Endophytes are microorganisms that live inside the plant tissue without causing external symptoms. All plants in nature harbor endophytes. Some endophytes produce and secrete biologically active compounds, known as secondary metabolites, which can help the host plant cope with bacterial, fungal, and other pest pathogens. Endophytes are isolated from aquatic plants and algae. Diseases are detrimental in the aquaculture industry where chemical pesticides and antibiotics are widely used in an attempt to cope with fish pathogens. However, the ability to prevent disease outbreaks in aquaculture is currently extremely limited. Here, we isolated 173 bacterial and fungal endophytes from 16 Mediterranean seaweed and 4 algae from fresh or thermo-mineral water. We found 88 endophytes (51%) with biological activity against four common aquaculture pathogens. Fifty endophytes (29%) caused mortality of at least one of these four pathogens. We identified 23 bioactive endophytes, 18 of which are from the Bacilli class. Our findings suggest that macroalgae from different aquatic environments can serve as a good source of potential biocontrol agents against aquaculture diseases. To the best of our knowledge, there are no published studies demonstrating the use of algal endophytes to control aquaculture diseases. Our study may lead to finding new molecules for use as novel environmentally friendly products that will solve one of the most challenging problems for the growing aquaculture industry: pathogens and pests.

Ulva is a commercially important marine macroalga. It hosts both epiphytes and endophytes. The latter are assumed to protect Ulva through secondary metabolites. Previously, we demonstrated bioactive endophytes from macroalgae with great potential to control diseases of aquaculture. In this study, we introduced a bioactive bacterial endophyte back into its original host (Ulva sp.) and demonstrated its survival over time in fresh and freeze-dried Ulva sp. We visualized the endophyte’s location and survival in the seaweed using a Green Fluorescent Protein (GFP) reporter gene. The isolate colonized the intercellular space and survived for at least 5 months in fresh, and 12 months in freeze-dried algae, while maintaining its bioactivity against the aquaculture pathogen Streptococcus iniae. We studied the influence of the endophyte on the bacterial community in the Ulva sp. We found that once introduced, the endophyte significantly changed algal microbiota diversity and abundance. Two of Ulva’s associated bacterial species were quantified over time, suggesting different trends in absolute abundance of these bacteria between treatments. To the best of our knowledge, this is the first report of the successful introduction of an endophytic microorganism into macroalgal tissue. These findings may be useful in applied research for the potential management of aquaculture diseases.