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 rea ctor region of Gabon are used to demonstrate the application of phylogeneti c methods to biodiversity assessment. Clones were provisionally placed in ' genera' using either the genus of the closest named EMBL entry, or by group ing clones at least 97.5% identical. The community is small, with 24 putati ve 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 31.3% (18.6-68.4%) Molecu lar biodiversity was estimated for all site combinations using genetic dive rsity (GD: probability of at least two alleles being present in the sequenc es preserved;ed), and confidence limits derived by standard phylogenetic bo otstrap sampling from the sequence dataset. Some combinations with fewer si tes preserved GD as well as combinations with larger numbers, although GD i s maximised by preserving as many sites as possible depending on choice of site. Some sire combinations did not differ significantly in GD preserved, and the conservation value of a site depends on the others selected. The st rongest predictor of molecular biodiversity is the observed number of 'clos et-match' genera, supporting the higher taxon richness concept for biodiver sity. 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 bel ow the surface. (C) 1999 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.