Molecular phylogenetic analysis of a soil microbial community in a soybean field

We report here the phylogenetic characterization of small subunit rRNA gene sequences obtained by polymerase chain reaction (PCR) amplification of mixed population DNA extracted directly from soil in a soybean field without culturing the organisms. The phylogenetic analysis of 17 soil clones by the neighbour-joining method shows that the soil sample contained broadly diverse prokaryotes; a clone related to archaea, a clone to gram-positive bacteria with high G+C contents, two clones to green sulphur bacteria, four clones to proteobacteria, and nine clones were not in clusters of any previously reported bacterial groups, which suggests they belong to members of novel groups in Bacteria. In addition, the archaeal sequence, FIE16, is phylogenetically similar to ANTARCTIC 12, a clone obtained from surface waters of Antarctica by PCR. Their occurrence in both the ocean and soil suggests a global distribution of this archaeal group. In conclusion, rRNA gene sequences recovered from soil biomass document the occurrence of many more bacterial lingeages than have been recognized previously through cultivation-based techniques.