Urban Microbial Dynamics and Metagenomics

Project Location

Students sample the urban environment and characterize bacterial diversity in the sample using a molecular approach.

Student Audience

Introductory, Advanced, Major, Non-major

Scientific Domain

  • Ecology
  • Genetics/Genomics
  • Microbiology

Nature of the Research

  • Wet lab/bench research
  • Field research
  • Informatics/computational research
  • Basic research

Core Concepts

  • Evolution: The diversity of life evolved over time by process of mutation, selection, and genetic change.
  • Information Flow and Exchange: The growth and behavior of organisms are activated through the expression of genetic information in context.
  • Systems: Living systems are interconnected and interacting.

Core Competencies

  • Applying the process of science
  • Using quantitative reasoning
  • Tapping into the interdisciplinary nature of science
  • Communicating and collaborating

Guiding Questions

  • What is the microbial diversity of an urban environment?
  • To what extent is microbial diversity stable over time?
  • How do environment factors such as rainfall, traffic, etc., influence microbial diversity?

Learning Objectives

  • Conduct and explain molecular genetic techniques such as PCR
  • Describe the limitations of culturing for determining bacterial diversity
  • Characterize the bacterial diversity of an environment
  • Interpret metagenomic data to determine bacterial diversity and relative abundance


The goal of the urban metagenomics project is to involve undergraduates in determining the microbial community composition of common sites, such as streets, sidewalks, parks, and to get a sense of the diversity and stability of these communities by sampling multiple locations over time and across seasons. The project is divided into five steps, starting with 1) sampling of microorganisms from the environment by swabbing, 2) extraction and purification of the total genomic DNA from the sample, 3) PCR amplification of 16S rRNA variable gene regions using universal primer set and clean-up of the resulting amplicon, 4) submitting 16S amplicon for pyrosequencing and 5) analysis of sequencing data. Each lab section is divided into small teams of 4 to 6 students. The project is carried out over 8-10 weeks of the 14-week lab, with an introduction to microbial diversity and metagenomics at the outset of the course and time built in for troubleshooting and repeating steps when things do not work. Student teams can be at different steps of the project in the same lab session and because there are other smaller projects and microbiological techniques being covered in the course the students are always active and not waiting for other teams to reach the same point each week. It should be noted that urban microbial community dynamics is the largest project that is carried out in the lab, but there are other less extensive research-based projects that the students work on in parallel during the semester. In some semesters we have used a directed approach where the microbiology course coordinator has worked with the lab instructors to determine what urban sites should be sampled, while we have also run lab sections where the students, working in their groups, were given the choice of determining what sites to sample. In these cases, students were asked to select sites they thought would have the greatest potential to serve as reservoirs for human pathogens, and they chose to look at local playground equipment and subway stations.

Getting Started

There are three starting points: (1) students do all of the work - collect samples, conduct PCR, send samples to a core facility for sequencing, and then analyze the data; (2) students collect samples, send them to the home site at CUNY, CUNY completes the molecular work and sends out for sequencing, and send the data back for students to analyze; or (3) students examine existing CUNY datasets using bioinformatics approaches. Agreements may need to be generated to cover the costs.