Molecular evidence for the presence of novel actinomycete lineages in a temperate forest soil

PCR primers were designed to selectively recover partial (similar to 1100 bp) actinomycete 16S ribosomal DNA sequences from a temperate forest soil, A gene library was made and colony PCR was used to identify clones containing inserts, Unique clones were identified and partial or complete insert sequences were determined for 53 clones, Phylogenetic analyses revealed that 46 (87%) of the clones sampled contained 16S rDNA sequences which fell within the actinomycete radiation, The largest group of 34 sequences formed two closely related monophyletic groups in the 16S rRNA tree, which in turn formed a weakly supported sister group with the sequence from Actinomadura madurae, Four novel 16S rDNA lineages were detected in Mycobacterium, one in Propionibacterium and one in Corynebacterium, Three novel sequences weakly grouped with Sporichthya polymorpha, Two sequences formed an isolated lineage not closely related to any of the reference actinomycetes. Our results lend strong support to the hypothesis that cultured (and sequenced) actinomycetes do not adequately describe the diversity of this group in the environment.