Black Excellence Day 2025 (Oct 15, 2025)
Dr. Jesse McNichol, St. Francis Xavier University
eDNA Sequencing for Exploring Microbial Ecosystems!
Bacteria and other microbes cause nasty diseases...
Typhoid fever (bacterial)
Potato blight (eukaryotic)
Yellow fever (viral)
Cyanobacteria bloom (Nodularia), Baltic Sea
Bacteria are everywhere
Cyanobacteria bloom, Lake Erie
Bacteria are everywhere
Grand Prismatic hot spring, Yellowstone
Bacteria are everywhere
"Black smoker" at deep-sea hydrothermal vent (Atlantic ocean)
Bacteria are everywhere
When were microbes first discovered?
- The 1900s
- The 1800s
- The 1600s
- The 1200s
When were microbes first discovered?
- The 1900s
- The 1800s
- The 1600s
- The 1200s
Sample placed on pin
Spherical lens
The first microscope
Seeing is believing
Red blood cells
Spiral bacteria
Giardia parasite
Seeing is believing
https://foldscope.com/
A "$1 microscope"! Tool for education, diagnosis (e.g. Malaria in blood smears)
Seeing is believing
Eukaryotic microbes are pretty...
Diatom morphological diversity
(Taylor lab, Rynearson lab, Wipeter CCA)
What are their cells made of?
Why would this be useful?
Dinoflagellate morphological diversity
Cellulose armor ("thecal plates")
Complex behaviour (predation)
Have "eyespots" for phototaxis
(Wikimedia commons)
Eukaryotic microbes are pretty...
- Food / oxygen production (base of food webs)
- Nutrient regeneration
- Greenhouse gas production / consumption
- Influence geology, climate, chemistry, and biology of Earth
Microbial life
Microbes are critical in marine systems
But what about the future?
Microbial life
But what about the future?
How will climate change and coastal pollution affect "ecosystem services" that microbes provide to us?
NASA PACE
How to monitor these dynamic and changing systems?
How to monitor these dynamic and changing systems?
ESA Copernicus
Early sequencing
"Next Generation Sequencing" (NGS)
DNA sequencing is now very cheap!
An avalanche of data!
Image credit: Chavez et al., 2021
Cheap DNA sequencing → "eDNA profiles"
Image credit: Chavez et al., 2021
Cheap DNA sequencing → "eDNA profiles"
Modern (Micro)biology Driven by Biotechnology
These 2 technologies allowed us to go beyond cultivation and enter the "molecular age"
PCR (polymerase chain reaction)
DNA sequencing (Sanger sequencing)
Depends on an enzyme from hot springs
Grand Prismatic hot spring, Yellowstone
Thermus aquaticus, a thermophilic bacterium from Yellowstone gave rise to the "Taq" DNA polymerase that is used in all PCR reactions to this day!
- Isolated by Thomas Brock, a famous environmental microbiologist
Text credit: Kirchman, Processes in Microbial Ecology
A nice metaphor
How PCR Works (overall)
PCR = polymerase chain reaction
How PCR Works (overall)
PCR = polymerase chain reaction
How PCR Works (thermocycling)
Modern thermocycler (original invention used water baths)
How PCR Works (thermocycling)
How PCR Works (overall)
PCR = polymerase chain reaction
How PCR Works (overall)
PCR = polymerase chain reaction
Metaphor credit: Kirchman, Processes in Microbial Ecology
To emphasize the metaphor...
Microbe art: @claudia_traboni
3. PCR
4. Sequencing
1. Sampling
2. DNA extraction
Returning to environmental microbiology
Vincent and Vardi, 2023
eDNA profiles → ecosystem monitoring across time & space
- Accessible to non-experts, community organizations, affordable and sustainable
- Leading to collaborative, interdisciplinary research asking exciting new questions
- A record of changing ecosystems, and a possible warning for state changes
eDNA sequencing's future
After the lapse of many years, possibly a century, the student of the future will have access to the original record of faunal conditions in California."
-Annie Montague Alexander, from "Why Ecology Needs Natural History"
Today's data will help us understand the future
Thanks for your attention!
Microbe art: @claudia_traboni
stfxmicroeco.ca | jmcnicho@stfx.ca
