Introduction
Atlantic salmon (Salmo salar ) aquaculture continues to grow and intensify in line with a continually expanding world population. Such demand for sustainable protein sources has driven the expansion of land-based production in recirculating aquaculture systems (RAS) . Microbes associated with fish mucosal surfaces are an important component of health and immunity and have become of increasing interest in recent year , particularl y in RAS where microbes are also a key component in maintaining high water quality. External mucosal surfaces, skin and gill, are the first lines of defence against opportunistic pathogens as they are in constant contact with surrounding water, but the stability of mucosal microbiomes over time in RAS is unknown.
Materials and methods
We analysed the temporal dynamics of the microbial communities associated with skin and gill mucus in Atlantic salmon during smoltification in a commercial RAS facility and following transfer to a commercial sea site. Mucus swabs were taken from 6 fish from triplicate tanks at 4 timepoints in freshwater (FW1-4) and at 1- and 4-weeks post-seawater transfer (SW1/SW2). Sequencing of the V3/V4 variable region of the bacterial 16S gene was carried out on the Illumina MiSeq platform. DADA2
was used to determine microbial composition in skin and gill mucus , water and diet samples at the level of amplicon sequence variants (ASVs). Functionality was inferred using Piphillin
.
Results
Microbial diversity and richness were temporally dynamic in both skin and gill mucus (p<0.001) with a distinct and significant drop at FW2 followed by a rising trend to FW4 and stability post-SWT. The drop in diversity in FW was the result of a surge in relative abundance of two taxa belonging to the genus Hydrogenophaga . These dynamics were mirrored in tank water samples. Beta diversity revealed more separation between sampling points than between tissues at a single sampling point.
The numbers of identified core microbial taxa (present in >9 0% of samples) generally increased over time in both skin and gill mucus, and overlap was observed between the two. However, c oincident with the surge in Hydrogenophaga at FW2 , few core taxa were identified and all of these cores were also identified in tank water.
Functional inference identified metabolic pathways associated with microbial communities. Coincident with the surge in Hydrogenophaga at FW2, ‘Xenobiotics biodegradation and metabolism’ increased in contribution at the detriment of ‘Carbohydrate metabolism’ in both skin and gill mucus.
Discussion and conclusions
Microbial diversity in skin and gill mucus were temporally dynamic in fish reared in a FW RAS during the parr – smolt transformation. A distinct drop in diversity was identified at FW2 , coincident with a spike in the relative abundance of two taxa belonging to the genus Hydrogenophaga and suggested the occurrence of a dysbiotic event.
Hydrogenophaga is an autotrophic de-nitrifier associated with RAS biofilters
. Previous work in RAS has shown that biofilter-associated taxa are not restricted to the biofilter and have the potential to colonise fish mucus
. The Hydrogenophaga spike was associated with ‘Xenobiotics biodegradation and metabolism’ , suggesting a role for this genus in metabolism and bioremediation of potentially harmful inorganic compounds in RAS tank water and mucosal surfaces.
Despite disruption of the mucosal microbiota , no adverse impacts on health or growth were observed, indicating functional redundancy and potentially protective functions of individual genera. This study highlights the importance of considering temporal dynamics when interpreting results of microbiome studies and inferring wider significance.
This work was funded by BBSRC grant RobustSmolt (BB/S004270/1). The authors would like to thank John Richmond, MOWI and ARCH-UK for their contributions to this work.
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