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Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches.
Syst Appl Microbiol. 2010 Jun; 33(4):222-31.SA

Abstract

Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580m, were subjected to DNA extraction and 16S rRNA amplification targeting the V3 region. Denaturing gradient gel electrophoresis (DGGE) showed several heterogeneous profiles and 27 single bands were excised and sequenced. Sequence analysis revealed the presence of Firmicutes, Actinobacteria and Chloroflexi in 26% of the DGGE bands and a predominance of sequences affiliated to cultivable and uncultivable clones of Gammaproteobacteria (55%). To corroborate these findings, cultivation attempts were performed that allowed the isolation of 87 strains assigned to the proteobacterial classes. Identification was achieved by means of automated ribosomal intergenic spacer analysis (ARISA) and by 16S rDNA sequencing. The isolates were related to the gamma, alpha and beta subclasses of Proteobacteria with respective percentages of 77, 17 and 6%. The most predominant Gammaproteobacteria isolates, assigned to the Psychrobacter marincola and P. submarinus clade (n=53) and to Halomonas aquamarina (n=14), showed a huge intraspecific diversity with 29 distinct ARISA haplotypes. The detection by both approaches of these psychrophilic and moderately halophilic species and their extensive microdiversity indicated their predominance in Tyrrhenian Sea sediments where they constituted the indigenous microflora.

Authors+Show Affiliations

Laboratoire Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université Tunis El Manar, Campus Universitaire, 2092 Tunis, Tunisia.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

20413241

Citation

Ettoumi, Besma, et al. "Gammaproteobacteria Occurrence and Microdiversity in Tyrrhenian Sea Sediments as Revealed By Cultivation-dependent and -independent Approaches." Systematic and Applied Microbiology, vol. 33, no. 4, 2010, pp. 222-31.
Ettoumi B, Bouhajja E, Borin S, et al. Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches. Syst Appl Microbiol. 2010;33(4):222-31.
Ettoumi, B., Bouhajja, E., Borin, S., Daffonchio, D., Boudabous, A., & Cherif, A. (2010). Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches. Systematic and Applied Microbiology, 33(4), 222-31. https://doi.org/10.1016/j.syapm.2010.02.005
Ettoumi B, et al. Gammaproteobacteria Occurrence and Microdiversity in Tyrrhenian Sea Sediments as Revealed By Cultivation-dependent and -independent Approaches. Syst Appl Microbiol. 2010;33(4):222-31. PubMed PMID: 20413241.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches. AU - Ettoumi,Besma, AU - Bouhajja,Emna, AU - Borin,Sara, AU - Daffonchio,Daniele, AU - Boudabous,Abdellatif, AU - Cherif,Ameur, Y1 - 2010/04/22/ PY - 2009/08/10/received PY - 2010/02/20/revised PY - 2010/02/22/accepted PY - 2010/4/24/entrez PY - 2010/4/24/pubmed PY - 2010/8/10/medline SP - 222 EP - 31 JF - Systematic and applied microbiology JO - Syst Appl Microbiol VL - 33 IS - 4 N2 - Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580m, were subjected to DNA extraction and 16S rRNA amplification targeting the V3 region. Denaturing gradient gel electrophoresis (DGGE) showed several heterogeneous profiles and 27 single bands were excised and sequenced. Sequence analysis revealed the presence of Firmicutes, Actinobacteria and Chloroflexi in 26% of the DGGE bands and a predominance of sequences affiliated to cultivable and uncultivable clones of Gammaproteobacteria (55%). To corroborate these findings, cultivation attempts were performed that allowed the isolation of 87 strains assigned to the proteobacterial classes. Identification was achieved by means of automated ribosomal intergenic spacer analysis (ARISA) and by 16S rDNA sequencing. The isolates were related to the gamma, alpha and beta subclasses of Proteobacteria with respective percentages of 77, 17 and 6%. The most predominant Gammaproteobacteria isolates, assigned to the Psychrobacter marincola and P. submarinus clade (n=53) and to Halomonas aquamarina (n=14), showed a huge intraspecific diversity with 29 distinct ARISA haplotypes. The detection by both approaches of these psychrophilic and moderately halophilic species and their extensive microdiversity indicated their predominance in Tyrrhenian Sea sediments where they constituted the indigenous microflora. SN - 1618-0984 UR - https://www.unboundmedicine.com/medline/citation/20413241/Gammaproteobacteria_occurrence_and_microdiversity_in_Tyrrhenian_Sea_sediments_as_revealed_by_cultivation_dependent_and__independent_approaches_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0723-2020(10)00038-X DB - PRIME DP - Unbound Medicine ER -