Transcriptome analysis of the growth-promoting effect of volatile organic compounds produced by Microbacterium aurantiacum GX14001 on tobacco (Nicotiana benthamiana)

Abstract

Background: Plant growth-promoting rhizobacteria (PGPR) release volatile organic compounds (VOCs), which promote plant growth.

Results: A potential PGPR strain GX14001 was isolated from marine samples, and the VOCs produced by GX14001 significantly promoted tobacco (Nicotiana benthamiana) growth in a plate experiment. Based on 16S rRNA sequence alignment and physiological and biochemical characterization, GX14001 was identified as Microbacterium aurantiacum. Comparative transcriptome analysis was conducted between GX14001 VOCs-treated tobacco and the control; it was found that 1286 genes were upregulated and 1088 genes were downregulated. Gene ontology (GO) analysis showed that upregulated genes were involved in three biological processes: polysaccharide metabolic, polysaccharide catabolic and carbohydrate metabolic. The downregulated genes were involved in six biological processes, namely cell redox homeostasis, cellular homeostasis, carbohydrate metabolic process, homeostatic process, obsolete electron transport, and regulation of biological quality. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that 190 upregulated differentially expressed genes were mainly involved in plant hormone signal transduction, phenylpropyl biosynthesis, plant-pathogen interaction, and flavonoid biosynthesis. The 148 downregulated differentially expressed genes were mainly involved in plant hormone signal transduction and the metabolism of ascorbic, aldehyde, and pyruvate acids. Further analysis revealed that many genes were differentially expressed in the metabolic pathways of plant hormone signals, which were speculated to be the main reason why GX14001 VOCs promoted tobacco growth. To further study its regulatory mechanism, we found that GX14001 promoted plant growth through auxin, salicylic acid, and gibberellin in Arabidopsis mutant experiments.

Conclusion: The VOCs produced by Microbacterium aurantiacum GX14001 may promote the growth of tobacco through the auxin, salicylic acid and gibberellin pathways.

Keywords: Plant growth promoting rhizobacteria (PGPR); Plant growth promotion; Promotional mechanisms; Transcriptome analysis; Volatile organic compounds (VOCs).

Fig. 1

A The I-plate was used to co-culture tobacco seedlings and sterile water culture without physical contact; B The I-plate was used to co-culture tobacco seedlings and Microbacterium aurantiacum culture without physical contact; C Growth promoting effect of GX14001-VOCs on tobacco. CK was non-treated with bacteria and GX14001 was bacterial-treated with GX14001-VOCs. "*" refers to significant difference between treatments, P < 0.05, "**" refers to P < 0.01. The unit of leaf length and width and root length is cm; the unit of fresh weight is g; the unit of lateral root number is number

Fig. 2

The Neighbor-Joining tree based on the 16S rRNA gene sequences showing the phylogenetic relationship of GX14001 with related taxa. The evolutionary distances were computed using the p-distance method and are in the units of the number of base differences per site. The sequence of Agrococcus jenensis DAM9580^T (X92492) was used as an outgroup. Bootstrap support values were calculated from 1000 replicates and only values above 50% are shown. Bar, 0.005 substitutions per nucleotide position. Evolutionary analyses were conducted in MEGA6 [23]

Fig. 3

A Differential gene expression profile; “N” was treatment group, “CK” was control group. B Results of gene function annotation

Fig. 4

A Enrichment Column Diagram of Differential Gene GO; B Enrichment Column Diagram of Up-regulated Gene GO; C Enrichment Column Diagram of Down-regulated Gene GO. “N” was treatment group, “CK” was control group. BP: biological processes, CC: cellular components, MF: molecular function

Fig. 5

A KEGG pathway up-regulated gene top20 enrichment scatter plot; B KEGG pathway down-regulated gene top20 enrichment scatter plot; C KEGG pathway differential gene enrichment scatter plot

Fig. 6

Relative expression levels are shown as induction fold in GX14001-VOCs treatment compared with control. Error bars represent standard deviation from triplicate repeats. XM_009780502, auxin response factor 5, ARF5; XM_019383693, ethylene-responsive transcription factor 1B-like, ERF1; XM_019391388, Nicotiana attenuata protein gene, TIFY-10A; KP941063, Auxin responsive gene, GH3.6; XM_019398799, Nicotiana attenuata regulatory protein gene, NPR5; XM_019386038, Nicotiana attenuata auxin-responsive protein gene, SAUR50; OIT03335, auxin-responsive protein gene, SAUR32; XM_016628419, Nicotiana tabacum histidine protein kinase gene, HPK3; XM_016639077, XM_019410474, XM_016604946, Nicotiana tabacum auxin-induced protein gene, AIP5.

Fig. 7

Plant hormone signal transduction pathways. The colors in the figure represent differentially significant genes. Red shows genes that are significantly upregulated. Green shows genes that are significantly downregulated. Blue indicates that there are both significantly up-regulated and down-regulated genes

Fig. 8

A Growth-promoting effect of strain GX14001 on wild A. thaliana; B Growth-promoting effect of strain GX14001 on etr1 mutant; C Growth-promoting effect of strain GX14001 on arf1 mutant; D Growth-promoting effect of strain GX14001 on npr1 mutant; E Growth-promoting effect of strain GX14001 on gai1 mutant. "*" refers to significant difference between treatments, P < 0.05, "**" refers to P < 0.01. The unit of leaf length and width and root length is cm; the unit of fresh weight is g