Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia
Identifieur interne : 000820 ( Main/Curation ); précédent : 000819; suivant : 000821Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia
Auteurs : Afef Najjari ; Panagiota Stathopoulou ; Khaled Elmnasri ; Faten Hasnaoui ; Ines Zidi ; Haitham Sghaier [Tunisie] ; Hadda Imene Ouzari ; Ameur Cherif ; George TsiamisSource :
- Biology [ 2079-7737 ] ; 2021.
Abstract
In the current investigation, we determine the archaeal diversity from halite-crystal salts sampled from Chott Djerid and Chott Douz, two saline Chotts in the Tunisian Sahara, using both culture-dependent and independent approaches citing DGGE (V3 regions), 16S rRNA-gene (full length gene ~ 1500 bp) based clone libraries and high-throughput sequencing technology of Illumina MiSeq platform (V3–V4 regions). The amalgamation of all results yielded a comprehensive view of the archaeal diversity represented by members of
A thorough assessment of the phylogenetic diversity and community structure of halophilic archaea from three halite-crystal salts, processed from two separated saline systems of Southern Tunisia has been performed using culture dependent and independent methods targeting different regions of 16S rRNA gene sequences including DGGE, 16S rRNA clone libraries and Illumina Miseq sequencing. Two samples, CDR (red halite-crystal salts) and CDW (white halite-crystal salts), were collected from Chott-Eljerid and one sample CDZ (white halite-crystal salts) from Chott Douz. Fourteen isolates were identified as
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DOI: 10.3390/biology10050397
PubMed: 34064384
PubMed Central: 8147861
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia</title><author><name sortKey="Najjari, Afef" sort="Najjari, Afef" uniqKey="Najjari A" first="Afef" last="Najjari">Afef Najjari</name><affiliation><nlm:aff id="af1-biology-10-00397">Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia;<email>faten.hasnaoui@etudiant-issbat.utm.tn</email> (F.H.);<email>ines.zidi@istmt.utm.tn</email> (I.Z.);<email>imene.ouzari@fst.utm.tn</email> (H.I.O.)</nlm:aff></affiliation></author><author><name sortKey="Stathopoulou, Panagiota" sort="Stathopoulou, Panagiota" uniqKey="Stathopoulou P" first="Panagiota" last="Stathopoulou">Panagiota Stathopoulou</name><affiliation><nlm:aff id="af2-biology-10-00397">Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece;<email>panstath@upatras.gr</email> (P.S.);<email>gtsiamis@upatras.gr</email> (G.T.)</nlm:aff></affiliation></author><author><name sortKey="Elmnasri, Khaled" sort="Elmnasri, Khaled" uniqKey="Elmnasri K" first="Khaled" last="Elmnasri">Khaled Elmnasri</name><affiliation><nlm:aff id="af3-biology-10-00397">Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia;<email>khaled.elmnasri@fst.utm.tn</email> (K.E.);<email>haitham.sghaier@cnstn.rnrt.tn</email> (H.S.);<email>ameur.cherif@uma.tn</email> (A.C.)</nlm:aff></affiliation></author><author><name sortKey="Hasnaoui, Faten" sort="Hasnaoui, Faten" uniqKey="Hasnaoui F" first="Faten" last="Hasnaoui">Faten Hasnaoui</name><affiliation><nlm:aff id="af1-biology-10-00397">Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia;<email>faten.hasnaoui@etudiant-issbat.utm.tn</email> (F.H.);<email>ines.zidi@istmt.utm.tn</email> (I.Z.);<email>imene.ouzari@fst.utm.tn</email> (H.I.O.)</nlm:aff></affiliation></author><author><name sortKey="Zidi, Ines" sort="Zidi, Ines" uniqKey="Zidi I" first="Ines" last="Zidi">Ines Zidi</name><affiliation><nlm:aff id="af1-biology-10-00397">Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia;<email>faten.hasnaoui@etudiant-issbat.utm.tn</email> (F.H.);<email>ines.zidi@istmt.utm.tn</email> (I.Z.);<email>imene.ouzari@fst.utm.tn</email> (H.I.O.)</nlm:aff></affiliation></author><author><name sortKey="Sghaier, Haitham" sort="Sghaier, Haitham" uniqKey="Sghaier H" first="Haitham" last="Sghaier">Haitham Sghaier</name><affiliation><nlm:aff id="af3-biology-10-00397">Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi 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Tunis El Manar, 2092 Tunis, Tunisia;<email>faten.hasnaoui@etudiant-issbat.utm.tn</email> (F.H.);<email>ines.zidi@istmt.utm.tn</email> (I.Z.);<email>imene.ouzari@fst.utm.tn</email> (H.I.O.)</nlm:aff></affiliation></author><author><name sortKey="Cherif, Ameur" sort="Cherif, Ameur" uniqKey="Cherif A" first="Ameur" last="Cherif">Ameur Cherif</name><affiliation><nlm:aff id="af3-biology-10-00397">Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia;<email>khaled.elmnasri@fst.utm.tn</email> (K.E.);<email>haitham.sghaier@cnstn.rnrt.tn</email> (H.S.);<email>ameur.cherif@uma.tn</email> (A.C.)</nlm:aff></affiliation></author><author><name sortKey="Tsiamis, George" sort="Tsiamis, George" uniqKey="Tsiamis G" first="George" last="Tsiamis">George Tsiamis</name><affiliation><nlm:aff id="af2-biology-10-00397">Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece;<email>panstath@upatras.gr</email> (P.S.);<email>gtsiamis@upatras.gr</email> (G.T.)</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">34064384</idno><idno type="pmc">8147861</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8147861</idno><idno type="RBID">PMC:8147861</idno><idno type="doi">10.3390/biology10050397</idno><date when="2021">2021</date><idno type="wicri:Area/Pmc/Corpus">000051</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000051</idno><idno type="wicri:Area/Pmc/Curation">000051</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000051</idno><idno type="wicri:Area/Pmc/Checkpoint">000022</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000022</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:34064384</idno><idno 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de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia;<email>faten.hasnaoui@etudiant-issbat.utm.tn</email> (F.H.);<email>ines.zidi@istmt.utm.tn</email> (I.Z.);<email>imene.ouzari@fst.utm.tn</email> (H.I.O.)</nlm:aff></affiliation></author><author><name sortKey="Stathopoulou, Panagiota" sort="Stathopoulou, Panagiota" uniqKey="Stathopoulou P" first="Panagiota" last="Stathopoulou">Panagiota Stathopoulou</name><affiliation><nlm:aff id="af2-biology-10-00397">Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece;<email>panstath@upatras.gr</email> (P.S.);<email>gtsiamis@upatras.gr</email> (G.T.)</nlm:aff></affiliation></author><author><name sortKey="Elmnasri, Khaled" sort="Elmnasri, Khaled" uniqKey="Elmnasri K" first="Khaled" last="Elmnasri">Khaled Elmnasri</name><affiliation><nlm:aff id="af3-biology-10-00397">Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia;<email>khaled.elmnasri@fst.utm.tn</email> (K.E.);<email>haitham.sghaier@cnstn.rnrt.tn</email> (H.S.);<email>ameur.cherif@uma.tn</email> (A.C.)</nlm:aff></affiliation></author><author><name sortKey="Hasnaoui, Faten" sort="Hasnaoui, Faten" uniqKey="Hasnaoui F" first="Faten" last="Hasnaoui">Faten Hasnaoui</name><affiliation><nlm:aff id="af1-biology-10-00397">Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia;<email>faten.hasnaoui@etudiant-issbat.utm.tn</email> (F.H.);<email>ines.zidi@istmt.utm.tn</email> (I.Z.);<email>imene.ouzari@fst.utm.tn</email> (H.I.O.)</nlm:aff></affiliation></author><author><name sortKey="Zidi, Ines" sort="Zidi, Ines" uniqKey="Zidi I" first="Ines" last="Zidi">Ines Zidi</name><affiliation><nlm:aff id="af1-biology-10-00397">Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia;<email>faten.hasnaoui@etudiant-issbat.utm.tn</email> (F.H.);<email>ines.zidi@istmt.utm.tn</email> (I.Z.);<email>imene.ouzari@fst.utm.tn</email> (H.I.O.)</nlm:aff></affiliation></author><author><name sortKey="Sghaier, Haitham" sort="Sghaier, Haitham" uniqKey="Sghaier H" first="Haitham" last="Sghaier">Haitham Sghaier</name><affiliation><nlm:aff id="af3-biology-10-00397">Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia;<email>khaled.elmnasri@fst.utm.tn</email> (K.E.);<email>haitham.sghaier@cnstn.rnrt.tn</email> (H.S.);<email>ameur.cherif@uma.tn</email> (A.C.)</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="af4-biology-10-00397">Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), 2020 Sidi Thabet, Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory “Energy and Matter for Development of Nuclear Sciences” (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), 2020 Sidi Thabet</wicri:regionArea></affiliation></author><author><name sortKey="Ouzari, Hadda Imene" sort="Ouzari, Hadda Imene" uniqKey="Ouzari H" first="Hadda Imene" last="Ouzari">Hadda Imene Ouzari</name><affiliation><nlm:aff id="af1-biology-10-00397">Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia;<email>faten.hasnaoui@etudiant-issbat.utm.tn</email> (F.H.);<email>ines.zidi@istmt.utm.tn</email> (I.Z.);<email>imene.ouzari@fst.utm.tn</email> (H.I.O.)</nlm:aff></affiliation></author><author><name sortKey="Cherif, Ameur" sort="Cherif, Ameur" uniqKey="Cherif A" first="Ameur" last="Cherif">Ameur Cherif</name><affiliation><nlm:aff id="af3-biology-10-00397">Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia;<email>khaled.elmnasri@fst.utm.tn</email> (K.E.);<email>haitham.sghaier@cnstn.rnrt.tn</email> (H.S.);<email>ameur.cherif@uma.tn</email> (A.C.)</nlm:aff></affiliation></author><author><name sortKey="Tsiamis, George" sort="Tsiamis, George" uniqKey="Tsiamis G" first="George" last="Tsiamis">George Tsiamis</name><affiliation><nlm:aff id="af2-biology-10-00397">Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece;<email>panstath@upatras.gr</email> (P.S.);<email>gtsiamis@upatras.gr</email> (G.T.)</nlm:aff></affiliation></author></analytic><series><title level="j">Biology</title><idno type="eISSN">2079-7737</idno><imprint><date when="2021">2021</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Simple Summary</title><p>In the current investigation, we determine the archaeal diversity from halite-crystal salts sampled from Chott Djerid and Chott Douz, two saline Chotts in the Tunisian Sahara, using both culture-dependent and independent approaches citing DGGE (V3 regions), 16S rRNA-gene (full length gene ~ 1500 bp) based clone libraries and high-throughput sequencing technology of Illumina MiSeq platform (V3–V4 regions). The amalgamation of all results yielded a comprehensive view of the archaeal diversity represented by members of <italic>Halobacteria</italic> and <italic>Nanohaloarchaea</italic> classes.</p></sec><sec><title>Abstract</title><p>A thorough assessment of the phylogenetic diversity and community structure of halophilic archaea from three halite-crystal salts, processed from two separated saline systems of Southern Tunisia has been performed using culture dependent and independent methods targeting different regions of 16S rRNA gene sequences including DGGE, 16S rRNA clone libraries and Illumina Miseq sequencing. Two samples, CDR (red halite-crystal salts) and CDW (white halite-crystal salts), were collected from Chott-Eljerid and one sample CDZ (white halite-crystal salts) from Chott Douz. Fourteen isolates were identified as <italic>Halorubrum</italic>, <italic>Haloferax</italic>, <italic>Haloarcula</italic>, and <italic>Halogeometricum</italic> genera members. Culture-independent approach revealed a high diversity of archaeal members present in all samples, represented by the Euryarchaeal phylum and the dominance of the Halobacteria class. <italic>Nanohaloarchaea</italic> were also identified only in white halite samples based on metagenomic analysis. In fact, a total of 61 genera were identified with members of the <italic>Halorhabdus</italic>, <italic>Halonotius</italic>, <italic>Halorubrum</italic>, <italic>Haloarcula</italic>, and unclassified. <italic>Halobacteriaceae</italic> were shared among all samples. Unexpected diversity profiles between samples was observed where the red halite crust sample was considered as the most diverse one. The highest diversity was observed with Miseq approach, nevertheless, some genera were detected only with 16S rRNA clone libraries and cultured approaches.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Stivaletta, N" uniqKey="Stivaletta N">N. Stivaletta</name></author><author><name sortKey="Barbieri, R" uniqKey="Barbieri R">R. Barbieri</name></author><author><name sortKey="Picard, C" uniqKey="Picard C">C. Picard</name></author><author><name sortKey="Bosco, M" uniqKey="Bosco M">M. Bosco</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Javor, B" uniqKey="Javor B">B. Javor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kamekura, M" uniqKey="Kamekura M">M. Kamekura</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oren, A" uniqKey="Oren A">A. 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