Intercropping with Potato-Onion Enhanced the Soil Microbial Diversity of Tomato

Abstract

Intercropping can achieve sustainable agricultural development by increasing plant diversity. In this study, we investigated the effects of tomato monoculture and tomato/potato-onion intercropping systems on tomato seedling growth and changes of soil microbial communities in greenhouse conditions. Results showed that the intercropping with potato-onion increased tomato seedling biomass. Compared with monoculture system, the alpha diversity of soil bacterial and fungal communities, beta diversity and abundance of bacterial community were increased in the intercropping system. Nevertheless, the beta-diversity and abundance of fungal community had no difference between the intercropping and monoculture systems. The relative abundances of some taxa (i.e., Acidobacteria-Subgroup-6, Arthrobacter, Bacillus, Pseudomonas) and several OTUs with the potential to promote plant growth were increased, while the relative abundances of some potential plant pathogens (i.e., Cladosporium) were decreased in the intercropping system. Redundancy analysis indicated that bacterial community structure was significantly influenced by soil organic carbon and pH, the fungal community structure was related to changes in soil organic carbon and available phosphorus. Overall, our results suggested that the tomato/potato-onion intercropping system altered soil microbial communities and improved the soil environment, which may be the main factor in promoting tomato growth.

Keywords: Illumina MiSeq sequencing; intercropping; potato-onion; soil microbial community; tomato.

Figure 1

Soil microbial abundances of bacteria (a) and fungi (b) in monoculture (M) and intercropping (I) systems. Different letters indicate significant differences (p < 0.05; Student’s t-test.).

Figure 2

Alpha diversity based on Illumina MiSeq sequencing of bacterial (a) and fungal (b) communities in tomato monoculture (M) and intercropping (I) systems. Operational taxonomic units (OTUs) were delineated at 97% sequence similarity. Different letters indicate significant differences (p < 0.05; Student’s t-test.).

Figure 3

Beta diversity of bacterial (a,c) and fungal (b,d) communities in the monoculture (M) and intercropping systems (I) based on Bray–Curtis distances at the OTU level. Different letters indicate significant differences (p < 0.05; Student’s t-test.).

Figure 4

Relative abundances of the main bacterial phyla and proteobacterial classes (a) and fungal phyla (b) and the top 20 classified bacterial genera (c) and fungal genera (d) in monoculture (M) and intercropping (I) systems. * represents significance (p < 0.05) between the soil samples from the monoculture and intercropping systems according to Student’s t-test.

Figure 5

Histogram of the linear discriminant analysis (LDA) scores computed for differentially abundant bacterial (a) and fungal (b) genera between the monoculture system (M) and intercropping system (I). The threshold employed on the logarithmic LDA score for discriminative features was 2.0.

Figure 6

Response ratio analysis of changes in the relative abundances of the top 20 classified bacterial OTUs (a) and fungal OTUs (b) in response to intercropping with potato-onion compared to the monoculture system at 95% confidence interval. Error bars plotted to the right of the dashed line indicate that the relative abundance increased, while those on the left side indicate that the relative abundance decreased.

Figure 7

Redundancy analysis (RDA) depicting the relationship between the bacterial (a) and fungal (b) communities and environmental variables in monoculture (M) and intercropping (I) systems.