Lignolytic-consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization

Eduardo C Moraes,Neil Dixon,Gabriela C Ematsu,Camila Caldana,Thabata M Alvarez,Livia B Brenelli,Douglas A A Paixão,Timothy D H Bugg,Juliana A Aricetti,Fabio M Squina,Geizecler Tomazetto,Gabriela F Persinoti

doi:10.1186/s13068-018-1073-4

Abstract

BackgroundLignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bio-derived products for the chemical industry. However, the inherent structural complexity and recalcitrance of lignin makes its conversion into valuable chemicals a challenge. Natural microbial communities produce biocatalysts derived from a large number of microorganisms, including those considered unculturable, which operate synergistically to perform a variety of bioconversion processes. Thus, metagenomic approaches are a powerful tool to reveal novel optimized metabolic pathways for lignin conversion and valorization.ResultsThe lignin-degrading consortium (LigMet) was obtained from a sugarcane plantation soil sample. The LigMet taxonomical analyses (based on 16S rRNA) indicated prevalence of Proteobacteria, Actinobacteria and Firmicutes members, including the Alcaligenaceae and Micrococcaceae families, which were enriched in the LigMet compared to sugarcane soil. Analysis of global DNA sequencing revealed around 240,000 gene models, and 65 draft bacterial genomes were predicted. Along with depicting several peroxidases, dye-decolorizing peroxidases, laccases, carbohydrate esterases, and lignocellulosic auxiliary (redox) activities, the major pathways related to aromatic degradation were identified, including benzoate (or methylbenzoate) degradation to catechol (or methylcatechol), catechol ortho-cleavage, catechol meta-cleavage, and phthalate degradation. A novel Paenarthrobacter strain harboring eight gene clusters related to aromatic degradation was isolated from LigMet and was able to grow on lignin as major carbon source. Furthermore, a recombinant pathway for vanillin production was designed based on novel gene sequences coding for a feruloyl-CoA synthetase and an enoyl-CoA hydratase/aldolase retrieved from the metagenomic data set.ConclusionThe enrichment protocol described in the present study was successful for a microbial consortium establishment towards the lignin and aromatic metabolism, providing pathways and enzyme sets for synthetic biology engineering approaches. This work represents a pioneering study on lignin conversion and valorization strategies based on metagenomics, revealing several novel lignin conversion enzymes, aromatic-degrading bacterial genomes, and a novel bacterial strain of potential biotechnological interest. The validation of a biosynthetic route for vanillin synthesis confirmed the applicability of the targeted metagenome discovery approach for lignin valorization strategies.

Highlights

Lignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bioderived products for the chemical industry
The hypothesis under investigation was whether the sugarcane field soil covered by straws, after the plants were harvested, could be a potential source of novel lignolytic enzymes, because it is expected that the microbial population involved in degradation of plant biomass polymers is enriched in this environment (Fig. 1)
Based on the 16S rRNA gene comparison, the analysis revealed that the strain HW13 shares 96.8% 16S rRNA gene sequence similarity with P. ureafaciens DSM 20126T as the closest related species with a valid nomenclature (Additional file 1: Figure S9)

Summary

Introduction

Lignin is a heterogeneous polymer representing a renewable source of aromatic and phenolic bioderived products for the chemical industry. Lignocellulosic biomass is the most abundant carbon-based material in nature, representing an attractive renewable source to replace oil derivatives and to provide aromatic building blocks for the chemical industry [1,2,3]. Controlled deconstruction of the macromolecule to produce lower molecular weight compounds is critical in lignin valorization strategies [5, 7]. Examples of chemical depolymerization or acidification treatment of lignin to produce low-molecular-weight aromatic compounds have proven to be methods of interest for adding value to lignin streams [8,9,10]. The depolymerization of lignin into monomers such as guaiacyl, syringyl, vanillin, and syringaldehyde is of commercial interest due to the potential for application of these molecules in the biofuel, food, cosmetic, and other industrial sectors [11]

Methods

Results

Conclusion