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Genes 2018, 9(1), 55; https://doi.org/10.3390/genes9010055

Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs

1
Sequencing and Bioinformatics Service, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia 46020, Spain
2
Center for Advanced Research in Public Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Valencia 46020, Spain
3
Chemical Engineering Faculty, Exact Sciences and Engineering Campus, Autonomous University of Yucatán (UADY), Mérida, Yucatán 97050, Mexico
4
Biological Sciences Academic Division, Autonomous University Juárez de Tabasco (UJAT), Villahermosa, Centro, Tabasco 99630, Mexico
*
Author to whom correspondence should be addressed.
Received: 7 November 2017 / Revised: 12 January 2018 / Accepted: 13 January 2018 / Published: 22 January 2018
(This article belongs to the Special Issue Genetics and Genomics of Extremophiles)
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Abstract

New biotechnology applications require in-depth preliminary studies of biodiversity. The methods of massive sequencing using metagenomics and bioinformatics tools offer us sufficient and reliable knowledge to understand environmental diversity, to know new microorganisms, and to take advantage of their functional genes. Villa Luz caves, in the southern Mexican state of Tabasco, are fed by at least 26 groundwater inlets, containing 300–500 mg L−1 H2S and <0.1 mg L−1 O2. We extracted environmental DNA for metagenomic analysis of collected samples in five selected Villa Luz caves sites, with pH values from 2.5 to 7. Foreign organisms found in this underground ecosystem can oxidize H2S to H2SO4. These include: biovermiculites, a bacterial association that can grow on the rock walls; snottites, that are whitish, viscous biofilms hanging from the rock walls, and sacks or bags of phlegm, which live within the aquatic environment of the springs. Through the emergency food assistance program (TEFAP) pyrosequencing, a total of 20,901 readings of amplification products from hypervariable regions V1 and V3 of 16S rRNA bacterial gene in whole and pure metagenomic DNA samples were generated. Seven bacterial phyla were identified. As a result, Proteobacteria was more frequent than Acidobacteria. Finally, acidophilic Proteobacteria was detected in UJAT5 sample. View Full-Text
Keywords: metagenomics; bTEFAP; Proteobacteria; Acidobacteria metagenomics; bTEFAP; Proteobacteria; Acidobacteria
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D’Auria, G.; Artacho, A.; Rojas, R.A.; Bautista, J.S.; Méndez, R.; Gamboa, M.T.; Gamboa, J.R.; Gómez-Cruz, R. Metagenomics of Bacterial Diversity in Villa Luz Caves with Sulfur Water Springs. Genes 2018, 9, 55.

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