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. 2025 Mar 12:16:1554644.
doi: 10.3389/fmicb.2025.1554644. eCollection 2025.

Root separation modulates AMF diversity and composition in tomato-potato onion intercropping systems

Musawar Ibrahim #  1 , Asad Ullah #  1 , Xinjie Pan  1 , Jianzeng Lu  1 , Musaddiq Ibrahim  2   3 , Kunpeng Cao  1 , Shouwei Liu  1 , Xingang Zhou  1 , Fengzhi Wu  1 , Danmei Gao  1
Affiliations

Root separation modulates AMF diversity and composition in tomato-potato onion intercropping systems

Musawar Ibrahim et al. Front Microbiol. .

Abstract

Plant-plant interactions shape arbuscular mycorrhizal fungi (AMF) communities in rhizosphere soil, with tomato/potato-onion intercropping emerging as a promising agro-ecological strategy to optimize resource utilization. However, the role of root separation methods in modulating AMF diversity within intercropping systems remains unclear. Specifically, whether the AMF community in the rhizosphere of tomato and potato-onion intercropping differs from monoculture and how root separation methods modulate these effects. This study evaluates the effects of various root separation methods (no separation, 0.45 μm nylon membrane, 38 μm nylon membrane, and solid separation) on AMF diversity and composition in tomato/potato-onion intercropping and monoculture systems. High-throughput Illumina MiSeq sequencing was used to assess AMF diversity indices (Ace, Chao1, Shannon, and Simpson), and Principal Coordinate Analysis evaluated community structure. Results showed that the non-separation mode achieved the highest Ace and Chao1 indices, indicating greater richness, while intercropping lowered Shannon and Simpson indices. Intercropping significantly reduced Glomerales but increased Paraglomerales, under the non-separation mode. Similarly, it decreased Glomus while increasing Paraglomus in the rhizosphere of both crops. Principal Coordinate Analysis revealed that root separation distinctly altered AMF community structure, reflecting specific barrier effects on AMF interactions. Intercropping increased AMF abundance in the tomato rhizosphere but reduced it in potato-onion as shown by 18S rRNA gene abundance. These findings emphasize that minimizing root separation in intercropping enhances AMF diversity and functionality, providing valuable insights for sustainable agricultural management. Understanding the role of root interactions in shaping AMF communities can help optimizing intercropping strategies to improve soil health and nutrient dynamics.

Keywords: AMF; CMNs; intercropping; plant-plant interaction; root barrier; soil microbial community.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Schematic diagram of experimental design in different barrier treatments. (A) No barrier (C); (B) 0.45 μm nylon mesh barrier (M); (C) 38 μm nylon mesh barrier (N); (D) Solid barrier (S).
FIGURE 2
FIGURE 2
Experimental workflow for the methodology of AMF (Arbuscular Mycorrhizal Fungi) research.
FIGURE 3
FIGURE 3
Effects of different root separation methods on the relative abundance of AMF community under order and genus levels in the rhizosphere of mono- and intercropping systems. C, M, N, S represent no separation treatment; 0.45 μm nylon membrane separation treatment; 38 μm nylon membrane separation treatment; solid separation treatment, respectively. O, OT, T, TO: monocropped potato-onion treatment; intercropped potato-onion treatment; monocropped tomato treatment; intercropped tomato treatment, respectively (P < 0.05).
FIGURE 4
FIGURE 4
Effects of different root separation methods on the relative abundance of AMF dominant orders in the rhizosphere of mono-and intercropping systems. Panels (A–D) represent the relative abundance of Archeosporales, Paraglomales, Glomerales, and Diversisporales, respectively. C, M, N, S represent no separation treatment; 0.45 μm nylon membrane separation treatment; 38 μm nylon membrane separation treatment; solid separation treatment, respectively. O, OT, T, TO: monocropped potato-onion treatment; intercropped potato-onion treatment; monocropped tomato treatment; intercropped tomato treatment, respectively. Lowercase letters indicate the significant difference between different planting patterns under the same separation method (P < 0.05).
FIGURE 5
FIGURE 5
Effects of different root system separation methods on the relative abundance of dominant genera in the rhizosphere of mono-and intercropping systems. Panels (A–E) represent the relative abundance of Paraglomus, Ambispora, Archaeospora, Glomus and Diversispora respectively. C, M, N, S represent no separation treatment; 0.45 μm nylon membrane separation treatment; 38 μm nylon membrane separation treatment; Solid separation treatment, respectively. O, OT, T, TO: monocropped potato-onion treatment; intercropped potato-onion treatment; monocropped tomato treatment; intercropped tomato treatment, respectively. Lowercase letters indicate the significant difference between different planting patterns under the same separation method (P < 0.05).
FIGURE 6
FIGURE 6
Indicator genera of AMF based on IndVal analysis. Genera with an indicator value > 0.4 and p < 0.05 were identified as indicators. The heatmap shows the relative abundances of these AMF taxa in different treatments: no separation (C), 0.45 μm nylon mesh (M), 38 μm nylon mesh (N), and solid barrier (S).
FIGURE 7
FIGURE 7
Effects of different root separation modes on the a-diversity index of rhizosphere AMF communities in mono-and intercropping systems. Panels (A–D) represent the relative abundance of Ace, Chao, Shannon, and Simpson respectively. C, M, N, S represent no separation treatment; 0.45 μm nylon membrane separation treatment; 38 μm nylon membrane separation treatment; Solid separation treatment, respectively. O, OT, T, TO: monocropped potato-onion treatment; intercropped potato-onion treatment; monocropped tomato treatment; intercropped tomato treatment, respectively. Lowercase letters indicate the significant difference between different planting patterns under the same separation method (P < 0.05).
FIGURE 8
FIGURE 8
PCoA analysis of AMF community structure in the rhizosphere of mono- and intercropping tomato/potato-onion under different root separation methods. C, M, N, S represent no separation treatment; 0.45 μm nylon membrane separation treatment; 38 μm nylon membrane separation treatment; Solid separation treatment, respectively. O, OT, T, TO: monocropped potato-onion treatment; intercropped potato-onion treatment; monocropped tomato treatment; intercropped tomato treatment, respectively (P < 0.05).
FIGURE 9
FIGURE 9
Effects of different root system separation methods on the abundance of AMF communities in the rhizosphere of mono-and intercropping systems. C, M, N, S represent no separation treatment; 0.45 μm nylon membrane separation treatment; 38 μm nylon membrane separation treatment; Solid separation treatment, respectively. O, OT, T, TO: monocropped potato-onion treatment; intercropped potato-onion treatment; monocropped tomato treatment; intercropped tomato treatment, respectively. Lowercase letters indicate the significant difference between different planting patterns under the same separation method (P < 0.05).
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