Rotation and organic fertilization alleviate soil microbial phosphorus limitation and improve soil health and productivity in a continuous cropping pineapple orchard

Long-term pineapple monoculture severely degrades soil in tropical regions, necessitating sustainable remediation strategies. This study evaluated the effectiveness of crop rotation and organic fertilization in improving soil health and productivity through a field experiment in a decade-long continuously cropped pineapple orchard, with four treatments: continuous pineapple (PP, control); PP with 30 % organic fertilizer substitution (OP); Alpinia officinarum– pineapple rotation (GP); banana–pineapple rotation (BP). Soil health was evaluated using three metrics: the soil quality index (SQI) derived from conventional biochemical indicators, and soil multifunctionality (SMF) based on seven enzymatic activities, and microbial community structure via phospholipid fatty acid (PLFA) profiling. Microbial metabolic limitation was determined via extracellular enzyme stoichiometry. Compared to PP, both remediation strategies significantly alleviated microbial phosphorus (P) limitation, increasing EEA N:P by 12.4 16.6 % and reducing the vector angle by 20.1 27.7 %. Consequently, they enhanced microbial abundance (PLFA increased 30.9–84.1 %) and diversity, with increases in SQI (21.2 47.4 %), SMF (26.8 45.7 %), and pineapple yield (9.3 25.5 %). Crop rotation, particularly BP, consistently outperformed organic fertilization across these metrics—e.g., BP rotation increased total PLFA by 84.1 %, markedly exceeding the 30.9 % increase under OP. Structural equation modeling (SEM) analysis confirmed a critical pathway whereby P limitation alleviation enhanced microbial abundance and SMF, directly boosting yield. Thus, while both strategies were beneficial, crop rotation was superior, with BP most improving soil health and productivity. These findings inform sustainable tropical agriculture and soil health indicator selection. • Rotation or organic fertilization alleviate soil microbial P limitation. • Rotation or organic fertilization enhance soil health and productivity. • BP shows the most significant effects in improving soil health & productivity. • Alleviation of microbial P limitation is vital for soil health & productivity.