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Agricultural yields are under constant jeopardy as climate change and abiotic pressures spread worldwide. Using rhizospheric microbes as biostimulants/biofertilizers is one of the best ways to improve agro-agriculture in the face of these things. The purpose of this experiment was to investigate whether a native arbuscular mycorrhizal fungi inoculum (AMF-complex) might improve caper (Capparis spinosa) seedlings' nutritional status, their morphological/growth performance and photosynthetic efficiency under water-deficit stress (WDS). Thus, caper plantlets inoculated with or without an AMF complex (+AMF and −AMF, respectively) were grown under three gradually increasing WDS regimes, i.e., 75, 50 and 25% of field capacity (FC). Overall, measurements of morphological traits, biomass production and nutrient uptake (particularly P, K+, Mg2+, Fe2+ and Zn2+) showed that mycorrhizal fungi inoculation increased these variables significantly, notably in moderate and severe WDS conditions. The increased WDS levels reduced the photochemical efficiency indices (Fv/Fm and Fv/Fo) in −AMF plants, while AMF-complex application significantly augmented these parameters. Furthermore, the photosynthetic pigments content was substantially higher in +AMF seedlings than −AMF controls at all the WDS levels. Favorably, at 25% FC, AMF-colonized plants produce approximately twice as many carotenoids as non-colonized ones. In conclusion, AMF inoculation seems to be a powerful eco-engineering strategy for improving the caper seedling growth rate and drought tolerance in harsh environments. [ABSTRACT FROM AUTHOR]