Effects of live feed manipulation with algal‐derived antimicrobial metabolites on fish larvae microbiome assembly: A molecular‐based assessment

Abstract

Opportunistic microorganisms acquired through rearing water or live feed ingestion are believed to underpin high mortality rates of fish larvae, constituting a production bottleneck for the aquaculture industry. We employed 16S rRNA gene sequencing to determine whether treatment of live feed (rotifers and Artemia) with algal-derived, antibacterial metabolites could alter bacterial community structure of gilthead seabream (Sparus aurata) larvae in a larviculture facility. Owing to a large degree of sample-to-sample variation, pronounced 'legacy effects' of live feed manipulation on the total fish larvae bacterial community could not be verified. Notwithstanding, the approach induced shifts in relative abundance of specific bacterial phylotypes in both the live feed and fish larvae. Some phylotypes representing opportunistic taxa such as Stenotrophomonas, Pseudomonas and Klebsiella displayed reduced abundances in the bacterial community of fish larvae fed metabolite-treated vs. control live feed.Conversely, potentially beneficial phylotypes in the Alphaproteobacteria clade were consistently-although not significantly-promoted in the treated larval samples. These outcomes encourage future microbiome manipulation attempts to improve fish larviculture. However, successful host colonization and competition with resident symbionts are primary barriers that need to be overcome if live feeds are to be used as effective delivery systems of beneficial bacteria to fish larvae.

Vibriosis Outbreaks in Aquaculture: Addressing Environmental and Public Health Concerns and Preventive Therapies Using Gilthead Seabream Farming as a Model System

“…Aquaculture facilities constitute a high-density species environment where the use of live feed, the stress and the animals' physical proximity increase the propagation of parasites and diseases (Guidi et al, 2018 ; Sanches-Fernandes et al, 2021a ). Therefore, monitoring quality, safety, and microbiological indicators, across all production stages, will play a decisive role in the development of future, sustainable and cost-effective aquaculture practices (FAO, 2020 ).…”

“…Therefore, monitoring quality, safety, and microbiological indicators, across all production stages, will play a decisive role in the development of future, sustainable and cost-effective aquaculture practices (FAO, 2020 ). One main problem to be overcome is the fact that most fish species display very low survival rates during larval rearing, which can be partially attributed to the spread of bacterial diseases (Snoussi et al, 2008 ; Sanches-Fernandes et al, 2021a ). In fact, bacterial diseases are responsible for mass stock mortalities in fish farms throughout Mediterranean waters, independently of the reared species and host developmental stage (Bordas et al, 1996 ; Akayli and Timur, 2002 ; Kahla-Nakbi et al, 2006 ), resulting in a significant production bottleneck.…”

Assessing the Effects of Rotifer Feed Enrichments on Turbot (Scophthalmus maximus) Larvae and Post-Larvae Gut-Associated Bacterial Communities

“…In addition to the importance of providing nutritionally complete live diets, the continuous production of marine finfish fingerlings is frequently affected by stochastic episodes of mass mortalities in the first weeks of life [ 2 , 15 ]. These outbreaks have typically been associated with pathogens belonging to genera Vibrio , Photobacterium , and Tenacibaculum that naturally inhabit the microbial communities of rotifers, copepods, and artemia [ 16 , 17 , 18 ].…”

“…Furthermore, the process of disinfection affects the microbial community as a whole, creating a more unstable environment, which will favor the development of fast-growing opportunistic r-strategists and increase the probability of pathogen proliferation and fish larvae infection [ 22 ]. Despite the perception that the disinfection processes can have significantly adverse effects on the larviculture microbiome, there is a scarce amount of information on how live feed enrichments affect the initial microbe recruitment of newly hatched larvae [ 15 , 23 , 24 , 25 ].…”

“…The establishment of larval microbial communities is a multifactorial process, driven by both extrinsic (e.g., environment) and intrinsic processes (e.g., phylogeny and host genetics; [ 26 , 27 , 28 ]), in which diet plays a crucial role [ 25 , 29 , 30 ]. In larviculture, the rearing water and feed are the earliest sources of bacteria that colonize the skin and gastrointestinal tracts of fish [ 15 , 24 , 29 , 31 ]. There is, however, a lack of information on how larval bacterial communities are influenced by different commercial live feed enrichments.…”