1. Wood Chemistry PSE 406
Decay

2. Introduction to Deterioration
Plant matter is constantly under attack by fungi, insects, bacteria, marine borers and the weather.
It is estimated that roughly 1/10 of the forest products generated each year are destroyed.

3. PSE 406 Emphasis
While weathering, insects and marine borers cause substantial damage, we are going to focus on decay caused by fungi and bacteria.
In particular, we are going to discuss some of the biology involved but mostly the chemistry.

4. Fungi The wood deteriorating fungi are organized into three groups:
White rot fungi
Brown rot fungi
Soft rot fungi

5. White Rot Fungi
This group of organisms is known as white rot because of their ability to degrade lignin.
The decaying wood looks white.
Cellulose and hemicelluloses are also degraded.
Largest number of species belong to Basidiomycotina.
White rot fungi typically decay hardwoods
They will decay softwoods but hardwoods are their food of choice.
Simultaneous decay: all the cell components are degraded simultaneously from lumen outwards.
Preferential decay: lignin and hemicelluloses are removed selectively across the cell wall leaving cellulose.
White rot fungi produce unique extracellular oxidative enzymes that degrade lignin, as well as related compounds found in explosive-contaminated materials, pesticides, and toxic wastes.
White rot fungi White rot fungi can degrade all cell wall components, including lignin. They often cause a bleaching of normal wood coloration. Their ability to metabolize large amounts of lignin in wood is unique among microorganisms. The thousands of species that cause white rots are a heterogeneous group that may degrade greater or lesser amounts of a specific cell wall component. Some species preferentially remove lignin from wood leaving pockets of white, degraded cells that consist entirely of cellulose, while others degrade lignin and cellulose simultaneously. Degradation is usually localized to cells colonized by fungal hyphae and substantial amounts of undecayed wood remains even after advanced decay has occurred. A progressive erosion of the cell wall occurs when components are degraded simultaneously or a diffuse attack of lignin may occur by species that preferentially remove lignin . Strength losses are not significant until late stages of decay. White-rot fungi are common parasites of heartwood in living trees and are aggressive decomposers of woody debris in forest ecosystems.

6. White Rot Fungi (2) hypha ML?
1) Cross section of an oak tree with white rot. The fungus has decayed the sapwood and dark heartwood turning it white. This white rot fungus attacked all cell wall components.
2) Scanning electron micrograph showing the hypha of a white rot fungus in the cell lumen of a wood cell. Extracellular enzymes are degrading all of the cell wall components simultaneously causing erosion troughs to form in the cell wall.
3) A cross section of wood from a white-pocket area of decayed wood showing delignified wood cells. These cells have no middle lamella (this is the area between cells that has high lignin concentration). Only the cellulose-rich secondary walls remains after advanced decay.
ML?
Cross section of an oak tree with white rot.
The fungus has decayed the sapwood and
dark heartwood turning it white.
Scanning electron micrograph showing the
hypha of a white rot fungus.
A cross section of wood from a white-pocket
area of decayed wood showing delignified
wood cells.

7. Brown Rot Fungi
With brown rot fungi, cellulose and hemicelluloses are degraded with only limited lignin degradation.
Decayed wood is brown and crumbly.
Most species belong to Basidiomycotina.
Brown rot fungi typically decay softwoods.
Attack starts at the cell lumen and works outwards.
Cellulose is rapidly degraded.
Brown rot fungi Brown-rot fungi depolymerase cellulose rapidly during incipient stages of wood colonization. Considerable losses in wood strength occur very early in the decay process, often before decay characteristics are visually evident. Cell wall carbohydrates are degraded extensively during decay leaving a modified, lignin-rich substrate . The residual wood is brown and often cracks into cubical pieces when dry. Brown-rot fungi commonly cause decay in living trees, downed timber and wood used in buildings. Since large losses of wood strength result from brown rot, living trees with this decay can be hazardous and wood in service may fail. Commonly, this type of decay has been referred to as dry rot. This term, apparently first used to describe any deterioration of dead wood or wood in service is misleading because moisture must be present for the decay to occur.

8. Brown Rot Fungi (2) Brown-rooted wood.
1) A closer view of brown- rooted wood is shown in this photo. In advanced stages of decay the wood cracks and checks into cubicle pieces. Little to no integrity remains in this decayed wood.
2) Scanning electron micrograph of brown-rotted wood. Only slight pressure causes the wood cell walls to crumble into minute fragments.
Brown-rooted wood.
Wood cracks and checks into cubicle pieces.
Scanning electron micrograph of brown-rotted wood.
Only slight pressure causes the wood cell walls to
crumble into minute fragments.

9. Soft Rot Fungi
Soft rot occurs in areas where plant matter is in contact with excessive amounts of moisture.
The term soft rots comes from the soft appearance of the decayed surface.
When dry the wood surface is cracked.
Members: Ascomycetes and Fungi Imperfect.
Degradation is mainly though cavity formation in the secondary wall.
Soft rot fungi attack holocellulose; lignin protects the plant.
Soft rot fungi Fungi that cause soft-rot are taxonomically classified in the subdivisions, Ascomycota and Deuteromycota. Soft rot was first characterized as a soft, decayed surface of wood in contact with excessive moisture. However, soft rots can occur in dry environments and may be macroscopically similar to brown rot. Two distinct types of soft rot are currently recognized. Type 1 is characterized by longitudinal cavities formed within the secondary wall of wood cells and Type 2 used to describe an erosion of the entire secondary wall. The middle lamella is not degraded (in contrast to cell wall erosion by white-rot fungi), but may be modified in advanced stages of decay. Large strength losses in wood can be associated with soft rot attack. Cavities formed in the wood as well as extensive cellulose degradation can result in extremely poor strength characteristics when soft-rot wood is visually evident. As decay progresses, extensive carbohydrate loss occurs and lignin concentrations increase in the residual wood.

10. Soft Rot Fungi (2) Soft rot in wood often appears brown
Soft rot in wood often appears brown and can be confused with decay caused by brown rot fungi.
Soft rot is different from other types of wood decay. Chains of cavities are produced inside the cell wall. This micrograph taken of a section from soft-rotted wood and viewed with a light microscope shows cavities within the cell walls.
Soft rot in wood often appears brown
and can be confused with decay
caused by brown rot fungi.
This micrograph taken of a section from soft-rotted wood
and viewed with a light microscope shows cavities
within the cell walls.

11. Molds and Blue Stain Fungi
Wood is often stained by these organisms with little loss of structural integrity.
Particularly in softwoods, some strength loss in hardwoods.
Molds: Aspergillus, Penicillium etc.
Blue Stain Fungi: Philaphora, etc.
These organisms typically attack non lignified parenchyma cells and pit membranes.

12. How Does This Happen? This is a picture of highly degraded wood.
What you see are the fungal bodies known as hyphae. They grow through the plant matter like little worms.
The organisms arrive as spores (transported by a variety of methods).

13. Movement of Hyphae
This SEM picture shows fungal hyphae inside hardwood xylem.
The hyphae enter the cells though openings (pits, etc) or can bore directly through the wall (chemically).

14. How Do Fungi Destroy the Cell Wall Material?
This is a very complex question which is not well understood.
The process is enzymatic. Fungi possess a wide variety of cell wall degrading enzymes:
Cellulases, hemicellulases, etc.

15. How do Enzymes Function?
Enzymes are very large proteins.
Enzymes have very specific functions: they cause chemical reactions to occur in exact fashions.
A very large number of enzymes have been isolated from fungi and their functions identified.
Fungal hyphae release enzymes to degrade cell wall components: this reaction is extra cellular.
Enzymes are too large to penetrate into the cell wall structure and react with cell wall components. How does degradation occur?
This is the big unknown question.

16. Enzyme Function
There are a large number of fungal enzymes responsible for the breakdown of each wood component. Each enzyme plays specific roles:
Cellobiohydrolase (CBH), acts on the end of the molecule successively cleaving off the disaccharide cellobiose.
Endo-beta-1,4-glucanase acts within the chain, breaking it into smaller units and providing more "ends" for CBH.
Beta-glucosidase (or cellobiase) which cleaves cellobiose to two glucose units.
These enzymes working together produce glucose which is consumed by the fungi. *

17. What Happens to the Chemicals Unloved by the Fungi?
Basically the question is what happens to all of the organic material that is not consumed by the organisms?
In this picture, the log is rotting leaving a pile of organic material on top of the soil.
Does this organic material simply disappear?

18. Soil Organics
The answer to the question on the last slide is of course not, the organic material doesn’t disappear it is simple changed into the soil organics: Fulvic Acids, Humic acids, and Humins. These materials are classified by their solubility.
Fulvic Acids (Acid soluble fraction)
Humic acids (Alkali soluble fraction/ acid insoluble)
Humins (Insoluble organics)

19. Soil Organics II These materials are very important to the soil.
The amounts of these compounds is very soil type dependent.
60-70% of soils organics are humin, humic acids and fulvic acids.
Soil organic matter ranges from 0.5 to 20 % of the soil material.

20. Structure of Soil Organics
These soils organics are large polymers and thus like lignin structural determination is somewhat difficult.
Fulvic acid Mw~2000+, humic acids higher, humins as high as 300,000?
These materials are more difficult than lignin for structural studies because they are produced from so many different materials (unlike lignin: 3 possible precursors).

21. Proposed Humic Acid Structure
This is a proposed segment of humic acid by Stevenson*
Notice the phenolics, the sugars, and the peptides
It is obvious that this molecule does not arise directly from any component but is built from pieces of other components.

22. Proposed Fulvic Acid Structure
This is a proposed structure for a fulvic acid fragment by Buffle.

23. Formation of Soil Organics
There is a tremendous amount not known about this process.
This figure (borrowed from a website) shows 4 proposed routes to humic substances.