Elle Barnes

Assistant Professor

Thomas H. Gosnell School of Life Sciences

College of Science

embsbi@rit.edu

585-475-2483

Office Location

BRN-1125

Elle Barnes

Assistant Professor

Thomas H. Gosnell School of Life Sciences

College of Science

Bio

I am a community and microbial ecologist interested in anthropogenic effects on environmental health and disease. I apply molecular, computational, and theoretical techniques to explore how host-microbe-environment interactions influence biodiversity patterns across space and time. I am especially interested in applying modern 'omic techniques (e.g., genomics) traditionally used in human medicine to issues in wildlife conservation--expanding the toolkit of conservation practitioners through less invasive and cheaper environmental methods.

In my lab, we use salamander-associated microbiomes as model systems to ask: how do you build a beneficial microbiome? We do this through field and lab-based experiments that empirically test core eco-evolutionary theories, such as community assembly theory. We are also a group that is extremely passionate about science education and literacy and advocates of mental health and diversity in STEM.

embsbi@rit.edu

585-475-2483

Personal Links

Personal Website

Google Scholar

Twitter

Select Scholarship

Halliday, F. W., Barnes, E. M., Ojima, M. N., & Stiver, I. (2024). On the hunt for facilitation in symbiont communities. Trends in Ecology & Evolution. DOI: 10.1016/j.tree.2024.07.009

Barnes, E. M., Hartman, K., Chiniquy, D., Zhao, W., Liu, P., Creech, C., ... & Tringe, S. G. (2024). Abiotic stress reorganizes rhizosphere and endosphere network structure of Sorghum bicolor. Phytobiomes Journal. DOI: 10.1094/PBIOMES-02-24-0012-R

Stroud, J. T., Delory, B. M., Barnes, E. M., Chase, J. M., De Meester, L., Dieskau, J., ... & Fukami, T. (2024). Priority effects transcend scales and disciplines in biology. Trends in Ecology & Evolution. DOI: 10.1016/j.tree.2024.02.004

Qiao, Z., Barnes, E.M., Tringe, S., Schachtman, D. P., & Liu, P. (2023). Poisson hurdle model-based method for clustering microbiome features. Bioinformatics, 39(1), btac782. DOI: 10.1093/bioinformatics/btac782

Barnes, E. M., & Tringe, S. G. (2022). Exploring the roles of microbes in facilitating plant adaptation to climate change. Biochemical Journal, 479(3), 327-335. DOI: 10.1042/BCJ20210793

Barnes, E. M., Kutos, S., Naghshineh, N., Mesko, M., You, Q., & Lewis, J. D. (2021). Assembly of the amphibian microbiome is influenced by the effects of land???use change on environmental reservoirs. Environmental Microbiology, 23(8), 4595-4611. DOI: 10.1111/1462-2920.15653

Chiniquy, D., Barnes, E. M., Zhou, J., Hartman, K., Li, X., Sheflin, A., ... & Tringe, S. G. (2021). Microbial community field surveys reveal abundant Pseudomonas population in sorghum rhizosphere composed of many closely related phylotypes. Frontiers in microbiology, 12, 598180. DOI: 10.3389/fmicb.2021.598180

Barnes, E. M., Carter, E. L., & Lewis, J. D. (2020). Predicting microbiome function across space is confounded by strain-level differences and functional redundancy across taxa. Frontiers in Microbiology, 11, 101. DOI: 10.3389/fmicb.2020.00101

Currently Teaching

BIOL-295

Biology Research

1 - 4 Credits

This course is a faculty-directed student project or research involving laboratory work, computer modeling, or theoretical calculations that could be considered of an original nature. The level of study is appropriate for students in their first three years of study.

BIOL-298

Biology Independent Study

1 - 4 Credits

This course is a faculty-directed tutorial of appropriate topics that are not part of the formal curriculum. The level of study is appropriate for student in their first three years of study.

BIOL-301

Undergraduate Teaching Experience

1 - 4 Credits

This course allows students to assist in a class or laboratory for which they have previously earned credit. The student will assist the instructor in the operation of the course. Assistance by the student may include fielding questions, helping in workshops, and assisting in review sessions. In the case of labs, students may also be asked to help with supervising safety practices, waste manifestation, and instrumentation.

BIOL-471

Environmental Microbiology

4 Credits

This course presents the relationships between microbes and their environments, as well as techniques to study them. It will cover the diverse microbiology of different habitats, ranging from soils and aquatic environments, to anthropized and extreme environments. Topics include the roles of microbes in nutrient and biogeochemical cycles, evolutionary aspects, as well as the relationships between environmental microbes and humans with regard to health impacts and biotechnological applications. Laboratory experiments will explore the types of bacteria in different environmental samples using a range of techniques from culturing and coliform counting, to metagenomic approaches. Impacts of microbes on the environment and human health will be highlighted through biogeochemical techniques and antibiotic resistance testing.

BIOL-495

Advanced Biology Research

1 - 4 Credits

This course is a faculty-directed student project or research involving laboratory or field work, computer modeling, or theoretical calculations that could be considered of an original nature. The level of study is appropriate for students in their final two years of study.

BIOL-498

Advanced Biology Independent Study

1 - 4 Credits

This course is a faculty-directed tutorial of appropriate topics that are not part of the formal curriculum. The level of study is appropriate for student in their final two years of study.

BIOL-599

Research Based Writing

3 Credits

This course is intended for students with significant research experience to work closely with their faculty mentors to prepare a manuscript for publication or write a proposal for external funding. Students will devote significant time to writing, revision and peer review. A submission-quality manuscript or proposal is expected at the end of the semester.

BIOL-798

Grad Biology Independent Study

1 - 4 Credits

This course is a faculty-directed, graduate level tutorial of appropriate topics that are not part of the formal curriculum.

ENVS-790

Environmental Science Thesis

1 - 4 Credits

The thesis option will be available to environmental science graduate students only with prior written approval of program faculty. Students will submit a proposal to a faculty member who agrees to serve as the student's thesis committee chair. The proposal will describe the basic research question to be investigated and the experimental protocols to be employed. Proposals will be reviewed by the program faculty who will give permission to register for thesis credit. This course may be taken several times over the course of a student's graduate program, for variable credits. A written thesis and oral defense are required at the completion of the thesis research.

ENVS-795

Environmental Science Graduate Research

1 - 4 Credits

This course is a graduate level, faculty-directed, student project or research involving laboratory or field work, computer modeling, or theoretical calculations that could be considered of an original nature. The level of study is appropriate for students in Environmental Science graduate program.

ENVS-798

Advanced Environmental Science Independent Study

1 - 4 Credits

This course is a faculty-directed tutorial of appropriate topics that are not part of the formal curriculum. The level of study is appropriate for student in the Environmental Science graduate program.

In the News

March 21, 2024

Genomics lab allows scientists and students to help protect the local ecosystem

Within Brown Hall on RIT’s campus, newly renovated lab spaces house state-of-the-art equipment allowing for essential research. One such space is the genomics lab, where Elle Barnes, assistant professor in the Thomas H. Gosnell School of Life Sciences, is working to help protect one of the key members of the local ecosystem: salamanders.

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