Microbial Communities in the Baltimore Inner Harbor
I am super grateful to be apart of the IMET summer internship. Initially my cousin had sent the link to me, saying it sounded like something I’d be interested in and that I should apply, but I was nervous and doubted my strength as an applicant. It wasn’t until the lab manager at the Bruns Lab, Ally Kido encouraged me to apply, as she is an incoming Masters student in Dr. Eric Schott’s lab at UMBC/IMET. I’m really glad I did, as this was a valuable experience for me to gain exposure to the estuarine system, continue to sharpen my skills as a researcher, and experience the dynamics of a multi-institutional site.
IMET is an institution that is a collaboration between multiple schools. It’s primarily UMCES and UMBC, but also there are people from UMD-CP, UMB, and Towson. This environment allowed me to explore the collaborative side of science— not just working together with other people, but the large scale connections that people make to get institutions to work together on projects they deem and propose as important. I also got to see an aspect of ecology and biology in industry. I worked in the Chen lab which was under a DOE contract as well as a contract with a biotech company (HiTechBio). It was really interesting to see how the work they did was directly applicable.
This summer with the Chen Lab I worked closely with Jeffery Jiao, a master’s student with UMD-CP studying biodiversity change in the Inner Harbor. He is interested in how microbial biodiversity shifts along with seasonal change. I supported this project by starting cultures for summer samples and doing a characterization analysis on some winter samples.
I was successfully able to characterize one sample from the winter collection as Chlorella vulgaris, a green microalgae species that is known to thrive in freshwater. I presented my work at the end of the summer to friends, family, and colleagues at the Summer Intern Symposium on August 5th. Feel free to read my posts below which are a recollection of my experience during the program!
For more, check out IMET’s blog for the interns.
Presenting my work on August 5th.
Getting awarded my certificate of completion with Lauren Forsyth, Lauren Wagner, and Jeffery Jiao (left to right).
Chronology of Methods (What I’ve done so far!)
June 6 First day, orientation
June 8 Practice taking Inner Harbor water sample
June 9 Make SN-15 (saltwater-like) medium
June 10 Make BG-11 (freshwater-like) medium and pour agar plates
June 14 Sample collection and spreading onto plates
June 15-now Microscopy on winter samples
June 22 PCR on a winter sample; practice for me (first gel in 2 years!)
June 23 STEAM Poetry session
June 29 Creation of figure, seminars on Adobe Illustrator
June 30 More microscope; had to troubleshoot some scale bar issues
July 7 Resolved the scale bar issue! more microscope
July 20 Finished and compiled BG-11 winter photos. Start SN-15 photos
July 21 Take new Inner Harbor samples to redo summer data; scale up existing colonies from ‘failed’ summer plates
July 25 Start PCR . Tried on a few BG-11 winter samples. No dice so far
July 28 Got one good PCR product out of like 10 we tried.
August 1 Learned how to use MEGA11 software to create a phylogenetic tree
August 5 Presented work at Summer Intern Symposium.
8.5.22
IMET’s Summer Intern Symposium was today! We got to present our work to our friends and family that we invited, as well as our mentors and other colleagues at IMET.
I presented about my isolation and characterization of the B5 sample that I identified as Chlorella vulgaris.
I also got to show my family where I got to work all summer! It was really fun.
7.28.22
Finally a good one!!
7.27.22
I had a dream about running a PCR the other day. It was so satisfying in my dream and all the products came out. Sadly, real life is not that beautiful. I’m worried I won’t get PCR product from some winter samples before my internship is over! That sucks.
my failed PCR. hopefully it will work better when i try it again!
C2 : large circular algae morph
D2 : filamentous morph
E6 : walnut-like morph
F2 : filamentous morph (cyanobacteria)
7.8.22
More microscope photos! I figured out how to make a scale bar in Illustrator using a photo I took of a micrometer under the microscope. Scale bars are in red (light) and blue (UV) and represent 10 um. Something disappointing is that my plates aren’t growing! It’s been a month and by now they should have some growth, but now there’s basically nothing. So we are trying to figure out what went wrong.
green algae under light microscope; 40X
green algae under light microscope; 100X
green algae under UV light; 40X
green algae under UV light; 100X
7.1.22
Been taking microscope photos of the winter samples. For some reason the scale bar has been glitching, so it’s not on there, but I’m working on it. The top two photos are pennate scenedesmus-like algae, and are each about 10 micrometers long. The bottom two are circular green algae, and around about 5 micrometers in diameter.
40X magnification; pennate scenedesmus-like with UV blue light.
100X magnification; pennate scenedesmus-like.
40X magnification; circular green algae.
100X magnification; circular green algae with UV blue light.
6.28.22
We got a better microscope! So now we can take much better photos for determining the types of algae and bacteria we are looking at before we perform PCR and sequence them.
6.29.22
Learning how to improve as a science communicator! Created this graphic to try to show what my experiment is about.
Statement in the corner: “What is the connection between astronomically high gas prices and increases in human health conditions due to unclear water?
Both these issues have the potential to be solved by algae. This is possible because algae are relatively easy to work with, consume products found in wastewater, and are able to produce a form of diesel as a byproduct. However, there are millions of unique species that we struggle to effectively utilize and more we have yet to discover.
Therefore, it is important to increase our understanding of algal species by characterizing those that grow locally in the Inner Harbor to optimize how we engineer them and find more uses for them.”
6.23.22
The group of interns and I met with Dr. Kathleen Gillespie where she taught us how science can be blended with Poetry!
We got to create some of our own. It was very embarrassing as I am not the most creative writer.
Blackout poem created from a paper of Dr. Chen’s (Xu et al., 2015) that I’ve read for background on my project.
Free Write (10 min) I was given 10 min to free write a poem using the following words.
terms: estuary, picocyanobacteria, psychrotolerant
Other words: experiment, green, water, library, quiet, pensive
The estuary is home
To the smallest resident
The funkiest little guy
The picocyanobacteria
They poke at him
They prod at him
They experiment
Why is he not green?
They call him names
Too hot
Too cold
Too.. psychrotolerant
Not his fault they’re not as unyielding as he
But Mr. Pico wants to go home
To his dirty water and fecal matter
Where they treat him like one of their own
6.22.22
PCR! Did this with Jeffery and got to try PCR for the first time in about 2 years. It’s been a while for me so I was pretty rusty but now I’m ready to go!
Gel from PCR. Was essentially a practice run for me, so I wasn’t given the DNA ladder scale to put onto the photo. [once I get that I’ll add it hopefully]
6.14.22
I am setting up my experiment! The goal is to characterize microbes that we grow from a water sample taken from the Inner Harbor. Since this sample is taken in the summer, we will compare the data to the sample taken in the winter by Jeffery.
Experimental design:
Figure displaying the amount of plates made and what medium and treatment they are receiving. All plates are spread with sampled water from the Inner Harbor that was collected on June 14th, 2022.
Set up:
Example incubator set up. Grow light on the rack above, plates directly below. Did this for 15, 25, and 30 degrees C treatments.
Set up for 10 degree Celsius treatment. is it in the freezer. The stacked cups that the grow light is on top of are the same height as the racks in the incubator. Light intensity was measured to confirm all plates are receiving about the same amount of light.
Was the same for 20 degree treatment, however that was in the normal lab (which is at about room temperature ~22 degrees ish) with a cardboard box over the set up to prevent light interference from ambient lighting.
