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Open AccessArticle

A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Via Amendola 122/O, 70126 Bari, Italy
Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona 4, 70126 Bari, Italy
Stazione Zoologica Anton Dohrn, Via dei Mille 46, 98057 Milazzo (Messina), Italy
Institute for Biological Resources and Marine Biotechnology, CNR, Spianata San Raineri 86, 98122 Messina, Italy
Authors to whom correspondence should be addressed.
These authors have contributed equally to this work.
Microorganisms 2020, 8(6), 936;
Received: 21 May 2020 / Revised: 15 June 2020 / Accepted: 18 June 2020 / Published: 22 June 2020
(This article belongs to the Special Issue Extremophiles 2.0)
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 Bacteria and Archaea, 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 Archaea 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 Bacteria and at 24.1% salinity for Archaea. While Bacteria 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, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters. View Full-Text
Keywords: halophiles; extremophiles; microbiota; saltern halophiles; extremophiles; microbiota; saltern
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Leoni, C.; Volpicella, M.; Fosso, B.; Manzari, C.; Piancone, E.; Dileo, M.C.; Arcadi, E.; Yakimov, M.; Pesole, G.; Ceci, L.R. A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy). Microorganisms 2020, 8, 936.

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