Compost and vegetation cover drive soil fertility, microbial activity, and community in organic farming soils

Aims Organic amendments and vegetation cover enhance soil health, biodiversity, and resilience in organic farming. However, their differential effects on microbial biomass, activity, and community structure vary, requiring tailored management. This study examines compost and vegetation interactive effects on soil quality, fertility, and microbes over short (4 months) and medium (12 months) periods, evaluating their combined impact over time. Methods A pot experiment was conducted using soil from an organic olive farm. A 2 × 3 factorial design was applied to 36 pots, testing for interactive effects between two factors: (1) compost application (~ 50 t ha −1 ), and (2) three vegetation covers: Herbaceous, Herbaceous + shrub, and Natural. Soil properties, microbial biomass, enzyme activity, and community structure were measured at both times. Results Compost significantly increased total carbon, nitrogen, phosphorus, potassium, and microbial biomass, with stronger effects after 12 months. Initially, it reduced dehydrogenase and β-glucosidase activity (by 50% and 20%), though this effect lessened over time. Compost enhanced bacterial diversity and evenness but slightly reduced fungal diversity and markedly decreased arbuscular mycorrhizal fungi richness. Compost-amended soils had higher plant pathogen abundance, likely due to pre-existing populations. Vegetation cover had a smaller effect but influenced fungal community composition, with spontaneous vegetation promoting saprotrophic and mycoparasitic fungi. Conclusions Compost and vegetation cover combined application did not consistently produce synergistic or non-additive effects across all evaluated parameters. Alone, compost presented the highest impact on soil properties highlighting the need to monitor biological quality of amendments, while vegetation cover presented moderately effects mainly on fungi. These results stress integrated management that balances benefits and potential microbial trade-offs in organic farming.