Derome, N. J. A. | bioRxiv Science

bioRxiv2022

Fish-microbe systems in the hostile but highly biodiverse Amazonian blackwaters

Amazonian blackwaters are extremely biodiverse systems containing some of the most naturally acidic, dissolved organic carbon-rich and ion-poor waters on Earth. Physiological adaptations of fish facing these ionoregulatory challenges are unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response of 964 fish-microbe systems from four blackwater Teleost species along a natural hydrochemical gradient, using dual RNA-Seq and 16S rRNA of gill samples. We find that responses to blackwaters are host-species-specific, but occasionally include the overexpression of Toll-receptors and integrins associated to interkingdom communication. Blackwater gill microbiomes are characterized by a transcriptionally-active betaproteobacterial cluster potentially interfering with epithelial permeability. We explore further blackwater fish-microbe interactions by analyzing transcriptomes of 320 axenic zebrafish larvae exposed to sterile, non-sterile and inverted (non-native bacterioplankton) blackwater. We find that axenic zebrafish do not survive well when exposed to sterile/inverted blackwater, suggesting an essential role of endogenous symbionts in blackwater fish physiology.

ecology↗

bioRxiv2021

The Amazon River microbiome, a story of humic carbon.

The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear and black waters. Black waters contain important loads of allochthonous humic dissolved organic carbon (DOC), mostly coming from bacteria-mediated lignin degradation, a process that remains understudied. Here, we identified the main bacterial taxa and functions associated with contrasting Amazonian water types, and shed light on their potential implication in the lignin degradation process. We performed an extensive field bacterioplankton sampling campaign from the three Amazonian water types, and combined our observations to a meta-analysis of 90 Amazonian basin shotgun metagenomes used to build a tailored functional inference database. We showed that the overall quality of DOC is a major driver of bacterioplankton structure, transcriptional activity and functional repertory. We also showed that among the taxa mostly associated to differences between water types, Polynucleobacter sinensis particularly stood out, as its abundance and transcriptional activity was strongly correlated to black water environments, and specially to humic DOC concentration. Screening the reference genome of this bacteria, we found genes coding for enzymes implicated in all the main lignin degradation steps, suggesting that this bacteria may play key roles in the carbon cycle processes within the Amazon basin.

ecology↗