Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

Abstract

Summary White‐rot fungi, such as Dichomitus squalens, degrade all wood components and inhabit mixed‐wood forests containing both soft‐ and hardwood species. In this study, we evaluated how D. squalens responded to the compositional differences in softwood [guaiacyl (G) lignin and higher mannan content] and hardwood [syringyl/guaiacyl (S/G) lignin and higher xylan content] using semi‐natural solid cultures. Spruce (softwood) and birch (hardwood) sticks were degraded by D. squalens as measured by oxidation of the lignins using 2D‐NMR. The fungal response as measured by transcriptomics, proteomics and enzyme activities showed a partial tailoring to wood composition. Mannanolytic transcripts and proteins were more abundant in spruce cultures, while a proportionally higher xylanolytic activity was detected in birch cultures. Both wood types induced manganese peroxidases to a much higher level than laccases, but higher transcript and protein levels of the manganese peroxidases were observed on the G‐lignin rich spruce. Overall, the molecular responses demonstrated a stronger adaptation to the spruce rather than birch composition, possibly because D. squalens is mainly found degrading softwoods in nature, which supports the ability of the solid wood cultures to reflect the natural environment.

Colonies of the fungus Aspergillus niger are highly differentiated to adapt to local carbon source variation

“…Intracellular proteins and metabolites were released from the ground mycelia using 500 μl of extraction buffer (50 mM potassium phosphate buffer pH 7, 5 mM MgCl 2 , 5 mM β-mercaptoethanol and 0.5 mM EDTA) with inversion of the tube followed by centrifugation (20 000 × g, 4 C and 5 min), before mixing 300 μl of the supernatant with 1.5 ml of cold 2:1 (v/v) chloroform: methanol. The rest of the procedure was described previously (Daly et al, 2018).…”

“…The intracellular proteome was analysed using equal amounts of proteins from each sample and normalized for total signal intensity, whereas the extracellular proteins collected from the liquid in the compartments was analysed using equivalent volumes of liquid without any normalization for total signal intensity. Sample preparation was performed as previously described (Daly et al, 2018). The intracellular samples were all diluted to a concentration of 0.1 μg μL −1 in water for analysis by LC-MS as described previously (Daly et al, 2018).…”

“…Sample preparation was performed as previously described (Daly et al, 2018). The intracellular samples were all diluted to a concentration of 0.1 μg μL −1 in water for analysis by LC-MS as described previously (Daly et al, 2018). In order to analyse the extracellular samples using equivalent volumes from each compartment, the highest concentrated sample was identified in the extracellular sample set and it was diluted to 0.1 μg μL −1 and the remainder of the set was diluted using the same volumes as this sample.…”

“…The aqueous phase, containing the polar metabolites, obtained from the chloroform:methanol extractions was processed for using GC-MS-based metabolomics data generation and analysis using pipelines described previously (Daly et al, 2018;Khosravi et al, 2018). Meta-boAnalyst (Xia et al, 2015) was used for the principal component analysis of the metabolite abundances.…”

An Italian Research Culture Collection of Wood Decay Fungi

“…Dichomitus squalens is a model species for studies about the selectivity of white rot and its enzymatic basis [57][58][59][60]. Despite being reported all throughout the boreal emisphere, it appears scattered and is commonly found in the northern parts of Europe, North America and Asia [61]; the GBIF [54] places the wide majority of records in the Fennoscandian region.…”