Assessment of three methods for detection and quantification of nitrite-oxidizing bacteria and Nitrobacter in freshwater sediments (MPN-PCR, MPN-Griess, immunofluorescence)

Nitrification in freshwater, a key process in the nitrogen cycle, is now we ll known to take place predominantly on suspended particles and in sediment . Nitrobacter is the most commonly isolated nitrite oxidizing bacteria from water environments. Three methods for counting nitrite oxidizing communiti es (especially Nitrobacter) in sediment were investigated: MPN-Griess, fluo rescent antibodies (immunofluorescence), and a more recent molecular method coupling specific DNA amplification by PCR and statistical MPN quantificat ion. After preliminary adjustments of the MPN-PCR technique, the detection level and the yield of each method were determined by inoculating a sedimen t with a pure Nitrobacter culture. The best recovery yield was obtained wit h the immunofluorescence technique (21.3%) and the lowest detection level w as reached with the MPN-Griess method (10(3) Nitrobacter/g dry weight sedim ent). The MPN-PCR method resulted in the lowest recovery yields and needs f urther adaptation to become a reliable and precise tool for investigations of nitrifying bacteria in sediment.