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?

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.

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.

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.
— Erica Dasi

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.

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.

 

Accounts of a microbial hunter in France: Introduction

Standing in front of the laboratory in Marseille, France.

Standing in front of the laboratory in Marseille, France.

I am currently conducting research at the Centre National de la Recherche Scientifique (CNRS), located in Marseille, France. I am working there with Dr. Emmanuel Talla to identify the microbial community structure in engineered systems aimed to biologically remove nitrate from small community drinking water systems.

This blog series encompasses my experiences at CNRS. I hope that it serves as a useful resource for those interested in pursuing research opportunities abroad, incorporating an interdisciplinary component to their research, navigating through challenges, and much more. This post serves as an introduction of the research I am pursuing at CNRS. I want to take the time to prime my audience on the basis of this research in efforts to provide context for subsequent posts. Thank you for taking the time to join this journey with me!

Small communities are especially vulnerable to health impacts associated with the consumption of nitrate contaminated drinking water

In 2016, I spent the summer in Ghana working with a team to develop a low-cost and sustainable filter for treating contaminated drinking water.

In 2016, I spent the summer in Ghana working with a team to develop a low-cost and sustainable filter for treating contaminated drinking water.

My passion surrounds providing potable water and treating wastewater in communities around the globe. As an Environmental Engineering PhD student at the University of South Florida, my research seeks to develop low-cost, simple, and sustainable systems for treating nitrate contamination in small community drinking water systems. The consumption of nitrate contaminated water is a concern because it has been linked to causing an illness known as methemoglobinemia, which is fatal in infants and can lead to spontaneous abortion in pregnant women. Small communities are especially vulnerable to these impacts as financial and technological resources are often limited or unavailable. This makes it difficult for these communities to employ traditional physical and chemical methods of nitrate removal.

Denitrification using sulfur-bearing minerals is a promising technology for treating nitrate contaminated drinking water supplies in small communities

Holding a sulfur-bearing mineral specimen in the laboratory.

Holding a sulfur-bearing mineral specimen in the laboratory.

My research harnesses a natural biological process known as denitrification in engineered systems. Microbes known as denitrifiers are drivers of this process and are responsible for transforming nitrate into nitrogen gas, which is an environmentally benign product. Denitrifiers are ubiquitous throughout the planet. Therefore, the introduction of these organisms into engineered systems can create a potentially affordable and sustainable nitrate removal technology for small communities.

Previous research has demonstrated that sulfur-bearing minerals can mediate wastewater denitrification. However, few studies have evaluated the use of these minerals for drinking water denitrification. My research involves assessing and comparing the performances of various sulfur-bearing minerals to promote drinking water denitrification. The use of sulfur-bearing minerals is specifically attractive because they are abundant and widespread. Therefore, the acquisition and application of these minerals in engineered systems can be achieved with relative ease.

The biological mechanisms governing denitrification facilitated by sulfur-bearing minerals is unclear

Examples of engineered systems containing sulfur-bearing mineral. These systems were used in previous experiments that assessed the performance of sulfur-bearing minerals in promoting drinking water denitrification.

Examples of engineered systems containing sulfur-bearing mineral. These systems were used in previous experiments that assessed the performance of sulfur-bearing minerals in promoting drinking water denitrification.

As mentioned previously, denitrifiers are the drivers for denitrification. The underlying biological mechanisms that occur when these minerals are employed for this process are poorly understood. Studying microbial community structure can provide insights into these mechanisms, which can be harnessed to refine the design of engineered systems for enhancing nitrate removal. My research takes an interdisciplinary approach in attempt to treat nitrate contaminated drinking water. Fundamentals of environmental engineering are employed to develop novel engineered systems containing sulfur-bearing minerals for denitrification. Furthermore, molecular and computational tools are used to examine microbial community evolution in these systems.

Next generation sequencing (NGS) technologies are used to study microbial community structure during denitrification mediated by sulfur-bearing minerals

Over of the course of several months, small volumes of sample were removed from the engineered systems to: ( 1 ) monitor how the nitrate concentration changed throughout the experimental period; and ( 2 ) examine the evolution of the microbial community structure. Combining information acquired from both of these tasks can help in gaining a comprehensive view of this specific nitrate removal process. Molecular biology tools and techniques were applied to isolate DNA from the collected samples. Following this, NGS was applied on the samples to obtain data that could be subsequently analyzed to identify microbes within the samples. NGS is a technique that is applied for ancestry kits, such as 23andMe® or AncestryDNA®, which are used to discover a persons family history.

Processing NGS data to obtain information on the microbial community structure in the engineered systems used in this investigation

Dr. Talla and I using a computational tool to analyze our next generation sequencing data.

Dr. Talla and I using a computational tool to analyze our next generation sequencing data.

I am receiving training in bioinformatics at CNRS. Bioinformatics is a multi-disciplinary field that includes molecular biology and computer science. Dr. Talla is advising me through using bioinfomatics to analyze the NGS data representing samples that were previously collected. I am gaining hands-on experience with handling big data obtained from NGS, using computational tools to perform quality control and analysis, and troubleshooting these tools. By the end of this experience, I will have the ability to describe: ( 1 ) the impact of the microbial community on denitrification performance using different sulfur-bearing minerals; and ( 2 ) identify populations that are dominant during peak periods of nitrate removal. This information can be applied in the development of future engineered systems to foster conditions that promote the growth of these dominant populations. This can assist in optimizing nitrate removal efficiencies of these systems during pilot testing within a small community setting.

Acknowledgements

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.

Thank you for your time and stay tuned for my next post of this series! If you have any questions or concerns feel free to comment below.

Louis Stoke's Alliance for Minority Participation Research Symposium

Celebrating the Legacy of Congressman Stokes and 25 years of Success

Photo courtesy of Laura Lee.

Photo courtesy of Laura Lee.

Congressman Stokes’ legacy lives on in the students, faculty, and staff who have benefitted from LSAMP.
— Dr. France Córdova, NSF Director

A few weeks ago, I had the opportunity to attend the Louis Stoke's Alliance for Minority Participation (LSAMP) Research Symposium at the National Harbor in Maryland. The program is named after the late Congressman Stokes who used his elected positions to advocate tirelessly for equal rights and opportunities for African Americans. LSAMP is a program of the National Science Foundation (NSF) that was established in 1991. It is a program dedicated to increasing the quality and quantity of minorities who complete baccalaureate degrees in Science, Technology, Engineering, and Mathematics (STEM). Furthermore, LSAMP aims to increase the number of minority students who continue onto graduate studies in STEM. 

During this conference, students and faculty from various LSAMP institutions as well as a number of individuals from NSF and industry came together to celebrate the legacy of Congressman Stokes and reflect on the 25 years of success of the LSAMP program. In addition, LSAMP fellows had the opportunity to share their research during the conference. The Conference also featured performances by the Lepquinm Gumilgit Gagoadim (Our Own Dance in Our Heart) Tsimshian dancers and Johnny Walker, and speakers that included Dr. Samuel Betances, Dr. Vincent TintoDr. France Córdova, and Dr. Jo Handelsman. Near the end of the conference, a panel of Alumni LSAMP fellows shared their personal narratives of how the LSAMP program enhanced their graduate school experience.

Attending the the LSAMP research conference was such an rewarding experience. Presenting at the conference gave me the opportunity to practice talking about my research to a diverse audience. Being able to communicate your research to a non-technical audience is an essential skill every scientist should have and I am currently working on refining it myself. In addition, I had the opportunity to meet other LSAMP students and hear about research in other disciplines that include chemical engineering, environmental science, civil engineering. Listening to their research allowed me to learn and gain an appreciation about work centered on creating non-invasive technologies for measuring blood glucose levels, understanding biodiversity within the environment, and creating technologies for reducing the concentration of fluoride in water within a developing country. 

 

Much thanks and appreciation goes out to the people who are involved in organizing the LSAMP program. More specifically, I would like to thank the program directors, Dr. Tasha Inniss and Dr. James Hicks for their hard work in creating the opportunity for students like myself to pursue a graduate degree. I look forward to future LSAMP events and also moving forward in my graduate career as a LSAMP fellow!