Multi-omic analyses of extensively decayed Pinus contorta reveal expression of diverse array of lignocellulose degrading enzymes

Fungi play a key role cycling nutrients in forest ecosystems but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNAseq and LC-MS/MS, respectively. Following de novo metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to to basidiomycete transcripts dominated and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate active enzymes (CAzymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases including highly expressed cellulases or hemicellulases. The CAzymes also included 162 genes encoding redox enzymes classified within Auxiliary Activity (AA) families. Eighteen of these were manganese peroxidases, key components of ligninolytic white rot fungi. Expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radical. The latter has been implicated as a diffusible oxidant responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of logdepole pine.IMPORTANCE The deconstruction of recalcitrant woody substrates is a central component of carbon cycling and forest health. Laboratory investigations have contributed substantially toward understanding mechanisms employed by model wood decay fungi, but few studies have examined the physiological processes in natural environments. Herein, we identify the functional genes present in field samples of extensively decayed lodgepole pine (Pinus contorta), a major species distributed throughout the North American Rocky Mountains. The classified transcripts and proteins revealed a diverse array of oxidative and hydrolytic enzymes involved in the degradation of lignocellulose. The evidence also strongly supports simultaneous attack by fungal species employing different enzymatic strategies.

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