Scheda di dettaglio – i prodotti della ricerca
| Dato | Valore |
|---|---|
| Title | EFFICIENCY OF FLUORESCENCE IN SITU HYBRIDIZATION FOR BACTERIAL CELL IDENTIFICATION IN TEMPORAY RIVER SEDIMENTS WITH CONTRASTING WATER CONTENT |
| Abstract | We studied the efficiency of two hybridization techniques for the analysis of benthic bacterial community composition under varying sediment water content. Microcosms were set up with sediments from four European temporary rivers. Wet sediments were dried, and dry sediments were artificially rewetted. The percentage of bacterial cells detected by fluorescence in situ hybridization with fluorescently monolabeled probes (FISH) significantly increased from dry to wet sediments, showing a positive correlation with the community activity measured via incorporation of 3H leucine. FISH and signal amplification by catalyzed reporter deposition (CARD-FISH) could significantly better detect cells with low activity in dried sediments. Through the application of an optimized cell permeabilization protocol, the percentage of hybridized cells by CARD-FISH showed comparable values in dry and wet conditions. This approach was unrelated to 3H leucine incorporation rates. Moreover, the optimized protocol allowed a significantly better visualization of Gram-positive Actinobacteria in the studied samples. CARD-FISH is, therefore, proposed as an effective technique to compare bacterial communities residing in sediments with contrasting water content, irrespective of differences in the activity state of target cells. Considering the increasing frequencies of flood and drought cycles in European temporary rivers, our approach may help to better understand the dynamics of microbial communities in such systems. |
| Source | Systematic and applied microbiology (Print) 30 (6), pp. 463–470 |
| Keywords | Freshwater sedimentsTemporary riversCARD-FISHBacteriaActinobacteria |
| Journal | Systematic and applied microbiology (Print) |
| Editor | Elsevier., Jena, Germania |
| Year | 2007 |
| Type | Articolo in rivista |
| DOI | 10.1016/j.syapm.2007.03.003 |
| Authors | FAZI S. (a); AMALFITANO S. (a); PIZZETTI I. (a); PERNTHALER J. (b) |
| Text | 42137 2007 10.1016/j.syapm.2007.03.003 ISI Web of Science WOS 000249273300004 Scopus 2 s2.0 34547191211 Freshwater sediments Temporary rivers CARD FISH Bacteria Actinobacteria EFFICIENCY OF FLUORESCENCE IN SITU HYBRIDIZATION FOR BACTERIAL CELL IDENTIFICATION IN TEMPORAY RIVER SEDIMENTS WITH CONTRASTING WATER CONTENT FAZI S. a ; AMALFITANO S. a ; PIZZETTI I. a ; PERNTHALER J. b a IRSA CNR; b Limnological Station, University of Zurich, Switzerland We studied the efficiency of two hybridization techniques for the analysis of benthic bacterial community composition under varying sediment water content. Microcosms were set up with sediments from four European temporary rivers. Wet sediments were dried, and dry sediments were artificially rewetted. The percentage of bacterial cells detected by fluorescence in situ hybridization with fluorescently monolabeled probes FISH significantly increased from dry to wet sediments, showing a positive correlation with the community activity measured via incorporation of 3H leucine. FISH and signal amplification by catalyzed reporter deposition CARD FISH could significantly better detect cells with low activity in dried sediments. Through the application of an optimized cell permeabilization protocol, the percentage of hybridized cells by CARD FISH showed comparable values in dry and wet conditions. This approach was unrelated to 3H leucine incorporation rates. Moreover, the optimized protocol allowed a significantly better visualization of Gram positive Actinobacteria in the studied samples. CARD FISH is, therefore, proposed as an effective technique to compare bacterial communities residing in sediments with contrasting water content, irrespective of differences in the activity state of target cells. Considering the increasing frequencies of flood and drought cycles in European temporary rivers, our approach may help to better understand the dynamics of microbial communities in such systems. 30 Efficiency of FISH Fazi_SAM_07.pdf Articolo in rivista Elsevier. 0723 2020 Systematic and applied microbiology Print Systematic and applied microbiology Print Syst. appl. microbiol. Print Systematic and applied microbiology. Print stefano.amalfitano AMALFITANO STEFANO stefano.fazi FAZI STEFANO TA.P02.002.003 Ruolo di comunita microbiche nella degradazione della sostanza organica e nella circolazione del carbonio nei sistemi acquatici |