Citrus microbiota in the Canary Islands: How soil management shapes root endosphere and rhizosphere communities

A cover crop was introduced to an anthropogenic volcanic sorriba citrus orchard and monitored for three years. Soil chemical analyses, microbial activity, active microbial biomass, community level-physiological profiles (CLPP) and metabarcoding of bacteria and fungi were conducted. Compared to a tilled bare soil, the cover crop raised soil pH from 7.8 to 8.2, boosted soil organic carbon by 50% and lowered exchangeable calcium by 15% via organic-acid chelation and incorporation into microbial or organo-mineral pools. Soil of cover crops exhibited enhanced microbial activity and biomass, with 2- and 2.3-fold increases in basal and glucose-induced respiration, respectively. However, the metabolic quotient (qCO₂) showed a time-dependent response: it did not differ between treatments after two years, but increased under cover crops after three years, indicating a shift in respiratory allocation as cover-crop inputs accumulated. Multiple-substrate-induced respiration increased by 68%, amino-acid catabolism tripled and simple-carbohydrate use almost doubled, while high activity on α-cyclodextrin and syringic acid indicated enrichment of taxa able to mine mineral-protected organic carbon. The presence of cover crops increased the diversity and evenness of bacterial and fungal communities in the citrus roots and influenced bacterial structure in endosphere and rhizosphere, and fungal structure in rhizosphere. Specific taxa showed differential abundance by management. The cover crop microbial networks had more positive links and keystone taxa. Soil factors such as pH, phosphorous and electrical conductivity under cover crop influenced the bacterial and fungal community, respectively. These findings show that species-rich cover crops enhance chemical fertility and microbial functional breadth . They improved microbial diversity, network complexity and community structuring, offering a low-input path to greater resilience of Canary Islands citrus orchards.