Impacts of the Marine Hatchery Built Environment on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail King sh, Seriola Lalandi

Jeremiah Minich (  jjminich@ucsd.edu ) Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA https://orcid.org/0000-0002-7202-965X Barbara Nowak University of Tasmania Abigail Elizur University Sunshine Coast Rob Knight University of California San Diego Stewart Fielder NSW DPI: New South Wales Department of Primary Industries Eric Allen University of California San Diego


Abstract Background
Microbial succession in vertebrates has primarily focused on vertical transmission and ontogenetic development in the mammalian gut. Teleosts comprise the majority of vertebrate diversity, yet little is known about how the microbiome develops in sh, particularly when vertical transmission is limited or absent for broadcast spawners. Biological factors such as diet, age, phylogeny, and trophic level along with environmental factors such as water salinity, temperature, and depth have been shown to in uence the mucosal microbiomes of sh. Here we investigate how various microbial-rich surfaces from the built environment 'BE' in uence the development of the mucosal microbiome (gill, skin, and digesta) of an economically important marine sh, yellowtail king sh, Seriola lalandi, over time.

Results
For the rst experiment, we sampled gill and skin microbiomes from 36 sh reared in three tank conditions, and demonstrate that the gill is more in uenced by the surrounding environment than the skin. In a second experiment, sh microbiomes (gill, skin, and digesta) and the BE (tank side, water, inlet pipe, airstones, and air diffusers) were sampled from indoor reared sh at three ages (43 dph, 137 dph, 430 dph; n=12 per age). At 430 dph, 20 additional sh were sampled from an outdoor ocean net pen. A total of 304 samples were processed for 16S rRNA gene sequencing. Gill and skin alpha diversity increased while gut diversity decreased with age. Diversity was much lower in sh from the ocean net pen compared to indoor sh. We quanti ed the change in community dynamics driven by the BE and show that the gill and skin are most in uenced by the BE early in development, with aeration equipment having more impact in later ages, while the gut microbiome becomes increasingly differentiated from the environment over time.

Conclusions
Our ndings suggest that sh mucosal microbiomes are differentially in uenced by the built environment with a high turnover and rapid succession occurring in the gill and skin while the gut microbiome is more stable. We demonstrate how individual components of a hatchery system, especially aeration equipment, may contribute directly to microbiome development in a marine sh. In addition, results demonstrate how early life (larval) exposure to stressors in the rearing environment may in uence sh microbiome development which is important for animal health and aquaculture production.

Full Text
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However, the manuscript can be downloaded and accessed as a PDF.  Niche differentiation within body sites over time. Beta diversity distances (weighted normalized UniFrac) of a) gill, b) skin, and c) digesta samples compared to six different hatchery built environment putative microbial sources (water, inlet pipe, tank side, air diffuser, airstone, and rst feed (rotifers). Statistical comparison of microbiome differentiation across three BE comparisons (water, inlet pipe, rst feed) over time and calculated independently across three body sites: d) gill, e) skin, and f) digesta (Statistical test: Kruskal-Wallis, P value and KW test statistic reported in gure panel. f) Results from the Kruskal-Wallis test for (d,e,f) depicted as effect size to demonstrate the rate of microbial community niche differentiation.

Figure 5
SourceTracker2 analysis of individual microbiome contributions from the built environment onto various mucosal body sites across time: a) 43 dph, b) 137 dph, c) 430 dph indoor, and d) 430 dph seapen. Features with less than 100 counts across all samples excluded. 'Unknown' indicates source population was not sampled or included thus would be the percentage of a given sample which has source microbes from an unknown location or undetermined source.

Supplementary Files
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