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 : 000005 ( PubMed/Corpus ); précédent : 000004; suivant : 000006Assessment 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 ; Hadda Imene Ouzari ; Ameur Cherif ; George TsiamisSource :
- Biology [ 2079-7737 ] ; 2021.
Abstract
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 Halorubrum, Haloferax, Haloarcula, and Halogeometricum 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. Nanohaloarchaea 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 Halorhabdus, Halonotius, Halorubrum, Haloarcula, and unclassified. Halobacteriaceae 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.
DOI: 10.3390/biology10050397
PubMed: 34064384
PubMed Central: PMC8147861
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last="Cherif">Ameur Cherif</name><affiliation><nlm:affiliation>Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia.</nlm:affiliation></affiliation></author><author><name sortKey="Tsiamis, George" sort="Tsiamis, George" uniqKey="Tsiamis G" first="George" last="Tsiamis">George Tsiamis</name><affiliation><nlm:affiliation>Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2021">2021</date><idno type="RBID">pubmed:34064384</idno><idno type="pmid">34064384</idno><idno type="doi">10.3390/biology10050397</idno><idno type="pmc">PMC8147861</idno><idno type="wicri:Area/PubMed/Corpus">000005</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000005</idno></publicationStmt><sourceDesc><biblStruct><analytic><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:affiliation>Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia.</nlm:affiliation></affiliation></author><author><name sortKey="Stathopoulou, Panagiota" sort="Stathopoulou, Panagiota" uniqKey="Stathopoulou P" first="Panagiota" last="Stathopoulou">Panagiota Stathopoulou</name><affiliation><nlm:affiliation>Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece.</nlm:affiliation></affiliation></author><author><name sortKey="Elmnasri, Khaled" sort="Elmnasri, Khaled" uniqKey="Elmnasri K" first="Khaled" last="Elmnasri">Khaled Elmnasri</name><affiliation><nlm:affiliation>Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia.</nlm:affiliation></affiliation></author><author><name sortKey="Hasnaoui, Faten" sort="Hasnaoui, Faten" uniqKey="Hasnaoui F" first="Faten" last="Hasnaoui">Faten Hasnaoui</name><affiliation><nlm:affiliation>Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia.</nlm:affiliation></affiliation></author><author><name sortKey="Zidi, Ines" sort="Zidi, Ines" uniqKey="Zidi I" first="Ines" last="Zidi">Ines Zidi</name><affiliation><nlm:affiliation>Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia.</nlm:affiliation></affiliation></author><author><name sortKey="Sghaier, Haitham" sort="Sghaier, Haitham" uniqKey="Sghaier H" first="Haitham" last="Sghaier">Haitham Sghaier</name><affiliation><nlm:affiliation>Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), 2020 Sidi Thabet, Tunisia.</nlm:affiliation></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:affiliation>Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia.</nlm:affiliation></affiliation></author><author><name sortKey="Cherif, Ameur" sort="Cherif, Ameur" uniqKey="Cherif A" first="Ameur" last="Cherif">Ameur Cherif</name><affiliation><nlm:affiliation>Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia.</nlm:affiliation></affiliation></author><author><name sortKey="Tsiamis, George" sort="Tsiamis, George" uniqKey="Tsiamis G" first="George" last="Tsiamis">George Tsiamis</name><affiliation><nlm:affiliation>Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Biology</title><idno type="ISSN">2079-7737</idno><imprint><date when="2021" type="published">2021</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 <i>Halorubrum</i>, <i>Haloferax</i>, <i>Haloarcula</i>, and <i>Halogeometricum</i> 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. <i>Nanohaloarchaea</i> 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 <i>Halorhabdus</i>, <i>Halonotius</i>, <i>Halorubrum</i>, <i>Haloarcula</i>, and unclassified. <i>Halobacteriaceae</i> 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.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">34064384</PMID><DateRevised><Year>2021</Year><Month>06</Month><Day>15</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Print">2079-7737</ISSN><JournalIssue CitedMedium="Print"><Volume>10</Volume><Issue>5</Issue><PubDate><Year>2021</Year><Month>May</Month><Day>04</Day></PubDate></JournalIssue><Title>Biology</Title><ISOAbbreviation>Biology (Basel)</ISOAbbreviation></Journal><ArticleTitle>Assessment of 16S rRNA Gene-Based Phylogenetic Diversity of Archaeal Communities in Halite-Crystal Salts Processed from Natural Saharan Saline Systems of Southern Tunisia.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">397</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/biology10050397</ELocationID><Abstract><AbstractText>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 <i>Halorubrum</i>, <i>Haloferax</i>, <i>Haloarcula</i>, and <i>Halogeometricum</i> 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. <i>Nanohaloarchaea</i> 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 <i>Halorhabdus</i>, <i>Halonotius</i>, <i>Halorubrum</i>, <i>Haloarcula</i>, and unclassified. <i>Halobacteriaceae</i> 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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Najjari</LastName><ForeName>Afef</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stathopoulou</LastName><ForeName>Panagiota</ForeName><Initials>P</Initials><Identifier Source="ORCID">0000-0003-3941-0990</Identifier><AffiliationInfo><Affiliation>Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Elmnasri</LastName><ForeName>Khaled</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hasnaoui</LastName><ForeName>Faten</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zidi</LastName><ForeName>Ines</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sghaier</LastName><ForeName>Haitham</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), 2020 Sidi Thabet, Tunisia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ouzari</LastName><ForeName>Hadda Imene</ForeName><Initials>HI</Initials><AffiliationInfo><Affiliation>Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092 Tunis, Tunisia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cherif</LastName><ForeName>Ameur</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Higher Institute for Biotechnology, University Manouba, BVBGR-LR11ES31, Biotechpole Sidi Thabet, 2020 Ariana, Tunisia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tsiamis</LastName><ForeName>George</ForeName><Initials>G</Initials><Identifier Source="ORCID">0000-0001-5616-8505</Identifier><AffiliationInfo><Affiliation>Department of Environmental Engineering, Laboratory of Systems Microbiology and Applied Genomics, University of Patras, 2 Seferi Str., 30100 Agrinio, Greece.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2021</Year><Month>05</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Biology (Basel)</MedlineTA><NlmUniqueID>101587988</NlmUniqueID><ISSNLinking>2079-7737</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">16S rRNA gene libraries</Keyword><Keyword MajorTopicYN="N">DGGE</Keyword><Keyword MajorTopicYN="N">archaea</Keyword><Keyword MajorTopicYN="N">culture approach</Keyword><Keyword MajorTopicYN="N">metagenomic</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2021</Year><Month>03</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2021</Year><Month>03</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2021</Year><Month>03</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2021</Year><Month>6</Month><Day>2</Day><Hour>1</Hour><Minute>9</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2021</Year><Month>6</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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