Diversity and Co-occurrence Patterns of Soil Bacterial and Fungal Communities in Seven Intercropping Systems

Abstract

Intercropping plays a vital role in greenhouse production, and affects soil physicochemical properties and soil microbial communities structure, but influences of intercropping on the relationship of microorganisms are reported in continuous cropping soil rarely. Here, we investigated the effects of seven intercropping systems [alfalfa (Medicago sativa L.)/cucumber, trifolium (Trifolium repens L.)/cucumber, wheat (Triticum aestivum L.)/cucumber, rye (Secale cereale L.)/cucumber, chrysanthemum (Chrysanthemum coronrium L.)/cucumber, rape (Brassica campestris L.)/cucumber, mustard (Brassica juncea L.)/cucumber] on soil bacterial and fungal communities compared to the cucumber continuous cropping system in the greenhouse. The results showed that intercropping increased microbial OTU richness and fungal communities diversity, soil bacterial communities diversity was abundant in the trifolium-cucumber and mustard-cucumber systems. Nevertheless, there was no significant differences of microbial communities structure between intercropping and monoculture systems. Redundancy analysis indicated that soil microbial communities composition was indirectly influenced by soil properties. In addition, network analysis demonstrated that simple inter-relationships of fungal taxa were observed in the intercropping soil, and trifolium, wheat, and mustard intercropping systems had a complex connection between bacterial taxa. Taken together, trifolium and mustard as the intercrops significantly increased cucumber continuous cropping soil bacterial and fungal communities diversity. Moreover, intercropping strongly changed the relationships of microbial taxa, though did not shape notably soil microbial communities structure.

Keywords: bacteria; co-occurrence networks; fungi; intercropping; soil microbe.

Figure 1

The abundances of bacterial 16S rRNA gene (A) and fungal ITS gene (B) under different treatments in the spring (S) and fall (F) cropping seasons. Data with different letters in each column indicate significantly different between treatments at 0.05 level.

Figure 2

Changes in the relative abundances of bacterial and fungal phyla under different treatments in the spring (S) and fall (F) cropping seasons. Others includes phyla below 0.1% of relative abundance and the unclassified phyla.

Figure 3

Heatmap of top 50 genera of soil bacterial and fungal communities in the spring (S) and fall (F) cropping seasons. Legends showed the Z-scores, demonstrating all samples were represented by the median-centered Z-scores as the relative abundance levels.

Figure 4

Nonmetric multidimensional scaling (NMDS) based on euclidean distance plot of all soil bacterial and fungal communities in the spring (S) and fall (F) cropping seasons.

Figure 5

Redundancy analysis (RDA) demonstrating the relationships between soil environmental factors and soil microbial communities during spring (S) and fall (F) cropping seasons in the control (CM), alfalfa (A), trifolium (T), wheat (W), chrysanthemum (C), rye (Ry), mustard (M), and rape (Ra). *P < 0.05, **P < 0.01, ***P < 0.001.

Figure 6

Network of co-occurring bacterial genera based on correlation analysis for intercropping cultivations and cucumber monoculture. A connection stands for a strong (Spearman's ρ > 0.6) and significant (P < 0.01) correlation. The size of each node is proportional to the degree, the thickness of each edge is proportional to the value of Spearman's correlation coefficients. Nodes colored by taxonomy.

Figure 7

Network of co-occurring fungal genera based on correlations analysis for intercropping cultivations and cucumber monoculture. A connection stands for a strong (Spearman's ρ > 0.6) and significant (P < 0.01) correlation. The size of each node is proportional to the degree, the thickness of each edge is proportional to the value of Spearman's correlation coefficients. Nodes colored by taxonomy.