Loyola University Chicago

Department of Biology

Miguel Rojas Thesis Defense: Project Description

Title: Biotic and abiotic factors influence benthic microbial communities in urban habitats


Microbial biofilms can be found on virtually all submerged surfaces in aquatic habitats, including rivers and streams. Biofilms are complex, taxonomically diverse communities of microorganisms (including algae and bacteria) that colonize solid surfaces and support a wide range of metabolic activities. Biofilms are critical components of river and stream ecosystems because they are key drivers of nutrient cycling processes (including nitrogen cycling) and because they serve as an important food source for higher trophic levels. Biofilms in urban streams are subject to a number of anthropogenic stressors, but research on the ecology of urban biofilms and their response to stressors has been limited. With the work from my thesis, I seek to improve our understanding of these important but understudied communities.
My thesis project has two main components that will address two hypotheses related to biofilms in urban streams. Hypothesis 1 predicts that the type of algae present in a biofilm will influence both the taxonomic composition and activity of bacteria within
the biofilm. Hypothesis 2 predicts that the taxonomic composition and activity of bacterial communities within urban streams will be affected by anthropogenic pollutants.
Two main components will address these two hypotheses.  Component 1 tests Hypothesis 1 through a laboratory experiment in which monocultures of four different algal species were grown in the laboratory with a mixed bacterial community collected from a field site. Next-generation sequencing of bacterial communities to assess the effects of algal species identity on the development of biofilm bacterial communities. Analysis of the sequence data shows that denitrifier community composition was significantly impacted by the identity of the algal species present.
Component 2 of my project tests Hypothesis 2 with a field study in which I analyzed the composition and function of microbial communities collected from 3 stream sites in Baltimore, MD. These three sites are located along a previously studied urbanization gradient. I compared the microbial communities at these sites with concentrations of anthropogenic pollutants (pharmaceuticals and personal care products) to assess linkages between stressors and bacterial community responses.
The results of this analysis suggests linkages exist between urbanization and the activity and composition of stream biofilm communities. Component 2 of my project will provide novel insight into the potential effects of anthropogenic pollutants on microbial communities within urban streams, and my project as a whole will add to our understanding of the factors that can influence microbial communities in urban habitats.



I would like to acknowledge the support and encouragement I received in preparation for my degree. First, I would like to express my sincere gratitude to my advisor Dr. Kelly for the continuous support of my studies and related research, for his patience, motivation, and immense knowledge. Without his assistance and dedicated involvement throughout the process, this defense would have never been accomplished. Because of him, I was able to learn many of the skills required to complete my research projects and had the opportunity to share my findings every year and collaborate with scientists across the country.
A very special thanks goes out to past members of the Kelly Lab, who not only offered friendship and helped make my stay at Loyola more enjoyable, but also helped with the completion of some aspects of my projects. Bradley Drury and Undergraduate Diana De Avila who helped me get settled and taught me some of the techniques used in the lab when I first arrived. Undergraduates Sana Iqbal and Francis Cocjin who assisted in the completion of some of laboratory work including making plates needed for bacterial counts and setting up and counting slides for microscopic counts. Alexandra Ozaki who provided guidance when I first began my writing and a special thanks to former Kelly Lab post-doc, Dr. Binh Chu Thi Thanh, who offered guidance and advice while I conducted the analysis of my research projects and with drafts during the early stages of my writing.
I must also acknowledge Dr. Emma Rosi-Marshall of the Cary Institute and the members of her lab who welcomed me and provided with invaluable guidance and support while I tried to complete a major part of my research project in Baltimore, MD. They offered advice and helped in planning my field experiment, travel, set up, and taught me some techniques which were necessary for the completion of the analysis of my experiment.
I would also like to show gratitude to my committee, Dr. Christopher Peterson and Dr. Timothy Hoellien. I appreciate the valuable advice and feedback they have provided during my research and during my time writing my thesis. They both raised points in our discussion of my research projects and helped me address several roadblocks while I was conducting my projects.
Most importantly, none of this could have happened without the support and encouragement my family and friends through every step of the process. I am especially grateful to have had Alicia Ortiz by my side, who sometimes went out of her way to make sure she was always there for me, cheering me on and never letting me give up.
Finally, I recognize that the work done on this thesis could not have been possible without the financial assistance from Loyola University Chicago, a National Science Foundation (NSF) Graduate Research Fellowship awarded to Miguel Rojas (award number: DGE-1257295), a National Science Foundation (NSF) award to John J. Kelly and Christopher Peterson and Kimberly Gray, a National Science Foundation (NSF) award to Emma Rosi-Marshall and an Illinois Water Resources Center grant awarded to Dr. Kelly.


Miguel Rojas earned a Bachelor of Science in Biological Sciences at DePaul University in 2010. As an undergraduate he served as a research assistant in Dr. Aguirre’s Lab at DePaul University with a focus on the ecology and evolution of fish beginning in September 2009. There he studied the microgeographical distribution of divergent mtDNA haplotypes in threespine stickleback, Gasterosteus aculeatus, and the phylogenetic relationships of freshwater fishes in western Ecuador inferred from mtDNA sequence data.
Beginning in the summer of 2009 thru the summer of 2010, Miguel began an internship and later became staff at the Field Museum working for Dr. Matt von Konrat in the Botany Department. He contributed to the Biological Research Collections (BRC) Project, aimed at improving the current bryophyte and lichen collection and making it more accessible to other researches. Mentoring high school students that came to the museum to work as interns.  During his time here he also participated the collection and counting of macro fungi within previously set up experimental plots for an ongoing project studying the impacts of atmospheric nitrogen deposition on soil fungal communities with Patrick Leacock and also collected macro fungi for a separate project with the aim of documenting the diversity of fungi within the Midwest region and to add to current knowledge of biogeography.
Miguel came to Dr. John J. Kelly’s lab in 2010 where he began to work on his Master of Science in Biology at Loyola University Chicago. Here he had the opportunity to learn new techniques while contributing to a variety of different research projects. His work has allowed him to serve as coauthor to four peer reviewed journal articles and has work that is in the process of being written up for publication. The work from his thesis has been presented at the General Meeting of the American Society for Microbiology (2011, 2012, and 2013) and a Joint Aquatic Sciences Meeting (2014). He played a role in serving as a mentor and overseeing the independent research being conducted by undergraduate students working in the Kelly lab.  During his time at Loyola, Miguel was also able to expand his interest in education by being involved in leading classroom demonstrations, participating in career day events where he would speak about his research and experience, and serve a judge for science fairs at Rachel Carson Elementary.  


Committee Members:

Dr. John J. Kelly
Dr. Christopher Peterson
Dr. Timothy Hoellein