ACCESS 2025: Coastal Microbial Interactions

Dr. Jesse McNichol (May 29th, 2025)

Towards Holistic Coastal Microbial Ecology: Integrating Across Domains, Scale, and Genetic Diversity to Track Microbial Ecosystem Function

or... "How I learned to stop worrying and love the madness of the microbiome"

1. Part I: "Carl Sagan" intro
2. Part II: Coastal Complexity
3. Part III: Microbiome madness
4. Part IV: How not to go mad: CAFCA
   1. Contextualized
   2. Affordable / Accessible
   3. FAIR
   4. Comprehensive
   5. Archived
5. My thoughts on the future of coastal microbial ecology
6. Questions / discussion

Talk outline

Part I: "Carl Sagan" intro

If you could step back to the edge of the solar system...

...and look at the light passing through our atmosphere...

...what would you see?

Chemical signatures of a living planet!

• Primary production
• Nutrient cycling
• GHG production / consumption
• Influence geology, climate, chemistry, and biology of Earth

Microbial life

Microbial life keeps the big wheel turning...

But what about the future?

Microbial life

But what about the future?

(Micro)

Kump, Kasting, and Crane, The Earth System

Microbial life

But what about the future?

(Micro)

Kump, Kasting, and Crane, The Earth System

What is the role of microbial ecology / microbiome science in an age of crisis?

 NASA PACE

Coastal ecosystems cover huge spatial scales

Coastal ecosystems are incredibly dynamic

Coastal ecosystems are incredibly dynamic

Land-sea interactions and temporal variability

Data: Environment Canada

Land-sea interactions and temporal variability

Yeo et al., 2013

Normal

Land-sea interactions and temporal variability

Image: Google Maps

Complex coastal geometry → spatial heterogeneity

Image: J. McNichol

Complex coastal geometry → spatial heterogeneity

Image: J. McNichol

Complex coastal geometry → spatial heterogeneity

Image: J. McNichol

Complex coastal geometry → spatial heterogeneity

Image: J. McNichol

Complex coastal geometry → spatial heterogeneity

Image: J. McNichol

Complex coastal geometry → spatial heterogeneity

Finkel et al., 2010

For microbes, spatial heterogeneity extends to the microscale

Davis Laundon /  De Tommasi et al

Living at the microscale - plankton

Jalaluddin et al., 2025

Living at the microscale - sand grains

Jalaluddin et al., 2025

Microscale biogeochemical partitioning (sand grains)

Wilbanks et al., 2014

found in salt marshes near Woods Hole, but I've yet to see them here!

Microscale biogeochemical partitioning ("pink berries")

Why do I like studying coastal systems?

 NASA PACE

Vincent and Vardi, 2023

Can experiment across scales, depending on question

"Model ecosystems"

A "model ecosystem" in Cape Breton

• Stratified basin with anoxic, sulfidic waters ~ 17 m
• Using metabarcoding, metagenomics to understand taxa present, their dynamics, and functional potential
  • Ultimate goal: use experiments to understand how resilient microbial "ecosystem services" are to disturbance (i.e. climate change, eutrophication)

A "model ecosystem" in Cape Breton

The era of cheap DNA sequencing

For a few thousand dollars, can get billions of "reads"

The era of cheap DNA sequencing

Image credit: Chavez et al., 2021

Cheap DNA sequencing → "eDNA assays" ( = amplicon sequencing = metabarcoding)

Image credit: Chavez et al., 2021

Cheap DNA sequencing → "eDNA assays" ( = amplicon sequencing = metabarcoding)

The era of arguing about methods

The era of arguing about methods

• Intercalibration using standard reference material / mock communities so we know which methods really are best

My opinion: Arguing about methods will only end with community intercalibration efforts

Let's enter the era of "what does it all mean?"

Easy to get overwhelmed! Remainder of presentation = my thoughts on how to navigate this complexity

Complex ecosystems + complex methods / data

1. Part I: "Carl Sagan" intro
2. Part II: Coastal Complexity
3. Part III: Microbiome madness
4. Part IV: How not to go mad: CAFCA
   1. Contextualized
   2. Affordable / Accessible
   3. FAIR
   4. Comprehensive
   5. Archived
5. My thoughts on the future of coastal microbial ecology
6. Questions / discussion

CAFCA

1.  
2.  
3.  
4. Part IV: How not to go mad: CAFCA
   1. Contextualized
   2. Affordable / Accessible
   3. FAIR
   4. Comprehensive
   5. Archived
5.  
6.  

Contextualized: metadata-rich time-series

Contextualized: collaborate!

Microbial ecology

Contextualized: focus on "bold hypotheses" that build knowledge

• Generating sequencing data: easy
• Developing a good question: hard

https://royalsocietypublishing.org/doi/full/10.1098/rstb.2019.0240

Accessible: Use open-source workflows

https://metagenome-atlas.github.io/

https://github.com/jcmcnch/eASV-pipeline-for-515Y-926R

Accessible: Use open-source workflows

https://app.pr2-database.org/pr2-database/

Accessible: Use expert-curated databases

https://simonscmap.com/catalog/datasets/GRUMP

Accessible: Use expert-curated datasets

McNichol, Williams, et al., 2025 (in revision)

Affordable: My "quiver" of DIY methods

• Kit-free, non-toxic DNA extraction with linear acrylamide as co-precipitant, allows for recovery of very small amounts of DNA for PCR (~10 mL seawater*)
• Cheap, simple protocol for removal of PCR inhibitors with linear acrylamide
• Protocols for decontamination of reusable plasticware for molecular protocols (reduce waste, guarantee quality)
• 1-step PCR reaction for library prep in lab (advantages = speed, lower cost, flexibility)

*Other methods for as little as 1 µL exist

Wilkinson et al., 2016

FAIR

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"

FAIR data and Natural History

Microbe art: @claudia_traboni

Comprehensive: whole-community methods

Microbe art: @claudia_traboni

18S

p16S

e16S

Comprehensive: whole-community methods

Sample y: dominated by eukaryotes (e.g. Southern Ocean)

Comprehensive: absolute units

Jones-Kellett et al., 2024

• Near perfect match between high-quality flow cytometry data and our eDNA quantification method with internal standards
• Workshop on internal standard methods with Dr. Julie Laroche (Sept 12-13th 2025, Halifax)

Archived

• DNA extracts from time-series studies may be incalculably valuable in future (new technologies, ecological restoration)
• Current methods of long-term preservation are energy intensive and/or not stable in very long term - should we be archiving DNA to create "microbial herbaria" as a long-term record?

• 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

My vision for microbial ecology in the Anthropocene

The future

Zakem, McNichol, Weissman et al., 2025

The future

• Global eDNA data used as a "scaffold"
• GTDB genome data recruited to predict growth rates, niches
• Compared with models, showing high correspondence
• Observations → "bold hypotheses" about basic biology & microbe - climate interactions

The future: closing thought

At a time when forces are trying to distract and disrupt the scientific enterprise, doing the important work of finding and sharing the truth is now a great act of resistance."

 

-H. Holden Thorp, 2025 (link)

Questions?

Thanks to:

• Current and former CBIOMES collaborators (Fuhrman, Follows, Levine, Zakem labs)
• Dr. Bruce Hatcher (CBU)
• Katherine Rutherford and Jillian Davies (StFX)
• All of you for listening!

stfxmicroeco.ca | jmcnicho@stfx.ca

slides.com/jcmcnch/access-2025-plenary

Interested in aquatic microbial research at StFX?

stfxmicroeco.ca | jmcnicho@stfx.ca

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