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| Fourquez, Marion; Obernosterer, Ingrid; Blain, Stephane. |
| Heterotrophic bacteria are key players in the biogeochemical cycle of iron (Fe) in the ocean, but the capability of different bacterial groups to access this micronutrient is ignored thus far. The aim of our study was to develop a protocol for the combined application of microautoradiography (MICRO) and catalyzed reporter depositionfluorescence in situ hybridization (CARD-FISH) using the radioisotope 55Fe. Among the different washing solutions tested, Ti-citrate-EDTA was the most efficient for the removal of extracellular 55Fe providing sufficiently low background values. We further demonstrate that the washing of cells with Ti-citrate-EDTA and the fixation with paraformaldehyde or formaldehyde do not induce leakage of intracellular 55Fe. Incubating... |
| Tipo: Text |
Palavras-chave: Microautoradiography; 55Fe; CARD-FISH; Marine bacteria. |
| Ano: 2012 |
URL: https://archimer.ifremer.fr/doc/00143/25403/23555.pdf |
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| Pizzetti, Ilaria; Gobet, Angelique; Fuchs, Bernhard M.; Amann, Rudolf; Fazi, Stefano. |
| The phylum Planctomycetes is involved in important processes, such as the mineralization of algal biomass and the removal of nitrogen. Using a combination of 16S rRNA sequence analysis and in situ hybridization, we analyzed the diversity and dynamics of Planctomycetes in a shallow meso-eutrophic lake, Lago di Paola, Italy. Planctomycetes detected by the probe PLA46 accounted for 1 to 5% of prokaryotic picoplankton. Abundances were higher in the coastal lake than in the adjacent marine waters. In the surface waters of the lake, the numbers of Planctomycetes fluctuated greatly, reaching a maximum of 1.5 x 10(6) cells ml(-1) in July. The hypoxic bottom waters had less variable cell abundances. The Planctomycetes counts were positively correlated with... |
| Tipo: Text |
Palavras-chave: Coastal lake ecology; Planctomycetes; Bacterial diversity; FISH; CARD-FISH; 16S rRNA gene sequencing. |
| Ano: 2011 |
URL: https://archimer.ifremer.fr/doc/00488/59948/63196.pdf |
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| Riou, Virginie; Périot, Marine; Biegala, Isabelle. |
| Oligonucleotide probes are increasingly being used to characterize natural microbial assemblages by Tyramide Signal Amplification-Fluorescent in situ Hybridization (TSA-FISH, or CAtalysed Reporter Deposition CARD-FISH). In view of the fast-growing rRNA databases, we re-evaluated the in silico specificity of eleven bacterial and eukaryotic probes and competitor frequently used for the quantification of marine picoplankton. We performed tests on cell cultures to decrease the risk for non-specific hybridization, before they are used on environmental samples. The probes were confronted to recent databases and hybridization conditions were tested against target strains matching perfectly with the probes, and against the closest non-target strains presenting one... |
| Tipo: Text |
Palavras-chave: TSA-FISH; Probes; Specificity; Marine; Prokaryotes; Eukaryotes; Oligonucleotide; CARD-FISH. |
| Ano: 2017 |
URL: https://archimer.ifremer.fr/doc/00640/75208/75339.pdf |
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