Earth's Systems / Biological processes / Terrestrial ecosystem functioning / Living soil system / Saprotrophic fungi / White-rot and brown-rot fungi: two routes to lignin and cellulose decay
White-rot and brown-rot fungi: two routes to lignin and cellulose decay
How wood and litter fungi attack lignified plant material. White-rot fungi use peroxidases and laccases to oxidize lignin; brown-rot fungi use Fenton chemistry to depolymerize cellulose and leave modified lignin. Mineral nitrogen from decomposition feeds back by repressing ligninolytic enzymes.
Boundary: where this process starts
Starts with: White-rot basidiomycetes secrete class II peroxidases (lignin, manganese, versatile) and laccases that oxidize lignin and leave a pale, cellulose-rich residue
Boundary: where it ends
Ends after: Hypothesis: class II peroxidases arose about 295 million years ago, coinciding with the end of major coal formation (competing explanations exist); Partly oxidized lignin fragments and fungal melanin enter the dissolved pool and can become humic precursors
Line thickness = size of impact (1 to 5)% on a line = chance a fork takes that branch📄 = pieces of evidence on a stepNegative effectLoops backHypothesisResource used up (arrow into the step)Resource used, not used upResource made or released (arrow out of the step)
What am I looking at? The concepts on every map
- Participant
- Someone or something that takes part in a process or influences it: a plant, a microbe, a river, a machine, a force. Participants are the rows of a map.
- Resource
- Something a step uses or uses up: water, oxygen, sunlight, a tool. Each step has an arrow down to the resources it uses.
- Step
- One thing that happens in a process. Every step has at least one participant and carries evidence.
- Decision fork
- A step where the process can go several ways. Every outcome is labeled with a percentage, and the percentages add up to 100%. It is not limited to yes or no.
- Loop
- A line that carries the process back to an earlier step. We record whether it reinforces or balances, how strong it is (weak, moderate, strong), and its gain (0 to 1): the share of the effect that returns on each pass.
- Size of impact
- Every line says how much the earlier step affects the next one (1 to 5), in which direction (+, -, 0), and why. Thicker lines mean bigger impact.
- Evidence
- The support for a claim: a source and what it shows. Every step, line, change and vote needs it. Click any step or line to read its evidence.
- Boundary
- Where a process starts and where it ends. Every process, and every subprocess, has a start and an end.
- Subprocess
- A step that is itself a whole process, with its own boundary, steps and lines. Click a step marked ↘ to open it. Subprocesses nest as deep as the evidence goes.
- Description
- A plain-language summary of what a process is and what it covers.
- Hypothesis
- A proposed new connection between two parts of the map that nobody has linked. It carries a prediction, a way to test it, and a count of papers on each topic and on both. It is an unverified idea until someone tests it.
Every step, with its evidence
The same information as the map, as a list you can search and share. Click a participant or resource to see everywhere it appears.
White-rot basidiomycetes secrete class II peroxidases (lignin, manganese, versatile) and laccases that oxidize lignin and leave a pale, cellulose-rich residue
Evidence (1) · added by Ember
- Floudas et al. 2012, Science 336:1715: Class II peroxidases are the signature enzymes of white-rot Agaricomycetes. (confidence 0.85)
Manganese peroxidase oxidizes Mn(II) to Mn(III) chelated by oxalate, a diffusible oxidant that attacks lignin beyond the enzyme's reach
Evidence (1) · added by Ember
- Hofrichter 2002, Enzyme and Microbial Technology 30:454, Review: lignin conversion by manganese peroxidase: Chelated Mn(III) acts as a diffusible mediator oxidizing phenolic lignin units. (confidence 0.85)
Brown-rot fungi lack class II peroxidases and use Fenton chemistry (Fe2+ + H2O2 gives hydroxyl radicals) to depolymerize cellulose, leaving modified lignin
Evidence (1) · added by Ember
- Eastwood et al. 2011, Science 333:762, The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi: Brown-rot genomes have reduced oxidative and cellulolytic enzyme sets and rely on oxidative radical chemistry. (confidence 0.85)
Hypothesis: class II peroxidases arose about 295 million years ago, coinciding with the end of major coal formation (competing explanations exist)
Evidence (1) · added by Ember
- Floudas et al. 2012, Science 336:1715: Molecular clock places the origin of lignin-degrading peroxidases near the Carboniferous-Permian boundary. (confidence 0.6)
Lignin is co-metabolized: fungi need cellulose or another carbon source and H2O2 from oxidases; lignin alone does not support growth
Evidence (1) · added by Ember
- Kirk & Farrell 1987, Annual Review of Microbiology 41:465, Enzymatic combustion: the microbial degradation of lignin: Ligninolysis is a secondary-metabolic, co-metabolic process that exposes cellulose rather than feeding on lignin. (confidence 0.8)
Partly oxidized lignin fragments and fungal melanin enter the dissolved pool and can become humic precursors
Evidence (1) · added by Ember
- Kogel-Knabner 2002, Soil Biology and Biochemistry 34:139, The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter: Lignin-derived and microbial residues contribute aromatic and phenolic structures to soil organic matter. (confidence 0.7)
Mineral nitrogen released as litter decays represses ligninolytic enzymes and phenol oxidase in lignin-rich litter, slowing late-stage decay while speeding early cellulose decay
Evidence (1) · added by Ember
- Carreiro, Sinsabaugh, Repert & Parkhurst 2000, Ecology 81:2359, Microbial enzyme shifts explain litter decay responses to simulated nitrogen deposition: N additions raised cellulase but lowered phenol oxidase activity in high-lignin litter, slowing late-stage decay. (confidence 0.8)