Microbiome Differences in Sugarcane and Metabolically Engineered Oilcane Accessions and Their Implications for Bioenergy Production

Themes: Feedstock Production, Sustainability

Keywords: Biomass Analytics, Metabolomics

Citation

Yang, J., Sooksa-nguan, T., Kannan, B., Cano-Alfanar, S., Liu, H., Kent, A., Shanklin, J., Altpeter, F., Howe, A. March 30, 2023. Data from: “Microbiome Differences in Sugarcane and Metabolically Engineered Oilcane Accessions and Their Implications for Bioenergy Production.” NIH – BioProject. DOI: 10.1186/s13068-023-02302-6.

Overview

Hierarchical clustering heatmap of Bray–Curtis distance dissimilarity in the bacterial microbiomes. A leaf, B root, and C rhizosphere microbial community composition. The red color indicates a high dissimilarity. Letters *** on the dendrograms denote significant differences in Bray–Curtis dissimilarity indices between accessions at a p-value < 0.05 as assessed by hierarchical agglomerative clustering using Ward’s minimum variance method (Ward.D2) with 10,000 bootstrap resampling. WT and 17 T, 1565, 1566, and 1569 represent the wild-type sugarcane and different oilcane accessions, respectively.

Oilcane is a metabolically engineered sugarcane (Saccharum spp. hybrid) that hyper-accumulates lipids in its vegetable biomass to provide an advanced feedstock for biodiesel production. The potential impact of hyper-accumulation of lipids in vegetable biomass on microbiomes and the consequences of altered microbiomes on plant growth and lipid accumulation have not been explored so far. Here, we explore differences in the microbiome structure of different oilcane accessions and non-modified sugarcane. 16S SSU rRNA and ITS rRNA amplicon sequencing were performed to compare the characteristics of the microbiome structure from different plant compartments (leaf, stem, root, rhizosphere, and bulk soil) of four greenhouse-grown oilcane accessions and non-modified sugarcane. Significant differences were only observed in the bacterial microbiomes. In leaf and stem microbiomes, more than 90% of the entire microbiome of non-modified sugarcane and oilcane was dominated by similar core taxa. Taxa associated with Proteobacteria led to differences in the non-modified sugarcane and oilcane microbiome structure. While differences were observed between multiple accessions, accession 1566 was notable in that it was consistently observed to differ in its microbial membership than other accessions and had the lowest abundance of taxa associated with plant-growth-promoting bacteria. Accession 1566 is also unique among oilcane accessions in that it has the highest constitutive expression of the WRI1 transgene. The WRI1 transcription factor is known to contribute to significant changes in the global gene expression profile, impacting plant fatty acid biosynthesis and photomorphogenesis. This study reveals for the first time that genetically modified oilcanes associate with distinct microbiomes. Our findings suggest potential relationships between core taxa, biomass yield, and TAG in oilcane accessions and support further research on the relationship between plant genotypes and their microbiomes.

Data

NIH – BioProject: Includes sequence data, BioSample

Download (5.5 KB) includes:

    • Taxa Relative Abundance
    • PERMANOVA
    • Expression Analysis

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