Analysis of three molecular methods to describe sea Yucatan, Mexico environmental prokaryotic taxa

Authors

  • Laura Espinosa-Asuar Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, México 04510
  • Ana E. Escalante Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, México 04510
  • Luisa I. Falcón Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, México 04510
  • Germán Bonilla-Rosso Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, México 04510
  • Santiago Ramírez-Barahona Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, México 04510
  • Luis E. Eguiarte Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, México 04510
  • Valeria Souza Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, México 04510

Keywords:

Cloning, prokaryotic diversity, NGS, shotgun, T-RFLPs.

Abstract

In this study we describe a prokaryotic community from a seawater sample obtained in the Yucatan Channel, using for this purpose three molecular methods: 1) T-RFLPs. 2) Sequencing of amplicons (clone libraries). 3) Metagenome shotgun sequencing; the three are useful for the determination of microbial diversity. We also present a comparison of the scope and limits of each method. The comparison took into account three criteria: the number of taxonomic units detected, the taxonomic assignment accuracy and the cost of the study. The most abundant taxa were Candidatus Portiera OTU 3744 (equivalent to SAR86 clade) and Candidatus Pelagibacter. The results showed that the shotgun sequencing strategy is the most powerful in terms of detected taxonomic units, while the data obtained by T-RFLPs and clone library methods represent only a subsample of the shotgun fragment library. Regarding phylogenetic resolution (taxonomical determination), the more accurate approach is the sequencing of clone libraries. The costs of the three strategies vary considerably, but so does its scope. Therefore, it is important to consider that one, or another methodology, can only specifically answer some ecological and evolutionary questions.

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Published

2017-01-03

How to Cite

Espinosa-Asuar, L., Escalante, A. E., Falcón, L. I., Bonilla-Rosso, G., Ramírez-Barahona, S., Eguiarte, L. E., & Souza, V. (2017). Analysis of three molecular methods to describe sea Yucatan, Mexico environmental prokaryotic taxa. HIDROBIOLÓGICA, 24(3), 257–270. Retrieved from https://hidrobiologica.izt.uam.mx/index.php/revHidro/article/view/602

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