Quick Question: White Rot Fungi

[irregular]

Hello,

I'm interested in pursuing a project which uses white rot fungi. Before I settle on it, I have to make sure that I'll be able to get all of the materials. So, my question is, where do you think that I will be able to obtain/purchase the white rot fungi?

Thanks.

[donnahardy2]

Hi Irregular,

Welcome back! It sounds like you have selected another fascinating and challenging topic for your next science fair project. Here’s some background information on white rot fungi. There are a number of species in this group of fungi. The first article is a review article from one of the Wikipedia website references on this topic. I don’t have access to it right now, but I will try to get it for you because review articles are always a good place to start for background reading

Indian J Exp Biol. 2005 Apr; 43(4):301-12.

http://botit.botany.wisc.edu/toms_fungi/may97.html

http://www.cib.csic.es/repositorio_bd/p ... 43-368.pdf

http://www.fungaldiversity.org/fdp/sfdp/15-3.pdf

http://ncsu.edu/bioresources/BioRes_04/ ... SF_371.pdf

Here some information on the taxonomy of these fungi commonly known as basidiomyctes.

http://www.fpl.fs.fed.us/documnts/pdf1998/burds98a.pdf

Fortunately, white rot fungi are ubiquitous, so one or two cultures should not be difficult to obtain. You could contact the mycology department of a local University and ask for a culture. If you find a reference article written by a local author, you can e-mail that individual and explain that you are doing a science project and request a culture. Do you have any paper pulp mills in your local area? If so, contact the company and ask if they have a sample or can refer you to someone doing research in this area. Or, if I were you, I would look for a local source. Are you close to a local park or forest that has decaying trees? You can identify white rot fungi on decaying wood that is lighter than the original color. Or, you could look for a rotting apple. Here are some photographs to help you identify white rot fungi in the wild:

How to identify:

http://www.world-of-fungi.org/Mostly_My ... tfungi.htm

http://www.caf.wvu.edu/kearneysville/di ... hiter.html

http://www.flickr.com/photos/52467126@N05/5680362473/

http://woodwildpark.org/fungi/inventory05.htm

Here is information on growing isolating white rot fungi.

http://www.trisanita.org/jases/asespape ... 1y2011.pdf

Here is a recipe for potato dextrose agar, the standard medium for growing fungi.

http://www.shroomery.org/forums/showfla ... er/4308913

Here is information from the Science Buddies website on microbiological techniques. White rot fungi are not pathogenic, but you would want to avoid breathing spores that can be present in high numbers in pure cultures. You will need to maintain a stock culture of an organism to use throughout your experiments.

https://www.sciencebuddies.org/science- ... Agar.shtml

https://www.sciencebuddies.org/science- ... ains.shtml

To growth this type of organism, you will need a 30 degree incubator, Petri dishes, agar, a method of aerating broth cultures, and it would be great to have a microscope, microscope slides and coverslips.

Let me know what you are thinking about doing for an experiment.

Donna Hardy

[irregular]

Hello,

Sorry for the late response. Thanks for all of the information and links, I really appreciate it!

At the moment I need a little bit of help developing my idea. I was originally interested in using white rot fungi to degrade lignin (I branched off from last year's project; lignin was a part of my project last year, but I didn't really concentrate on it). I also have read about the biodegradation of quinoline, insectisides, and nylon using white rot fungi and find those interesting. I have read quite a few various papers on these topics and on white rot fungi, but I'm having some difficulty understanding them (e.g. the processes which white rot fungi uses in order to biodegrade, hydrolytic vs. oxidative process, manganese peroxide). Some papers I've been reading:

ftp://124.42.15.59/ck/2011-01/165/012/6 ... TRATES.pdf

http://www.ncbi.nlm.nih.gov/pmc/article ... 8-0184.pdf

http://soe.stanford.edu/pubs/Gao%20et%2 ... )_5408.pdf (review article)

http://www.ncbi.nlm.nih.gov/pmc/article ... 630329.pdf

http://aem.asm.org/cgi/reprint/64/4/1366.pdf

http://www.aseanbiodiversity.info/Abstract/51004187.pdf

I have a a vague idea of what I want to do (I've mentioned above). My challenge right now is finding a specific aspect of this area which I want to concentrate on, finding what I can actually DO in that field (which is original), and develop this into an advanced project.

Thank you very much!

[donnahardy2]

Hi Irregular,

These look like good articles; I will print them out and read them and look for an idea for you. Is there any local environmental problem involving molecules that could be degraded by lignin-hydrolyzing fungi that you could work on? A project like this would make your research more relevant.

You need to understand the chemical structure of lignin and how it is degraded by microorganisms. Without reading all of the text, look at the structures included in these references. The key feature of lignin is that is has the 6-carbon ring structure that is impossible for most microorganisms to hydrolyze. However, the lignin degraders have various enzymes that will break the 6-carbon ring bond and eventually break the molecule down to very small metabolites. The fungus is doing this to derive the energy that is stored in the chemical bonds.

http://www.riken.go.jp/lab-www/library/ ... 42_039.pdf

This article has a table that lists the specific activity of the lignin-degrading enzymes:

http://www.fpl.fs.fed.us/documnts/pdf1997/hamme97a.pdf

Now, look at the chemical structure for bisphnol A, which is used to manufacture polycarbonate plastic items. You will see that is has the hard-to-degrade 6 carbon ring structure also. This is just one example; many pesticides and herbicides also have this 6- carbon ring in their structure.

http://en.wikipedia.org/wiki/Bisphenol_A

The enzymes in lignin degrading fungi have the ability to degrade the 6-carbon ring structures of many pesticides.

What kind of science class are you taking this year?

Have you identified a source of white rot fungi yet?


Donna Hardy

[irregular]

Hi!

Thank you so much for the great information, I'll read and understand lignin degradation so I can further understand my papers and look for ideas and conduct research throughout today and tomorrow. Something interesting I saw was that white rot fungi degrades lignin, and brown rot fungi decays cellulose; one idea is to choose a project where I could experiment with both fungi.

There is a researcher who lives 2-3 hours away and had helped me in the written portion of my project as well last year. He would like to work with me throughout my experiment this year, so I will be meeting with him on Wednesday and would like to make sure that I understand everything and have a rough plan chalked out.

In my high school there is only one grade 9 general science class offered which covers introductory biology, chemistry, physics and cosmology/earth science. However this summer I have been educating myself on high school biology, chemistry and physics using online videos.

FInding a white rot fungi source shouldn't be that hard since there is one nearby paper mill I believe, I live close to a provincial park and can look over there, I have found a professor at a nearby university who has done research on white rot fungi and could ask him, and, if any of those don't work, I could simply contact an author of a reference article who lives nearby (as you suggested). I will to find my definite source tomorrow.

Thank you!

EDIT: I'm sorry, two of the links I sent you didn't work. Here they are:

ftp://124.42.15.59/ck/2011-01/165/012/6 ... TRATES.pdf

http://soe.stanford.edu/pubs/Gao%20et%2 ... 9_5408.pdf

EDIT:

All Ideas:
- quinoline degradation
- insecticide/pesticide/herbecide degradation
- nylon degradation
- lignin degradation (newspaper degradation, like last year's project)
- experimentation of brown rot fungi/white rot fungi/soft rot fungi/antinomycetes
- finding a way to speed up lignolysis as it is a slow process
- degradation of leaves

I started working with what rough ideas I have and digging into them and finding more specific research. For example, the nylon degradation article was done using white rot fungi - has nylon degradation using brown rot fungi been tested? This will be the hard part - choosing one out of all of my ideas.

Thanks!

[donnahardy2]

Hi Irregular,

This is great that you have a local mentor who is willing to work with you and a local professor who is an expert in the topic. The professor should be able to help you get access to pure cultures of white rot fungi. You can contact the paper pulp mill and ask if there are any associated researchers from a university who are studying the paper pulp mill process. The paper pulp itself should be a good source of the specific organisms you are interested in.

All of your topics are good and worthwhile doing. The combination brown rot/white rot, soft rot/ actinomyces topic is appealing, but might get too complicated to be able to do a controlled experiment. The herbicide/pesticide/insecticide degradation project would be environmentally significant, but you would need a method of measuring your analyte. The nylon and quinoline degradation projects would be good, but not as environmentally significant. It would be fantastic if you could figure out a way to speed up lignolysis as this is a major problem, but more background reading is needed to come up with an idea on how to do this.

Have you looked into the fungal media and incubators you will need to do this project? This might limit the scope of your project to something you can do. Would the professor you know be able to facilitate access to a microbiology laboratory for you? That would be very helpful for this project.

Good luck with your meeting tomorrow!


Donna Hardy

[irregular]

Hi!

It's been a while since we exchanged a message last! At the moment, I'm exploring the storage unit for the fungi and how to measure degradation with my mentor and his team, and am in touch with a mycologist to answer any questions I have and to obtain the fungi (which he will provide me by about the end of the month). I'm basically trying to find out how the project will work itself (e.g. we realized that an incubator won't be needed, are looking for the possibility to use an HPLC for data analysis, weight loss measurement and CO2 measurement methods to measure degradation). My school will be helping me with equipment, and overall equipment shouldn't be an issue since I can contact companies, my mentor, the mycologist, or my father's workplace for help.

My mentor and his team are helping me out incredibly well in designing the experiment. I haven't been able to find a mycologist who specifically works in degradation of materials. However, I am still not completely satisfied with my exact project idea and would like to still make it more complex and original and challenging. The main idea in mind at the moment is to compare degradation of newspaper and possibly nylon with white-rot, brown-rot and soft-rot fungi. I am still interested in dealing with degradation of lignin/hemicellulose/cellulose as I want to continue on from the newspaper train of thought. I am also now better understanding how the degradation works.

Something interesting I noticed with my mentor was that in the paper "A critical review of the application of white rot...." they mention using lasers and UV radiation to enhance degradation, and that this field needs further research as well.

Here's an inventory of my scientific literature for this project (although some of the papers are not directly related to my project so far, e.g. quinoline/pesticide degradation):

Cellulose Degradation by Cellulose-Clearing and Non-Cellulose-Clearning Brown-Rot Fungi
http://www.ncbi.nlm.nih.gov/pmc/article ... 2-0167.pdf

Lignocellulosic Residues: Biodegradation and Bioconversion by fungii
ftp://124.42.15.59/ck/2011-05/165/068/3 ... nocell.pdf

Studies on QUinoline Biodegradation By a White Rot Fungus in Liquid and Solid State Substrates
ftp://124.42.15.59/ck/2011-01/165/012/6 ... TRATES.pdf

Lignin degradation and roles of white rot fungi: Study on an efficient symbiotic system in fungus-growing termites and its application to bioremediation
http://www.riken.go.jp/lab-www/library/ ... 42_039.pdf

Fungal Degradation of Lignin
http://www.fpl.fs.fed.us/documnts/pdf1997/hamme97a.pdf

Nylon Biodegradation By Lignin-Degrading Fungi
http://www.ncbi.nlm.nih.gov/pmc/article ... 630329.pdf

A critical review of the application of white rot fungus to environmental pollution control
http://soe.stanford.edu/pubs/Gao%20et%2 ... )_5408.pdf

Evidence for cleavage of lignin by a brown rot basidiomycete
http://www.fpl.fs.fed.us/documnts/pdf20 ... lle001.pdf

Purification and Characterization of Nylon-Degrading Enzyme
http://aem.asm.org/cgi/reprint/64/4/1366.pdf

Degradation of Contrasting pesticides by white rot fungi and its relationship with ligninolytic potential
http://www.aseanbiodiversity.info/Abstract/51004187.pdf

Quantitative Changes in Structural Components of Conifer Woods During Decay by White- and Brown-Rot Fungi
http://www.apsnet.org/publications/phyt ... 1_1338.pdf

Some Articles which I also have and find useful:
http://forestpathology.cfans.umn.edu/microbes.htm
http://ehp03.niehs.nih.gov/article/fetc ... p.93101232
http://www.biology.ed.ac.uk/research/gr ... odrots.htm
http://www.hawaii.edu/abrp/Technologies/fungus.html

If you have any input it would be great.

Thanks!

[donnahardy2]

Hi Irregular,

You are making great progress, and I’m happy to hear you will be able to start soon since the white and brown rot fungi grow more slowly compared to the yeast and microbial fuel cell organisms that you have worked with previously. Thanks for including your bibliography. I have printed out all of the articles and I will read through them to see if I can help identify a unique idea for your project. It would probably be a good idea to settle on a significant topic. I understand your continued interest in newspapers, but I’m not sure if there is enough significance for newspapers. Would the world be a better place if you could figure out how to degrade newspaper lignin more quickly than previous methods? Please explain what you are thinking about with this material. If you are expecting the lignolytic fungi to degrade the lignin to release the cellulose, which can be then be used for biofuel production, then I understand the purpose. The selection of a synthetic polymer like nylon, which is a growing environmental concern, is obviously a good topic for your project.

I’ll have more comments tomorrow.

Donna Hardy

[irregular]

Hello,

Thanks so much for helping me out! The reason I'd like to somewhat continue on from last year's project is because I am planning on applying for ISEF, and I'm not sure if I will submit the celluosic ethanol or this new one, or combine both as one project if that's possible. Hopefully I can produce an interesting and challenging project right now to submit for ISEF. Not only this, but as you know I'm indeed interested in the concept of degradation as well. However, I feel that simply degrading is not enough as the experimental procedure seems quite simple. By "continuing on from last year's project", I don't have to include newspaper, but primarily I'm interested in lignin/cellulose/hemicellulose and that interest branched off into nylon as well. I have to keep in mind the environmental applications of this project as well, as you've mentioned, and I agree with you in the biofuel production example. The different fungi play a part in this as well - the different types (white-, brown-, soft-rot) degrade different things (e.g. white-rot degrades lignin, brown-rot modifies ligni and degrades cellulose, soft-rot modifies lignin. By the way, it would be great if I could have some confirmation on the matter of which fungi degrades what from you. The information in my material varies, one article says that white-rot degrades hemicellulose, cellulose and lignin in fact.)

Thank you!