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

Abstract

Here, 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. 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. 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. In conclusion, 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.

Authors:
; ; ; ; ; ; ; ORCiD logo;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1440261
Alternate Identifier(s):
OSTI ID: 1462903
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Published Article
Journal Name:
Plant and Soil
Additional Journal Information:
Journal Name: Plant and Soil Journal Volume: 429 Journal Issue: 1-2; Journal ID: ISSN 0032-079X
Publisher:
Springer Science + Business Media
Country of Publication:
Netherlands
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Cellulose; Cell wall alteration; Endo-1,4-ß-glucanase; Microbiome; Metabolome; Populus

Citation Formats

Veach, Allison M., Yip, Daniel, Engle, Nancy L., Yang, Zamin K., Bible, Amber, Morrell-Falvey, Jennifer, Tschaplinski, Timothy J., Kalluri, Udaya C., and Schadt, Christopher W. Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants. Netherlands: N. p., 2018. Web. doi:10.1007/s11104-018-3692-8.
Veach, Allison M., Yip, Daniel, Engle, Nancy L., Yang, Zamin K., Bible, Amber, Morrell-Falvey, Jennifer, Tschaplinski, Timothy J., Kalluri, Udaya C., & Schadt, Christopher W. Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants. Netherlands. doi:10.1007/s11104-018-3692-8.
Veach, Allison M., Yip, Daniel, Engle, Nancy L., Yang, Zamin K., Bible, Amber, Morrell-Falvey, Jennifer, Tschaplinski, Timothy J., Kalluri, Udaya C., and Schadt, Christopher W. Mon . "Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants". Netherlands. doi:10.1007/s11104-018-3692-8.
@article{osti_1440261,
title = {Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants},
author = {Veach, Allison M. and Yip, Daniel and Engle, Nancy L. and Yang, Zamin K. and Bible, Amber and Morrell-Falvey, Jennifer and Tschaplinski, Timothy J. and Kalluri, Udaya C. and Schadt, Christopher W.},
abstractNote = {Here, 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. 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. 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. In conclusion, 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.},
doi = {10.1007/s11104-018-3692-8},
journal = {Plant and Soil},
number = 1-2,
volume = 429,
place = {Netherlands},
year = {2018},
month = {6}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1007/s11104-018-3692-8

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