CBIOMES 2026 Annual Meeting Update

Jesse McNichol, St. Francis Xavier University (StFX)

Implications of Prokaryotic Microdiversity for Ecosystem Functional Resilience - an Empirical Approach

 NASA PACE

A "model ecosystem" in Cape Breton

A "model ecosystem" in Cape Breton

A "model ecosystem" in Cape Breton

Source: Stormy Vandenplas, MSc. Thesis

A "model ecosystem" in Cape Breton

Source: Stormy Vandenplas, MSc. Thesis

A "model ecosystem" in Cape Breton

A "model ecosystem" in Cape Breton

Me aboard Dr. Bruce Hatcher's research vessel Exocet in 2024

• Stratified basin with anoxic, sulfidic waters ~ 17 m (historically ~1000 μM H₂S)
• Temperature and oxygen gradients very steep at redoxcline, system has recently overturned in winter 2024/2025 causing aquaculture mortality in 2024
• With Dr. Katherine Rutherford (StFX) we are using metabarcoding, metagenomics to understand taxa present, dynamics, functional potential

A "model ecosystem" in Cape Breton

A "model ecosystem" to ask questions about the link between diversity and function

Lots of genetic diversity, but relationship between diversity & function poorly known (some exceptions, e.g. Prochlorococcus)

A "model ecosystem" to ask questions about the link between diversity and function

...it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions."

• In this ecosystem, sulfur oxidation is an "ecosystem service"
• "Microbial firewall"
• Prediction: stable stratification means limited functional diversity
• If disturbance (e.g. water overturning) occurs → limited resilience of function
• Goal: experiments to generate empirical data to test this prediction

How resilient are microbial ecosystem services to disturbance?

Does high genetic "microdiversity" observed in natural microbial ecosystems confer functional resilience of H₂S detoxification during deep water mixing, or will rapid changes in environmental conditions slow or stop this critical ecosystem service?"

A simple question

Whycocomagh Bay

Establishing the Whycocomagh Euxinia Time-Series (WET)

Whycocomagh Bay

• María Alas Romero, BSc Honours project: "The Resilience of Arcobacter in Sulfidic Environments [as determined by metagenomics]"

Establishing the Whycocomagh Euxinia Time-Series (WET)

Whycocomagh Bay

Joanna Martinsen, BSc Honours project: "Isolation and Characterization of Sulfur-Detoxifying Prokaryotes in a Coastal Euxinic Basin"

Establishing the Whycocomagh Euxinia Time-Series (WET)

Whycocomagh Bay

Leslie Tran, undergrad research assistant: will be working on HCR-FISH analyses

Establishing the Whycocomagh Euxinia Time-Series (WET)

Establishing the Whycocomagh Euxinia Time-Series (WET)

Sampling depth

Extreme euxinia has disappeared, but plenty of evidence for active sulfur cycling

pre / post turnover

Establishing the Whycocomagh Euxinia Time-Series (WET)

Sampling depth

Extreme euxinia has disappeared, but plenty of evidence for active sulfur cycling (and water column sulfate reduction)

pre / post turnover

Establishing the Whycocomagh Euxinia Time-Series (WET)

Sampling depths

a.k.a. "SUP05"

Extreme euxinia has disappeared, but plenty of evidence for active "cryptic" sulfur cycling

pre / post turnover

Julia Kadel, Unsplash

Does "microdiversity" buffer changes at WET?

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

Ecologically-relevant annotations aggregate complex ASV data into sensible groupings

• Bacterioplankton
• Phytoplankton
  • Prochlorococcus  (ecotype)

McNichol, Williams, et al., 2025

What is the right level for understanding ecosystem function? 

One strategy: aggregate to broad "guild" level

Does "microdiversity" buffer changes at WET?

Does "microdiversity" buffer changes at WET?

Does "microdiversity" buffer changes at WET?

Does "microdiversity" buffer changes at WET?

Does "microdiversity" buffer changes at WET?

Ecosystem

Ecosystem

Does "microdiversity" buffer changes at WET?

Vincent and Vardi, 2023

A "middle way" for testing microdiversity

Vincent and Vardi, 2023

A "middle way" for understanding microdiversity

Short-term incubation experiments of seawater

Pro: Generate empirical data for testing hypotheses

Con: The longer you incubate, the less the composition resembles the natural community. Need very short-term incubations, and single-cell activity measurements

McNichol, Dyksma et al., 2022

A "middle way" for understanding microdiversity

rRNA-FISH & FACS + ¹⁴CO₂ =

• taxon-specific C-fixation
• response to different chemical conditions in short-term incubations

How we plan to do the work

Katherine Rutherford (StFX)

Bruce Hatcher (CBU)

3DMB=3-domain metabarcoding, FL-16S=full-length 16S (PacBio)

SRF=surface, RXL=redoxcline, EUX=Euxinic (sulfide-rich waters)

How we plan to do the work

How we plan to do the work: in situ growth rates

FISH probes + FODC method → OOI growth rate (including microdiverse subclusters)

Could be compared with MAG estimates (gRodon)

How we plan to do the work: incubations

How we plan to do the work: organism-specific respiration

FISH probes + Redox Sensor Green → OOI respiration rate changes after short-term incubations

Munson-McGee et al., 2022

Possible outcomes (null)

Killed

NIC

RXL @ RXL

NIC=No incubation control + RSG | RXL @ RXL=redoxcline water incubated at in situ conditions

RXL @ SRF=redoxcline water incubated at surface conditions (increased O₂, temp)

RXL @ SRF

Possible outcomes (limited resilience)

Killed

NIC

RXL @ RXL

NIC=No incubation control + RSG | RXL @ RXL=redoxcline water incubated at in situ conditions

RXL @ SRF=redoxcline water incubated at surface conditions (increased O₂, temp)

RXL @ SRF

Possible outcomes (more activity with upwelling)

Killed

NIC

RXL @ RXL

NIC=No incubation control + RSG | RXL @ RXL=redoxcline water incubated at in situ conditions

RXL @ SRF=redoxcline water incubated at surface conditions (increased O₂, temp)

RXL @ SRF

Possible outcomes (incubations not working)

Killed

NIC

RXL @ RXL

NIC=No incubation control + RSG | RXL @ RXL=redoxcline water incubated at in situ conditions

RXL @ SRF=redoxcline water incubated at surface conditions (increased O₂, temp)

RXL @ SRF

Next steps

Summer 2026:

Identify targets from bioinformatics, optimize FISH probes

Fall 2026 / Spring 2027:

Apply incubation approach with FISH probes targeting organisms of interest

What knowledge we can gain?

• An inventory of sulfur oxidation potential in system from metagenomics (Illumina + Nanopore)
• Spatiotemporal diversity patterns (stochastic? predictable?)
• In situ growth and respiration rates (FODC, RSG)
• Resilience to realistic disturbances across diversity
• "Traits" we can use to model future disturbance

STAY TUNED over the next 2-3 years!

Does high genetic "microdiversity" observed in natural microbial ecosystems confer functional resilience of H₂S detoxification during deep water mixing, or will rapid changes in environmental conditions slow or stop this critical ecosystem service?"

Much to learn!

Questions?

Thanks to:

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

stfxmicroeco.ca | jmcnicho@stfx.ca

https://slides.com/jcmcnch/cbiomes-annual-meeting-update-2026

Summary of incubation conditions

Ecosystem maps from eDNA

Ecosystem DNA

Vincent and Vardi, 2023

Ecosystem maps from eDNA → tackling big questions

Ecosystem maps can be cheaply generated from a "quiver" of DIY methods that I like to use

• 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 (for difficult samples, Zymo 1-step is cheap & works)
• 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

A story about ecosystem maps + meta'omics + models

Zakem, McNichol, Weissman, Raut et al., 2025

Figure 1: Overview of sampling and data processing workflow. Oxygen and sulfide depth profiles shown in blue and orange, respectively. SRF=surface, RXL=redoxcline, EUX=euxinic. 3DMB=3-domain metabarcoding, MAGs = metagenome assembled genomes, FL-16S = full-length 16S. OOI = organism of interest. FISH = fluorescence in-situ hybridzation.

Vincent and Vardi, 2023

Coastal systems are flexible: experiment across scales, depending on question

GRUMP 2.0 = a story about absolute units

Slide credits: Dr. Lexi Jones-Kellett (aejk@alum.mit.edu)

GRUMP 2.0 = a story about absolute units

Slide credits: Dr. Lexi Jones-Kellett (aejk@alum.mit.edu)