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

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.

Climatic Aridity Gradient Modulates the Diversity of the Rhizosphere and Endosphere Bacterial Microbiomes of Opuntia ficus-indica

“…Predominant DGGE bands were excised, reamplifed, and sequenced. Sequences and phylogenetic analysis of the rRNA 16S sequences were performed as previously reported (BenAbdallah et al, 2018).…”

“…Sequencing of PCR amplicons of 16S rDNA was conducted with the Illumina MiSeq platform (CBS, Sfax, Tunisia) targeting the V3-V4 hypervariable regions using prokaryotic universal (Pro341/Pro805R) primer sets (Takahashi et al, 2014) for 2 × 300 bp paired-end sequencing (Illumina). The amplification of PCR products and Illumina library preparations were achieved as previously reported (BenAbdallah et al, 2018). Raw data acquired from the Illumina MiSeq sequencing platform were analyzed using the QIIME software package 1.9.1 (Caporaso et al, 2010) as previously described (BenAbdallah et al, 2018).…”

“…The amplification of PCR products and Illumina library preparations were achieved as previously reported (BenAbdallah et al, 2018). Raw data acquired from the Illumina MiSeq sequencing platform were analyzed using the QIIME software package 1.9.1 (Caporaso et al, 2010) as previously described (BenAbdallah et al, 2018). Plant chloroplast and mitochondrial OTUs were removed from all sequences samples.…”

Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China

“…Halophiles thrive in hypersaline niches and have potential applications in biotechnology [1,2]. Microbial diversity in most hypersaline environments is often studied using culture-dependent and -independent methods [3][4][5][6][7]. Previous studies have shown that the taxonomic diversity of microbial populations in terrestrial saline and hypersaline environments is relatively low [8,9].…”

Satellite-based monitoring of surface water dynamics

“…Particularly for lakes with strong dynamics within a month, this uncertainty increases. respectively, strong differences between two datasets correspond to months with rapid water changes in response to erratic rainfall events (Ben Abdallah et al 2018;Bryant 1999). These examples demonstrate that a low to moderate correlation between both datasets does not necessarily imply a poor accuracy of MODIS SWF, but rather that MODIS allows to capture rapid temporal changes.…”