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

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.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1073-4) contains supplementary material, which is available to authorized users.

Lignin catabolic pathways reveal unique characteristics of dye‐decolorizing peroxidases in Pseudomonas putida

“…However, their instability, complex protein synthesis systems and immature genetic systems restrict their application in industrial lignin bioconversion (Li et al ., ; Sondhi et al ., ; de Gonzalo et al ., ). Several bacteria (e.g., Pseudomonas , Sphingomonas and Rhodococcus ) with the ligninolytic capacity have been identified (Ahmad et al ., ; Bugg et al ., ; Lin et al ., ; Moraes et al ., ). Among them, Pseudomonas have attracted particular attention (Linger et al ., ; Salvachua et al ., ) due to their strong capacity to accumulate energy storage components [e.g., polyhydroxyalkanoate (PHA)] (Wang et al ., ), ability to easily adapt to different environments (Mazurkewich et al ., ), and the availability of genetic manipulation systems (Sun et al ., ).…”

Biotransformation of lignin: Mechanisms, applications and future work

“…117 ing and degradation as well as a PHA biosynthetic gene cluster were discovered in its genome, which served as a basis for further studies. 43 Moraes et al 135…”

“…two dicarboxylic acids were in the range of 80-125 mg/L. Moraes et al135 collected soil samples from a sugarcane plantation in Brazil and established lignin-degrading consortium with microorganisms from such soil samples. 129 5 | ADVANCED TECHNIQUES IN LIGNIN BIOCONVERSION RESEARCH 5.1 | Screening of new lignin degraders Until now, many microorganisms have been extensively studied as lignin degraders, and an increasing number of species are being identified with lignin-degrading ability, such as Ochrobactrum tritici, 130 Neurospora discrete, 131 Bjerkandera adusta, 132 Cedecea lapagei, 133 etc.…”

Explorando as relações entre estrutura e função das hidrolases de glicosídeos das famílias 9, 48 e 74

“…Inúmeros microrganismos são capazes de utilizar celulose, hemicelulose e lignina como fonte de carbono por meio da hidrólise enzimática. 13,14 Para isso, eles utilizam uma sofisticada maquinaria para produzir um arsenal de enzimas líticas e oxidativas. [15][16][17] As bactérias e fungos, por exemplo, utilizam dois mecanismos de produção.…”

“…i) Secretam um conjunto de CAZymes independentes entre si; 15 ii) secretam complexos multi enzimáticos formando uma estrutura supramolecular chamada celulossoma; 17 e por fim, iii) secretam uma mistura de CAZymes constituídas por diversos módulos catalíticos em uma mesma cadeia polipeptídica. 16 Essas enzimas estão envolvidas na bioconversão de celulose, hemicelulose e compostos aromáticos, 13,14 assim como polissacarídeos da microbiota intestinal de ruminantes 18 e de humanos. 19 CAZYmes: distribuição, especificidade por substratos e modo de ação.…”