Monitoring a widespread bacterial group: in situ detection of planctomycetes with 16S rRNA-targeted probes

The group of planctomycetes represents a separate line of descent within th e domain Bacteria. Two phylum-specific 16S rRNA-targeted oligonucleotide pr obes for planctomycetes have been designed, optimized for in situ hybridiza tion and used in different habitats to detect members of the group in situ, The probes, named PLA46 and PLA886, are targeting all or nearly all member s of the planctomycete line of descent. Planctomycetes could be detected in almost all samples examined, e.g. a brackish water lagoon, activated sludg e, and other wastewater habitats. In situ probing revealed quite uniform mo rphology and spatial arrangement of the detected cells but profound differe nces in abundance ranging from less than 0.1% to several percentage of the total cells. Single coccoid cells with diameters between 1 and 2.5 mu m wer e dominating in most samples with the exception of the lagoon, in which ros ettes of pear-shaped cells were abundant. The planctomycetes showed general ly no hybridization signals with the bacterial probe EUB338, which is in ac cordance with base changes in their 165 rRNA sequences. A discrete ultrastr ucture of planctomycete cells was suggested by double staining with rRNA-ta rgeted probes and the DNA-binding dye 4',6-diamidino-2-phenylindole (DAPI), The probe-conferred fluorescence was distributed in a ring-shaped manner a round a central DAPI spot, The two probes developed extend the existing set of group-specific rRNA-targeted probes and help to elucidate the basic com position of bacterial communities in a first step of differential analysis. In situ hybridization of environmental samples indicated widespread presen ce of planctomycetes in different ecosystems.