Detection and characterization of Pasteuria 16S rRNA gene sequences from nematodes and soils

1 Soil and Water Science Department, University of Florida, Gainesville, FL 32611-0290, USA 3 Microbiology and Cell Science Department, University of Florida, Gainesville, FL 32611-0290, USA 2 Entomos LLC, Gainesville, FL, USA Correspondence A. V. Ogram avo{at}mail.ifas.ufl.edu Various bacterial species in the genus Pasteuria have great potential as biocontrol agents against plant-parasitic nematodes, although study of this important genus is hampered by the current inability to cultivate Pasteuria species outside their host. To aid in the study of this genus, an extensive 16S rRNA gene sequence phylogeny was constructed and this information was used to develop cultivation-independent methods for detection of Pasteuria in soils and nematodes. Thirty new clones of Pasteuria 16S rRNA genes were obtained directly from nematodes and soil samples. These were sequenced and used to construct an extensive phylogeny of this genus. These sequences were divided into two deeply branching clades within the low-G+C, Gram-positive division; some sequences appear to represent novel species within the genus Pasteuria . In addition, a surprising degree of 16S rRNA gene sequence diversity was observed within what had previously been designated a single strain of Pasteuria penetrans (P-20). PCR primers specific to Pasteuria 16S rRNA for detection of Pasteuria in soils were also designed and evaluated. Detection limits for soil DNA were 100–10 000 Pasteuria endospores (g soil) -1 . Published online ahead of print on 12 July 2002 as DOI 10·1099/ijs.0·02303-0. The GenBank accession numbers for the sequences reported in this paper are AY081911 – AY081940 . A table showing sequence similarities of all clones described in this paper is available as supplementary data in IJSEM Online ( http://ijs.sgmjournals.org ).