Fungal Endophytes Are Associated with Improved Salinity Responses Across Quinoa Ecotypes

Soil salinity is a major constraint on global crop productivity, highlighting the importance of strategies to enhance plant stress tolerance. This study investigated whether root-associated fungal endophytes derived from a salt-tolerant quinoa ecotype could establish associations with a salt-sensitive ecotype and confer systemic physiological and molecular stress-mitigation responses. Fungal endophytes—two Alternaria spp. and one Setophoma sp.—were isolated from roots of Pandela (salt-tolerant genotype) and inoculated BO75 (salt-sensitive ecotype) under severe salt stress (400 mM NaCl). Physiological (potential photochemical efficiency, survival), biochemical (malondialdehyde, proline), molecular (expression of ion transporter genes CqSOS1 and CqNHX1), and elemental (Na+, K+, Cl− distribution by μ-XRF) responses were evaluated. In the salt-sensitive BO75 genotype, endophyte inoculation was associated with improved stress performance, evidenced by reduced oxidative damage (lower MDA), higher proline accumulation, and enhanced photochemical efficiency. Furthermore, the reduced expression of CqSOS1 and CqNHX1 suggests an improved ionic balance in inoculated plants. Conversely, re-inoculating Pandela yielded negligible effects, suggesting that these endophytes primarily benefit genotypes lacking inherent salt tolerance. These findings indicate that transferring fungal endophytes from halophytic ecotypes can significantly mitigate stress in sensitive genotypes, highlighting their potential for enhancing crop resilience in saline environments.