Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database

Abstract

Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.

Keywords: Aromatic metabolism; Bioconversion; Catabolic pathways; Database; Ecological niche; Lignin.

Fig. 1

Schematic representation of the lignin microbial niche. In this model of the niche, lignin is mineralized by two subgroups: lignolytic species and aromatic degrading species. Some species degrade or modify lignin to access the hemi-/cellulose on which they grow (subgroup 1), and other species catabolize the aromatic lignin fragments that result from the enzymatic depolymerization (subgroup 2). There is also some overlap between the subgroups, with species capable of both lignolysis and aromatic degradation. Yellow circles represent the different origins of isolation reported for this niche. The poplar lignin structure was adapted from Vanholme et al. (2010)

Fig. 2

Schematic overview of the eLignin database. The figure illustrates that eLignin is a microorganism- and substrate-focused database and that every entry type (organism, substrate, gene, enzyme, pathway, reaction) is accessible from each of these point-of-entries

Fig. 3

Schematic distribution of the known pathways for aromatic catabolism currently indexed in the eLignin database. Please note that this representation should be seen as a hypothetical map of the existing possibilities within aromatic catabolism, and not as a map of a “superbug.” Funneling pathways refer to routes that reduce larger/more substituted aromatic compounds down to the different catabolic nodes from where ring fission occurs (here called fission pathways). The three routes that funnel compounds derived from the primary monolignols (S, H, G) are indicated in dotted boxes: the sinapyl (S), p-coumaryl (H), and coniferyl (G) branches

Fig. 4

a Substrates that can be utilized by > 10 organisms listed in the database; the numbers represent the number of strains in the database that utilize each compound. Total number of substrates that satisfied the > 10 cutoff—32; total number of substrates in dataset—141. b Number of species that can degrade natural and technical lignins, and di- and oligomeric aromatic compounds, sorted by phylum. To distinguish the bacteria from the representatives of the other two kingdoms, the fungal phyla are presented with stripes and the only archaeal phylum is in solid black

Fig. 5

Distribution of putative funneling pathway branches in the eLignin bibliome, inferred from reported substrates, sorted by phylum. Because of the overall linear nature of the aerobic funneling pathways (Fig. 3), it is possible to use the substrates reported in the literature for a given organism and correlate that to a funneling pathway branch (i.e., a collection of funneling pathways). The small group of species that has been reported to degrade aromatics anaerobically has all been clustered in the anaerobic branch in order not to generate false positives in the other branches. To distinguish the bacteria from the representatives of the other two kingdoms, the fungal phyla are presented with stripes and the only archaeal phylum is in solid black. A detailed outcome of the prediction for each species with links to the different references is found online at www.elignindatabase.com under each organism entry page. Please note that the results are theoretical and it is up to everyone to assess the probability of these inferences, e.g., by reading the primary references for each organism