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Intestinal Microbiota of White Shrimp Penaeus vannamei Under Intensive Cultivation Conditions in Ecuador

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Abstract

The goal of the study was to characterize the intestinal tract bacterial microbiota composition of Penaeus vannamei in intensive commercial ponds in Ecuador, comparing two shrimp-farming phases: nursery and harvest. Bacterial microbiota was examined by sequencing amplicons V2–V3 of the 16S rRNA using Ion Torrent technology. Archaea sequences were detected in both phases. Sequence analyses revealed quantitative and qualitative differences between the nursery phase and the harvest phase in shrimp intestinal microbiota composition. The main differences were observed at the phylum level during the nursery phase, and the prevailing phyla were CKC4 (37.3%), Proteobacteria (29.8%), Actinobacteria (11.6%), and Firmicutes (10.1%). In the harvest phase, the prevailing phyla were Proteobacteria (28.4%), Chloroflexi (19.9%), and Actinobacteria (15.1%). At the genus level, microbiota from the nursery phase showed greater relative abundances of CKC4 uncultured bacterium (37%) and Escherichia-Shigella (18%). On the contrary, in the microbiota of harvested shrimp, the prevailing genera were uncultured Caldilinea (19%) and Alphaproteobacteria with no other assigned rate (10%). The analysis of similarity ANOSIM test (beta diversity) indicated significant differences between the shrimp microbiota for these two farming phases. Similarly, alfa-diversity analysis (Chao1) indicated that the microbiota at harvest was far more diverse than the microbiota during the nursery phase, which showed a homogeneous composition. These results suggest that shrimp microbiota diversify their composition during intensive farming. The present work offers the most detailed description of the microbiota of P. vannamei under commercial production conditions to date.

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Acknowledgements

The authors wish to thank the SENESCYT Ecuador for their contribution and also to Messrs. Avila, owners of the shrimp farm. Fondecyt nos. 1140734 and 1171129 supported this work.

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Authors and Affiliations

  1. Doctorado en Acuicultura, Programa Cooperativo, Universidad de Chile, Universidad Católica del Norte y Universidad Católica de Valparaíso, Coquimbo, Chile

    Oreste Gainza

  2. Laboratorio de Biotecnología, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Avda. El Líbano 5524, Santiago, Chile

    Carolina Ramírez

  3. Granja de Cultivo Intensivo San Ana, Vía Arenillas Huaquilla, El Oro, Ecuador

    Alfredo Salinas Ramos

  4. Laboratorio de Biotecnología, Unidad de Alimentos, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Avda. El Líbano 5524, Santiago, Chile

    Jaime Romero

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Gainza, O., Ramírez, C., Ramos, A.S. et al. Intestinal Microbiota of White Shrimp Penaeus vannamei Under Intensive Cultivation Conditions in Ecuador. Microb Ecol 75, 562–568 (2018). https://doi.org/10.1007/s00248-017-1066-z

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