Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis

Abstract

In order to investigate the genetic diversity of streptomycetes in an acid forested soil sample from Mt. Coot-tha, Brisbane, Australia, cells were mechanically lysed within the soil matrix and genomic DNA was isolated and purified. 16S ribosomal (r)DNA was amplified by the polymerase chain reaction (PCR) method using one primer conserved for members of the domain Bacteria and a second designed specifically for streptomycetes and related taxa. PCR amplification products were cloned into phage vector M13 mp19 and the diversity of 16S rDNA genes was determined by sequence analysis and oligonucleotide probing of the resultant clone library. Comparison of partial 16S rDNA sequences with published sequences revealed that few sequences originated from streptomycetes. The majority of sequences belonged to members of the alpha subclass of Proteobacteria. Other clones were related to planctomycetes, actinomycetes, or represented novel lines of descent. Bacteria that are customarily isolated from soil of pH 4-7 such as thiobacilli, bacilli, spore- and nonsporeforming actinomycetes, and pseudomonads are represented in the clone library in small numbers or were not detected at all. Parameters influencing the recovery, amplification, quantification, and interpretation of genetic information from natural sites are discussed.