Dietary rayon microfibers differentially reshape rearing water and host associated microbiomes of farmed European sea bass (Dicentrarchus labrax)

TL;DR

This study shows how rayon microfibers in fish diets change the water and microbial communities of farmed sea bass, with effects varying based on microfiber dose.

Contribution

The study reveals a dose-dependent and threshold response in microbial communities of European sea bass and their environment due to dietary rayon microfibers.

Findings

Higher rayon microfiber doses increased starch- and hydrocarbon-degrading bacteria in water.

Gut and skin microbial diversity decreased with intermediate microfiber doses but recovered at high doses.

Certain bacteria correlated with host inflammation and muscle regeneration markers.

Abstract

Viscose-rayon microfibres (RFs) are cellulosic microfibres widely dispersed throughout aquatic environments. Whether ingested by or suspended in the surrounding environment, these microfibres may impact both wild and farmed animals. A previous study on European sea bass (Dicentrarchus labrax) showed that the increased presence of RFs in aquafeeds (CTRL—no RFs; RF1—0.001 g/kg; RF2—0.01 g/kg; RF3—0.1 g/kg) was linked to an exponential increase of RFs in water, intestine and skeletal muscle. This finding was associated to a fatty liver and tissue-specific transcriptional changes, depicting the up-regulation of hepatic lipogenic enzymes and intestinal/head kidney inflammatory markers. The aim of the present study was to extend this evaluation by investigating changes in associated microbial communities after the ingestion of RFs in the diet, employing a multi-layered approach for the integrative profiling of gut, skin, and environmental water microbiome using the Nanopore platform.

Amplicon-sequencing identified ~2800 taxa across water, skin and gut microbiomes. Gut and skin microbiomes were more similar to each other, but increasing RF exposure shifted the skin community toward the water microbiome. Moreover, RF induced the highest taxonomic variation in water (691 taxa), followed by skin (253) and gut (99), while microbial diversity Shannon and Simpson indexes declined from 4 down to 3.3 under RF2 and RF3 in a dose-dependent manner. Major exponents of this trend were the decrease of Synechococcus and Flavobacteriales in association with the increase of starch- and hydrocarbon-degrading taxa (Ardenticatenaceae and Gracilibacteria). In both gut and skin, bacterial richness decreased in fish fed low to intermediate RF doses, whereas RF3 fish resembled controls. Thus, compositional and discriminant analyses consistently grouped CTRL and RF3 samples, suggesting the existence of a dose threshold occurring in parallel with host counter-regulatory responses. Such feature was reflected by abundant skin-associated bacteria (Exiguobacterium and Planococcus) with at least the genetic potential to be linked to vitamin B6 biosynthesis and host-driven muscle regeneration markers, whereas predominant gut taxa with the same pattern (Microbacterium and Achromobacter) was associated with polysaccharide degradation and correlated with host gene inflammatory mechanisms.

This study revealed a concomitant dose-dependent and dose-threshold response among the bacterial communities composing the holobiont of European sea bass in response to dietary RFs ingestion, highlighting novel bacterial taxa and pathways through which microplastic exposure may differentially reshape rearing water and host-associated microbial communities.

The online version contains supplementary material available at 10.1186/s40793-026-00851-5.

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