Genotypic and Phenotypic Diversity within Species of Purple Nonsulfur Bacteria Isolated from Aquatic Sediments

Abstract

To assess the extent of genotypic and phenotypic diversity within species of purple nonsulfur bacteria found in aquatic sediments, a total of 128 strains were directly isolated from agar plates that had been inoculated with sediment samples from Haren and De Biesbosch in The Netherlands. All isolates were initially characterized by BOX-PCR genomic DNA fingerprinting, and 60 distinct genotypes were identified. Analyses of 16S rRNA gene sequences of representatives of each genotype showed that five and eight different phylotypes of purple nonsulfur bacteria were obtained from the Haren and De Biesbosch sites, respectively. At the Haren site, 80.5% of the clones were Rhodopseudomonas palustris, whereas Rhodoferax fermentans and Rhodopseudomonas palustris were numerically dominant at the De Biesbosch site and constituted 45.9 and 34.4% of the isolates obtained, respectively. BOX-PCR genomic fingerprints showed that there was a high level of genotypic diversity within each of these species. The genomic fingerprints of Rhodopseudomonas palustris isolates were significantly different for isolates from the two sampling sites, suggesting that certain strains may be endemic to each sampling site. Not all Rhodopseudomonas palustris isolates could degrade benzoate, a feature that has previously been thought to be characteristic of the species. There were differences in the BOX-PCR genomic fingerprints and restriction fragment length polymorphisms of benzoate-coenzyme A ligase genes and form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes between benzoate-degrading and non-benzoate-degrading genotypes. The ability to distinguish these two Rhodopseudomonas palustris groups based on multiple genetic differences may reflect an incipient speciation event resulting from adaptive evolution to local environmental conditions.Many species of bacteria in the environment, particularly in soil, are composed of genetically distinct and diverse clones (5,13,21,22,27,28,52). This diversification has resulted from evolutionary processes (4,28,30,35,41) that occur during adaptive evolution to local conditions in heterogeneous environments that contain a range of ecologically distinct habitats (28). This is in contrast to what is observed with many pathogenic and commensal bacterial species, which often exhibit clonal population structures that are correlated to differences in host environmental specificity and geographic differences (1,7,12,27,29,40,43,51).There have been numerous studies to assess the genetic diversity in closely related bacteria by PCR-based genome analysis techniques, including repetitive-sequence-based PCR (rep-PCR), amplified fragment length polymorphism, and random amplified polymorphic DNA techniques. The species studied include human-, animal-, and plant-associated bacteria, such as Escherichia coli (7,17), Helicobacter pylori (2), Bradyrhizobium sp. (47, 48), Pseudomonas syringae (24, 25), Rhizobium sp. (6, 23), and several species of the genus Xanthomonas (32,33). These studies were ai...

Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at “Evolution Canyons” I and II, Israel

“…This procedure impedes linkage of varying geographical distance to varying ecology. Interestingly, other studies have observed indications of natural selection (16)(17)(18); however, the results were not linked either to ecology (17) or to the effect of geographic distance (18).…”

Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris

“…This is the largest number of RND pumps observed in any bacterium to date and may explain the high intrinsic resistance of R. palustris to antibiotics. R. palustris has been isolated in high numbers from polluted environments 36 . Heavy metal efflux transporters should allow R. palustris to live in a variety of environments and still acquire the necessary nutrients while resisting heavy metal toxicity.…”

Intrageneric relationships of members of the genus Rhodopseudomonas

“…Members of the genus Rhodopseudomonas are characterized by having budding cell morphology, lamellar photosynthetic membranes, bacteriochlorophyll a and carotenoids of the sprilloxanthin series as the photopigments, and ubiquinone-10 as the major quinone. They are physiologically versatile and inhabit a wide variety of natural environments such as soil, freshwater, hot springs, and wastewater treatment systems (Hiraishi and Kitamura, 1984;Hisada et al, 2007;Oda et al, 2002Oda et al, , 2003aOkubo et al, 2005). In natural habitats, members of Rhodopseudomonas grow well in polluted waters and may have a higher affi nity to organic substrates compared to other PPNS bacteria such as those of the genus Rhodobacter (Okubo and Hiraishi, 2007;Okubo et al, 2006).…”