A Differential Metabarcoding Approach to Describe Taxonomy Profiles of <i>Bacteria</i> and <i>Archaea</i> in the Saltern of Margherita di Savoia (Italy)
Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine p...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-06-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/6/936 |
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| author | Claudia Leoni Mariateresa Volpicella Bruno Fosso Caterina Manzari Elisabetta Piancone Maria C.G. Dileo Erika Arcadi Michail Yakimov Graziano Pesole Luigi R. Ceci |
| author_facet | Claudia Leoni Mariateresa Volpicella Bruno Fosso Caterina Manzari Elisabetta Piancone Maria C.G. Dileo Erika Arcadi Michail Yakimov Graziano Pesole Luigi R. Ceci |
| author_sort | Claudia Leoni |
| collection | DOAJ |
| description | Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of <i>Bacteria</i> and <i>Archaea</i>, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of <i>Archaea</i> in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for <i>Bacteria</i> and at 24.1% salinity for <i>Archaea</i>. While <i>Bacteria</i> showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, <i>Salinibacter</i> was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal <i>Haloquadratum</i> (~43% at 36.0% salinity) and <i>Natronomonas</i> (~18% at 13.1% salinity) and the bacterial “<i>Candidatus</i> Aquiluna” (~19% at 14.5% salinity). Interestingly, “<i>Candidatus</i> Aquiluna” had not been identified before in thalassohaline waters. |
| first_indexed | 2024-03-10T18:58:48Z |
| format | Article |
| id | doaj.art-ed69ab6f3b9f4e349ebfe05c8f24a4bb |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T18:58:48Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-ed69ab6f3b9f4e349ebfe05c8f24a4bb2023-11-20T04:36:13ZengMDPI AGMicroorganisms2076-26072020-06-018693610.3390/microorganisms8060936A Differential Metabarcoding Approach to Describe Taxonomy Profiles of <i>Bacteria</i> and <i>Archaea</i> in the Saltern of Margherita di Savoia (Italy)Claudia Leoni0Mariateresa Volpicella1Bruno Fosso2Caterina Manzari3Elisabetta Piancone4Maria C.G. Dileo5Erika Arcadi6Michail Yakimov7Graziano Pesole8Luigi R. Ceci9Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 122/O, 70126 Bari, ItalyInstitute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 122/O, 70126 Bari, ItalyInstitute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 122/O, 70126 Bari, ItalyInstitute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 122/O, 70126 Bari, ItalyDepartment of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona 4, 70126 Bari, ItalyDepartment of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona 4, 70126 Bari, ItalyStazione Zoologica Anton Dohrn, Via dei Mille 46, 98057 Milazzo (Messina), ItalyInstitute for Biological Resources and Marine Biotechnology, CNR, Spianata San Raineri 86, 98122 Messina, ItalyInstitute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 122/O, 70126 Bari, ItalyInstitute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 122/O, 70126 Bari, ItalyMicroorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of <i>Bacteria</i> and <i>Archaea</i>, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of <i>Archaea</i> in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for <i>Bacteria</i> and at 24.1% salinity for <i>Archaea</i>. While <i>Bacteria</i> showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, <i>Salinibacter</i> was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal <i>Haloquadratum</i> (~43% at 36.0% salinity) and <i>Natronomonas</i> (~18% at 13.1% salinity) and the bacterial “<i>Candidatus</i> Aquiluna” (~19% at 14.5% salinity). Interestingly, “<i>Candidatus</i> Aquiluna” had not been identified before in thalassohaline waters.https://www.mdpi.com/2076-2607/8/6/936halophilesextremophilesmicrobiotasaltern |
| spellingShingle | Claudia Leoni Mariateresa Volpicella Bruno Fosso Caterina Manzari Elisabetta Piancone Maria C.G. Dileo Erika Arcadi Michail Yakimov Graziano Pesole Luigi R. Ceci A Differential Metabarcoding Approach to Describe Taxonomy Profiles of <i>Bacteria</i> and <i>Archaea</i> in the Saltern of Margherita di Savoia (Italy) Microorganisms halophiles extremophiles microbiota saltern |
| title | A Differential Metabarcoding Approach to Describe Taxonomy Profiles of <i>Bacteria</i> and <i>Archaea</i> in the Saltern of Margherita di Savoia (Italy) |
| title_full | A Differential Metabarcoding Approach to Describe Taxonomy Profiles of <i>Bacteria</i> and <i>Archaea</i> in the Saltern of Margherita di Savoia (Italy) |
| title_fullStr | A Differential Metabarcoding Approach to Describe Taxonomy Profiles of <i>Bacteria</i> and <i>Archaea</i> in the Saltern of Margherita di Savoia (Italy) |
| title_full_unstemmed | A Differential Metabarcoding Approach to Describe Taxonomy Profiles of <i>Bacteria</i> and <i>Archaea</i> in the Saltern of Margherita di Savoia (Italy) |
| title_short | A Differential Metabarcoding Approach to Describe Taxonomy Profiles of <i>Bacteria</i> and <i>Archaea</i> in the Saltern of Margherita di Savoia (Italy) |
| title_sort | differential metabarcoding approach to describe taxonomy profiles of i bacteria i and i archaea i in the saltern of margherita di savoia italy |
| topic | halophiles extremophiles microbiota saltern |
| url | https://www.mdpi.com/2076-2607/8/6/936 |
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