Adjunct of post doctoral research, Erin Carr, is set to name new species and genera in the next couple of months.
Carr’s hypothesis is that these previously undiscovered fungi are interacting with local algae and cyanobacteria in the environment. Both algae and cyanobacteria can produce a carbon source through photosynthesis, with the cyanobacteria also providing a nitrogen source.
“If you have a cyanobacteria and algae friend right next to you, then you’ve got your carbon and your nitrogen, and that’s all you need to live,” Carr said.
This process is similar to how lichen survives on trees, rocks, soil, houses, tombstones, cars, old farm equipment and even the University of Nebraska-Lincoln’s campus. The fungi that Carr is researching can also be found on campus at the Beadle Center, which coincidentally is where her lab is located.
“Outside of Beadle, black sludge you see as you’re walking in from the bus stop, that’s my fungi,” she said.
Carr originally acquired 25 fungi and 40 algae from Steven Harris, an adjunct professor at UNL, after Harris returned from Canada with nine soil samples in hand. It became Carr’s job to isolate the fungi and algae.
It was with Harris that she became involved as a research assistant and a manager for the fly genetics lab in her early years at UNL. She later applied and got accepted to be a graduate student in biological sciences, mentored by Harris.
Her original area of work was co-culturing, or growing, fungi and algae in combination.
“I was just smashing them together and seeing if they stuck,” Carr said.
With the samples acquired from Harris, her primary focus for them was to use sequencing capabilities provided by the Joint Genome Institute to define exactly what kinds of fungi and algae they were working with.
“Our grant was to sequence six fungi, two algae and metagenomes for soil samples,” Carr said. “From there, my PhD focused on just those six fungi because that’s enough work as it is fully characterizing them.”
The characterizing process involves phenotyping the fungi and establishing what their DNA sequence looks like through extractions and extensive mapping of genes to identify what genes are actually present.
"Phenotyping involves conducting experiments to find out what temperatures these fungi grow at, what nitrogen or carbon sources they can grow on, what their favorite food source is, any UV or metal resistance and more," Carr explained.
“The reason why we did all this is to try and figure out how these fungi are growing in places where there are no carbon or nitrogen sources available,” Carr said.
Because there are many kinds of fungi being studied at once, it’s important to not get them mixed up. For ease of keeping the species separate, Carr decided to have a little fun naming the fungi with informal names that make it simple to distinguish them with the naked eye.
“Dr. Harris couldn’t keep them straight, so I named them with colloquial names. They are Goopy, Slimy, Fuzzy, Lumpy, Dopey and Crusty, based on how I felt about them and their phenotype [how they looked],” she said.
Making official scientific names for these new fungi would be a much harder process, according to Carr.
Goopy and Slimy were originally categorized as separate species but fell below the threshold of matching enough to be considered the same species. While they are closely related, they are not the same.
“We named them Goopy and Slimy in Latin. They are actually the same species, it turns out. They look really different under the microscope, but their DNA is the same,” Carr said.
Lumpy and Dopey do not fit within any existing genera at the moment, so that prohibited Carr and her team from being able to tell what order they are in. Currently, Carr is declaring they are between two genera and proclaiming a new one.
“It’s like if you [had] a human and a monkey and you didn’t know where the apes fit,” Carr said. “Yeah, they look kind of like humans, but they also kind of look like monkeys. They fit somewhere in between, so you have to create a new group for them.”
“There’s a whole process of naming new species, and then there’s slightly not much more relief to naming a new genus,” Carr said.
While all of these fungi have fun casual names, another commonality they share is that they are all melanized fungi, also known as black yeast fungi or polyextremotolerant fungi.
These special fungi can withstand extreme conditions as well as mesophilic conditions, which are conditions optimal for human life. Without the presence of melanin, these fungi would not be able to withstand all of the conditions that they do.
What adds complexity to this discovery is that melanin is still a mystery in the scientific community. Scientists are currently unable to figure out melanin’s true chemical structure because of its light absorbing properties.
“We can’t say for sure the chemical structure of melanin because the way we test it involves light, which melanin absorbs,” said Quin Barton, a sophomore undergraduate researcher on Carr’s team.
Barton added that the original melanin extraction protocol was found from another researcher’s paper, but it only worked with Goopy and Slimy, which contain a specific kind of melanin. For Creamy and the other fungi mutants, the original protocol for melanin extraction did not work.
Because of this, Carr had to create her own method, almost from scratch, and it worked. Now, due to Carr’s research, there are two different protocols for melanin extraction.
Carr’s research of these new fungi is currently in review at “G3: Genes, Genomes, Genetics.” Her publication, once the reviewing process is complete, will be published on their website in the following months.
In the meantime, Carr and her team are working to fulfill the requirements for declaring her new fungi species and genus. This is done through one or two of the worldwide fungal organizations, such as MycoBank, which is a part of the Westerdijk Institute. She will be depositing portions of the fungi so it’s publicly available for other scientists to research.
“You have to go through the process of yelling at other scientists to say ‘Hey, no, this is really going on,’” Carr said.
Carr has to provide proof that this is a new species or new genus with the support of DNA, phylogenetic trees, its origins, the discovery of similar organisms, the morphology (or its appearance) and more.
“I basically did all this myself with the help of undergrads,” Carr said.
A lot of the model organisms, such as yeast and E. coli, have been worked with frequently, so there are papers and research readily available to follow protocols and edit to get new results.
“Obviously, she discovered Exophiala viscosa [a new fungus] so she can’t just google ‘how do I do this,’” Barton said. “She is an absolute legend — everything she does is frontier work. There is so much that we are doing that doesn’t have an outline. She has been pioneering shit left and right for six, eight years.”