Microbial colonization and community stability in a marine post-smolt RAS inoculated with a commercial starter culture

K Drønen,I Roalkvam,H Dahle,H Nilsen,A.B Olsen,H Wergeland

doi:10.1016/j.aqrep.2021.100745

K Drønen, I Roalkvam + Show 4 more

Open Access

https://doi.org/10.1016/j.aqrep.2021.100745

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Abstract

The performance of a commercial starter culture was investigated in a new marine post-smolt RAS, analyzing the microbial communities of 100 samples collected monthly over a year from biofilter biofilm carriers, tank wall biofilm, production water and fish skin. Totally 139 operational taxonomic units (OTUs) were defined in the starter culture, of which the classified members of Rhodobacterales, Bacteroidetes, Alteromonadales and Planctomycetes were largely the first colonizers of the biofilter carriers. Early colonizing OTUs that dominated biofilter biofilm carriers (> 5% relative abundance) were stably present over time, but the development went slowly from a few OTUs with very high relative abundance to several dominant ones with lower relative abundance. Operating taxonomic units not associated with the starting culture became prominent on the biofilter biofilm carriers only towards the end of the trial period. These were termed environmental OTUs. Comparing the two OTU quantitives in a ratio, where counts were based on all OTUs in the sample, the starter culture OTUs:environmental OTUs were 1.2 and 0.9 at the first and last sampling time for the biofilter biofilm carriers. Correspondingly, for all defined OTUs in the RAS sampling sites together, the ratio changed from 0.8 to 0.6 during experiment. Independent of origin, omniscient OTUs at a sampling site, did also have the highest relative abundances and were normally shared between biofilter biofilm carriers and the production water. New and lost OTUs between sampling times were on average 44 % of the OTUs defined, and this OTUflow was strongest for low abundant environmental OTUs. The maturation of the biofilter with respect to nitrification took long time, and the Nitrospira strain in the starter culture was not adapted to marine salinities. Still, we report a controlled colonization of the marine RAS by the starter culture.

Highlights

Microbiome studies from recycling aquaculture systems (RAS), based on next-generation 16S rRNA gene sequencing, is a powerful and increasingly used approach to predict processes that influence water quality and fish health. (Bartelme et al, 2019; Gonzalez-Silva et al, 2021; Ma et al, 2020; Martins et al, 2013; Mekuchi et al, 2019; Menanteau-Ledouble et al, 2020; Minich et al, 2020; Minniti et al, 2017; Perry et al, 2020; Ruan et al, 2015; Schmidt et al, 2016; Wang et al, 2021)
The biofilter biofilm carriers in a new marine post-smolt RAS were inoculated with microbes from a commercial starter culture prior to the first fish stocking
Other dominating operational taxonomic units (OTUs) on the biofilter biofilm carriers that were not defined at all sampling times were classified as Planctomycetes (2 and 3), Lewinella (2), Desulforomonadales (3 and 5), Nannocystaceae (3 and 5), Thioalkalispira (4), Dasania (5), Nitrospira (5) and Alteromonadales (5), and they dominated on the biofilm carriers in the production cycles as indicated within the brackets

Summary

Introduction

Microbiome studies from recycling aquaculture systems (RAS), based on next-generation 16S rRNA gene sequencing, is a powerful and increasingly used approach to predict processes that influence water quality and fish health. (Bartelme et al, 2019; Gonzalez-Silva et al, 2021; Ma et al, 2020; Martins et al, 2013; Mekuchi et al, 2019; Menanteau-Ledouble et al, 2020; Minich et al, 2020; Minniti et al, 2017; Perry et al, 2020; Ruan et al, 2015; Schmidt et al, 2016; Wang et al, 2021). (Bartelme et al, 2019; Gonzalez-Silva et al, 2021; Ma et al, 2020; Martins et al, 2013; Mekuchi et al, 2019; Menanteau-Ledouble et al, 2020; Minich et al, 2020; Minniti et al, 2017; Perry et al, 2020; Ruan et al, 2015; Schmidt et al, 2016; Wang et al, 2021) Most of these studies reports from fresh water or brackish water systems. The major goal for further development of RAS technology is to maintain stable good water quality during a whole salmon life cycle. This goal does not necessarily demand a long-time stable RAS microbiome. The normal variations in the RAS microbiome without influencing growth and health perfor mance in the fish needs to be understood, and what causes the dynamics in the RAS microbiomes (Sauer et al, 2007)

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