Inquiry Lab: Identifying Bacteria using Morphology, Physiology, and Molecular Data

Overview & Concepts

Bacteria are prokaryotic organisms that can be found almost anywhere on earth.  Identifying prokaryotic species can be difficult in a high school lab.  The purpose of this lab it to use information that is known about bacteria cell wall composition, size, shape, arrangements, enzymatic activity, colony growth, and molecular data (DNA) to identify species (or group of prokaryotes) of known and unknown bacterial samples.  

Grade Level: 

Concepts Covered: 

  • Prokaryotic cell wall structure
  • Gram staining
  • Bacteria colony morphology
  • Bacteria shapes
  • Bacteria arrangements
  • enzymatic activity in prokaryotes
  • PCR

Prior Knowledge Required: 

  • DNA structure and genes
  • Domain Bacteria characteristics including cell wall structure, cell shapes and arrangements, metabolism, and respiration
  • Evolution
  • Gene expression
  • Genetic engineering including PCR
Activity Notes

Days to Teach: 

one week to complete the lab


  • Petri plates to grow bacteria
  • agar
  • Ecoli (known sample)
  • inoculating loops
  • sterile swabs for collecting bacteria
  • computer
  • Taq polymerase
  • PCR primers (see protocol)
  • PCR buffer
  • dNTP
  • distilled water
  • thermocycler
  • microcentrifuge tubes
  • agarose gel
  • electrophoresis chamber
  • power supply
  • loading dye
  • ladder (marker)
  • TBE buffer solution
  • gram stain materials (including crystal violet, safranin, iodine, and ethanol)
  • microscope slides
  • microscope
  • hydrogen peroxide
  • pipettes
  • micropipettes


Teaching Tips / Activity Overview: 

In order to avoid wasted class time, students can learn about Domain Bacteria while they are working on the lab. The lab work will take about a week, but will not take an entire class period every day.  During waiting periods, students can be researching information about Domain Bacteria.  Have supplemental activities they can work on like charts and concept maps to compare and contrast Archaea to Bacteria.  


  • Completion of known lab- using Ecoli to go through all the lab procedures (days 1 and 2)
  • Start thinking about lab design (days 1 and 2)
  • Lab design (second part of day 2)
  • Collect bacteria (second part of day 2)
  • Begin inquiry lab testing (days 3-5)
  • Work on lab write-up or poster presentation (days 3-5)
  • Work on supplemental activities about Domain Bacteria and Domain Archaea (days 3-5)


  • Work on lab write-up  or poster presentation (due one week after lab work in complete) There will be no more class time to work on the lab write-up or poster presentation after day 5.


  • If you are short on time, the following can be made ahead of time: 
  1. Agar plates
  2. Master mix for PCR (completed before start of class)
  3. Agarose gels
  • Do not give the students too many ideas about what they can test.  This should be an inquiry lab and you want the students to be engaged and creative.
  • Make sure you are clear about lab safety before students complete this lab.  (i.e. where to put contaminated materials)



  • Students will be taking an EXAM on lab content and information they collect about Domain Bacteria and Domain Archaea while completing this lab.
  • Students will be assessed on a lab write-up or poster presentation. 


  • have students construct a phylogenetic tree based on the information they obtained about the different prokaryotic groups
  • students can complete the AP Biology transformation inquiry lab


Additional Information: 

This lab would only be completed with an Advanced or AP Biology course.  Since most general biology classes do not cover classification, gram-staining, and bacteria shapes and arrangments would not be necessary.  This lab could be modified to include more of an emphasis on PCR and cloning if it were to be completed with a general biology course.  

Academic Standards
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