Microbial strategies for deconstruction of bark components

Doctoral thesis, 2023

Bark is the outermost part of a tree, and it is a protective layer against external threats such as microorganisms and environmental stressors. Bark consists of various polymers including lignin, cellulose, hemicellulose, and it also contains a large fraction of compounds known as extractives. The polymers and extractives are assembled into a heterogenous complex matrix, forming a highly recalcitrant material. Despite its protective role, bark is degraded in nature by microorganisms, yet little is known about the specific microorganisms involved and how they affect bark composition.

In this thesis, I have investigated different strategies that individual species and microbial communities employ to degrade bark and how enzymes hydrolyze pure polysaccharides and extractive compounds, focusing on spruce bark degradation. I analyzed a microbial community growing on spruce bark over six months and observed significant effects on the extractives, especially resin acids at the start of the cultivation. The community was dominated by bacteria, and guided by metagenomics, a new Pseudomonas species was isolated, sequenced, and shown to degrade the major resin acids present in spruce bark. The role of filamentous fungi in the microbial community was unclear, despite their reputation as exceptional lignocellulose degraders. Therefore, I studied fungi from the Basidiomycota and Ascomycota phyla known to employ different lignocellulose degradation strategies. I showed that the Basidiomycetes can degrade/modify resin acids, while the Ascomycetes instead appeared to tolerate resin acids. All fungi investigated were able to degrade the bark polysaccharides, with significant differences in pectin and xylan degradation. To understand xylan degrading mechanisms in more detail, I studied the growth of taxonomically different yeasts and biochemically characterized their xylanases. One of the yeasts, Wickerhamomyces canadensis, grew poorly on xylan but its growth was boosted when co-cultured with another yeast, Blastobotrys mokoenaii. This suggests that W. canadensis is a secondary degrader of xylan. For in-depth studies of extractive-degrading enzymes, I biochemically characterized three tannases from the bacterium Clostridium butyricum and demonstrated their ability to cleave oak bark tannins. My work contributes to our understanding of the microbial degradation of bark and the strategies employed by microbial communities, individual species, and enzymes to degrade bark.