Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood

Abstract

The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.

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

“…S3). Tláskal et al ( 1 ) in their pangenome analysis determined that the Sodalis deadwood guild shared an average of 1,596 genes from 1,519 gene clusters, which was 28.4% per average genome for each member.…”

“…In the family Bruguierivoracaceae , the genus Sodalis can be grouped generally into three guilds: deadwood associated isolates, endosymbionts associated with the tsetse fly, and endosymbionts of other insects, such as long-horned beetles, louse flies, and bees ( 1 – 4 ). The genus was established by Dale and Maudlin ( 5 ) with the description of species S. glossinidius strain M1, which was the first isolated insect secondary endosymbiont.…”

“…There is a total of three free-living Sodalis members identified to date: S. praecaptivus ( 13 ), Sodalis ligni dw23, and Sodalis sp. dw96 ( 1 ). S. praecaptivus was isolated from an infected wound of a person whose hand had been impaled by a dead crab apple tree branch, suggesting that S. praecaptivus was either a pathogen or saprophyte residing on the bark or woody tissue of the plant ( 14 ).…”

“… Sodalis ligni dw23 and Sodalis sp. dw96 were both isolated from decomposing deadwood ( 1 ). Bacteria isolated from decomposing wood or plant litter on the soil surface are part of a much larger microbial community that includes members that depolymerize lignin to access cellulose or hemicellulose components of plant material, that consume the lignin-derived monomers, or can do both functions ( 15 ).…”

Deadwood-Inhabiting Bacteria Show Adaptations to Changing Carbon and Nitrogen Availability During Decomposition

“…In line with this, we cultivated two Rhizobiales strains containing the nitrogenase nifHDK operon. The other two nitrogen fixers are enterobacteria from the genus Sodalis, and both are closely related to Sodalis insect endosymbionts that lack nitrogenase genes (Tláskal et al, 2021b). After almost 40 years, non-symbiotic N 2 -fixing Sodalis and Rhizobiales strains widen a small group of cultivated deadwood diazotrophic bacteria successfully retrieved from naturally decomposing CWD (Seidler et al, 1972;Spano et al, 1982).…”