Featured Research

from universities, journals, and other organizations

Treading into gray area along spectrum of wood decay fungi

Date:
June 23, 2014
Source:
DOE/Joint Genome Institute
Summary:
A fungus that can break down all the components of plant cell walls is considered a white rot fungus. If it can only break down cellulose and hemicellulose, it's a brown rot fungus. A research team suggests that categorizing wood-decaying fungi may be more complicated, broadening the range of fungal decay strategies to be explored for commercializing biofuels production.

The white rot Jaapia argillacea was one of the four fungi whose genomes were recently sequenced as part of the study. It has characteristics of a white rot fungus but not all of the expected traits. Researchers grew the fungus on pine wood and it broke down the cell walls in localized areas, removing the cellulose, hemicellulose and lignin.
Credit: Benjamin Held, University of Minnesota

One of the most basic rules for playing the game "Twenty Questions" is that all of the questions must be definitively answered by either "yes" or "no." The exchange of information allows the players to correctly guess the item in question.

Fungal researchers have been using a variation of Twenty Questions to determine if wood-decaying fungi fall under one of two general classes. If a fungus can break down all the components -- cellulose, hemicellulose and lignin -- of plant cell walls it is considered a white rot fungus. If a fungus can only break down cellulose and hemicellulose but not lignin, they classify it as a brown rot fungus. Known white rot fungi produce certain lignin-degrading enzymes called class II peroxidases (PODs) and a variety of enzymes that go after crystalline cellulose.

In a study published online the week of June 23, 2014 in the Proceedings of the National Academy of Sciences, a team led by U.S. Department of Energy Joint Genome Institute (DOE JGI) fungal researchers suggests that categorizing wood-decaying fungi as either white rot or brown rot may not be as clear-cut as previously thought. The discovery complicates but also broadens the range of fungal decay strategies to be explored for commercializing the process of biofuels production.

This finding emerged after researchers analyzed 33 basidiomycete fungal genomes, 22 of which are wood decayers, four of which had been recently sequenced by the DOE JGI. Based on previously sequenced genomes, the team observed that two of the new fungi, Botryobasidium botryosum and Jaapia argillacea, had the cellulose-attacking enzymes characteristic of white rot fungi, but lacked PODs, making them similar to brown rot fungi. Applying a statistical process called Principal Components Analysis (PCA) to find similarities in fungi based on their plant biomass degrading genes, they found that the two new fungi grouped close to Phanerochaete chrysosporium, the first white rot species sequenced. This was a curious finding because the new fungi were phylogenetically distant from P. chrysosporium, and, moreover, didn't have PODs.

The team then grew isolates of B. botryosum and J. argillacea on pine and aspen wood. They found that the fungi superficially degraded the wood surfaces but in localized areas, went further and broke down the cell walls and removed cellulose, hemicellulose and lignin.

"[They] show similarities to white rot fungi in … all predicted carbohydrate- and lignin-active enzymes and can degrade all components of wood, but they do so without the PODs that are a hallmark of white rot," the team reported in their paper. They also found a correlation between secondary metabolism genes, which are crucial for fungal survival, and brown rot fungi. These results, they added, suggest that the perceived dichotomy of white rot and brown rot is too simplistic and suggest that fungal wood decay capabilities be categorized instead on a continuum.

DOE JGI Fungal Genomics head Igor Grigoriev noted this wasn't the first time they'd seen a genome that appeared to blur the definitions between white rots and brown rots. "We thought we saw an anomaly with a previously sequenced white rot fungus Schizophyllum commune," he said. "Now we see a trend. This is the value of having multiple data points and so many fungal genome sequences. This is the whole point of doing fungal genomics at scale."

Dan Eastwood, a fungal researcher at Swansea University who was not involved in the study, pointed out that fungi don't have to follow rules to exhibit a decay form. "The manuscript is very timely and provides evidence for what many people in the field have suspected for some time -- that simple descriptors of wood decomposition do not necessarily reflect the diversity in decay strategies exhibited by fungi," he said. "This is particularly the case when discussing the brown rot wood decay mechanism where distantly related species have evolved superficially similar decay mechanisms. This manuscript uses whole genome sequence information to outline the argument for advancing our understanding of wood decomposition away from a simplistic white versus brown rot dichotomy."

"This is the first time we see patterns of white rot without this particular enzyme," Grigoriev added. "That tells us these fungi degrade lignin using other means, which tells us POD is not the only marker for white rot. Now that it's clear that it's not the only player, we should broaden our search for enzymes that have bioenergy applications. It is important to identify a whole range of enzymes sourced from nature that can be used to develop second-generation biofuels in terms of breaking down lignin and other components in plant cell walls."

Eastwood added that the work allows researchers to start to understand decay strategies in complex habitats. "Wood is a complex substrate in a complex environment," he said. "Evolution of decay mechanisms will be complex also, and the diversity in gene compliment will reflect the polyphyletic nature of superficially similar decay strategies. The future challenges are to better define the chemical environment during wood decomposition in conjunction with enzyme activity of different species that appropriately reflect their specific ecology."


Story Source:

The above story is based on materials provided by DOE/Joint Genome Institute. Note: Materials may be edited for content and length.


Journal Reference:

  1. R. Riley, A. A. Salamov, D. W. Brown, L. G. Nagy, D. Floudas, B. W. Held, A. Levasseur, V. Lombard, E. Morin, R. Otillar, E. A. Lindquist, H. Sun, K. M. LaButti, J. Schmutz, D. Jabbour, H. Luo, S. E. Baker, A. G. Pisabarro, J. D. Walton, R. A. Blanchette, B. Henrissat, F. Martin, D. Cullen, D. S. Hibbett, I. V. Grigoriev. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proceedings of the National Academy of Sciences, 2014; DOI: 10.1073/pnas.1400592111

Cite This Page:

DOE/Joint Genome Institute. "Treading into gray area along spectrum of wood decay fungi." ScienceDaily. ScienceDaily, 23 June 2014. <www.sciencedaily.com/releases/2014/06/140623154755.htm>.
DOE/Joint Genome Institute. (2014, June 23). Treading into gray area along spectrum of wood decay fungi. ScienceDaily. Retrieved July 28, 2014 from www.sciencedaily.com/releases/2014/06/140623154755.htm
DOE/Joint Genome Institute. "Treading into gray area along spectrum of wood decay fungi." ScienceDaily. www.sciencedaily.com/releases/2014/06/140623154755.htm (accessed July 28, 2014).

Share This




More Plants & Animals News

Monday, July 28, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Traditional African Dishes Teach Healthy Eating

Traditional African Dishes Teach Healthy Eating

AP (July 28, 2014) Classes are being offered nationwide to encourage African Americans to learn about cooking fresh foods based on traditional African cuisine. The program is trying to combat obesity, heart disease and other ailments often linked to diet. (July 28) Video provided by AP
Powered by NewsLook.com
Asteroid's Timing Was 'Colossal Bad Luck' For The Dinosaurs

Asteroid's Timing Was 'Colossal Bad Luck' For The Dinosaurs

Newsy (July 28, 2014) The asteroid that killed the dinosaurs struck at the worst time for them. A new study says that if it hit earlier or later, they might've survived. Video provided by Newsy
Powered by NewsLook.com
Raw: Sea Turtle Hatchlings Emerge from Nest

Raw: Sea Turtle Hatchlings Emerge from Nest

AP (July 27, 2014) A live-streaming webcam catches loggerhead sea turtle hatchlings emerging from a nest in the Florida Keys. (July 27) Video provided by AP
Powered by NewsLook.com
Russia Saves Gecko Sex Satellite, Media Has Some Fun With It

Russia Saves Gecko Sex Satellite, Media Has Some Fun With It

Newsy (July 27, 2014) The satellite is back under ground control after a tense few days, but with a gecko sex experiment on board, the media just couldn't help themselves. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins