Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853)
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Abstract
Symbiotic relationships between host and microbiome can play a major role in local adaptation. Previous studies with freshwater organisms have shown that microbiome performs numerous important biochemical functions for the host, playing a key role in metabolism, physiology or health. Experimental studies in fish groups have found an effect of enzymatic activity of gut microbiota on a variety of metabolic processes. The goal of this study was to compare stomach microbiome from cave and surface Astyanax mexicanus, in order to evaluate the potential response of microbiota to locally contrasting environmental conditions and physiological adaptations of the host. Stomach biopsies were obtained from three different populations: Pachón cave, and two surface rivers (Rascón and Micos rivers). The stomach microbiome was analyzed using the Ion 16S Metagenomic kit considering seven variable regions: V2, V3, V4, V6-7, V8 and V9. A high diversity was observed across samples, including 16 phyla, 120 families and 178 genera. Gammaproteobacteria, Firmicutes, Bacteroidetes and Betaprotobacteria were the most abundant phyla across the samples. Although the relative abundance of the core OTUs at genus level were highly contrasting among populations, we did not recover differences in stomach microbiome between contrasting habitats (caves vs surface rivers). Rather, we observed a consistent association between β-diversity and dissolved oxygen concentration in water. Therefore, and unexpectedly, the microbiota of A. mexicanus is not linked with the habitat but results from water conditions.
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2018. Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853) PeerJ Preprints 6:e27058v1 https://doi.org/10.7287/peerj.preprints.27058v1Author comment
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Figure S1
Rarefaction curves of observed species of 16S rDNA genes for the different fish samples. Symbol abbreviations: R, Rascón; M, Micos; P, Pachón; M, male; F, female.
Figure S2
Venn diagrams showing the numbers of shared and unique genus OTUs (at 97% of similarity) from stomach microbiome among fish samples from the same population: a) Rascón, b) Micos, and c) Pachón. Symbol abbreviations: R, Rascón; M, Micos; P, Pachón; M, male; F, female.
Figure S3
Distribution of bacterial taxonomic groups from mapped reads among the different hypervariable regions of 16S rRNA for each fish sample. The number of reads for each region is indicated in parentheses. Symbol abbreviations: R, Rascón; M, Micos; P, Pachón; M, male; F, female.
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Patricia Ornelas-García conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Silvia Pajares conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.
Víctor M. Sosa-Jiménez performed the experiments, approved the final draft.
Sylvie Rétaux authored or reviewed drafts of the paper, approved the final draft.
Ramsés A. Miranda-Gamboa performed the experiments, approved the final draft.
Animal Ethics
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
SEMARNAT: SGPA/DGVS/02438/16
Field Study Permissions
The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):
Field collection permit was approved by the Secretaria del Medio Ambiente y Recursos Naturales (SEMARNAT: SGPA/DGVS/02438/16).
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
Data Deposition
The following information was supplied regarding data availability:
Funding
This work was supported by UNAM-PAPIIT IA203017 and Ecos-Nord CONACYT exchange program grant No. 279100. RGM Grad student Fellowship at the Posgrado en Ciencia e Ingeniería de Materiales, Universidad Nacional Autónoma de México. VMSJ Grad student Fellowship at the Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.