title: In situ analysis of native microbial communities in complex samples with high particulate loads.
abstract: In the present study a procedure combining a cell extraction method and Fluorescence In Situ Hybridization (FISH) for molecular monitoring and quantification of bacteria in soil and aquifer samples is presented. FISH was applied to bacterial cells extracted from the matrix by density gradient centrifugation. This separation method was applied to soil and aquifer samples and produced high cell recovery of 76.5%+/-4.4 and 78.0%+/-3.2, respectively. FISH, performed on the harvested cells, permitted a perfect visualization and quantification of bacteria. This approach is therefore promising for in situ detection of indigenous bacterial communities in complex samples.
authors.affiliation: Water Research Institute, CNR, Via Reno 1, 00198 Rome, Italy. caraccio@irsa.cnr.it
authors.forename: Anna
authors.initials: A
authors.lastname: Barra Caracciolo
authors.forename: Paola
authors.initials: P
authors.lastname: Grenni
authors.forename: Cinzia
authors.initials: C
authors.lastname: Cupo
authors.forename: Simona
authors.initials: S
authors.lastname: Rossetti
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D001431:Bacteriological Techniques; D002499:Centrifugation, Density Gradient; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D017753:Ecosystem; D005456:Fluorescent Dyes; D017404:In Situ Hybridization, Fluorescence; D007211:Indoles; D007472:Iohexol; D012988:Soil Microbiology; D014871:Water Microbiology
chemical_list: D004269:DNA, Bacterial; D005456:Fluorescent Dyes; D007211:Indoles; D007472:Iohexol; C007293:DAPI