World Record Largest Myxomycete Found On BRIT Campus

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Fuligo septica, dog-vomit slime mold

And there it was—a myxomycete fruiting body about 30 inches by 22 inches, round like a pancake and filled with spores, found in BRIT’s front yard growing on bark mulch in bioswale #3. This discovery was recently published in the 2016 Summer Issue (Volume 9, No. 2) of FUNGI magazine, a popular publication for amateurs and professional mycologists (people who study fungi and fungal-like organisms). There were more than 20 smaller fruiting bodies scattered on the surface of the bark mulch, but this fruiting body eclipsed the former world record by several inches.

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What is a myxomycete? They are often referred to by mushroom collectors as “slime molds” because of a soft, jelly-like, amorphous stage called a plasmodium that creeps over the surface of bark mulch feeding on microorganisms, mostly bacteria, eventually developing into a fruiting body structure that forms spores. There are animal-like life cycle stages that are motile, tiny amoebae or swimming cells as well as plant-like or fungal like stages with spores. Most of the species have fruiting bodies that are tiny, less than 0.1 of an inch in diameter.

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This myxomycete species, Fuligo septica, is common in the Fort Worth area, growing on piles of leaves, compost heaps or piled grass clippings, wood chips, decomposing tree stumps, living grass in yards, and bark mulching around the base of trees. It is not a disease pathogen and poses no problem attacking and killing lawn grass or shrubbery. It is sometimes a scary nuisance as in the case of a Garland, Texas, homeowner that discovered the plasmodial stage growing and getting larger, that was called “the Texas Blob,” portrayed as a mutant bacterium that might take over the earth, and made newspaper headlines throughout the country.

This one has a sad face...

This one has a sad face…

How did this myxomycete get to this site? The spores are wind-blown and probably were already present on the oak bark mulch when it was placed in the bioswale around the trees. This article has weather data compiled from a BRIT weather station that includes the temperatures, precipitation, and the time course of fruiting body formation for the period March 1st to April 15th, 2016.

The discoverers by the now old plasmodium.

The discoverers by the now old plasmodium.

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Keller, H.W., B. O’Kennon, and G. Gunn. 2016. World record myxomycete Fuligo septica fruiting body (aethalium). FUNGI 9(2):6-11.

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BRIT’s Computer Vision(aries)

This summer, four high school students from Trinity Valley School interned at BRIT through our Junior Volunteer/Intern program. These students were given the task of applying their computer science background to the challenge of helping BRIT create a quick and easy way to determine the fullness of our herbarium cabinets. By better understanding the details of the capacity of the cabinets, BRIT will be able to strategically plan for future growth and management of the herbarium collections.

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L to R: Ashia White, Kevin James, Jason Best, and Jacob Haydel

I worked with students Grace Beasley, Jacob Haydel, Kevin James, and Ashia White to explore the process of using computer vision technology to analyze images of the open cabinets. We set out to extract details of each cabinet’s structure and the height of each stack of specimens within the cubbies of the cabinet to determine how much space is available for use in the cabinets. The students also created a powerful graphical interface for visualizing the cabinet data once they are generated.

The students already had experience with Processing, a software platform which facilitates the creation of software with rich and dynamic user interfaces, so we chose this as our primary tool for the project. Fortunately, Processing also has a number of additional modules which helped the team manipulate and analyze the images. In particular we used two modules that are focused on computer vision technology: OpenCV and BoofCV.

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The popular app FaceSwap involves similar technologies as those being used for this project. Photo credit: John Woods (Woodsie TV @ YouTube)

Computer vision technologies are used for many applications ranging from self-driving cars, to robotics, to entertainment, and much more. For our particular challenge, we used computer vision techniques to analyze the images of open cabinets to first find the boundaries of the cabinets and the cubbies, then to identify and measure the spaces that were filled with specimens. The computer vision modules provided all the tools we needed to do this, but we still had to experiment a lot to find the right combination of tools and methods to get consistent and accurate results. We haven’t yet found the perfect formula, but we are very close to a solution that we hope to start using soon.

 

To perform a full herbarium capacity analysis, we’ll need to capture an image of every cabinet in the herbarium (something we hope to recruit our loyal volunteers to help with), then process them with our computer vision solution. In the end, we’ll have a dataset with a record for each cubby and the percentage fullness of that cubby, as well as a total fullness percentage of each cabinet. With those data, we’ll have a much better idea of how much room we have to grow and how to strategically organize our collection to more easily adopt orphaned collections. To better understand this huge amount of data, the team also created a graphical interface that helps visualize the data in a more intuitive format. In particular, we created a herbarium “heat-map” using Processing which can read all the capacity data and superimpose color-coded cabinets on a herbarium map (pictured below). The interface also lets you click on a cabinet and see the details of each cubby and eventually we’ll combine this with the herbarium inventory data to let you see what species are in the cabinet.

A heatmap of the BRIT herbarium showing cabinet fullness.

A heat-map of the BRIT herbarium showing cabinet fullness. This was created in Processing and uses simulated data, but the interface itself is fully functional.

The project still has a ways to go before we have a final, polished tool ready for use by the herbarium, but several of the students are eager to continue their efforts beyond the end of their summer break. Below, Jacob and Kevin share their summer experiences.

Jacob Haydel

Going into this project for BRIT, I didn’t really know what to expect. I hadn’t really done any work with computer vision, but I was eager to get started. The main thing I have learned from the project is that programing as a team is very different from working on an individual project. When working as a team you have to make sure everyone is on the same page and agrees on the direction the project should go. I also learned a lot about the problems that face BRIT in the digitization process. Taking a written format and converting it to a digital one can be a very tedious process; however there are huge benefits to digitization.

Working on the program, at first we had a really simple goal, to figure out how full the cabinets were. As we progressed we slowly started adding other goals to our original goal and expanded our idea of what this program could do. Despite this we were able to incorporate most of the ideas we came up with, and I think when the final program is done it will be much better than we initially imagined. I have really enjoyed working on what I would consider my first real world project in programing. It has definitely solidified my desire to pursue computer science as a career.

Kevin James

Going into this project, I wasn’t too sure how we were going to approach a project on such a large scale as this one. To begin, we learned the basics of computer vision and data visualization. Over the summer, we mainly worked on the data visualization aspect of the project, using fake data to test our program. We now have a heat map of the BRIT Herbarium, as well as a program that lets us view the fullness of individual cabinets. We hope to continue to expand this program, and we also hope to find a reliable method to obtain accurate data from the herbarium.

Our group faced the challenges that come with working on such large code as a team. This included changing specific parts of the code without unintentionally altering the entire program. We eventually learned how to work together more efficiently, and we managed to make a working program to display our herbarium data. This project was a very rewarding experience for me because I got an opportunity to use my computer skills in the real world.

 

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Data Entry, Insects, and Flying Cacti: My BRIT Internship

By Haley Rylander, BRIT Operations and Research Assistant.

Last summer (2015) I was a research intern at BRIT. I was first intrigued by BRIT – this strange and beautiful building of plants – during a field trip there for a Plant Biology class my junior year at TCU. I mean who wouldn’t want to spend the summer surrounded by fellow science nerds and doing ground-breaking and exciting research in a building made half of glass with an entire prairie on its roof? Naturally, my research internship was not quite this glamorous… But it was a priceless experience learning what really goes on behind scientific research, what it’s like working in a non-profit, and making valuable connections in the conservation science community.

Looking for rare species at a vernal pool at Elk Mountain, Oklahoma.

Looking for rare species at a vernal pool at Elk Mountain, Oklahoma.

I did a wide array of tasks in my internship. I helped with the long and intense herbarium inventory, entered data for Enchanted Rock and LBJ Grasslands species lists, went on a field day to the mountains in Oklahoma to document a rare species, entered more data…

A day on the living roof with BRIT researchers Heather Bass and Kim Taylor.

A day on the living roof with BRIT researchers Heather Bass and Kim Taylor.

I was also very fortunate to be trained to go onto the living roof. With three other researchers, I climbed onto the roof at the crack of dawn and helped record what species were growing. We also spent a lot of time clearing the lines that connect researchers to the roof via bungee cords and a harness. This primarily consisted of kicking cactus off the path and thoroughly confusing everyone in the building as cactus fell from the sky past their windows and crashed onto balconies. We even found a poor duck who had made her home in the brush on the roof and laid her eggs there! Apparently there was quite the panic later about what would happen to the ducklings if they hatched and tried to get off the roof, but (un)fortunately the roof was too hot and the eggs never hatched.

Objects of terror and tragedy: cacti that came flying off the roof and duck eggs that never hatched.

Objects of terror and tragedy: cactus that came flying off the roof and duck eggs that never hatched.

My primary project, however, was studying arthropod diversity on the living roof as compared to a native prairie upon which it was modeled. Before my internship, BRIT researchers installed pitfall traps on the living roof and counted and recorded everything that fell into them. Pitfall traps were then installed in a prairie near Benbrook Lake – and I was the lucky one who got to process these specimens! I counted thousands of ants, beetles, grasshoppers, spiders, and more, identifying them and grouping them by family/genus/species. After I had processed all these data I compared the species populations, diversity, and ratios of Benbrook Prairie to that of the roof and made a research poster of my results. It was an interesting project that gave some very useful information. The roof essentially had the same species as the prairie but in ratios mirroring a much earlier stage of succession.

A job of an intern: counting, counting, counting...

A job of an intern: counting, counting, counting…

My internship gave me so much valuable experience in my field. I met some awesome people, learned a lot of very different things, and felt that I made a lasting contribution to the organization – and it was pretty cool to know my research poster would continue to hang in the hallways after I left!

As a BRIT staff member, I now get to walk past my poster several times a day!

As a BRIT staff member, I now get to walk past my poster several times a day!

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Documenting Diversity: The First Step in Conservation

In the conservation community, there is often nothing more rewarding than walking through a landscape that you had a hand in saving and knowing that you did good. You saved this rare and valuable natural treasure for future generations. This is conservation at its finest and what most in the conservation community strive for. But there’s so much more that goes into the process, and believe it or not, it’s the early steps that I find most exciting.

And what is that first step? Documentation!

I know. It doesn’t sound that exciting, but we can’t protect what we don’t know. Before we can protect a piece of land, we need to know what we stand to lose if we fail; before we can restore a degraded prairie, we have to know what we are working towards; before we can protect a rare species, we need to know first that it exists and then that it is truly in need of protection. All of these conservation actions require that we know about the plants and ecosystems that we’re trying to conserve. Without this basic knowledge, we could easily squander our limited time and resources protecting a species or a piece of land that doesn’t need our protection. Cataloging diversity enables us to prioritize our efforts and identify what is truly at risk and what is truly unique.

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Kim Taylor documenting the plants at a private ranch in central Texas.

This idea of conservation through documentation has been a cornerstone of BRIT research for years. Our past projects in Peru, Jamaica, the Philippines, Papua New Guinea, and even right here in Texas have actively cataloged plant diversity. BRIT Biodiversity Explorer Dr. Sula Vanderplank is currently on the front lines of this work. Her biodiversity surveys in Baja California are working to catalog the total biodiversity of areas threatened by development or mining. Without these surveys there would be no evidence of the impact these developments would have on natural ecosystems and no sense of what was at stake. I was amazed when I saw that 29 species protected under Mexican law were in the proposed impact area for a gold mine inside the Sierra de la Laguna Biosphere Reserve. Sula’s work has brought the well-being of these treasures to the forefront. We now know what we stand to lose.

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Dr. Sula Vanderplank and her colleagues generated a report cataloging the diversity of a proposed impact area for a gold mine in Sierra La Laguna Biosphere Reserve.

The protection of any plant, animal, or ecosystem is contingent upon the ability to recognize that it exists in the first place. Many of our rare plants and ecosystems are still unknown to us. BRIT Vice President of Research, Dr. Peter Fritsch, recently described a new species of wintergreen (Gaultheria marronina) from the mountains of Sichuan, China. This new species is only known from two populations worldwide and is classified as endangered. Documenting the very existence of this species puts it on the radar for conservation. Without a name, this plant would forever live in obscurity and quite possibly be lost to extinction.

This same concept applies to ecosystems as well species. A plant community without a name can easily be overlooked. BRIT Biodiversity Explorer (and my mentor), Dr. Dwayne Estes, is working on the Pennyroyal Plain prairies, a little known prairie system in Tennessee and Kentucky. This system once spanned more than 200 miles, but today has only a few small remnants. The drastic contrast between this open grassland system and the surrounding forest landscape means that by its very nature, it harbors a unique set of plant species. With the loss of this system, many of the Pennyroyal Plain species, such as the rare Rudbeckia subtomentosa (sweet coneflower), are at risk. We will never know how many species were lost before scientists began documenting the diversity here. Without thorough documentation, this system could’ve gone unnoticed, and its remaining treasures lost forever.

Participants at the Mid-South Prairie Symposium learn about the Pennyroyal Plain prairies.

Participants at the Mid-South Prairie Symposium learn about the Pennyroyal Plain prairies.

Once we know that a plant or community exists, we have to determine if it’s truly in need of protection. Over the past six years I’ve worked to understand the distributions of rare and endemic species in Texas. We’ve shown that species which were previously thought to be rare, or not known to occur in our region, are actually common in certain habitats. We now know what truly needs to be done to conserve rare species like Dalea reverchonii (Comanche Peak Prairie Clover), Gratiola quartermaniae (Quarterman’s hedge hyssop), and Isoetes butleri (Butler’s quillwort). Currently, I’m documenting the distribution of four rare species in north Texas. This summer I began working on one of these, Pediomelum reverchonii (Reverchon’s scurfpea). When I first started the project there were only 10 known populations from the state of Texas (and only 15 outside of Texas, all from Oklahoma). During the course of the last month we’ve documented nine previously unknown populations, and we have only just begun. Finding and documenting these populations is the first step. Once we know where it grows, how abundant it is, and what habitat it prefers, we can begin to make informed decisions about the future of this rare species and work strategically towards its conservation. It’s an exciting process, and it all starts with documentation!

BRIT Research Assistant Haley Rylander (standing) and BRIT interns Lorena Cisneros (left) and Hanna Lieberman (right) survey a population of Pediomelum reverchonii.

BRIT Research Assistant Haley Rylander (standing) and BRIT interns Lorena Cisneros (left) and Hanna Lieberman (right) survey a population of Pediomelum reverchonii.

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Grey Fox: Exploring an Ancient Maya Center

Not all is as it appears! Bella the begonia visits Belize and helps Karen dig up potato root for collection.

Over the past two summers (2015 & 2016), BRIT Resident Research Associate Dr. Grace Bascopé, a Medical and Environmental Anthropologist, worked with the Maya Research Program’s (MRP) Blue Creek Archaeological Project to investigate the flora in far northwestern Belize. Working with her were Dr. Will McClatchey, former BRIT staff member and ethnobotanist, and Dr. Thomas Guderjan, Associate Professor of Anthropology (University of Texas, Tyler) and director of the MRP Blue Creek project.

For over two decades, MRP has undertaken annual archaeological field seasons in northwestern Belize to better understand the ancient Maya civilization that lived there from 900 BC to AD 900 and later. This effort has included major excavations of several ancient Maya centers and multi-disciplinary and multi-national studies of their agriculture systems. Besides Dr. Guderjan, others working on this project are Dr. Tim Beach, soil scientist and geographer (Georgetown University), Dr. Sheryl Luzzadder-Beach, hydrologist and geographer (George Mason University), and Dr. Nick Brokaw, forest ecologist (Universidad de Puerto Rico), among many others.

Trekking through high canopy in the rainforest toward the archaeological site core. This summer, the team did transects there to calculate the biodiversity.

MRP staff have witnessed the ongoing loss of forests and archaeological sites to clearing for modern agriculture and are taking steps to protect remaining sites. They recently purchased the “Grey Fox” site, one of only four Maya plaza-pyramid centers remaining in northwestern Belize. MRP is actively studying two of the other three sites—now only “forest islands” of 150 and 154 acres—and hopes to purchase for protection. While MRP’s primary interest is in protecting the archaeological materials within these sites, its members are also deeply concerned with protecting these forest remnants and treating them wisely as excavations go on.

Brokaw has completed an inventory of the trees of the high canopy at Grey Fox, to which Bascopé and McClatchey are adding the other plants of the region. They collect in duplicate for the BRIT herbarium and the National Herbarium of Belize (BRH) in Belmopan, and they also trained senior staff members of the MRP Project in collecting plant specimens and properly drying and storing them. This will allow the plant collections to grow even after those staff associated with BRIT leave the field. As a way of both saying thanks for allowing the research to be conducted in Belize and helping the resource-scarce National Herbarium, all specimens to be deposited there by the BRIT/MRP team are carefully mounted on archival paper and properly labeled.

Making collections for the BRIT herbarium and National Herbarium of Belize. The researchers wrote descriptions of the specimens and prepped them for pressing, drying, and labeling. Bella also lent a helping hand!

The overall goals of this joint BRIT/MRP project—benefiting BRIT, MRP, and the Belize National Herbarium—are (1) to contribute to BRIT’s collections from this Central American region; (2) to contribute to the national collections of Belize; (3) to provide a plant inventory so that archaeological work can continue with as little impact on the forest as possible; and (4) to provide an understanding of plants that are in the immediate area of the sites so these can be compared with pollen, phytolithic, and other plant material recovered during excavation. This also provides the archaeologists with a floristic baseline, which helps them address issues such as subsistence patterning and climate change.

The BRIT/MRP project has led to the discovery that a very large percentage of the plants found at Grey Fox are edible, and this possibly lends credibility to the argument that the Maya have long-engineered their own forest environments. Even site cores (the ceremonial centers full of large pyramids and other structures), not to mention the residential precincts of these ancient cities, may not simply have been sterile places covered over with white plaster, but more likely resembled temperature-lowering gardens full of edible and useful plants.

Working in the rainforest calls for impressive mosquito protection! But all is worth it when surrounded by such natural beauty.

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