Siya Sharma, Bipin Kumar Sati, Durgesh Pant, Shakti Kumar, Subhajit Basu
ABSTRACT Hydroponics is emerging as a promising method of controlled‐environment agriculture (CEA), known for its high yields and efficient use of water through continuous recycling within the channels. In hydroponic systems, commercially grown crops in soilless substrates can be cultivated year‐round with optimised nutrient delivery under CEA conditions. Despite these advantages, the structure and function of rhizospheric microbiomes in hydroponics remain inadequately characterised, particularly regarding their roles in plant health and disease resistance. This review critically examines the development and composition of the hydroponic rhizosphere microbiome based on current literature, with a specific focus on the challenges posed by fungal phytopathogens. A meta‐analysis of rhizospheric microbiomes associated with hydroponically grown Lactuca sativa (lettuce), Solanum lycopersicum (tomato) and Allium schoenoprasum (chive) across various cultivation systems identified 99 distinct bacterial genera. These taxa were primarily affiliated with the phyla Pseudomonadota, Bacteroidota, Actinobacteriota and Verrucomicrobiota. Importantly, the core microbiome genera are significantly fewer compared to system‐specific genera. Microbiome composition is strongly influenced by crop species, hydroponic system architecture, fertigation regimes, substrate type and greenhouse environmental conditions. Pathogen intrusion, particularly by opportunistic fungi such as Fusarium spp. and oomycetes such as Pythium and Phytophthora spp., was frequently associated with major disruptions to native microbiota, occasionally resulting in increased alpha‐diversity. This paradox suggests a transition towards rhizosphere dysbiosis rather than a stable microbial equilibrium. These observations underscore the need for targeted microbiome management strategies that account for ecological specificity and functional redundancy.