Intercropping is considered to be an environmentally friendly cropping system that can improve crop yield as well as water and nutrient-use efficiency32,33. Crops have different needs, so it is especially important to combine them in the right way to obtain yield improvements. As far as we know, the melon-cowpea intercropping system has not been studied in depth, nor have intercropping patterns between these two crops. However, this combination could be an important choice for sustainable agriculture management, given that cowpea is a legume, which fixes atmospheric nitrogen and thus supplies it to companion plants like watermelon or melon that at the same time provide soil shading to conserve water moisture34.
The intercropping system assayed was found to increase melon yield and the number of melons produced compared to melon monocrops starting from the first year of experimentation. Moreover, the intercrops used 30% less fertilization than the monocrop. This increase in melon yield could be due to a higher nitrogen disposal from cowpea rhizosphere, which, it is should be higher in soils with low N fertilization addition35. This fact has previously been observed in other cowpea intercrop relationships, such as cowpea-maize36, cowpea-sorghum37 and cowpea-cassava38. The cropping patterns and N fertilization rates can alter soil conditions, which subsequently influence the abundance of functional N-cycling genes39. In our study, we also observed a decreasing trend in nitrification and denitrification processes in the three intercropped systems compared to the monocrops. This decrease in the intercropping systems could allow for sustainable nutrient use, diminishing nitrate losses due to leaching and N oxide emissions40.
In general, legume crops included in intercropping systems improve P availability and soil organic carbon41, mostly through root exudates, nodules, and the sloughing off of root cells and root turnover during the growing season42. Roots excrete larger amounts of protons and carboxylates (malonate, malate, and citrate), which would facilitate root-borne phosphatases to hydrolyze organic P43. This could be supported by a high abundance of phosphate-solubilizing bacteria like Pseudomonas, which are more abundant in intercropped soils, as observed previously by44, that correlated with available P, TN and melon yield. Moreover, the presence of several phosphate-solubilizing bacteria like Bacillus in both the monocrops and intercropping systems could also influence in this behavior, as has been observed by Chen et al. (2006)45 and Panhwar et al. (2014)46.
It is important to note that soil microbial community composition is significantly correlated with changes in soil chemical properties47,48. In this study, the TN, available Na and P content, as AmoA abundance and melon crop yield play important roles in changes in the microbial community structure. Our findings could indicate that nutrient changes subsequently affect the carbon- and nitrogen-use efficiency of bacteria. Generally, an increase in soil microbial diversity is beneficial to soil function and health, but no differences were detected through diversity or richness estimators, indicating that our hypothesis was not validated. Until now, there is no consensus about changes in alpha diversity caused by intercropping systems, since some researchers have reported that some intercropping systems can increase diversity 1,49, while others have reported no significant changes 50,51.
On the other hand, we found significant differences in the bacterial community structure between intercropping and monocrop systems, although not between the different intercropping patterns. These differences showed the influence of cowpea on the bacterial structure of the melon crop, suggesting that cowpea could play an important role in maintaining agricultural ecosystem stability and improving crop growth52. The dominant taxonomic groups identified in the soils assayed were Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes, Gemmatimonadetes, Planctomycetes, Chloroflexi, Bacteroidetes and Nitrospirae, all depicted as common inhabitants of soil53. A higher relative abundance of Proteobacteria and Bacteriodetes and lower abundance of Actinobacteria in the intercropping systems than in the monocrop systems indicated that both plant species and planting patterns can change the abundance of dominant bacterial phyla50,54,55. Moreover, several plant beneficial microorganisms, identified as Pseudomonas, were higher in the intercropped soils, as were Bacillus, Streptomyces and Sphingomonas56,57.
LEfSe analysis indicated which microorganisms are significantly associated with the different cropping systems. The highest bacterial identified in the melon monocrop including Blastococcus, Geodermatophilus, Kineococcus, Actinoplanes, Kribella or Gemmatimonas. All of which have been reported as drought-resistant microorganisms 58,59. On the other hand, only five bacteria were associated with the intercropping system, which indicates that changes are occurring. Moreover, these changes do not depend too much on the specific intercropping pattern. The fact that these bacteria did not have a greater abundance than in the monocrops is likely due to the high resilience of bacterial community to changes60. These results indicate that one year of intercropping, which has been studied here, is not enough to result in a significant amount of associated microorganisms. It would be expected that repetitive intercropping in the same soils would increase a different microbial pattern.