Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant–Bacteria Interactions
Abstract
:1. Introduction
2. Results
2.1. Transcriptome Sequencing—An Overview
2.2. Transcriptome Analyses—An Overview
2.3. Transcriptome Analyses—Functional Genes Associated with Plant—Bacteria Interaction
2.3.1. Bacterial Initial Contact with Plants
2.3.2. Plant Growth-Promoting Genes
2.3.3. Secondary Metabolite Biosynthesis Gene Clusters
2.3.4. Defence and Stress Response Mechanisms Utilised by Barley Seedlings
2.3.5. Differentially Expressed Barley Transcripts Associated with Signal Transduction and Ethylene Biosynthesis
2.3.6. Differentially Expressed Barley Transcripts Associated with Nutrient Uptake and Metabolism
3. Discussion
3.1. Dual RNA-seq Analyses of Bacterial Strains and Barley Seedling Roots
3.2. Initial Contact Between Bacteria and Plants—Chemotaxis, Biofilm Formation and Plants’ Defence and Stress Response
3.3. Interactions between Bacteria and Plants—Plant Growth-Promoting Genes, Plant Nutrient Uptake and Metabolism, Signal Transduction and Ethylene Biosynthesis
3.4. Bacterial Secondary Metabolite
3.5. Specific Responses Associated with Bacterial Strains and Bacteria/Plant Species, and Their Implications for Enhanced Plant—Bacteria Interactions
4. Conclusions
5. Materials and Methods
5.1. Assay Design
5.2. Transcriptome Sequencing
5.3. Transcriptome Analyses
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample | Treatment | Medium | No. of Genes Passed the Abundance Filter | No. of Differentially Expressed Genes | |
---|---|---|---|---|---|
Bacteria | AR | Barley seedling | Nutrient Broth | 4009 | 1380 |
S25 | 5013 | 2945 | |||
S02 | 5266 | 2890 | |||
Burk’s N-free | 5032 | 2524 | |||
Plant | Barley seedling | AR | Nutrient Broth | 37,073 | 13,948 |
S25 | 35,365 | 13,648 | |||
S02 | 34,798 | 9129 | |||
Burk’s N-free | 31,502 | 10,806 |
Strain ID | Genome Size (bp) | No. of Genes |
---|---|---|
S02 (Paenibacillus sp.) | 6,060,529 | 5436 |
S25 (Paenibacillus sp.) | 5,958,851 | 5306 |
AR (Erwinia gerundensis) | 4,437,426 | 4091 |
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Li, T.; Mann, R.; Kaur, J.; Spangenberg, G.; Sawbridge, T. Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant–Bacteria Interactions. Plants 2021, 10, 1802. https://doi.org/10.3390/plants10091802
Li T, Mann R, Kaur J, Spangenberg G, Sawbridge T. Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant–Bacteria Interactions. Plants. 2021; 10(9):1802. https://doi.org/10.3390/plants10091802
Chicago/Turabian StyleLi, Tongda, Ross Mann, Jatinder Kaur, German Spangenberg, and Timothy Sawbridge. 2021. "Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant–Bacteria Interactions" Plants 10, no. 9: 1802. https://doi.org/10.3390/plants10091802