compare the numbers of common genotypes found at pairs of sampling locations, showed that there was substantial similarity between locations that were 1 cm apart (C(MH), >/=0.95) but there was almost no similarity between locations that were >/=9 m apart (C(MH), </=0.25). These calculations showed there was a gradual decrease in similarity among the five locations as a function of distance and that clones of R. palustris were lognormally distributed along the linear 10-m transect. These data indicate that natural populations of R. palustris are assemblages of genetically distinct ecotypes and that the distribution of each ecotype is patchy.

FIG. 1.

Sampling scheme. Sediment samples were collected at transect locations 1, 2 (1 cm from location 1), 3 (10 cm from location 1), 4 (100 cm from location 1), and 5 (1,000 cm from location 1).

FIG. 2.

Computer-assisted product-moment and unweighted pair group method using arithmetic averages cluster analysis of BOX-PCR genomic DNA fingerprints of 150 clones. Fingerprint patterns having r values of more than 0.8 (dotted line) were considered to be the same genotype. Clone designations (sampling location-clone number) are shown next to the BOX-PCR genomic fingerprints. The four genotypes with more than 10 clones were designated A, B, C, and D.

FIG. 3.

C_MH values for comparisons of populations of the four major genotypes of R. palustris between sampling location 1 and sampling locations 2, 3, 4, and 5 as a function of distance along a linear 10-m transect.