Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum

Abstract

The abundance and composition of bacteria of the phylum Acidobacteria were surveyed in subsurface sediments from uranium-contaminated sites using amplification of 16S rRNA genes followed by clone/sequence analysis. Analysis of sequences from this study and public databases produced a revised and greatly expanded phylogeny of the Acidobacteria phylum consisting of 26 subgroups.

FIG. 1.

Schematic tree of Acidobacteria phylum 16S rRNA gene sequence diversity based on maximum likelihood analysis of 405 sequences representative of types found in the present study (214 sequences) and in the database (191 sequences). Bootstrap support for the monophyly of groups determined by analysis of phylogenetic representatives of the sequences (before slash) versus that for all 700 of the sequences (after slash) is shown for results >70% by one or both analyses. Subgroups 1 to 8 are those described previously by Hugenholtz et al. (7), while groups 9 to 11 are those described previously by Zimmerman et al. (20). Numbering of groups above 11 was arbitrary. The shape of group “wedges” is indicative of sequence diversity observed within the group. Less than 70% bootstrap support was obtained for the order of branching of any groups above group 8 in the tree, as indicated by the single vertical line connecting the groups. The tree was rooted using the sequence of Escherichia coli as the outgroup. Subgroup wedges containing dots contain sequences from the U-contaminated sediments in this study. Subgroup wedges containing an “x” are those subgroups not detected using primer 31F.