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Arbuscular mycorrhizal (AM) fungi, Rhizobium bacteria and plant-growth-promoting rhizobacteria (PGPR) were isolated from a representative area of a desertified semi-arid ecosystem in the south-east of Spain. Microbial isolates were characterized and screened for effectiveness by a single-inoculation trial in soil microcosms. Anthyllis cytisoides L., a mycotrophic pioneer legume, dominant in the target mediterranean ecosystem, was the test plant. Several microbial cultures from existing collections were also included in the screening process. Two AM fungi (Glomus coronatum, native, and Glomus intraradices, exotic), two Rhizobium bacteria (NR4 and NR9, both native) and two PGPR (A2, native, and E, exotic) were selected. A further screening for the appropriate double and triple combinations of microbial inoculants was then performed. The parameters evaluated were biomass accumulation and allocation, N and P uptake, N-2-fixation (N-15) and specific root length. Overall, G. coronatum, native in the held site was more effective than the exotic G. intraradices in co-inoculation treatments. In general, our results support the importance of physiological and genetic adaptation of microbes to the whole environment, thus local isolates must be involved. Many microbial combinations were effective in improving either plant development, nutrient uptake, N-2-fixation or root system quality. Selective and specific functional compatibility relationships in plant response between the microbial inoculants, were observed. Despite the difficulty of selecting a multifunctional microbial inoculum, appropriate microbial combinations can be recommended for a given biotechnological input related to improvement of plant performance. This could be exploited in nursery production of target plant species endowed with optimized rhizosphere/mycorrhizosphere systems that can be tailored to help plants to establish and survive in nutrient-deficient, degraded habitats. The relevance of this microbial-based approach in the context of a reclamation strategy addressed to environmental sustainability purposes is discussed.