During the pandemic, I took a course on metagenomics with Dr. Noah Fierer and Dr. Hannah Holland-Mortiz where we obtained a time-series metagenomic dataset from CU Boulder Engineering professor Cresten Mansfeldt that was sampled from the sewage system of the CU Boulder campus. As a class we divided into groups to assess spatial trends, temporal trends, viral communities, and antibiotic resistance genes from the metagenomic data and the environmental variables that were collected with each sample. I was part of the spatial trends group, and I learned a lot about how to wrangle community data in R, use statistics appropriately for community datasets, and to make visualizations in R.
The manuscript is accessible at https://journals.asm.org/doi/10.1128/msystems.00651-22
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During an IQ Biology backpacking trip, I talked with several students in the geology department about their ongoing projects, and we dreamed up collaborations that I thought would never come to fruition. But, don't dream up big science ideas around go-getters unless you want something to happen. Geology PhD student, Tristan Caro, quickly brought me onto his soil microbial turnover project to do some marker gene sequencing work in the background of his main project. My role was to elucidate the microbial community composition so that Tristan could associate the lipids he measured to the groups of organisms in the soil that could be producing them. We had talked on the hike about how challenging it is to draw conclusions from lipid-based studies without that community composition data because for some reason or other you always want to know who is there.
In return, Tristan added biocrusts to the turnover project to allow me to see how adding water to the communities impacts their growth rate - with some of the fastest turnover rates measured for the biocrust cyanobacteria as compared to multiple other soil types. This was expected. We usually see rapid green-up and growth of the cyanobacteria community upon rewetting, but it was really cool to see the rate of that growth as compared to other community members and to see how dry-down affected the lipid composition of the soil as well. I look forward to working with Tristan in the future. Here is the preprint of our work Here is the published version of this work. At some point during COVID, I stumbled into the Microbes and Social Equity group, spearheaded by Dr. Sue Ishaq. Over the past few years, I have attended their Speaker Series and Symposia, and I co-authored a paper with them! It was truly a weird experience being half way through my PhD, without any published works, and jumping onto an on-going collaboration at the last minute to make sure that their paper, Twenty Important Research Questions in Microbial Exposure and Social Equity, did not leave out land degradation and differential exposure to infectious disease due to climate change and habitat destruction. I felt very lucky to work with Edauri Navarro-Perez on this writing and learned so much from the experience.
I am very much looking forward to this fall semester. I am taking one class on Teaching and Learning in STEM courses, teaching three sections of Biology & Society Lab, and am serving as co-organizer of the food for weekly EBIO Colloquia. My primary goals for the semester are to publish my work on biocrust natural recovery, draft a manuscript on cultivated biocrust for restoration, and to apply for research grants which will cover my summer salary (my final summer of my PhD). At this point, I am not looking to add more research projects. I am looking to give each project the time it deserves, but to also finish them and prepare for my next steps.
As I watch my classmates give their public talks and defend their dissertations, get married and/or pregnant, and then apply for and move on to new jobs, I realize how fleeting my time here at CU really is. All the people I have met and connected with, all the memories I have in various buildings and with specific instruments will be reduced to words on a page, published for a few people to read. I am not sure where I am headed next, or where inspiration will strike. My friend Meghann quit her job and travelled across America for the last 6 months. She has seen tide pools and lightning-sparked wildfires, laughed at amphibians hitching a ride on a dog and has felt the tumultuous joys of living out of one's car. I wonder if she feels intense purpose/drive now. I wonder if when we meet again it will feel as if nothing has changed, neither of us knowing exactly where we are headed but intensely grateful for the opportunities that have come our way and the people we've encountered as we ramble. I greatly appreciate funding from the IQ Biology Program to attend the Ecological Society of America (ESA) Conference this August in Montréal Canada. See my blog post on their website to read about my experience.
This month, a new student joined me in the laboratory. Violet will be with us in the Barger Lab for a year as she determines her research interests within soil science. We have been working through many different measurements for soils including pH, bulk density, soil texture, chlorophyll a, and exopolysaccharides. Soon we will be working on DNA extraction and marker gene sequencing as well. Violet has great talent in the laboratory, taking great care with each sample. I can't wait to see what questions she asks and what she decides to do in her time here with us.
I recently became an organizer for the Women in Soil Ecology (WiSE) and have been getting to know the other members of the leadership team including Michala Phillips, Courtney Collins, Kendall Beals, Lydia Bailey, Joy O'Brien, Ishwora Dhungana.
Our mission: "Our network is aimed at connecting women scientists to build a strong community and further the fight for equity of all those identifying as women in science. We aim to establish connections among senior and junior ecologists through meetups, workshops, and peer-to-peer mentorship." I am most excited to learn from other women soil ecologists in this group and to build a strong network of fellow scientists. The workshops that the leadership team organized last year are absolutely crucial for inclusively setting disciplinary expectations for the next generation of soil ecologists. I was so stoked to see women teaching women how to make our science stronger through reproducible code, collaboration, and mentorship. Recently, WiSE organized a career panel with women soil ecologists in non-profit, federal government, and academic roles. We look forward to meet-ups, reading groups, and more workshops in the future. Professors at CU offered some fantastic graduate level courses this semester. I took more credits than I should have including Data Science, Soil Ecology seminar, Restoration Ecology seminar, and Data Visualization. The seminars included reading scientific papers each week and discussing the ideas. For Restoration Ecology, we are working on two short opinion pieces for the SER call for short and spicy opinion pieces. This has been fun to put together with my lab-mate, Aly Ennis, and Sam Ahler. Data Science was geared toward ecology and evolutionary biology students and included algorithms for linear modeling. We used R, RStudio, and GitHub and conducted independent projects with Bayesian models. This was quite challenging for me, and I still consider myself a novice.
Data Visualization with Sebastian Kopf, a geology professor, was the best course I have taken at CU Boulder. Each week, students would bring an example of a published figure that they would like to replicate either with published data or with their own similar data. Seb would start at the beginning (data wrangling) and walk us all the way through to the final publication-ready figure in just one hour. This course also used RStudio and GitHub. The depth of knowledge that Seb has for plotting in R is incredible and it was awesome to see the coding style, techniques, and possibilities week after week. Truly inspiring! The Barger Lab renovation is almost complete. We now have a lounge space with a couch and table where we can meet all together. This week we started our Project Wall where we each keep track of the progress of our projects and communicate with one another about the overlap between projects or other issues we are having. We designed the wall with images from the website app.wombo.art which uses AI to generate beautiful imagery based on the words that you input. We've also considered including pressed flowers or dried mushrooms to represent the various projects. This winter break, I am preparing for my 5th semester exam which includes a <15 page proposal, a presentation, and questions from my committee. The proposal will be focused on a new topic for me, which I have been reading and preparing background information throughout the semester. The presentation is mostly about work I have already accomplished or will accomplish as my dissertation chapters. The highlight of this semester was my visit to the Forest-Rangeland Soil Ecology Lab with Dr.s Matt Bowker and Anita Antoninka at Northern Arizona University where we talked about exopolysaccharides in biological soil crust. It was a fantastic visit and all of the people there showed incredible hospitality and generosity to me. The biocrust community truly rocks! This fall I will be participating in the Letters to a Pre-Scientist program, which aims to inspire students to be curious about STEM fields. I'll be paired with a school kid and we'll exchange letters throughout the year. In preparation for letter writing, the program offers training on the systemic challenges that public education faces. I thought I would share a few of those resources here for those curious about systemic racism in public schooling, the science-gap in rural education, and ways to value and enhance skills/aptitudes that students already have as they learn what STEM is all about.
This TED Talk by Kandice Sumner is fantastic. I like the way she explains the challenges of teaching and learning with fewer resources and how we should be providing equal opportunity within public education. The 'achievement gap' is actually an education debt. She helped me see letter writing as part of paying that education debt. An article about science in rural America. An article about science equity nationally. An article about STEM camp and ways of helping students identify their own strengths and daily growth, providing external affirmation, and providing opportunities for students to identify with STEM. |
AuthorSierra is a graduate student in the Barger Lab at CU Boulder studying microbial ecology for dryland restoration. Archives
August 2023
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