Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches

Besma Ettoumi; Emna Bouhajja; Sara Borin; Daniele Daffonchio; Abdellatif Boudabous; Ameur Cherif

doi:10.1016/j.syapm.2010.02.005

Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches

Besma Ettoumi, Emna Bouhajja, Sara Borin, Daniele Daffonchio, Abdellatif Boudabous, Ameur Cherif^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

26 Scopus citations

Abstract

Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30. cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580. m, 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.

Original language	English (US)
Pages (from-to)	222-231
Number of pages	10
Journal	Systematic and Applied Microbiology
Volume	33
Issue number	4
DOIs	https://doi.org/10.1016/j.syapm.2010.02.005
State	Published - Jun 2010
Externally published	Yes

Bibliographical note

Funding Information:
This work was performed within the framework of the CIESM-SUB programme (CIESM Sur-Un-Bateau Cruise I). Pr. Laura Giuliano, who made this multidisciplinary research possible, Pr. Giorgio Budillon, the Chief Scientist of the expedition, Captain Angelo Barca and the crews of the R/V Universitatis are gratefully acknowledged. We thank Dr. Mirko Magagnini for his help in sample collection. This work was in part supported by the Ministries of High Education and Scientific Research and Technology of the Tunisian Republic , Grant LR MBA206 . The authors would also like to thank the two anonymous reviewers for their constructive comments on the manuscript.

Keywords

ARISA fingerprinting
DGGE
Deep-sea sediments
Gammaproteobacteria
Microdiversity

ASJC Scopus subject areas

Microbiology
Ecology, Evolution, Behavior and Systematics
Applied Microbiology and Biotechnology

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10.1016/j.syapm.2010.02.005

Cite this

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title = "Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches",

abstract = "Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30. cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580. m, 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.",

keywords = "ARISA fingerprinting, DGGE, Deep-sea sediments, Gammaproteobacteria, Microdiversity",

author = "Besma Ettoumi and Emna Bouhajja and Sara Borin and Daniele Daffonchio and Abdellatif Boudabous and Ameur Cherif",

note = "Funding Information: This work was performed within the framework of the CIESM-SUB programme (CIESM Sur-Un-Bateau Cruise I). Pr. Laura Giuliano, who made this multidisciplinary research possible, Pr. Giorgio Budillon, the Chief Scientist of the expedition, Captain Angelo Barca and the crews of the R/V Universitatis are gratefully acknowledged. We thank Dr. Mirko Magagnini for his help in sample collection. This work was in part supported by the Ministries of High Education and Scientific Research and Technology of the Tunisian Republic , Grant LR MBA206 . The authors would also like to thank the two anonymous reviewers for their constructive comments on the manuscript. ",

year = "2010",

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doi = "10.1016/j.syapm.2010.02.005",

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volume = "33",

pages = "222--231",

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AU - Borin, Sara

AU - Daffonchio, Daniele

AU - Boudabous, Abdellatif

AU - Cherif, Ameur

N1 - Funding Information: This work was performed within the framework of the CIESM-SUB programme (CIESM Sur-Un-Bateau Cruise I). Pr. Laura Giuliano, who made this multidisciplinary research possible, Pr. Giorgio Budillon, the Chief Scientist of the expedition, Captain Angelo Barca and the crews of the R/V Universitatis are gratefully acknowledged. We thank Dr. Mirko Magagnini for his help in sample collection. This work was in part supported by the Ministries of High Education and Scientific Research and Technology of the Tunisian Republic , Grant LR MBA206 . The authors would also like to thank the two anonymous reviewers for their constructive comments on the manuscript.

PY - 2010/6

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N2 - Bacterial diversity in Tyrrhenian Sea sediments was assessed using cultivation-dependent and -independent approaches. Samples collected from the different sediment layers (up to 30. cm) relative to four seamount and non-seamount stations, at depths from 3425 to 3580. m, 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.

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Gammaproteobacteria occurrence and microdiversity in Tyrrhenian Sea sediments as revealed by cultivation-dependent and -independent approaches

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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