Towards complete biodiversity assessment: an evaluation of the subterranean bacterial communities in the Oklo region of the sole surviving natural nuclear reactor
Groundwater bacterial rRNA sequences extracted from the natural nuclear reactor region of Gabon are used to demonstrate the application of phylogenetic methods to biodiversity assessment. Clones were provisionally placed in 'genera' using either the genus of the closest named EMBL entry, or by grouping clones at least 97.5% identical. The community is small, with 24 putative genera under the 'closest-match' criterion and an estimated number of 30.9 (25.8-49.7); estimated genus sample coverage is therefore 78% (48.3-92.8%). There were 36 genera under the 'threshold' criterion, with an estimated number of 87.2 (52.6-193.8), and sample coverage 41.3% (18.6-68.4%) Molecular biodiversity was estimated for all site combinations using genetic diversity (GD: probability of at least two alleles being present in the sequences preserved), and confidence limits derived by standard phylogenetic bootstrap sampling from the sequence dataset. Some combinations with fewer sites preserved GD as well as combinations with larger numbers, although GD is maximised by preserving as many sites as possible depending on choice of site. Some site combinations did not differ significantly in GD preserved, and the conservation value of a site depends on the others selected. The strongest predictor of molecular biodiversity is the observed number of 'closest-match' genera, supporting the higher taxon richness concept for biodiversity. The similarities between sites, and hence the molecular biodiversity characteristics of combinations of them, was associated with similarity in physical characteristics, the availability of organic carbon, and depth below the surface.
Crozier, Agapow, Pederson (1999). FEMS Microbial Ecology 28:325-334