| Title | Cultivation-indipendent assessment of the batthypelagic archaeal diversity of Tyrrhenian Sea:comparative study of rDNA-derived libraries and influence of samples decompression |
| Abstract | Two samples of the same bathypelagic bacterioplankton community (Tyrrhenian Sea at the depth of 3000 m) were collected during single cast by both traditional sampling with Niskin bottle and using a high pressure-maintaining HPSS sampler. Total RNA was isolated, reverse transcribed, amplified with Archaea-specific primers and cloned. Riboclones were sequenced, 117 riboclones from decompressed library and 104 rRNA-based riboclones retrieved from HPSS sampler. Both RNA libraries were additionally compared with 115 riboclones based on DNA obtained from the decompressed sample (16S rRNA genes). In terms of repetitive riboclones, obtained in all three libraries, the bathypelagic community was dominated by Crenarchaeota Marine Group I (52-64%). The combined analysis led to a characterization of sampling-specific phylotypes otherwise uncharacterized if only one type of library had been analyzed alone. Of the DNA riboclones, 22% were found only in this library and no close relatives of Euryarchaeota Marine Group II were detected in both RNA-based libraries, suggesting the dormant state of these organisms in deep-sea environment. For clones from the RNA libraries, one Crenarchaeota MG I phylotype did not indicate close relatives in the DNA library. In general, among 10 archaeal phylotypes recovered in total, 8, 7 and 6 of them were faced in DNA, RNA_HPSS and RNA decompressed libraries, respectively. Based on comparisons between all three libraries, our data indicate that (i) the short-term decompression of seawater samples during cast recovery and following treatments caused only slight changes in the total rRNA diversity and (ii) rRNA-based analysis is likely affected the characterization of phylotypes, present in deep-sea environment as the dormant cells, detected only on the DNA level. |
| Source | Deep-sea research. Part 2. Topical studies in oceanography 56 (11-12), pp. 768–773 |
| Keywords | * Phylogeny; * Deep Tyrrhenian Sea; * 16S rRNA; * Crenarchaeota Marine Group I; * Euryarchaeota Marine Group II |
| Journal | Deep-sea research. Part 2. Topical studies in oceanography |
| Editor | Pergamon,, Oxford, Regno Unito |
| Year | 2009 |
| Type | Articolo in rivista |
| DOI | 10.1016/j.dsr2.2008.07.025 |
| Authors | Violetta La Cono; Christian Tamburini, Lucrezia Genovese;Gina La Spada; Renata Denaro; Michail M. Yakimov |
| Text | 175145 2009 10.1016/j.dsr2.2008.07.025 Phylogeny; Deep Tyrrhenian Sea; 16S rRNA; Crenarchaeota Marine Group I; Euryarchaeota Marine Group II Cultivation indipendent assessment of the batthypelagic archaeal diversity of Tyrrhenian Sea comparative study of rDNA derived libraries and influence of samples decompression Violetta La Cono; Christian Tamburini, Lucrezia Genovese;Gina La Spada; Renata Denaro; Michail M. Yakimov Violetta La Cono CNR;Christian Tamburini Laboratoire Microbiologie, Geochimie et Ecologie Marines, Universite de la Mediterranee;Lucrezia Genovese CNR;Gina La Spada CNR; Renata Denaro CNR; Michail M. Yakimov CNR Two samples of the same bathypelagic bacterioplankton community Tyrrhenian Sea at the depth of 3000 m were collected during single cast by both traditional sampling with Niskin bottle and using a high pressure maintaining HPSS sampler. Total RNA was isolated, reverse transcribed, amplified with Archaea specific primers and cloned. Riboclones were sequenced, 117 riboclones from decompressed library and 104 rRNA based riboclones retrieved from HPSS sampler. Both RNA libraries were additionally compared with 115 riboclones based on DNA obtained from the decompressed sample 16S rRNA genes . In terms of repetitive riboclones, obtained in all three libraries, the bathypelagic community was dominated by Crenarchaeota Marine Group I 52 64% . The combined analysis led to a characterization of sampling specific phylotypes otherwise uncharacterized if only one type of library had been analyzed alone. Of the DNA riboclones, 22% were found only in this library and no close relatives of Euryarchaeota Marine Group II were detected in both RNA based libraries, suggesting the dormant state of these organisms in deep sea environment. For clones from the RNA libraries, one Crenarchaeota MG I phylotype did not indicate close relatives in the DNA library. In general, among 10 archaeal phylotypes recovered in total, 8, 7 and 6 of them were faced in DNA, RNA_HPSS and RNA decompressed libraries, respectively. Based on comparisons between all three libraries, our data indicate that i the short term decompression of seawater samples during cast recovery and following treatments caused only slight changes in the total rRNA diversity and ii rRNA based analysis is likely affected the characterization of phylotypes, present in deep sea environment as the dormant cells, detected only on the DNA level. 56 articolo pubblicato 1_s2_0_S0967064508003159_main_1.pdf Articolo in rivista Pergamon, 0967 0645 Deep sea research. Part 2. Topical studies in oceanography Deep sea research. Part 2. Topical studies in oceanography Deep sea res., Part 2, Top. stud. oceanogr. Deep sea research. Topical studies in oceanography LA SPADA GINA lucrezia.genovese GENOVESE LUCREZIA renata.denaro DENARO RENATA violetta.lacono LA CONO VIOLETTA |
