Relevant Probiotic and Functional Properties of Lactic Acid Bacteria Isolated from Aquaculture Environments on the Ivory Coast for Potential Aquaponic Applications

Aquaponics combines aquaculture and hydroponics, offering an integrated and sustainable food production system. This study investigated the probiotic properties, plant growth-promoting (PGP) activity, and nitrifying capacity of twelve lactic acid bacteria (LAB) strains isolated from an aquaculture farm environment on the Ivory Coast for their potential application in aquaponic systems. All isolates demonstrated antagonistic activity against key pathogenic indicator strains, except Vibrio cholerae, and displayed varying levels of surface hydrophobicity (5.50 ± 0.70% to 22.83 ± 1.17%) and auto-aggregation (32.50 ± 0.08% to 52.89 ± 0.39%) after 24 h. Antioxidant activity was significantly higher in cell-free supernatants (~71–79%) than in intact cells (~30–33%). Bile salt tolerance (0.3%, 4 h) ranged from 2.13 ± 0.76% to 40.87 ± 2.12%, and survival under pH 1.5 with pepsin for 3 h varied from 4.84 ± 0.26% to 53.98 ± 13.28%. All isolates produced lactic, acetic, citric, malic, and propionic acid and exhibited amylase and cellulase activity; none showed hemolytic activity. Only LAB 11 produced indole-3-acetic acid (17.72 ± 0.06 μg/mL), siderophores, and phosphate-solubilization activity for PGP traits, and this group significantly enhanced maize seed germination (86.66 ± 5.77%) and radicle length (7.00 ± 0.52 mm) compared to the control (63.33 ± 32.14% and 4.94 ± 1.52 mm), respectively. LAB 1 and LAB 10 demonstrated the highest ammonia-oxidizing capacity in vitro and in trout pond water. LAB 1, LAB 10, and LAB 11 were confirmed by whole genome sequencing analysis to be Enterococcus faecalis strains with a favorable-safety genomic profile and probiotic characteristics. These three strains therefore represent promising candidates for consortium-based applications in aquaponics systems.