Coupling Secretomics with Enzyme Activities To Compare the Temporal Processes of Wood Metabolism among White and Brown Rot Fungi

Abstract

Wood-degrading fungi use a sequence of oxidative and hydrolytic mechanisms to loosen lignocellulose and then release and metabolize embedded sugars. These temporal sequences have recently been mapped at high resolution using directional growth on wood wafers, revealing previously obscured dynamics as fungi progressively colonize wood. Here, we applied secretomics in the same wafer design to track temporal trends on aspen decayed by fungi with distinct nutritional modes: two brown rot-type (BR) fungi (, ) and two white rot (WR) (, ). We matched secretomic data from three zones of decay (early, middle, late) with enzyme activities in these zones, and we included measures of total protein and ergosterol as measures of fungal biomass. In line with previous transcriptomics data, the fungi tested showed an initial investment in pectinases and a delayed investment in glycoside hydrolases (GHs). Brown rot fungi also staggered abundance of some oxidoreductases ahead of GHs to produce a familiar two-step mechanism. White rot fungi, however, showed late-stage investment in pectinases as well, unlike brown rot fungi. Ligninolytic enzyme activities and abundances were also different between the two white rot fungi. Specifically, ligninolytic activity was delayed, explained almost entirely by the activity and abundance of five atypical manganese peroxidases, unlike more varied peroxidases and laccases in These secretomic analyses support brown rot patterns generated via transcriptomics, they reveal distinct patterns among and within rot types, and they link spectral counts with activities to help functionalize these multi-strain secretomic data. Wood decay, primarily driven by wood degrading basidiomycetes, is an essential component of global carbon cycles and decay mechanisms are essential for understanding forest ecosystem function. These fungi efficiently consolidate pretreatment and saccharification of wood at mild conditions, making them promising templates for low-cost lignocellulose conversion. Species are categorized as ligninolytic white rots and polysaccharide-selective brown rots, with considerable undescribed variability in decay mechanism that may manifest in the sequential variation in protein secretion over the progression of decay. Here we resolved spatially, a temporal progression of decay on intact wood wafers and compared secretome dynamics in two white and two brown rot fungi. We identified several universal mechanistic components among decay types including early pectinolytic "pretreatment" and later stage glycoside hydrolase-mediated saccharification. Interspecific comparisons also identified considerable mechanistic diversity within rot types, indicating there are multiple avenues to facilitate white and brown rot.

Fungal ecological strategies reflected in gene transcription ‐ a case study of two litter decomposers

“…Thus, the production of long‐chain acting enzymes seemed to increase as the pool of hydrolysable polysaccharides was depleted. These results partly agree with the dynamics of enzyme activities in other decomposition experiments (Šnajdr et al ., ; Presley et al ., ).…”

A Lytic Polysaccharide Monooxygenase from a White-Rot Fungus Drives the Degradation of Lignin by a Versatile Peroxidase

“…First, white-rot fungi have versatile extracellular H 2 O 2 -generating enzymes that participate in the lignin degradation reaction of class II peroxidase, such as aryl-alcohol oxidase (AAO) and glyoxal oxidase (GLOX) (23). The expression of H 2 O 2 -generating enzymes depends on the fungal isolate, wood substrate species, and physiological factors, and different H 2 O 2 -generating enzymes play roles in different stages of fungal decay (40,41). Some H 2 O 2 -generating enzymes, such as glyoxal oxidases, are lacking in some fungi, including Ceriporiopsis subvermispora, Fomitiporia mediterranea, and Heterobasidion annosum, but almost all white-rot fungi reported thus far have contained LPMOs (25).…”

The forgotten ecosystem engineers: community and functional ecology of pioneer wood decay fungi in the canopy of beech trees

“…Different white-rot species are known to differ in the range of ligninolytic enzymes they are capable of producing (Valmaseda et al 1990;Eastwood et al 2011) and in the identity and activity levels of enzymes expressed over time in relation to the initial capture of wood resource (Presley et al 2018). In addition, white-rot fungi like all saprotrophic microbes secrete a range of hydrolase enzymes as they degrade various carbohydrates in their surroundings and in the search for limiting nutrients (Baldrian 2009).…”

“…These dynamics are not well understood in any dead wood system and have never been examined in pioneer communities. During primary capture of wood resource by the early-secondary decay species T. versicolor and S. hirsutum, activities of laccase and the hydrolases β-glucosidase and β-galactosidase are higher in younger parts of the colony, with hydrolase levels dropping steadily with increasing decomposition (Presley et al 2018). Endochitinase, chitobiosidase and NAG activity levels also increase in older parts of the colony of many species of ligninolytic fungi following primary resource capture of woody resources (Lindahl & Finlay 2006) indicating that hydrolase enzymes associated with N acquisition may increase over decomposition gradients as colonisation times increase.…”

“…The enzymes assayed included a wide range of oxidoreductases utilised in lignin modification and hydrolases known to be utilised in the acquisition of nutrients by ligninolytic fungi (Baldrian 2009). There is, as yet, minimal understanding of the manner in which the suite of lignindegrading enzymes are employed to effect overall wood decomposition outside of biorefinery models (Zhang & Schilling 2017;Presley et al 2018). Attached dead branches, which represent the earliest stages of wood decay in natural woodland systems, are an ideal subject to explore this aspect of the functional ecology of wood decay.…”