Large amounts of chemical fertilizers are still used to suppress pathogens and boost agricultural productivity and food generation. However, their use can cause harmful environmental imbalance. Furthermore, plants typically absorb limited amounts of the nutrients provided by chemical fertilizers. Recent studies are recommending the use of microbiota present in the soil in different formulations, considering that several microorganisms are found in nature in association with plants in a symbiotic, antagonistic, or synergistic way. This ecological alternative is positive because no undesirable significant alterations occur in the environment while stimulating plant nutrition development and protection against damage caused by control pathogens. Therefore, this review presents a comprehensive discussion regarding endophytic and rhizospheric microorganisms and their interaction with plants, including signaling and bio-control processes concerning the plant's defense against pathogenic spread. A discussion is provided about the importance of these bioinputs as a microbial resource that promotes plant development and their sustainable protection methods aiming to increase resilience in the agricultural system. In modern agriculture, the manipulation of bioinputs through Rhizobium contributes to reducing the effects of greenhouse gases by managing nitrogen runoff and decreasing nitrous oxide. Additionally, mycorrhizal fungi extend their root systems, providing plants with greater access to water and nutrients.

Regenerative agriculture and the use of bioinputs have been gaining prominence in the global agribusiness sector, driven by the growing demand for healthier foods produced with minimal impact on ecosystems. In this context, compost and its derivatives (compost extracts and teas) are used to provide effective microorganisms to crops, although production processes affect the efficiency of compost extracts, as well as the soil microbiota. Thus, the hypothesis raised was that the organic matter source used for compost formation affects the agronomic efficiency of compost extracts. The objective of this study was to evaluate the effect of compost extracts based on litterfall of angiosperm (AC) and gymnosperm (GC) species, and the use of inoculation with the nitrogen-fixing bacteria Bradyrhizobium japonicum and Azospirillum brasilense (Bra+Azo), on soil quality, crop growth, grain yield, and disease control in soybean (Glycine max L.) crops. Using AC and GC resulted in varying effects on soybean growth and soil microbial biomass carbon (SMBC), confirming the hypothesis that the organic matter source affects the agronomic efficiency of compost extracts. Plants inoculated with Bra+Azo exhibited higher chlorophyll contents, resulting in a higher photochemical yield than for those treated with compost extracts (AC and GC). However, plants inoculated with AC and GC exhibited high plasticity in mitigating photochemical stress, reaching similar photosynthetic and transpiration rates to those observed in plants inoculated with Bra+Azo. Additionally, inoculation with Bra+Azo, overall, improved the photosynthetic efficiency of soybean plants, and the compost extracts (AC and GC) were more effective than the inoculation with Bra+Azo in increasing soybean 1000-grain weight, probably due to improvements in root development. The growth promotion observed with AC and GC is likely attributed to increases in SMBC by these compounds, denoting improvements in soil quality and biocontrol of damage caused by insect attacks.