Microbiology Resource of the Month: The Proteome of Fungus Philocephala scopiformis When Grown on Wood

Feb. 28, 2019

Announcement: The Foliar Endophyte Phialocephala scopiformis DAOMC 229536 Proteome When Grown on Wood Used as the Sole Carbon Source.
Resource: Proteome of the fungus P. scopiformis when grown with only pine wood chips

What is Phialocephala scopiformis?

Phialocephala scopiformis is a fungal endophyte that lives in conifer trees. Because P. scopiformis produces an anti-insect metabolite, rugulosin, many nurseries spray seedling trees with the fungus as a natural protectant. New research suggests P. scopiformis contributes to wood degradation, which was previously attributed to other microorganisms, and this discovery will contribute to our understanding of the carbon cycle.
The work was a collaboration between Jennifer Bhatnagar of Boston University, Grzegorz Sabat of the University of Wisconsin, and Daniel Cullen of the United States Department of Agriculture. The researchers provided insights into how they and others will use this new resource.
Shown here on malt extract agar is Phialocephala scopiformis DAOMC 229536, a well known endophyte of conifer needles and now proven to secrete an array of lignocellulose degrading enzymes.
Source: Jennifer Bhatnagar and Daniel Cullen

Why is it important to understand how microorganisms use wood as a carbon source?

Bhatnagar: Decomposition of dead wood is a critical process that determines how much carbon in the biosphere is released to the atmosphere as CO2, a greenhouse gas. Globally, dead wood contains approximately 7 times the amount of CO2-carbon released by humans annually through emissions. The decomposition of dead wood can lead to the release of this carbon as CO2 to the atmosphere (as decomposers respire) or it can be converted into stable soil carbon. Therefore, the way that wood decomposes influences exchange of carbon between the biosphere and the atmosphere on a global scale. Dead wood also stores nutrients that promote plant growth, like nitrogen, and is a hotspot for nitrogen accumulation, making its decomposition an important factor controlling forest productivity.
The microbial degradation of wood is a pivotal process in terrestrial carbon cycling and involves the activities of a diverse array of fungi and bacteria. Free-living saprophytic fungi possess the capacity to degrade 2 of the major polymers of wood, cellulose and hemicellulose.
Currently, ecosystem models are used by science and society to predict future atmospheric CO2 levels treat wood decay as a function of climate, subject only to the influence of rainfall, temperature, and the chemical composition of wood. However, these models cannot recapitulate some critical patterns of decomposition and CO2 release observed in field experiments, making it worthwhile to explore the wood decomposition mechanisms that are not represented in these models.
Traditionally, it has been assumed that wood is decomposed by a small group of bacteria and fungi that specialize on wood as a sole carbon source. However, recent observations of other types of microorganisms on and in wood are calling this assumption into question. In contrast to classic wood decomposers, Phialocephala scopiformis is a well-known endophyte of conifer needles. Nursery inoculation of conifer seedlings with P. scopiformis DAOMC 229536 limits spruce budworm damage, and persists in mature trees. Unexpectedly, metatranscriptome examination of extensively decayed Pinus contorta logs have shown that transcripts most closely related to P. scopiformis constitute the most abundant Ascomycetes present. This observation might be explained by specialized P. scopiformis variants. Alternatively, P. scopiformis may possess broad nutritional capacity, in which case a bona fide endophyte such as P. scopiformis DAOMC 229536 should be capable of utilizing wood as a sole carbon source. In support of the latter, the previously sequenced, P. scopiformis DAOMC 229536, is indeed capable of utilizing P. contorta wood as a sole carbon source and, in doing so, secretes an array of hydrolytic and oxidative enzymes.

What does the proteome of P. scopiformis tell you about its ability to degrade wood? 

Bhatnagar: To utilize lodgepole pine wood, we found that the spruce endophyte P. scopiformis DAOMC 229536 employed a diverse set of extracellular enzymes. Peptides corresponded to 590 proteins. 24% of the total extracellular proteins produced by P. scopiformis in culture were categorized as CAZymes, (including glycoside hydrolases (GHs), auxiliary activities and carbohydrate esterases), which catalyze the decomposition of abundant plant structural carbohydrates like cellulose.

Other GHs were more likely involved in the degradation of hemicellulose which, in conifers such as lodgepole pine, is primarily composed of O-acetylgalactoglucomannans and nonacetlylated arabinoglucuronoxylans. In addition to conventional hydrolases long known to degrade cellulose and hemicellulose, an array of extracellular oxidative enzymes and hypothetical proteins were unambiguously detected.

The precise role of some of these enzymes remains uncertain, but the impressive diversity suggests complex strategies involved in lignocellulose degradation. 

How will other scientists in the research community use this resource?

Bhatnagar: Dark septate endophytes (DSEs) such as P. scopiformis represent a large and widely distributed group considered nutritionally distinct from free-living saprophytes, like classic wood decomposers. However, accumulating evidence now shows that many DSEs exhibit unexpectedly broad substrate utilization patterns and expanded gene complements, all of which suggest latent saprotrophy.
This biochemical and genetic versatility may be widespread among DSEs. Given the enormous carbon pool in forest litter, twigs and logs, DSEs likely play an important role in the carbon cycle and merit consideration in current ecosystem models. Our P. scopiformis proteome identifies potential targets for future studies broadly relevant to lignocellulose degradation as well as enzymes for the conversion of woody biomass to high value products.

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Author: Julie Wolf

Julie Wolf
Dr. Julie Wolf is in science communications at Indie Bio, and was a former ASM employee. Follow Julie on Twitter for more ASM and microbiology highlights at @JulieMarieWolf.