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Molecular changes in the maize roots transcriptome due to soil microbes

ABSTRACT: The association between soil microbes and plant roots is present in all natural and agricultural environments. Microbes can be beneficial, pathogenic, or neutral to the host plant development and adaptation to abiotic or biotic stresses. Progress in investigating the functions and changes in microbial communities in diverse environments have been rapidly developing in recent years, but the changes in root function is still largely understudied. The aim of this study was to determine how soil bacteria influence maize root transcription and microRNAs (miRNAs) populations in a controlled inoculation of known microbes over a defined time course. At each time point after inoculation of the maize inbred line B73 with ten bacterial isolates, DNA and RNA were isolated from roots. The V4 region of the 16S rRNA gene was amplified from the DNA and sequenced with the Illumina MiSeq platform. Amplicon sequencing of the 16S rRNA gene indicated that most of the microbes successfully colonized maize roots. The colonization was dynamic over time and varied with the specific bacterial isolate. Small RNA sequencing and mRNA-Seq was done to capture changes in the root transcriptome from 0.5 to 480 hours after inoculation. The transcriptome and small RNA analyses revealed epigenetic and transcriptional changes in roots due to the microbial inoculation. This research provides the foundational data needed to understand how plant roots interact with bacterial partners and will be used to develop predictive models for root response to bacteria.

ORGANISM(S): Zea mays

PROVIDER: GSE214656 | GEO | 2023/05/01

REPOSITORIES: GEO

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Project description:BACKGROUND: The coevolution and interaction between plants and microorganisms have long been a subject of significant research interest. Dark septate endophytes (DSE) have garnered great attention in contemporary research due to their functional diversity, in vitro cultivation ability, and ability to establish symbiotic associations with host plants. In the present study, three DSE strains, namely Acrocalymma vagum, Zopfiella marina, and Phoma herbarum, which were obtained from the roots of Astragalus membranaceus, were introduced into maize plants through inoculation. We evaluated the effects of DSE inoculation on maize growth and root secretion activity through a multi omics methods, and proposed mechanisms for 'internal pathways' and 'external pathways'.RESULTS: The findings indicated that A. vagum exhibited superior growth-promoting ability on maize compared to Z. marina and P. herbarum.GO and KEGG enrichment analysis found that A. vagum inoculation resulted in significant enrichment of differentially expressed genes in annotation functions related to hormone regulation and lipid metabolism. A. vagum inoculation revealed that the gene pathways involved in plant hormone signaling and plant pathogen interactions play a crucial role in promoting host growth, and A. vagum inoculation group exhibited the highest number of differentially expressed genes, the most intricate protein-protein interaction (PPI) model, and the most pronounced relationship between differentially expressed genes. After the inoculation of A.vagum, the levels of salicylic acid, zeatin, and IAA in maize plants significantly increased. Additionally, the diversity and abundance of endophytic fungi, as well as the proportion of harmful bacteria and beneficial fungi, had significantly increased. Compared with Z. marina and P. herbarum, the net photosynthetic rate (Pn) and stomatal conductance (Gs) of A.vagum inoculated plants significantly increased. Inoculation with A.vagum could enhance the ability of corn roots to secrete lipids, sugars, and amino acids, resulted in a notable augmentation of beneficial bacteria and fungi, accompanied by a significant reduction in the proportion of harmful bacteria in the rhizosphere soil, such as Fusarium solani and Fusarium lacertarum, exhibited significant inhibition, whereas Bacillus niabensis and Bacillus nealsonii demonstrated enrichment trends. Soil pH, organic matter, available potassium content, acid phosphatase, alkaline phosphatase and urease activity exhibited significant increases following the inoculation of A. vagum. Variance decomposition and structural equation modeling (SEM) analysis indicated that the 'internal pathway', maize growth is mainly influenced by the interaction of endogenous hormones, endophytic microorganisms, and photosynthetic parameters, whereas within the 'external pathway', the interaction between soil microorganisms and soil physicochemical properties exerted a dominant influence. Compared with the Z. marina and P. herbarum inoculation, A. vagum inoculation showed a more significant impact on maize growth, both in terms of 'internal pathway' and 'external pathway', in terms of pathway level and quantity.CONCLUSIONS: These findings provide a new perspective for understanding the potential mechanisms of 'microbe-plant' interactions and also contribute to the exploration of targeted functional microorganisms that promote growth and stress resistance.

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Molecular changes in the maize roots transcriptome due to soil microbes

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