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Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assays

Manel Ben Abdallah 1 Fatma Karray 2, 1 Najwa Kallel Fabrice Armougom 3 Najla Mhiri 1 Marianne Quemeneur Jean-Luc Cayol 4 Gaël Erauso 4 Sami Sayadi 5
1 Laboratoire des Bioprocédés Environnementaux, LMI COSYS-Med
2 IGM - Institut de génétique et microbiologie [Orsay]
3 MAPIEM - Laboratoire Matériaux Polymères Interfaces Environnement Marin - EA 4323
4 MIO - Institut méditerranéen d'océanologie
5 Laboratoire des Bioprocédés Environnementaux
Abstract : Chott El Jerid is the largest hypersaline ephemeral lake in southern Tunisian Sahara desert and is one of the biggest depressions at the North of Africa. This study aimed to investigate the diversity and abundance of microbial communities inhabiting Chott El Jerid during wet season (when it was flooded), using molecular methods [Illumina Miseq sequencing, DGGE and qPCR (qPCR)]. 16S rRNA gene analyses revealed that bacterial community was dominated by Proteobacteria (especially Ralstonia species), followed by Firmicutes, Bacteroidetes, Cyanobacteria, Actinobacteria and Verrucomicrobia. The results obtained using prokaryotic universal primers showed low relative abundance of Archaea dominated by few OTUs related to Methanosarcinaceae and Methanomassiliicoccaceae families and the presence of sulfate-reducing Archaea affiliated with Archaeoglobus. However, the results obtained using Archaea-specific primers showed that archaeal community was mainly composed of aerobic Halobacteria (especially Halorubrum species) and anaerobic members of Methanomicrobia. These results also provided evidence for the presence of members of the genus Halohasta in this environment. qPCR results revealed that Archaea were more abundant in studied samples than Bacteria. The sulfate-reducing Bacteria were also found abundant (~ one-third of the bacterial community) and outnumbered methanogens, suggesting their potential important role in this sulfate-rich and hypersaline ecosystem.
Keywords : DGGE Hypersaline lake Illumina Miseq sequencing Methanogens Prokaryotic diversity Quantitative PCR Sulfate-reducing Bacteria
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Journal articles
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https://hal-amu.archives-ouvertes.fr/hal-01981823
Contributor : Jean-Luc Cayol <>
Submitted on : Tuesday, January 15, 2019 - 11:45:32 AM
Last modification on : Thursday, November 12, 2020 - 7:20:52 AM

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Manel Ben Abdallah, Fatma Karray, Najwa Kallel, Fabrice Armougom, Najla Mhiri, et al.. Abundance and diversity of prokaryotes in ephemeral hypersaline lake Chott El Jerid using Illumina Miseq sequencing, DGGE and qPCR assays. Extremophiles, Springer Verlag, 2018, 22 (5), pp.811-823. ⟨10.1007/s00792-018-1040-9⟩. ⟨hal-01981823⟩

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