Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants

Aims: We examined the effect of downregulating PdKOR1 gene, an endo-β-1,4-glucanase gene family member previously characterized to affect cellulose biosynthesis and cell wall composition in Populus, on the secondary metabolome and microbiome of field-grown Populus deltoides. Methods: We revealed differences in metabolite profiles of PdKOR1 RNAi and control roots using gas chromatography-mass spectrometry, and microbiome identification via Illumina MiSeq 16S and ITS2 rRNA sequencing in root endospheres and rhizospheres. Results: PdKOR1 RNAi root metabolites differed from control plants: free amino acids (valine, isoleucine, alanine) were reduced while caffeoyl-shikimates, salicylic-acid derivatives, and flavonoid metabolites increased in PdKOR1 RNAi roots. The Actinobacterial family Micromonosporaceae were more abundant in RNAi root endospheres, whereas Nitrospirae was reduced in PdKOR1 RNAi rhizospheres. Ascomycota were lower and Basidiomycota greater in PdKOR1 rhizospheres. Bacterial and fungal community composition, as measured by Bray-Curtis dissimilarity, differed between PdKOR1 RNAi and control rhizospheres and endospheres. Conclusions: These results indicate that modification of plant cell walls via downregulation of PdKOR1 gene in Populus impacts carbon metabolism in roots and concomitant alterations in root-associated microbial communities. Such an understanding of functional and ecological implications of biomass chemistry improvement efforts is critical to address the goals of sustainable bioenergy crop production and management.