Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum

Abstract

Steccherinum ochraceum is a white rot basidiomycete with wide ecological amplitude. It occurs in different regions of Russia and throughout the world, occupying different climatic zones. S. ochraceum colonizes stumps, trunks, and branches of various deciduous (seldom coniferous) trees. As a secondary colonizing fungus, S. ochraceum is mainly observed at the late decay stages. Here, we present the de novo assembly and annotation of the genome of S. ochraceum, LE-BIN 3174. This is the 8th published genome of fungus from the residual polyporoid clade and the first from the Steccherinaceae family. The obtained genome provides a first glimpse into the genetic and enzymatic mechanisms governing adaptation of S. ochraceum to an ecological niche of pre-degraded wood. It is proposed that increased number of carbohydrate-active enzymes (CAZymes) belonging to the AA superfamily and decreased number of CAZymes belonging to the GH superfamily reflects substrate preferences of S. ochraceum. This proposition is further substantiated by the results of the biochemical plate tests and exoproteomic study, which demonstrates that S. ochraceum assumes the intermediate position between typical primary colonizing fungi and litter decomposers or humus saprotrophs. Phylogenetic analysis of S. ochraceum laccase and class II peroxidase genes revealed the distinct evolutional origin of these genes in the Steccherinaceae family.

Purification and Characterization of Two Novel Laccases from Peniophora lycii

“…v1.0 (clade 9). It should be noted that a similar picture of the evolution of laccase genes-early multiple duplication with subsequent retention of an almost unchanged number of genes-was also described for fungi from the Core and Residual Polyporoid clades of the Polyporales order [13,[55][56][57]. Similar to the Polyporales order, since almost all detected gene duplications occurred in the common ancestor of all Peniophora spp., all 18 clades on the constructed tree can be regarded as well-defined orthology groups.…”

Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi

“…Agar plate assays of overall oxidative and cellulolytic activities were performed as previously described in [ 44 ]. The inoculum plugs (Ø 7 mm) were seized from the overgrown Petri dishes (see Section 2.2 ) and placed mycelium up into new Petri dishes (Ø 90 mm) containing 20 mL of the analytical medium consisting of 1% w / v agar and either 0.1% w / v 2,2′-azino-bis 3-ethylbenzothiazoline-6-sulfonic acid (ABTS; Sigma, St. Louis, MO, USA) for the overall oxidative activity assay or 1% w / v cellulose pulp (Sigma, St. Louis, MO, USA) for the overall cellulolytic activity assay.…”

The Conservation and Study of Macromycetes in the Komarov Botanical Institute Basidiomycetes Culture Collection—Their Taxonomical Diversity and Biotechnological Prospects

“…or decayed wood [94,95]. Information on the genetic and enzymatic mechanisms managing the adaptation of S. ochraceum LE-BIN 3174 to late stages of wood decomposition was obtained [96]. The study of Steccherinum strains was continued by evaluation of the oxidative enzyme activity and biodegradation potential of seventeen LE-BIN strains of S. ochraceum during their cultivation on different types of wood [97].…”