Modified lignin biosynthesis in field-grown Populus tremula x alba: Host genotype effects on the plant-associated bacterial microbiome

Abstract

Since their discovery and the onset of the industrial revolution, fossil fuels have powered global economical development and have been the world’s primary energy source. However, the continuous depletion of the fossil energy reserves for manufacturing and transport and the accompanying side-effects (environmental ramifications and energy security) has ultimately led to an everincreasing requirement of alternative and sustainable energy sources for our industrial economies and consumer societies. In the impending transition to a more bio-based economy, especially the need for biomass in the production of renewable energy and industrial feedstock applications is incessant and optimizing plant growth is required to ensure feed supply. Second-generation biofuels, produced from lignocellulosic non-food feedstocks, avoid competition with food crops but their commercial viability is severely limited by the recalcitrance of lignin polymers present in the plant cell walls. Therefore genetically modified (GM) energy crops, engineered to produce less lignin or more easily degradable lignin, have been utilized to partially overcome the recalcitrance of lignocellulosic biomass and to improve the commercial viability and cost-competitiveness of second-generation biofuels. In order to reduce/modify lignin polymers to generate feedstocks with diminished recalcitrance, genes have been cloned for each of the steps of the lignin biosynthetic pathway. Gene silencing of cinnamoyl-CoA reductase (CCR; EC 1.2.1.44), which catalyses the conversion of feruloyl-CoA to coniferaldehyde and is considered as the first enzyme in the monolignol-specific branch of lignin biosynthesis, represents an interesting target to reduce lignin levels. However, simultaneously gene silencing of CCR and by extension most of the genes silenced in the lignin biosynthesis, leads to flux changes in the phenylpropanoid and monolignol-specific pathways, most notably the accumulation of soluble phenolics (e.g. ferulic acid) and detoxicification products. In this way, the plant-associated microbiome is confronted with profound changes in the accessible carbon sources in the xylem vessels. The plant microbiome can be considered as an extension of the host genome or even as the plant’s second genome. Therefore, even small changes in the host genome (ecotypes, cultivars, genetically modified genotypes, etc.) may influence the plant microbiome, and these changes may even feed back to modulate the behaviour of the host. Furthermore, cell walls play major roles in the endophytic colonization of beneficial bacteria as well as in the resistance against pathogens. Since perturbations in the lignin biosynthesis via CCR downregulation lead to compositional alterations in the cell wall changes in the endophytic colonization may occur. Therefore, the main objective of the current work was to explore the general and specific host genotype effects exerted by CCR gene silencing in field-grown poplar trees (Populus tremula x alba) on the plant bacterial microbiome. Furthermore we also focussed on the microbiome niche differentiation between the different plant environments (rhizosphere, root, stem, leaf) and evaluated the potential of plant-growth promoting (PGP) bacteria to offset the negative repercussions on the biomass yield of ligninreduced genotypes.