Natural Communities of Achromatium oxaliferum Comprise Genetically, Morphologically, and Ecologically Distinct Subpopulations

Abstract

The diversity and ecology of natural communities of the uncultivated bacterium Achromatium oxaliferum were studied by use of culture-independent approaches. 16S rRNA gene sequences were PCR amplified from DNA extracted from highly purified preparations of cells that were morphologically identified as A. oxaliferumpresent in freshwater sediments from three locations in northern England (Rydal Water, Jenny Dam, Hell Kettles). Cloning and sequence analysis of the PCR-amplified 16S rRNA genes revealed that multiple related but divergent sequences were routinely obtained from theA. oxaliferum communities present in all the sediments examined. Whole-cell in situ hybridization with combinations of fluorescence-labelled oligonucleotide probes revealed that the divergent sequences recovered from purified A. oxaliferumcells corresponded to genetically distinct Achromatiumsubpopulations. Analysis of the cell size distribution of the genetically distinct subpopulations demonstrated that each was also morphologically distinct. Furthermore, there was a high degree of endemism in the Achromatium sequences recovered from different sediments; identical sequences were never recovered from different sampling locations. In addition to ecological differences that were apparent between Achromatium communities from different freshwater sediments, the distribution of different subpopulations of Achromatium in relation to sediment redox profiles indicated that the genetically and morphologically distinct organisms that coexisted in a single sediment were also ecologically distinct and were adapted to different redox conditions. This result suggests that Achromatium populations have undergone adaptive radiation and that the divergent Achromatiumspecies occupy different niches in the sediments which they inhabit.

Adaptation of sympatric Achromatium spp. to different redox conditions as a mechanism for coexistence of functionally similar sulphur bacteria

“…It was speculated that genetic diversity in coexisting Achromatium communities reflects exploitation of different redox-related niches. This second hypothesis was tentatively supported by the observation that differences in the distribution of different Achromatium species with depth were coincident with changes in redox chemistry (Gray et al ., 1999a).…”

“…Previous studies of the Achromatium community structure in Rydal Water sediments (Gray et al ., 1999a), used a combination of three oligonucleotide probes to distinguish different Achromatium spp. These three probes identified approximately 100% of cells purified from sediment samples taken between December 1997 and June 1998.…”

“…Examination of the partial RYKS 16S rRNA sequences revealed that they contained the target sequence reported for the oligonucleotide probe AHK655a that had previously been used to identify an Achromatium sp. from a different geographical location, Hell Kettles (Gray et al ., 1999a). Using this probe in combination with the three probes previously used to characterize the Rydal Water Achromatium community (ARY655a, specific for RY5; ARY655b, specific for RY8; ARY655c, specific for RY1; AHK655a, specific for RYKS.…”

“…Except for Achromatium sp. JD1 from Jenny Dam, for which few individual cells were measured, statistically significant differences in mean cell diameter were evident both in subpopulations coexisting in a single sediments and among all the subpopulations identified at different geographical locations (Gray et al ., 1999a). However, the mean cell diameter of the newly described Achromatium sp.…”

“…This has been achieved by examining the effect of oxic and anoxic conditions on Achromatium community structure and more specifically by examining the effect of nitrate, a putative electron acceptor for Achromatium spp. (Gray et al ., 1999a). The experimental strategy was based on the assumption that growth or maintenance of a particular Achromatium sp.…”