Open AccessDiscrepancies in the widely applied GAM42a fluorescence in situ hybridisation probe for Gammaproteobacteria
Author(s) -
Siyambalapitiya Nishanthi,
Blackall Linda Louise
Publication year - 2005
Publication title -
fems microbiology letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.899
H-Index - 151
eISSN - 1574-6968
pISSN - 0378-1097
DOI - 10.1016/j.femsle.2004.11.004
Subject(s) - gammaproteobacteria , biology , microbiology and biotechnology , alphaproteobacteria , activated sludge , bacteria , 16s ribosomal rna , wastewater , environmental engineering , genetics , engineering
Abstract A bacterial culture collection of 104 strains was obtained from an activated sludge wastewater treatment plant to pursue studies into microbial flocculation. Characterisation of the culture collection using a polyphasic approach indicated seven isolates, phylogenetically affiliated with the deep‐branching Xanthomonas group of the class Gammaproteobacteria , were unable to hybridise the GAM42a fluorescence in situ hybridisation (FISH) probe for Gammaproteobacteria . The sequence of the GAM42a probe target region in the 23S rRNA gene of these isolates was determined to have mismatches to GAM42a. Probes perfectly targeting the mismatches (GAM42a_T1038_G1031, and GAM42a_T1038 and GAM42a_A1041_A1040) were synthesised, and used in conjunction with GAM42a in FISH to study the Gammaproteobacteria community structure in one full‐scale activated sludge plant. Several bacteria in the activated sludge biomass bound the modified probes demonstrating their presence and the fact that these Gammaproteobacteria have been overlooked in community structure analyses of activated sludge.