Indigenous Microorganisms Offset Arbuscular Mycorrhizal Fungi-Induced Plant Growth and Nutrient Acquisition Through Negatively Modulating the Genes of Phosphorus Transport and Nitrogen Assimilation

Abstract

Arbuscular mycorrhizal (AM) fungi that promote plant growth and nutrient acquisition are essential for nutrient-deficient karst areas, while they inevitably regulate host plants jointly with indigenous microorganisms in natural soil. However, how indigenous microorganisms regulate AM-induced benefits on plant growth and nutrient acquisition remains unclear. In this study, the Bidens tripartita as the common plant species in the karst region was cultivated into three soil substrates treated by AM fungi inoculation (AMF), AM fungi inoculation combining with indigenous microorganisms (AMI), and the control without AM fungi and indigenous microorganisms (CK). The plant biomass and concentration of nitrogen (N) and phosphorus (P) were measured, and the transcriptomic analysis was carried out using root tissues. The results showed that AM fungi significantly enhanced the plant biomass, N, and P accumulation with the reduction of plants' N/P ratio; however, the indigenous microorganisms offset the AM-induced benefits in biomass and N and P acquisition. In addition, there are 819 genes in differentially expressed genes (DEGs) of AMF vs. AMI ∩ AMF vs. CK, meaning that AM fungi induced these genes that were simultaneously regulated by indigenous microorganisms. Furthermore, the enrichment analysis suggested that these genes were significantly associated with the metabolic processes of organophosphate, P, sulfur, N, and arginine biosynthesis. Notably, 34 and 17 genes of DEGs were related to P and N metabolism, respectively. Moreover, the indigenous microorganisms significantly downregulated these DEGs, especially those encoding the PHO1 P transporters and the glnA, glutamate dehydrogenase 2 (GDH2), and urease as key enzymes in N assimilation; however, the indigenous microorganisms significantly upregulated genes encoding PHO84 inducing cellular response to phosphate (Pi) starvation. These regulations indicated that indigenous microorganisms restrained the N and P metabolism induced by AM fungi. In conclusion, we suggested that indigenous microorganisms offset nutrient benefits of AM fungi for host plants through regulating these genes related to P transport and N assimilation.

Keywords: arbuscular mycorrhizal fungi; indigenous microorganisms; nitrogen assimilation; nutrients metabolism; phosphorus transport.

FIGURE 1

Nutrient acquisition of B. tripartita on nitrogen (N) (A) and phosphorus (P) (B); N/P ratio of B. tripartita seedlings (C). AMF = arbuscular mycorrhizal (AM) fungi inoculation treatment; AMI = AM fungi inoculation combining with indigenous microorganisms treatment; CK = the control without AM fungi and indigenous microorganisms. The different lowercase letters (a, b, and c) above the column indicate significant differences between AMF, AMI, and CK (P < 0.05). The dashed lines indicate the N/P ratio equal to 14 and equal to 16, respectively.

FIGURE 2

(A) The number of DEGs identified in the pairwise comparisons among the three treatments. The thresholds are q < 0.01 and |log₂⁡FoldChange| > 1. The red and blue columns indicate the numbers of upregulated and downregulated genes in the pairwise comparisons, respectively. (B) Venn diagram of the pairwise comparisons among the three treatments. AMF vs. AMI indicates that compared with the AMI, the genes upregulated or downregulated in the AMF; CK vs. AMI indicates that compared with the CK, the genes upregulated or downregulated in the AMI; CK vs. AMF indicates that compared with the CK, the genes upregulated or downregulated in the AMF.

FIGURE 3

Gene ontology (GO) enrichment analysis of the AM-induced genes regulated by indigenous microorganisms. The x-axis indicates various GO terms. The y-axis indicates the number of genes in GO terms. The color of column indicates the GO category to which GO term belongs.

FIGURE 4

The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the AM-induced genes upregulated (A) or downregulated (B) by indigenous microorganisms. The x-axis indicates the rich factors of pathways. The y-axis indicates various KEGG pathways. The size of the bubble indicates the number of genes enriched in this pathway. The color of the bubble indicates the significant degree of enrichment.

FIGURE 5

AM-induced genes regulated by indigenous microorganisms related to different categories. (A) AM-induced genes regulated by indigenous microorganisms related to P metabolism. (B) AM-induced genes regulated by indigenous microorganisms related to N metabolism. (C) AM-induced genes regulated by indigenous microorganisms related to amino acid metabolism. The horizontal axis represents the sample and the vertical axis represents the gene ID. The AMF, AMI, and CK mean the same as in Figure 1. Description and expression of genes related to different categories in AMF and AMI are listed in Supplementary Tables 3–5, respectively.