title: Catalyzed reporter deposition-fluorescence in situ hybridization allows for enrichment-independent detection of microcolony-forming soil bacteria.
abstract: Advances in the growth of hitherto unculturable soil bacteria have emphasized the requirement for rapid bacterial identification methods. Due to the slow-growing strategy of microcolony-forming soil bacteria, successful fluorescence in situ hybridization (FISH) requires an rRNA enrichment step for visualization. In this study, catalyzed reporter deposition (CARD)-FISH was employed as an alternative method to rRNA enhancement and was found to be superior to conventional FISH for the detection of microcolonies that are cultivated by using the soil substrate membrane system. CARD-FISH enabled real-time identification of oligophilic microcolony-forming soil bacteria without the requirement for enrichment on complex media and the associated shifts in community composition.
authors.affiliation: Department of Chemistry and Biomolecular Sciences, Division of Environmental and Life Sciences, Macquarie University, Sydney, NSW 2109, Australia. bferrari@rna.bio.mq.edu.au
authors.forename: Belinda C
authors.initials: BC
authors.lastname: Ferrari
authors.forename: Niina
authors.initials: N
authors.lastname: Tujula
authors.forename: Kate
authors.initials: K
authors.lastname: Stoner
authors.forename: Staffan
authors.initials: S
authors.lastname: Kjelleberg
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification*; D015373:Bacterial Typing Techniques; D015169:Colony Count, Microbial; D003470:Culture Media; D006735:Horseradish Peroxidase; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008567:Membranes, Artificial; D011076:Polycarboxylate Cement; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D012988:Soil Microbiology
chemical_list: D003470:Culture Media; D008567:Membranes, Artificial; D011076:Polycarboxylate Cement; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; C005506:polycarbonate; D006735:Horseradish Peroxidase