The hidden world of wood-decaying fungi

Dead wood in forests is a source of life. As wood decomposes, stored nutrients become available again for a new generation of trees. Fungi in particular thrive on wood and break it down. Many of these fungi form mushrooms, for example on dead tree stumps, but the actual breakdown is done by fungal threads inside the wood. It is therefore necessary to investigate what fungal threads do inside the wood and whether other organisms are involved.

This research did not really take off until the end of the last century when molecular-biological (DNA and RNA) and advanced chemical techniques were developed. These research techniques provide a better understanding of how wood decomposition takes place, what contribution dead wood makes to the storage of carbon, and what possible sustainable alternatives are for disease control in trees.

Wood decay

Wood consists mainly of sugar polymers (cellulose and hemicellulose) and of aromatic compounds (lignin). The difficulty to degrade wood is caused by lignin which lies as a protective layer around the other polymers. While cellulose and hemicellulose can be broken down using enzymes, lignin degradation requires reactive oxygen radicals. This is why wood hardly breaks down in an oxygen-free environment. The only organisms that can break down lignin completely with oxygen radicals are fungi causing white rot. This rot is named after the wood's change of colour from brown to lighter when lignin is being broken down.

Apart from white rot, brown rot fungi also exist. These cannot break down lignin completely, but they can damage it, and that is enough to give their enzymes access to the sugar polymers. As the sugar polymers disappear, the wood becomes increasingly richer in the lignin that remains and thus browner in colour. A cube-shaped crack pattern also forms. This is often easily seen on dead trunks of coniferous trees. Almost all white- and brown rot fungi belong to the club fungi (basidiomycetes) and contribute to the diversity of mushrooms in the forest.

Territory drive

Wood rot fungi are fighters that do not tolerate intruders in their occupied wood territory. Since fungal threads (hyphae) of different species can penetrate a large piece of wood from the soil, they encounter each other. To thwart intruders, the hyphs of wood rot fungi produce melanin, which the opponent cannot easily break down. In an undecided battle, borders are marked with that accumulated melanin and territories are easily seen. This can create beautiful patterns in wood carvings.

In a VENI project (2012-2016) for newly promoted researchers funded by the Dutch Research Council (NWO), Annemieke van der Wal found signs that battles between fungal species may play a role in how fast wood degrades in forests. She compared the decomposition rate of pedunculate oak stumps in Bergharen five years after felling and saw big differences. There were stumps virtually devoid of sapwood and stumps in which it appeared intact. DNA analysis showed that this correlated with differences in the composition and interactions between fungi.

In another study from this project, she showed that variation in breakdown rate and fungal composition can also be seen on trunk sections of recently felled larch and northern red oak that had been laid down at different locations in a forest (Schovenhorst) near Putten. The variation seems to be mainly due to chance. The fungal species that first colonised the trunks from the soil prevailed for the first few years. However, fungal species did vary for the two tree species, indicating selection by wood type. The findings fit well with research by other research groups: a high diversity of trees is accompanied by a high diversity of wood-degrading fungi. After the dynamic initial period, turkey tail (Trametes versicolor) dominated in the trunks of northern red oak after three years, while in the larch trunks the battle between different species was not yet decided.

Heterobasidium annosum

In larch, DNA of the pathogenic fungus Heterobasidium annosum was found in both trunks and stumps of the freshly cut wood. Remarkably, it managed to persist only in stumps and not in the sawn stem parts. This fungus can invade and kill roots of living trees from the roots of infected stumps. Interestingly, among the colonising fungi of trunk parts, the fungus Phlebiopsis gigantea was also found, but not in stumps. This species is used as a biological control agent against Heterobasidium annosum and thus may have also played a role in the disappearance from trunk parts via natural colonisation from the soil.

Love-hate relationship with bacteria

Bacteria are much smaller than fungi and are quicker to respond to new opportunities. Fresh wood, such as wind-blown branches, is therefore quickly colonised by bacteria. These grow on the limited amount of easily degradable sugars. For the invading fungi, those sugars are an important initial energy source to produce enzymes that will break down wood polymers.

Research by Larissa Folman in 2008 on the sulphur tuft (Hypholoma fasciculare), a common white rot fungus, showed that bacteria that had colonised beech wood blocks from the ground were virtually eradicated after entering the sulphur tuft’s fungal threads. This seems to be mainly caused by rapid, strong acidification of the wood by oxalic acid secreted by the fungus. Most bacterial pioneers are evidently not resistant to this.

NIOO researchers also found bactericidal activity in birch wood with fruiting bodies of the birch polypore (Piptoporus betulinus) and tinder fungus (Fomes fomentarius). These basidiomycetes continue the suppression of bacteria even after they have formed fruiting bodies. This is not the case with the sulphur tuft. Stumps of mushrooms of the sulphur tuft actually contain a lot of bacteria. These are different species than the pioneers that the fungus eradicated. These bacteria have adapted to acidic conditions and do not work against the fungus. Instead, they depend on the wood decomposition by the fungus for their growth. In return, the bacteria can be useful to the fungus, for example by fixing nitrogen from the air. Wood contains a lot of carbon but little nitrogen, which is a limiting factor for the growth of wood rot fungi.

NIOO's microbial collection contains many bacterial isolates derived from decaying wood. Since many of these bacteria have no inhibitory effect on fungi but fight against competing bacterial wood inhabitants, they are interesting for research into new antibacterial agents that leave eukaryotic cells (fungus, human) undisturbed. Thus, decaying wood in forests could potentially become another important contribution to finding much-needed new antibiotics.

Inspiration for sustainable agriculture

Unlike those in forest soils, the amount of fungal filaments in most arable soils is very limited. Although intensive tillage and fungicide use contribute to this, it is primarily the lack of degradable organic matter that limits fungal growth. We also see this in decommissioned fields on the Veluwe, where accumulation of organic matter and fungal growth remains limited over many years. As a result, important contributions of fungi to soil performance are missing. Examples include the formation of soil aggregates (better moisture retention capacity and reduced wind erosion), the regulation of the availability of mineral nutrients (including less leaching of nitrate), and increasing soil biodiversity (fungal part of the soil food web).

Inspired by the successful growth of fungi on wood in forests, Anna Clocchiatti spent her PhD research (2016-2021) investigating whether incorporating wood sawdust and chips into field soils stimulates fungal growth. It worked well! In particular, incorporation of hardwood material resulted in rapid and long-term stimulation of fungal filamentous growth. The fungi that develop are not the wood rot basidiomycetes found in forests, but ascomycetes (sac fungi) that have easy access to the cellulose polymers in shredded wood.

Stimulating fungi through wood addition fits well with more sustainable agriculture. It suppresses plant pathogenic fungi and the excess nitrogen, which might otherwise wash out, is captured by the fungi. It also increases the overall diversity of soil life by providing fungal-eating soil animals with a food source.

The use of wood as a soil improver is not yet widespread in agriculture. The government's incentive to create woody landscape elements such as hedgerows and girdles may also encourage the use of prunings to improve field soils. A little forest in the farmland will do the soil life good!

This article is part of a series on 70 years of ecological research by the Netherlands Institute of Ecology (NIOO-KNAW). This time, fungi are the common thread. Future editions will cover, for example, blue-green algae, bird rings and soil ecology. Find more on 70 years of ecology on the website of NIOO-KNAW.

Text: Wietse de Boer, NIOO-KNAW, in collaboration with Vakblad Natuur Bos Landschap
Photo's: NIOO-KNAW