Perception of beneficial microbes and pathogens, and their associated molecular patterns (bMAMP, PAMP) leads to changes in cytosolic calcium concentration ([Ca2+]cyt). The model plant Arabidopsis thaliana, expressing the bioluminescent Ca2+ reporter apoaequorin in the cytosol, was used to elucidate the role of cytosolic Ca2+ signaling in the beneficial (A. thaliana-P. indica) and pathogenic (A. thaliana-Alternaria brassicae) interactions. The biomolecule from P. indica-cell wall extract (Pi-CWE), which induces [Ca2+]cyt elevation in roots and stimulates the growth of Arabidopsis seedlings, was purified as a trisaccharide (Pi-504). The mutation is allelic and located in chromosome 1. Screening of EMS mutagenised aequorin populations resulted in the isolation of Pi-CYCAM mutants which do not induce [Ca2+]cyt elevation to Pi-504. The Pi-504- and the fungus- induced growth promotion is linked to enhanced nitrogen metabolism and phosphate uptake, and increased photosynthetic efficiency. The CYCAM mutants do not respond to exudate preparations from another endophytic beneficial fungus Acremonium alternatum, and pathogenic fungi e.g. A. brassicae, R. solani and F. solani; and the oomycete P. parasitica, but it responded to the CWE from Mortierella hyalina (Mh-CWE) and its biomolecule was purified as Mh-222. The cycam mutant is highly sensitive to abiotic (salt, water, drought) and biotic oxidative stress. The mutant contains increased levels of ABA, SA, JA and reactive oxygen species (ROS) upon A. brassicae infection. The evolutionarily conserved redox responsive transcription factor1 (RRTF1) amplifies ROS production. A. brassicae infection stimulates RRTF1 and represses ROS scavenging genes, while P. indica represses RRTF1 and activates ROS scavenging enzymes. Camalexin and indolic glucosinolates are important for the beneficial interaction between P. indica and A. thaliana. Furthermore, P. indica-derived auxin is not required for the growth response in Arabidopsis.