Influences of claywater and greenwater on the skin microbiome of cultured larval sablefish (Anoplopoma fimbria)

Emily T Dodd,Jonathan S F Lee,Melissa L Pierce,Rachel S Poretsky

doi:10.1186/s42523-020-00045-5

Abstract

BackgroundThe skin microbiome of marine fish is thought to come from bacteria in the surrounding water during the larval stages, although it is not clear how different water conditions affect the microbial communities in the water and, in turn, the composition and development of the larval skin microbiome. In aquaculture, water conditions are especially important; claywater and greenwater are often used in larval rearing tanks to increase water turbidity. Here, we explored the effects of these water additives on microbial communities in rearing water and on the skin of first-feeding sablefish larvae using 16S rRNA gene sequencing. We evaluated three treatments: greenwater, claywater, and greenwater with a switch to claywater after 1 week.ResultsWe observed additive-specific effects on rearing water microbial communities that coincided with the addition of larvae and rotifer feed to the tanks, such as an increase in Vibrionaceae in greenwater tanks. Additionally, microbial communities from experimental tank water, especially those in claywater, began to resemble larval skin microbiomes by the end of the experiment. The differential effects of the additives on larval sablefish skin microbiomes were largest during the first week, post-first feed. Bacteria associated with greenwater, including Vibrionaceae and Pseudoalteromonas spp., were found on larval skin a week after the switch to claywater. In addition to additive-specific effects, larval skin microbiomes also retained bacterial families likely acquired from their hatchery silos.ConclusionsOur results suggest that larval sablefish skin microbiomes are most sensitive to the surrounding seawater up to 1 week following the yolk-sac stage and that claywater substituted for greenwater after 1 week post-first feed does not significantly impact skin-associated microbial communities. However, the larval skin microbiome changes over time under all experimental conditions. Furthermore, our findings suggest a potential two-way interaction between microbial communities on the host and the surrounding environment. To our knowledge, this is one of the few studies to suggest that fish might influence the microbial community of the seawater.

Highlights

The skin microbiome of marine fish is thought to come from bacteria in the surrounding water during the larval stages, it is not clear how different water conditions affect the microbial communities in the water and, in turn, the composition and development of the larval skin microbiome
Reads per sample ranged mostly from 2000 to 30,000, but three water samples from claywater tanks and one water sample from a greenwater tank had fewer than 1000 reads, with a claywater sample having the fewest number of reads (285)
The effects of the water additives on larval skin microbiome variation were largest during the first week post first-feed, especially on day 3 between CC and GG treatments (R2 = 0.431, p = 0.004; Additional file 1), variation between treatments was low when phylogenetic distance was considered (R2 = 0.011, p = 0.99; Additional file 2)

Summary

Introduction

The skin microbiome of marine fish is thought to come from bacteria in the surrounding water during the larval stages, it is not clear how different water conditions affect the microbial communities in the water and, in turn, the composition and development of the larval skin microbiome. Inter- and intra-individual, regional, and seasonal variation have been observed in some species [13, 14, 16, 17] Extrinsic factors such as diet [18] and substances that are present in the water [19, 20] can shift the skin microbiomes of some species of marine and freshwater fish, including larvae. These interactions remain unclear, and the effects of environmental conditions and seawater microbiota on the skin microbiome of marine fish species such as sablefish (Anoplopoma fimbria) are not well understood

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