Happy Holidays!

Wishing all of you a safe and happy holiday season.  I will continue posting my research findings and other events after the new year.  I hope you stop back and see what interesting activities have taken place during the holiday break.

Hartley Wood Research: Initial Findings

I have now spent the better part of two weeks looking through the research database.  As a whole, it includes 612 collected specimens encompassing the phyla of Ascomycota (17%), Basidiomycota (78%), and Myxomycota (5%).  There were 130 genera and 199 species identified, not taking into account any repeats  or  unknown specimens found within the collection.  DNA has been extracted from voucher material with nearly 78% confirmed through gel electrophoresis.  The next step will be presenting the findings to my adviser and determining what extracted DNA to sequence.  My hunch is that all of the identified species will be sequenced and submitted into GenBank.  This should include species found within my sampling plots and those found randomly within the research site.  Once their identification has been confirmed using the ITS region of the DNA, a more confident approach can be made toward describing the species richness within the site.  Average temperature, precipitation, and relative humidity at the site during this two year study was examined with no obvious conclusion as to its impacts on the fruiting frequency of observed fungi.  This came as no surprise because most mycologists understand the ephemeral nature of the fruiting bodies and this study was based on collection/documentation of those fruiting structures.  More sorting and sifting through the database should disclose interesting associations among the specimens within the collection.  I will be sure to keep you all up to date on these findings as they become available.  Have a safe and happy holiday season!

Bacterial Blotch of Button Mushrooms

I have been backing up my research while preparing for the holiday season "rush" and came across some of my master's research data.  I received my MS degree in plant pathology in the Spring of 2007 and completed the entire program in about 18 months.  I was definitely in a "rush" to complete that program because my wife and I were eagerly awaiting the birth of our daughter Kaia.  The data acquired during that research was quite interesting and the method I developed to determine the severity of disease development for Bacterial Blotch on Agaricus bisporus using imaging software was very exciting.  I have provided a copy of my thesis defense seminar that I presented to the department of plant pathology in May of 2007.  Please click on the title of this post to view the entire PowerPoint slide show.  The image to the upper left shows an assay using the tissue of A. bisporus when challenged with variations of the causal agent, bacterium Pseudomonas tolaasii.  The acronyms for the variations are sterile distilled water (SDW) as a control, wild type (66W), pathogenic isolate (66S), and non-pathogenic revertant (66R).  The image to the middle left shows results of one Agar Well assay used to determine the inhibitory concentrations of hydrogen dioxide (Oxidate) on P. tolaasii grown in culture.  The image on the bottom left shows a histogram of the area of mushroom tissue post inoculation with the 66R isolate.  The results of my research objectives for this project are provided within the slide show and I wish there was audio to accompany it to provide a better understanding of the data.  Perhaps in the future I can re-post this presentation after a commentary has been added.

Potential New Species Discovered

 First, I would like to thank all of you for visiting this blog.  Within the last 30 days, there has been over 200 visitors from 5 different countries.  It is my pleasure providing information about my research and personal life with you all.  In the coming months I aim to post links to additional video clips, including those of me performing some original music.  Please stop back frequently to check for updates.

I am now performing the very tedious task of reviewing all of the unknown specimens in my collection of fungi and identifying them.  Most of this process is accomplished through the use of metadata recorded for each specimen in the collection.  Online sources and field guides are being used to aid in the identification of the majority of these unknowns.  However, there are many fungi within the collection that appear to be unnamed.  The images to the left are three of these potential new species.  The first is an Ascomycete and was only observed once within my research site.  It was growing at the base of a very large oak tree that has recently fallen during a snow storm.  The other two images are of fungi belonging to the phylum Basidiomycota and most likely the family Amanitaceae.  These specimens were observed once this past summer growing in the soils near a trail running through my study site.  When specific characteristics of these fungi were provided to a well known expert in this family, he indicated that he had never seen specimens like this before.  I am therefore extremely interested in pursuing the molecular identification of all three specimens to determine if they have been described and entered into NCBI.  If you would like to help me in the identification of these or future specimens, please e-mail me or leave a comment at the bottom of this post indicating your interest.  Stay tuned for the confirmation of these novel species.

Collection Database Management

Thank you all for visiting the blog after my brief absence during the Thanksgiving holiday.  I hope that you and your family had an enjoyable visit and that you all are eagerly anticipating the winter holiday season.  Now that I have returned to State College, PA and the Pennsylvania State University, I can continue organizing of electronic database.  I had initially entered data into a FileMaker Pro 10 database using the default templates.  This made data entry easy, but was very cumbersome when retrieving data of interest.  I therefore designed a template that used tabs to organize like metadata.  To the right are screen captures of the tab pages as they appear in the database.

Canadian Rockies Vacation 2009 Slideshow

Click on the post title to view the entire slide show of our recent adventures in Canada.

Hartley Wood Restoration Effort

It has been my pleasure to work with many individuals performing research within the Hartley Wood and to engage with others who are trying to manage this woodlot.  One such individual is Chip Clark, who serves as the Volunteer Coordinator for the Arboretum Woodland Restoration Corp. (AWRC). He stated that, " The mission of this group is to remove invasive non-native plants from the Hartley Wood and eventually replant with native species, as part of the overall area improvements coming with the Arboretum at Penn State".  Chip has accompanied me on several trips to my research site and has always provided me with fresh insights concerning the restoration of the woodlot.  He is currently attempting to determine the  usage of trails by mountain bikers so a management plan that would help protect those trails from erosion could be drawn.  In the images to the right, Chip and a mountain biker are discussing the recent addition of water bars on a steep portion of a popular trail entering the Hartley Wood.  These bars are put into place with the understanding that they will reduce the amount of erosion caused by the "ruts" produced by bike tires.  About Aaron D. Brown, Chip stated that he had, "the most complex and detailed research project ongoing in the Hartley Wood, and it is always a great learning experience for me when I accompany him on his visits in the Wood".  I always look forward to the next time I get to visit with Chip, whether it be during a hike or over a hot cup of coffee.  To access information about the AWRC click on the title of this post and drop Chip a line to let him know you appreciate his work.   

Visualizing Extracted DNA

I have spent the better part a week extracting DNA from dried tissue samples acquired during my research in the Hartley Wood.  There is over 600 specimens in the collection, of which 420 have had their DNA extracted.  Now begins the task of confirming the presence of DNA using gel electrophoresis.  This is not to say that if DNA is absent using this visual assay that it is physically absent, only that I could not observe the bands created during the electrophoresis process.  I have not standardized the concentration of extracted DNA before running the gels and therefore some bands are easy to see and others are quite faint.  Again, this assay is only being performed as a troubleshooting tool if my PCR products are not visible when run out on a gel.  Some of these terms might be foreign to some of you and I apologize, still the main point I am trying to express is the tedious nature of describing my collection through molecular techniques.  In today's field of mycology, these molecular characteristics (DNA sequences) are valuable sources of information used to identify and describe relationships between groups or species of fungi.  To the right is the image of a gel that has been stained with Ethidium bromide and photographed under UV illumination.  The "L" in the far left lanes are the 1Kb ladder used as a reference of size and the numbers above the remaining lanes indicate the extraction codes for the specimens.

Lake Louise, Banff AB Canada

It seems as if it were just yesterday when my wife, daughter, and in-laws made the 10 day journey from Vancouver to Calgary.  During this wonderful vacation through the Canadian Rockies, we encountered many sites to numerous to discuss in a single post.  So I have decided to give you a sample of just one  destination.  We took an entire day to visit Lake Louise in Banff, AB.  This day included a hike around the beautiful lakefront, a quick mycoblitz into the adjacent forest, and a fine dinner at the luxurious Fairmont Hotel.  Although it was mid-September, there were many individuals enjoying the scenery and some even partaking in water activities such as canoeing.  My daughter Kaia and I made our way through the evergreens via a well maintained dirt trail.  Along the way she would point out mushrooms and birds for me to identify.  Our "quick" hike ended up being nearly 30 minutes in length as we found ourselves getting drawn further and further into the forest landscape.  When we had emerged and located the other members of our party, it was off for a 45 minute hike around the perimeter of Lake Louise.  It was obvious to us how exhausting the day had been on our little girl as she soon fell asleep in the backpack carrier.  In fact, she slept through the group hike AND through the entirety of our lengthy, but enjoyable meal.  It was one of the first times my wife and I had eaten a meal together without any interruptions from our extremely active daughter.  The whole family was quite pleased with the vacation and were so happy to have had the opportunity to share it with each other.  Once the 1,500 images taken during the trip have been organized, a slide show will be provided within the blog for your viewing pleasure.                                      

Overuse of Pesticides: A Disney Cartoon

Although my research deals more specifically with the description of fungal communities with a wooded habitat, I am trained in the field of plant pathology.  This field investigates many of the pests that are destructive to valued crops, such as wheat, corn, and soybeans.  Often times the use of fungicides and/or pesticides are required to reduce diseases caused by these pests.  It is therefore extremely important to design an appropriate disease management plan with regards to the use of applied products.  In a short cartoon that was recently posted on my current research adviser's Face Book page,  Mickey Mouse experiences the drawbacks of overusing such chemical controls.  For all of you dedicated mycologists, there are several scenes in which giant mushrooms are visible!  Click on the title of this blog post to find out what happens to this iconic character.

Plot Disturbance From Recent Storms

While visiting my twenty-five plots this past week, I observed that nearly twenty-five percent of them had been effected by recent wind and snow storms.  Here in University Park, PA we received a record snowfall this October 15th.  It was the earliest recorded snowfall with standing accumulation and it caused lots of damage to trees.  In the Hartley Wood there were many large trees and branches downed from the weight of the snow.  Some of this woody debris fell onto my sampling plots and made it impossible for me to thoroughly investigate those areas.  I will not be including collections from this past month in any statistical analysis of the plots.  This should  eliminate any skewing effect caused by the reduction in sampling for these effected plots.  The image to the top left shows a sampling plot in the early part of October.  The image to the bottom left is the same plot post storm with debris covering the entire area of the plot.

Permanent Sampling Plot Layout

I had an opportunity to visit my research plots this past week and make my final collections for the year.  During that time in the woodlot I reflected on the amount of time it had taken me to arrive at the appropriate number and size of my permanent sampling plots.  I also thought about the layout of the plots and recalled how difficult it was to do so when the vegetation was at its most dense.  This encouraged me to create a short five minute tutorial on how to layout a circular sampling plot while the vegetation density has decreased.  If you are interested in learning how I created these permanent sampling plots, please click on the title of this blog post or click on "Sampling Plot Layout" under the Video Links section of this blog.  Let me know if you found the video informative and if you would like to see more video footage of my research.

Visit to the Mushroom Planet

Dr. Kathie Hodge, associate professor of mycology at Cornell University, lectures about the world of fungi.  Kathie is the director of the Cornell Plant Pathology Herbarium (CUP) and teaches multiple mycology courses at the university.  Her research includes the description of fungal diversity within insect pathogens.  She states that her lab uses "both modern molecular and classic morphological approaches to understand fungal relationships and make inferences about how they have evolved".  Please click on the title of this post to view her lecture and visit her Cornell Mushroom blog.

Coffee Grounds as Cultivation Substrate

Two Cal Berkley graduate students have developed a method of cultivating gourmet mushrooms on spent coffee grounds.  The process is similar to that used by mushroom companies cultivating fungi from substrate filled bags.  The difference is the ability for the mushrooms to be grown using materials that would normally be sent into a landfill.  This team of young men have entered into the BBC World Challenge 09 and are the only accepted entry from the United States of America.  Please check out this fascinating story by clicking on the title of this blog post and vote for these environmental innovators.

Maitake Workshop Spring 2009

I had the fortune to receive a few bags of maitake plugs from a friend this past spring.  The plugs are small segments of wooden dowels that have been colonized by the fungus Grifola frondosa.  This fungus is edible and a favorite of many students, faculty, and staff within our plant pathology department.  When word got out that I had some plugs, many individuals showed an interest in learning how to cultivate this fungus using oak logs as a substrate.  I immediately acquired freshly cut oak logs for use in a maitake inoculation workshop that I developed and instructed.  A small group of staff, faculty and students attended this 2 hour workshop and were given a inoculated log to take home with them.  I buried 2 large inoculated logs in a nearby woodlot and will monitor those locations for any fruiting body development.  The images to the right were taken by one of the workshop participants, Grace O'Keefe.  For a quick preview of the workshop  click on the title of this post.

Processing Fungal Specimens

After a long day of collecting fungi within my research site, I return to the lab and begin processing the collection.  Characteristics of the fungal specimens are described using basic tools, such as a stereoscope, microscope, and digital camera.  A description of ephemeral traits are recorded and images are taken of macroscopic and microscopic structures.  Spore prints are also prepared for many specimens within the collection and aide in their identification.  It takes roughly 2-4 days in the lab to process specimens collected during a single visit to my research site.  All data concerning the collection is entered into an electronic database and will be accessible in the future through a website.  The  first image has captured me entering data into a lab journal.  This information will then be compiled and entered into the electronic database.  The second image shows details of the pileus and gill tissue for an Inocybe sp.  Once the fungal specimens have been dried, tissue is removed for further DNA analysis, and a voucher is prepared.

Pumpkin Carving Session

My daughter and I had the best time this past Sunday while carving a large pumpkin on our kitchen floor.  She is nearly 2.5 years old and this was her first real experience with the carving process.  The previous Halloween she did have the chance to paint a pumpkin, but was not part of the carving process due to her age.  This year she was very interested in helping papa and mama create a jack-o-lantern and we agreed that it was time to show her how it was done.  After the "gutting" of the pumpkin, Kaia tried her hand at pulling all of the goo from within the pumpkin.  As one can see in the adjacent images, we had a great time and we were both happy to have caught the event with the digital camera, as mama was recovering from a cold and could not participate :(  

Cornell Plant Pathology Herbarium (CUP)

My visit to the Cornell Plant Pathology Herbarium (CUP) in June of 2009 was funded with a travel grant award distributed by the Penn State plant pathology department. The CUP facility had just celebrated its first year in its current location during this visit. The location was previously used for poultry research and was renovated to accommodate this herbarium. CUP has been described as the fourth or fifth largest mycological herbarium in North America. It houses approximately 400, 000 fungi and plant disease specimens, including over 7,000 types specimens and 60,000 historical photographs. CUP Curator, Robert Dirig, gave me an extensive tour of the facility. The knowledge gained during this brief visit will certainly be reflected in the proper preservation of specimens and vouchers collected during my research project in the Hartley Wood. The image to the right shows Robert inspecting the stability of a voucher packet from a collection.

Mycology Class Fall Foray

Two dedicated students from the PPATH 425 course of introductory mycology at Penn State met Aaron D. Brown for a guided foray. During the two hour walk through the Hartley Wood, adjacent to Sunset Park, many species of Basidiomycota were collected. Identification to genera and species was performed in the lab with the aide of multiple field guides. The "inky cap" mushroom can be seen here, prior to drying down for long-term storage.

Grape Picking at Happy Valley Vineyard

Graduate students from the Penn State plant pathology department volunteered there time to harvest grapes at the vineyard. The weather was delightful during this particular day of picking and the conversation among the students was quite entertaining. I am eagerly anticipating the final product from this years crop!

Whipple Damn Fall Foray 2009

Wonderful walk through Whipple Damn Park collecting array of fruiting fungal bodies. Some very informative instruction from local mushroom expert Bill Russell and Dr. Barrie Overton from Lock Haven University. It is my intention to create a comprehensive database of Pennsylvania fungi using species lists compiled during this foray and other forays throughout PA.

Genera of Fungi within Sampling Plots

There are twenty-five circular sampling plots uniformly distributed throughout the Hartley Wood. Image to the right indicates number of identified genera within each of the plots. The larger the circle shown, the more genera identified within the plot. The preliminary evaluation of raw data from this year's field season has yet to elude to any observable patterns or trends within the plots.

Collection of Forest Fungi

A fruiting body survey of fungi observed within an old-growth remnant forest will be used to generate a list of genera and species for the site. The image to the right shows Aaron D. Brown collecting fungal specimens from permanent sampling plot A02 during the fall 2009 season. Specimens are photographed, field characteristics recorded, and then placed into collection bags for short transport to lab. Final macro/micro photography of characteristics and identification of specimen completed in the laboratory.