ESTIMATION OF THE ABUNDANCE OF AN UNCULTURED SOIL BACTERIAL STRAIN BYA COMPETITIVE QUANTITATIVE PCR METHOD

Strain EA25 was identified in a clone library of bacterial 16S rRNA ge ne sequences that had been amplified from DNA extracted from soil coll ected in eastern Washington State. EA25 was subsequently shown to be r elated to members of the genera Planctomyces and Chlamydia and most cl osely related (93% similarity) to strain MC18, a strain identified in an Australian soil sample (W. Liesack and E. Stackebrandt, J. Bacterio l, 174:5072-5078, 1992), A competitive quantitative PCR method develop ed by Zachar et al, (V. Zachar, R. A. Thomas, and A. S. Goustin, Nucle ic Acids Res. 21:2017-2018, 1993) was used to estimate the abundance o f this uncultured strain in soil, An estimation of the abundance of EA 25 was based on the number of copies of the sequence in the DNA extrac ted and the efficiency of the DIVA extraction, In addition, amplificat ion rates of Escherichia coli DNAs added to soil were shown to be simi lar to those of DNAs from laboratory cultures of E. coli, The number o f EA25 16S rRNA genes was estimated to be 2.17 x 10(8) copies per g of soil, suggesting that strains similar to EA25 and the similar Austral ian strain could be widely distributed and present in significant numb ers in soils from temperate regions, This represents the first enumera tion of 16S rDNA copies from an uncultured strain in soil.