As the semester came to a close, I found myself with mixed emotions. Part of me was relieved, the semester was extremely busy and somewhat chaotic, I will now have so much more time to do research-uninterrupted research (the best kind!). On the other hand, I was going to miss the students and the awesome work that they were doing in class. As we gathered for our annual end of semester party, the excitement the students had for the class continued to show. One student made blue and white cupcakes, signifying the blue/white screen we had performed in class during transformations, and the white cupcakes even had an insert (cookie) inside! Another student had made dirt dessert in the form of our AMD site that we had visited earlier in the semester. These clever, and delicious, desserts not only exemplified their creativity, but their appreciation for a great semester. It was indeed a great semester! In fact, I spent most of the semester bragging about the students. I found myself telling everyone about the great projects that they had developed.
The blue and white cupcakes, signifying the blue/white transformation screen.
The students were given 10 weeks to design and execute a research project involving microbial communities found in abandoned mine drainage. This particular group of students, took the challenge and hit the ground running. Not only was there a nice mix of individual projects, but the students became invested in their projects right from the start. It was amazing to see the growth the students had over the course of the semester, not just growth in laboratory skills and knowledge, but personal growth. I watched individuals who struggled with confidence thrive, introverts come out of their shell, and organizational and planning skills meet optimum levels. It was extremely rewarding to see the students immerse themselves in their science.
Dirt dessert in the form of Lowber Passive Remediation System
So what are these great projects? I am so glad you asked! This semester some of the students isolated manganese and iron bacteria and identified them through Sanger sequencing. Others isolated bacteria from Lowber soil and compared it to soil from Duquesne. They than tested the isolated bacteria from both locations for metal resistance. Two groups looked at antibiotic resistance in bacteria isolated from Lowber compared to lab strains. Though there did not appear to be an increase in antibiotic resistance in bacteria isolated from the AMD, the students did find that lab strain Serratia marcescens exhibited increase resistance when grown in media made with AMD! The students were so excited about their findings that they are continuing their project this summer.
Other students looked at rhizosphere bacteria and the role they play in detoxifying the area around the plant roots. Another project that is being continued by the students next semester in our lab, is a study comparing sulfate reducing bacteria (SRB) found at Lowber (circum-neutral discharge) and Middle Branch (acidic discharge). The students worked this semester on isolating SRBs from both locations, and will identify them and run comparison tests next semester. A student going to grad school in the fall for bioinformatics (Go Nicole!), took her interest in bioinformatics and used 16S sequencing analysis to compare two passive systems to see if their populations were similar. She then focused on iron and sulfur bacteria to see if there was a significant difference between the two.
Despite their differences, there was teamwork even during the playoffs!!
Another student performed a series of stains on the bacteria from across the remediation site. This was right in her wheel house as this is what she is going to grad school for in the fall (YAY!). It was nice to see her incorporate her passions and interests into her independent project. Lastly, a student compared water and bacteria from upstream and downstream of the effluent from the passive system. She is going to law school in the fall, but remained a hard-working, dedicated scientist to the very last minute of class.
Marnie's transition from a scientist to a law student!
At the end of the semester the students presented their independent projects to the class in a powerpoint presentation. It was truly enjoyable watching them present their work. The students went above and beyond this semester to complete their projects and this was evident as they presented their work. I am so proud of all them!
So as the mixed emotions tossed and turned inside of me, I had a moment of clarity. I am a teacher, yes it is what I am contracted to do, but it is more than that. I am invested in the success of my students. I want to see everyone of them succeed and I celebrate their victories and stand by them in their defeats. I wasn't sure if I was going to like teaching, but it has become clear - I do! I am looking forward to the future where I get to do it all over again. Teaching truly is a rewarding experience.
The Superlab IV 2018 students celebrating at the end of the semester party
I remember the first time that I participated in novel research. How excited I was! That excitement quickly turned to pure terror. What do you mean no one has ever answered this question? We do not know the outcome? How do I know I am right? What happens if I am wrong? As I continued, I gained confidence in myself and in my work. It was then that I realized that this was what I wanted to do with the rest of my life, to seek out the unknown and make a difference through scientific discovery. This was my senior year of undergrad at Duquesne University and I was taken a 4 credit lab course, that has been coined "superlab".
Superlab comes in 2 parts, the first semester everyone takes the same course where the students are introduced to a range of lab techniques involving classic microbiology, molecular biology, and protein purification. The second semester comes in several concentrations (physiology, cell biology, and microbiology) where the students are exposed to an in-depth look at a specific topic. I had enrolled in Dr. Nancy Trun's microbiology superlab. This course provides the unique opportunity to engage in novel research, allowing the students to experience science in a way that they typically are not exposed too. They develop hypotheses, design experiments to test these hypotheses, and carry out the designed experiments. Allowing the students to "take the wheel" of their own education, encourages active involvement in the learning experience. They are not just going through the motions, in fact, each individual is creating their own path. I credit this course for the reason that I am in graduate school obtaining a Ph.D. with a concentration in microbiology.
Everybody loves field trip day! Brady, Benita, and Natalie (left to right) on the deck that crosses over the effluent.
I now have the opportunity to be a teaching assistant in the very lab course that inspired me to be where I am today. It provides me the unique perspective that allows me to relate with the students on a more personal level, as I was in their shoes not to long ago. I see the excitement and I see the fear. It is definitely a rollercoaster of emotions (for the students and myself), becoming a scientist is no easy feat! But the students quickly adapt and develop solid hypotheses and execute sound experimental design. It is truly a joy watching the students gain confidence and rise to the challenge, surpassing all of their (and mine) expectations.
Lowber Passive Remediation System.
The class focuses on bioremediation, specifically involving passive remediation systems designed to treat coal mine drainage . The students learn about passive systems, what is known, and what remains unknown. Over the course of the first 6 weeks they form hypotheses and design experiments. Then comes my favorite day of the semester.... (*drum roll please*) FIELD TRIP DAY. We get to take the students to a remediation site (Lowber, see "Field Sites") so that they can collect their own samples. This is always such a fun day, the students really enjoy being in the field. Its funny to hear what the students think the site was going to be like, one student said to me "I thought you climbed deep down into a cave to get to the site". I am sure spelunking was never mentioned in class!
Melissa (left) came ready to go in her boots and fanny pack, while Dania (right) took more of a fashion forward approach, staying pretty in pink.
I am not the only one that gets excited about field trip day, the students do too! Some students came decked out, ready to climb directly into the remediation site, while others were not quite sure what to expect. We started the day with a little background about the site, where Dr. Trun explained how the system worked and what to expect as we moved down through the system. The source pond, where the discharge surfaced from under ground, was a distinct green color. This pond contains high levels of iron and sulfate and has not yet had a chance to precipitate any of the iron. That will quickly change as it moves through the system, turning all of the ponds a bright orange color.
Dr. Trun talks to the students about Lowber and how the passive remediation system works
After the talk, we moved to the end of the system. That way we could work from the effluent, the end of the wetlands, back up to the beginning of the system (where our cars were). Along the way, I noticed that the ponds were orange well into the wetlands. This is not usually the case, but February has had a record amount of rainfall, ~5" alone in the week before we came out. Heavy rainfall increases flow rate, decreasing retention time and does not allow enough time for contaminants (iron especially) to precipitate out. Even the effluent remained tainted with orange.
The yellow boy (orange water) continuing well into the wetlands.
Even after passing through the entire system, the effluent remained orange.
The students really jumped in (some literally) and began to sample. All together we collected 50L of water across all of the 6 settling ponds, the wetlands, and the source pond. The samples will be used to make media, be plated on a variety of selective media types, stained to identify morphology and biochemical properties of bacteria present, and enriched to isolate sulfur, manganese, and iron bacteria. Plant growth and the relationship with rhizosphere bacteria, as well as Sewickley Creek were also sampled for further analysis.
The class disperses with bottles in hand.
Melissa just jumped right in and began to sample the wetlands.
Ali using the sampling pool to get a slurry sample..
Rasha sampling in pond 1. She really took a liking to sampling, jumping at every opportunity to collect slurry.
The system looked so much different from when I was here in January. Everything had thawed, the geese had returned, and biofilms were becoming more prevalent. As we moved from pond to pond, I tried to point out all of the changes that were occurring. Soon, the algae and cyanobacteria will begin to bloom and the wetlands will return to green. Spring is near!
Biofilms forming entering into pond 4 (left) and on the shore of pond 2 (right).
The geese have returned in preparation for spring.
The weather was beautiful and the field trip was a success. The students got to witness the devastation that was happening as a result of abandoned coal mine drainage (AMD). This leads the students to be even more invested in finding possible solutions to treating AMD. It is through this experience, that we (as educators) are able to take what was taught to them in class and materialize it in a way that you can't possibly experience in a classroom.
There is something so beautiful about an early morning following a winter snowfall. There is a sense of purity, for a few moments everything is new and untouched. The air appears cleaner and the world seems still. As Elizabeth Cochran, a masters student in my lab, and I approached Lowber I got a sense of peace, the remediation site had transferred from a place of destruction to a place of beauty overnight. Thats not to say that the devastation that was happening to the land was forgotten (the orange ponds were still prominent), but for one moment the land was once again beautiful, it was breathtaking.
Lowber passive remediation system in Lowber, PA (Winter 2018)
Picture taken in one of the troughs between the ponds
We started at the effluent of the system, the end of the wetlands, and worked our way forward. The wetlands was primarily frozen, but there was still water flowing through a narrow path. It made me wonder if the water was flowing underneath the ice or if water flow was truly limited to a narrow path all year. I think a dye test may be in order this summer to test the water flow from influent to effluent. In the mean time, the water was muddy and not very clear.
Elizabeth taking field measurements in the wetlands (effluent)
Lowber now showing its rendition of Swan Lake
After we sampled 6 liters of water/soil slurry, took field measurements, and freed a cattail from a block of ice, we moved to pond 3. Pond 3 is in the middle of the remediation system and we often study this pond because it serves as a potential inflection point (where contaminants and microbial communities shift). Pond 3 had no ice at all and was six degrees warmer than the effluent. This is to be expected, as the first couple ponds typically don't freeze because the mine discharge is from an underground mine and so it comes into the system fairly warm all year round. There was a few biofilms present as well. Another 6 liters of slurry was collected and Elizabeth found another interesting plant to sample for iron accumulation around the roots.
Pond 3 with no ice
Biofilms found in Pond 3
Here I am taking field measurements in pond 3
Our last stop was pond 1 where another 6 liters of slurry was collected and field measurements were taken. Pond 1 is the first settling pond of the system and was even warmer than pond 3 (~3 degrees warmer). There was a large manganese sheen at the influent of pond 1, suggesting the presence of leptothrix. There was also extensive biofilms growing around the edge of the pond. There was visible bubbles coming from the biofilms. There was a a distinct smell of "rotten eggs", the classic description of sulfide, present at this pond, where the other ponds lacked this lovely smell.
Pond 1 and its massive manganese sheen
Biofilm formation in pond 1, note the bubbles coming up to the surface
As we were walking past the giant mound of iron hydroxide that had been drudged from the ponds (that was now covered in snow), we noticed that there were crystals forming in the snow. Though I cannot explain what was causing this crystallization, it was really cool seeing them laying in the snow! It just confirmed the beauty that had formed at Lowber that cool winter morning.
Crystal formation on top of the iron hydroxide that had been drudged from the ponds
close up of the crystals
The samples collected on this trip will be used for enrichment cultures and lab-based studies to identify bacteria that may serve as bioindicators, as well as bacteria that may be resolubilizing contaminants in the system. mRNA will also be sequenced to track changes in metabolic genes, that could later be used to identify changes/shifts in the system.