Scripps Institution of Oceanography - The Invisible Life in the Oceans: Introduction to Marine Microbiology

Department: Marine Science

Instructors: Maitreyi Nagarkar and Rachel Diner
Instructor Emails:;
Prerequisites: None

Course Description

This course explores an unfamiliar aspect of ocean life: the millions of microbes that can be found within a single drop of seawater. We will cover introductory topics such as proper sterile technique when dealing with microbes, the preparation of culture media, and using DNA sequencing to identify as many microbial species as possible within a marine environment. Students will investigate microbes, including bacteria and algae, from a variety of different marine samples. Studying the microbiology within their surrounding environments will engage students and expand their conceptual understanding of the important role of microbes in all environments. Students will learn laboratory techniques that marine scientists and microbiologists use on a daily basis to explore and characterize microbial diversity from field samples. This course will immerse students in the scientific process as they formulate questions, collect data, and write up their findings.

Course Goals

The main objective of this course is to introduce high school students to the microscopic world around us and achieve an understanding of its fundamental importance to ocean ecosystems. Secondarily they will learn about the different challenges of studying microbial life and the methods, including the newest techniques of using DNA sequencing, scientists use to study marine microbes. By the end of the course, students should be able to (1) Identify the major categories of microbial life, (2) Describe the role of various microbes in the ocean ecosystem, (3) Collect and grow microbial species in a laboratory setting, (4) Understand and interpret DNA sequence data and what it can tell us about a microbial community, and (5) Formulate scientific questions and hypotheses and understand how to begin investigating them.

Course Expectations

We expect that students will come ready to learn and walk away with an appreciation for the vast diversity of microbes on our planet. Students should already have taken an introductory biology course at their high school, and this summer class will prepare them for the rigors of an Advanced Placement science course. Students should be prepared for learning in a variety of ways, including hands-on experience with lab work and sample collection as well as from lectures. Students will be expected to think critically about the world around them and connect prior scientific knowledge with the new microbiology content.

Course Outline

Week 1: Introduction to Microbiology and Lab Techniques

  • Introduction to microbes: prokaryotes and eukaryotes
  • Overview of lab safety and expectations
  • Tutorial on keeping a lab notebook
  • Preparing culture media and sterile technique
  • Separating microbes on streak plates
  • Description of bacterial morphology
  • Enumeration of bacteria by colony forming ability
  • Calculating viable cells in seawater
  • Field sampling trip #1

Week 2: Microbial Taxonomy, Molecular Biology, and Experimental Design

  • Identification of unknown bacteria
  • Amplicon sequencing of ribosomal subunit genes
  • Polymerase chain reaction (PCR); Agarose gel electrophoresis
  • BLAST analysis to identify unknown bacteria
  • Laboratory report on materials, methods and findings
  • Marine pathogens and water quality
  • Field sampling trip #2
  • Starting individual experiments

Week 3: Microbial Ecology and Interactions

  • Bacterial-Eukaryotic interactions
  • Tour of Scripps Institution of Oceanography
  • Observations of phytoplankton
  • Final project - Write ups and presentations of individual  experiments
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