Microbial community of salt crystals processed from Mediterranean seawater based on 16S rRNA analysis

Baati, Houda; Guermazi, Sonda; Gharsallah, Néji; Sghir, Abdelghani; Ammar, Emna

doi:10.1139/w09-102

Cited by 32 publications

(16 citation statements)

References 45 publications

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“…OTUs affiliated with Haloquadratum, retrieved in this study, were similar to those obtained from clone libraries recovered from solar salterns in Tunisia, Mexico, and Spain (Baati et al 2008;Dillon et al 2013;Fernández et al 2014). Halonotius-related pyrosequencing reads shared similarities with Halonotius pteroides isolated from Australian crystallizers and clones recovered from salt crystals processed from Mediterranean seawater (Burns et al 2004;Baati et al 2010). Strains belonging to genera Halorubrum and Haloarcula were isolated and related sequences detected by pyrosequencing indicating that it comprised a significant percentage of the archaeal portion of the communities.…”

Section: Discussionsupporting

confidence: 68%

“…The proportion of Archaea to Bacteria in the ponds was highly variable, but generally, the archaeal cells outnumbered the bacterial cells, as reported before (Maturrano et al 2006;Mutlu et al 2008;Boujelben et al 2012;Makhdoumi-Kakhki et al 2012). A vast number of the archaeal OTUs (~96 %) detected in the pyrosequencing data showed high-sequence similarity with known archaeal genera and have been previously cultured or detected within clone libraries from solar salterns sand salt lakes (Burns et al 2004;Walsh et al 2005;Baati et al 2008Baati et al , 2010Dillon et al 2013). However, the number of novel archaeal genera (19) was notable, even though they comprised small fractions overall of the archaeal communities in our sampling sites.…”

Section: Discussionmentioning

confidence: 83%

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Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey)

Çınar

Mutlu

2016

Extremophiles

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The prokaryotic communities of four salterns (Bingöl, Fadlum, Kemah, and Tuzlagözü) in Turkey were examined and compared using the cultivation and cultivation-independent methods [fluorescence in situ hybridization (FISH) and 454 pyrosequencing]. FISH analysis with universal probes revealed that feeding waters carried 1.6 × 10(2)-1.7 × 10(3) cells mL(-1), while crystallization ponds carried 3.8 × 10(6)-2.0 × 10(7) cells mL(-1) that were mostly haloarchaea, including square cells (except for Kemah). High-throughput 16S rRNA-based gene sequencing showed that the most frequent archaeal OTUs in Bingöl, Fadlum, Tuzlagözü, and Kemah samples were affiliated with Haloquadratum (76.8 %), Haloarcula (27.8 %), Halorubrum (49.6 %), and Halonotius (59.8 %), respectively. Bacteroidetes was the dominant bacterial phylum in Bingöl and Fadlum, representing 71.5 and 79.5 % of the bacterial OTUs (respectively), while the most abundant bacterial phylum found in the Kemah saltern was Proteobacteria (79.6 %). The majority of the bacterial OTUs recovered from Tuzlagözü belonged to the Cyanobacteria (35.7 %), Bacteroidetes (35.0 %), and Proteobacteria (25.5 %) phyla. Cultivation studies revealed that the archaeal isolates were closely related to the genera Halobacterium, Haloarcula, and Halorubrum. Bacterial isolates were confined to two phyla, Proteobacteria (Alphaproteobacteria and Gammaproteobacteria classes) and Bacteroidetes. Comparative analysis showed that members of the Euryarchaeota, Bacteroidetes, Proteobacteria, and Cyanobacteria phyla were major inhabitants of the solar salterns.

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Section: Discussionsupporting

confidence: 68%

Section: Discussionmentioning

confidence: 83%

Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey)

Çınar

Mutlu

2016

Extremophiles

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“…Only one of them (SR1) had a similarity 497% with S. ruber isolates, providing a new example of the biases imposed by cultivation even in 'culturable' species. Other Salinibacter-related phylotypes (see Table 1) presented the highest identities with environmental clones from medium salinity ponds in Tunisian salterns (Baati et al, 2008(Baati et al, , 2010(Baati et al, , 2011. Remarkably, some Salinibacter phylotypes, like SR4 and SR7, were detected only at specific temporal points from CM2 and CR41, respectively, underscoring the dynamic nature of the microbial communities in the salterns.…”

Section: Resultsmentioning

confidence: 91%

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

et al. 2014

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The microbiota of multi-pond solar salterns around the world has been analyzed using a variety of culture-dependent and molecular techniques. However, studies addressing the dynamic nature of these systems are very scarce. Here we have characterized the temporal variation during 1 year of the microbiota of five ponds with increasing salinity (from 18% to 440%), by means of CARD-FISH and DGGE. Microbial community structure was statistically correlated with several environmental parameters, including ionic composition and meteorological factors, indicating that the microbial community was dynamic as specific phylotypes appeared only at certain times of the year. In addition to total salinity, microbial composition was strongly influenced by temperature and specific ionic composition. Remarkably, DGGE analyses unveiled the presence of most phylotypes previously detected in hypersaline systems using metagenomics and other molecular techniques, such as the very abundant Haloquadratum and Salinibacter representatives or the recently described low GC Actinobacteria and Nanohaloarchaeota. In addition, an uncultured group of Bacteroidetes was present along the whole range of salinity. Database searches indicated a previously unrecognized widespread distribution of this phylotype. Single-cell genome analysis of five members of this group suggested a set of metabolic characteristics that could provide competitive advantages in hypersaline environments, such as polymer degradation capabilities, the presence of retinal-binding light-activated proton pumps and arsenate reduction potential. In addition, the fairly high metagenomic fragment recruitment obtained for these single cells in both the intermediate and hypersaline ponds further confirm the DGGE data and point to the generalist lifestyle of this new Bacteroidetes group.

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“…We used culture-independent approaches to analyze the viral assemblage of selected ponds from Sfax multipond solar salterns in southeast Tunisia. During the past 4 years, this thalassohaline system has been the object of many studies that have allowed the isolation and description of new halophilic bacterial and archaeal strains (7,56), as well as the description, using the rRNA approach, of the communities inhabiting pond waters (8,21,55), sediments (10), magnesium-rich brines (11), and salt crystals (9).…”

mentioning

confidence: 99%

Virioplankton Community Structure in Tunisian Solar Salterns

Boujelben

Yarza

Almansa

et al. 2012

Appl Environ Microbiol

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The microbial community inhabiting Sfax solar salterns on the east coast of Tunisia has been studied by means of different molecular and culture-dependent tools that have unveiled the presence of novel microbial groups as well as a community structure different from that of other coastal hypersaline environments. We have focused on the study of the viral assemblages of these salterns and their changes along the salinity gradient and over time. Viruses from three ponds (C4, M1, and TS) encompassing salinities from moderately hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in May and October 2009 and analyzed by transmission electron microscopy (TEM) and pulsed-field gel electrophoresis (PFGE). Additionally, for all three October samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios, increased along the salinity gradient, with around 10 10 virus-like particles (VLPs)/ml in close-to-saturation ponds, which represents the highest viral concentration reported so far for aquatic systems. Four distinct morphologies could be observed with TEM (spherical, tailed, spindled, and filamentous) but with various proportions in the different samples. Metagenomic analyses indicated that every pond harbored a distinct viral assemblage whose G؉C content could be roughly correlated with that of the active part of the microbial community that may have constituted the putative hosts. As previously reported for hypersaline metaviromes, most sequences did not have matches in the databases, although some were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide frequency analyses indicated that (i) factors additional to salinity could be structuring viral communities and (ii) every metavirome had unique gene contents and dinucleotide frequencies. Comparison with hypersaline metaviromes available in the databases indicated that the viral assemblages present in close-to-saturation environments located thousands of kilometers apart presented some common traits among them in spite of their differences regarding the putative hosts. A small core metavirome for close-to-saturation systems was found that contained 7 sequences of around 100 nucleotides (nt) whose function was not hinted at by in silico search results, although it most likely represents properties essential for hyperhalophilic viruses.

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Microbial community of salt crystals processed from Mediterranean seawater based on 16S rRNA analysis

Cited by 32 publications

References 45 publications

Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey)

Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey)

From community approaches to single-cell genomics: the discovery of ubiquitous hyperhalophilic Bacteroidetes generalists

Virioplankton Community Structure in Tunisian Solar Salterns

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