Seasonal and spatial dynamics of the intestinal microbiome in tropical freshwater fish: insights from Astyanax aeneus and Brycon costaricensis in the Peñas Blancas river basin, Costa Rica.

Abstract

Background: The intestinal microbiome plays a crucial role in fish development and health, facilitating essential functions such as nutrient uptake, immune system response, and disease resistance. However, the microbial communities of Neotropical freshwater fish, such as Astyanax aeneus and Brycon costaricensis, remain largely unexplored. Understanding how microbiomes vary in relation to environmental gradients is key to identifying potential sentinel species for ecosystem monitoring. To understand the dynamics of bacterial diversity and community structure, we collected intestinal content samples from 165 individuals of both species from six points along the Peñas Blancas river basin, Costa Rica, during the dry and rainy seasons and during an intermediate period.

Results: Metabarcoding analysis of the 16 S rRNA gene revealed that the intestinal microbial communities of both species were dominated primarily by the genera Cetobacterium, Clostridium, Romboutsia and Plesiomonas. No significant differences were detected in the relative abundance of taxa, metabolic pathways or community structure between the two species and only at the Dam site, a significant increase in the Shannon index was detected in B. costaricensis. Conversely, distinct differences in microbial network properties were found, with A. aeneus showing a lower clustering coefficient and modularity, a shorter average path length and a greater number of hubs. Site and season influenced the microbial community structure of A. aeneus but not the relative abundance of taxa. Similarly, differentially abundant metabolic pathways, including xenobiotic degradation, were enriched in A. aeneus.

Conclusions: The similarities in microbiome diversity and structure in both species could arise from parallels in taxonomy, habitat and diet. However, temporal and spatial shifts in the A. aeneus microbial community structure may be associated with sensitivity to changes in environmental stressors such as precipitation, temperature, and runoff. Microbial network analysis revealed that taxa in A. aeneus are more tightly interconnected and form fewer distinct clusters, making it a promising bioindicator for monitoring water quality and anthropogenic impacts.