Accounts of a microbial hunter in France:
Using research questions to “hunt” for microbes involved in water treatment
Here is a view of a sample collected from an engineered system that contained sulfur-bearing mineral. This mineral was applied to assess its ability to promote biological nitrate removal. I wonder who this critter is?
Welcome to the second blog post of the “Accounts of a Microbial Hunter in France” series! This series shares my experience at the Centre National de la Recherche Scientifique (CNRS), located in Marseille, France. I am actively searching for microbes (known as denitrifiers) that use sulfur-bearing minerals to biologically removing nitrate (i.e., denitrification) in engineered systems designed for treatment in small communities. Hence the “microbial hunter” part in the title of this blog series. The first blog post of this series serves as an introduction to my research at CNRS. This post is a resource for my audience to use for gaining context about the project (e.g., the motivation, an introduction to denitrification, and the research objectives). Especially, for those who are just joining the series and/or who are unfamiliar with denitrification. Feel free to access this post here.
I will be discussing my first week at CNRS, which involved proposing research questions. This post includes the approach that I used to pose these questions. It also features a reflection of how these questions have assisted me so far.
Prior to proceeding, I would like to extend my gratitude for taking the time to travel through this journey with me. I truly appreciate it. Buckle up and lets begin this ride!
Research questions were created to serve as a “map” for hunting microbes
During my first week, Dr. Talla (my mentor at CNRS) suggested creating research questions that would serve as a guide to:
I am working with Dr. Talla in the Laboratory of bacterial chemistry at CNRS, located in Maresille, France.
Search for denitirifiers involved in removing nitrate from contaminated water supplies
Identify the contribution of my research towards elucidating the biological processes that occur during the treatment process.
The approach that I used to create questions for my research involved thinking about valuable information that could be obtained and potentially applied to the engineered systems. Studying how the microbial community changes in response to the sulfur-bearing minerals within the engineered systems can provide important information. For example, details on how the denitrifiers responds to dynamic environmental conditions (e.g., varying nitrate concentrations) and to each other can be gained. This information can be applied to refine the design of the engineered systems in efforts to improve the treatment process. Therefore, the research questions that I proposed involved examining and comparing microbial community evolution when different sulfur-bearing minerals were used to mediate denitrification. Additional information on why these minerals were employed can be found here.
Formulating questions assisted with the selection of important research components
Example of a sampling session where I am taking a closer look at the microbes used in an engineered systems.
Once the research questions were posed, I was able to select samples suitable for answering them. The samples could then undergo next generation sequencing to obtain big data representing genetic information (i.e., DNA sequences) of organisms within each sample. Furthermore, these research questions assisted in including positive controls to perform a complete analysis. Positive controls are designed to produce an expected observation and are particularly useful in comparing these results to the experimental samples and validating the procedure.
Analyzing the microbial community throughout the experimental period can be an expensive and a long endeavor. Therefore, samples for specific time points were selected to analyze the microbial community structure. These samples were determined based on the observed nitrate concentrations measured during weekly sampling sessions over the course of three months.
“... revisiting the research questions have enabled me to return full circle and understand the main take home messages that my research community, peers, and the public will be interested in. ”
Reflection: Developing research questions beforehand have aided in providing organization and direction
Dr. Talla and I reviewing the big data that has been separated based on the research questions proposed.
These research questions have played a monumental role in gaining organization and direction, and fostering a forward thinking mindset. I have referred to these questions on many occasions to organize the big data representing microbes in the samples into small-groups to obtain clear results. These questions have also served as a reminder of the “big picture” that I am trying to learn about my research. There have been many moments where I became engrossed in the details of processing and analyzing the big data. However, revisiting the research questions have enabled me to return full circle and understand the main take home messages that my research community, peers, and the public will be interested in. Ultimately, reviewing the research questions at the end of the data analysis will aid in determining the denitrifiers that play key roles in the treatment process and pinpoint the contribution of this research to understanding the underlying biological mechanisms of denitrification.
Acknowledgments:
I would like to thank the Chateaubriand Fellowship, Alfred P. Sloan Foundation, and McKnight Doctoral Fellowship for supporting this project and encouraging opportunities for graduate students to pursue research abroad!
Thank you for your time and I hope that you were able to learn something new from this post. For any additional questions or comments feel free to leave your responses below.