Sodalis ligni Strain 159R Isolated from an Anaerobic Lignin-Degrading Consortium

Abstract

Novel bacterial isolates with the capabilities of lignin depolymerization, catabolism, or both, could be pertinent to lignocellulosic biofuel applications. In this study, we aimed to identify anaerobic bacteria that could address the economic challenges faced with microbial-mediated biotechnologies, such as the need for aeration and mixing. Using a consortium seeded from temperate forest soil and enriched under anoxic conditions with organosolv lignin as the sole carbon source, we successfully isolated a novel bacterium, designated 159R. Based on the 16S rRNA gene, the isolate belongs to the genus Sodalis in the family Bruguierivoracaceae. Whole-genome sequencing revealed a genome size of 6.38 Mbp and a GC content of 55 mol%. To resolve the phylogenetic position of 159R, its phylogeny was reconstructed using (i) 16S rRNA genes of its closest relatives, (ii) multilocus sequence analysis (MLSA) of 100 genes, (iii) 49 clusters of orthologous groups (COG) domains, and (iv) 400 conserved proteins. Isolate 159R was closely related to the deadwood associated Sodalis guild rather than the tsetse fly and other insect endosymbiont guilds. Estimated genome-sequence-based digital DNA-DNA hybridization (dDDH), genome percentage of conserved proteins (POCP), and an alignment analysis between 159R and the Sodalis clade species further supported that isolate 159R was part of the Sodalis genus and a strain of Sodalis ligni. We proposed the name Sodalis ligni str. 159R (=DSM 110549 = ATCC TSD-177). IMPORTANCE Currently, in the paper industry, paper mill pulping relies on unsustainable and costly processes to remove lignin from lignocellulosic material. A greener approach is biopulping, which uses microbes and their enzymes to break down lignin. However, there are limitations to biopulping that prevent it from outcompeting other pulping processes, such as requiring constant aeration and mixing. Anaerobic bacteria are a promising alternative source for consolidated depolymerization of lignin and its conversion to valuable by-products. We presented Sodalis ligni str. 159R and its characteristics as another example of potential mechanisms that can be developed for lignocellulosic applications.

Keywords: anaerobic catabolic pathways; aromatic compounds; aromatic metabolism; endosymbionts; lignocellulosic biofuel.

FIG 1

Reconstruction of the phylogenetic position of strain 159R based on 16S rRNA gene. Trees are presented as maximum-likelihood trees with bootstrap values. The tree was rooted in an outlier, Methanocaldococcus jannaschii (not shown in the tree).

FIG 2

Reconstruction of the phylogenetic position of Sodalis ligni str. 159R-based multi-locus sequence analysis (MLSA) via autoMLST. Trees are presented as maximum-likelihood trees with bootstrap values.

FIG 3

Reconstruction of the phylogenetic position of strain 159R based on (A) alignment similarity for a subset of 49 COG domains using KBase insert genome into species tree and (B) 400 conserved protein sequences using PhyloPhlan. The KBase insert genome species tree is presented as maximum-likelihood trees with bootstrap values.

FIG 4

Alignment analysis comparing the chromosome of Sodalis ligni str. 159R to S. ligni dw23 with the online tool, d-Genies, with 159R as the target and dw23 as the query (aligned with Minimap2).