Bucknell Faculty-student Team Discovers New Bacteria Strain
Biology Professor Emily Stowe and Emma Hundermark ’17 used genetic and traditional techniques to classify a previously unknown species.
This photo of the newly discovered cyanobacteria was taken with a confocal microscope using a laser to make the bacteria fluoresce. Photo by Adam Huff '17
January 13, 2017, BY Matt Hughes
You don't need to travel to the ends of the Earth or the depths of the sea to find new living things, says Bucknell Professor Emily Stowe, biology. You just need to look more closely in your own backyard.
For several years, Stowe and her student research partners have been looking very closely at the microscopic inhabitants of nearby waterways, and have recently classified a new form of bacteria that was previously unknown to science. By using both traditional observational and cutting-edge genomic techniques, they've verified that the bacteria, which they've dubbed Pseudanabaena strain Roaring Creek, is a bona fide new strain.
It has been six years since Stowe and student researcher Allison Mayhew '11 plucked the new strain of bacteria — or rather, its DNA — from a local stream, but it's taken that long to isolate and grow the bacteria in Stowe's laboratory and to piece together the DNA evidence needed to confirm it's something new. Stowe was interested in the strain because it is a cyanobacteria — a variety of bacteria that, like plants, uses photosynthesis to produce energy from sunlight — and Stowe studies how cyanobacteria use light as a developmental cue in acclimating to their environments.
But the cyanobacteria DNA found in those water samples (which were taken from Roaring Creek near Elysburg, Pa., about 20 miles from Bucknell) were mixed up with genetic material from countless other creatures. Isolating and growing the cyanobacteria was an iterative process of seeding petri dishes to produce new bacterial colonies. Student researcher Emma Hundermark '17 picked up the project this summer, isolating DNA from the colonies Mayhew had worked on, then trying to piece together fragmented segments of the bacteria's DNA produced in sequencing.
"I sent the genome out to be sequenced and it came back in pieces," Stowe said. "It's a process of taking really short sequences and trying to build longer and longer ones."
Once they had reassembled enough of the bacteria's DNA sequence, Stowe and Hundermark confirmed that the cyanobacteria had not previously been catalogued by cross-referencing its genome with those stored in GenBank, an annotated collection of all publicly available DNA sequences managed by the National Institutes of Health. Researchers use a specific gene as an index, and any species whose DNA for that gene is less than 97 percent identical to any other is considered new, Stowe explained.
Now that they knew they had something novel on their hands, the researchers turned to more traditional, observational methods to identify its place in the tree of life.
"There's a rubric with all these different characteristics," said Hundermark, a biology major. "Does it grow on its own or does it grow in filaments? If it grows in filaments, like this one does, some of them have a mucus sheet around the outside. This one didn't. You just follow the rubric."
The rubric led them to one of two genuses, at which point they returned to genetic evidence to further refine their search.
"We looked at conserved genes across species," Hundermark continued. "These are genes that all bacteria have and that haven't changed a lot over time. You look at that gene in one species and compare it to another. If they're in the same genus, you'd expect those genes to be very similar. I looked at my options and found that this bacteria had a really high similarity to a species of [the genus] Pseudanabaena that had already been named."
Bingo — the researchers had identified the bacteria. They gave it the name Pseudanabaena strain Roaring Creek, after the location where it was collected. Stowe and Hundermark have since uploaded the bacteria's genomic sequence to the GenBank database, and Hundermark is planning to publish her work first as an honor's thesis, and then in an academic journal as well. The project has already proven a transformational educational experience for her.
"I got to be involved in the naming and classification of a species, which you don't get to do every day," Hundermark said.
"It has also been interesting to learn about cyanobacteria," she continued. "These are organisms that are around us all the time and are so important for oxygen production and in the food chain, but they aren't something we think about a lot."
For Stowe, the discovery was more ancillary to her primary research interest, but it remains a powerful reminder of just how much biodiversity still remains to be discovered, right under our noses. In fact, Stowe and another student, Brianna Bjordhal '19, are currently working to classify another cyanobacterium they found in the Susquehanna River last summer.
Biologists generally agree that less than 1 percent of bacteria have been classified, with some estimates putting the number as low as 0.1 percent, Stowe said.
"We don't know the true diversity," she said. "There are thousands of people studying hundreds of different ecosystems and we don't know enough to even necessarily call these species. We know when one thing is not the same as other things, but we have no idea what it really is.
"That includes humans as an ecosystem," she added. "You could have more than 400 different bacteria in your mouth — and that's if you brush your teeth a lot. The communities in your belly button are different from the communities in your ear. That kind of diversity is hard to picture. You can appreciate 20 different kinds of trees in a forest — you can see that difference. But with microbial diversity, it's hard to appreciate how much there is, and how much that's left to learn."
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