Marine Microbial Ecology at StFX

StFX Biology department, March 31st, 2021

Jesse McNichol, PhD, Biological Oceanography

Postdoctoral Scholar, USC

The microbial tree of life

• Microbes are a "living fossil record" of biosphere evolution
• Have mapped diversity but cannot yet explain it
  • What is the "logic" behind the tree's structure (traits, niches)?
  • What are the ecological and environmental implications?

Ecosystem-centred research

• Goal = holistic under-standing of ecosystem
• Methods = puzzle pieces
• Whole puzzle = "sketch" of traits / niche

Proposed program

1. Holistic program driven by broad vision
2. Accomplished with diverse methods (range of depths / breadths)
3. Built with iterative and interconnected research projects
   • Different experience levels and (inter)departmental collaborations

Methods

• Diverse techniques that represent different parts of the puzzle

Areas of research

1. Cultivation:
   • Genomics, Physiology
2. Barcoding surveys
3. Process studies

Cultivation

• Pure cultures are essential for interpreting environmental 'omics data
  • Isolation is a great introductory project:
    • Most microbes are unknown to science
    • Develop based on interests / strengths

Cultivation & genomics

• Sequencing genomes of multiple isolates shows how speciation and evolution may occur in nature

Cultivation & physiology

• Develop and test hypotheses about biochemical basis of ecological niches

Cultivation @ StFX

Barcoding surveys

• Barcoding data is used to map microbes across time and space
  • 515Y / 926R primers target all cellular life

Barcoding surveys

• Our work is extending observations across oceans

Barcoding surveys @ StFX

• Set up bioinformatic infrastructure
• Develop "bite-size" projects:
  • Biogeographic, time-series data
  • Analysis, interpretation, "data science"
  • Contribute to modelling work
• Med. term: Build lab infrastructure (eDNA)
• Long term: Apply to local "model systems"

Process studies (hydrothermal vents)

• How much CO₂ do hydrothermal vent microbes fix?
• What factors influence their growth?

• Barcoding showed major shift due to oxygen
• FISH + SIP quantified CO₂ fixation at single-cell level (NanoSIMS)

Process studies (hydrothermal vents)

• Set up lab infrastructure for FISH
• Medium term:
  • Investigate Whycocomagh bay as model system:
    • Water anoxic at 10 - 15 m, contains sulfide
    • These conditions favour chemoautotrophs
  • (Inter)departmental collaborations (microbiomes?)

Process studies @ StFX

• Methods inform and interact with one another
• Points to "microbial natural history"

Holistic picture

Native Microbiota CURE

• Based on undergraduate botany experience (Native Flora)
• Students collect microbial "herbaria":
  • Characterize with barcoding
  • Visualize with FISH
  • Attempt to cultivate
• Goal: Develop "microbial natural history"
  • Bring new scientists into the fold
    • EDI objectives
  • X-Oceans Outreach
    
  • Discover new taxa, study sites

Summary

• Samples / data:
  • Global barcoding data
  • Vent strains / samples
  • (meta)genomic data
• Wet lab skills:
  • HTS* library prep
  • Low O₂ cultivation
  • FISH (& probe design)
  • Analytical chemistry
• Bioinformatics skills:
  • Barcoding (qiime2)
  • 'omics (anvi'o)
  • R/python/bash, snakemake**

Why microbial ecology at StFX?

• Opportunity to focus on fundamental biological research
  • Build model (eco)systems, interdepartment collaborations
• Diverse questions / techniques fits with liberal arts education
  • Flexible, student-centred projects; CURE
• Maritimes offers a wealth of natural marine environments
  • Collaborations in oceanography, ecosystem monitoring

Acknowledgements

WHOI: Stefan Sievert, Jeff Seewald, Niculina Musat, Craig Taylor

CUHK/Academia Sinica: Haiwei Luo, Annie Wing-Yi Lo, Benny Chan

USC: Jed Fuhrman, Yi-Chun Yeh, Bruce Yanpui Chan, Paul Berube, Steven Biller, Mick Follows, Enrico Ser-Giacomi

Works cited (ideas and images)

Unless otherwise noted, images are either my own work, ⓒWHOI, or from wikimedia commons

Understand to protect

• Microbes are the "wires" connecting global chemical cycles
  • Climate, nutrient cycling, habitability

A microbial ecology lab at StFX

• Ultimate goal:
  • Niche / traits of marine bacteria
• Long-term, iterative program:
  • Undergrads, grad students, postdocs
  • (Inter)departmental collaborations
• Bring materials, expertise, collaborations:
  • Quickly begin research with 'omics / barcoding data
  • Samples (e.g. for cultivation)
• Longer term goals once established:
  • Model ecosystem (Whycocomagh bay?)
  • Native Microbiota CURE
  • Monitoring collaborations

My experience

• B.Sc., Biology, Mount Allison (2003 - 2008)
• Government researcher (2008-2011)
  • Environment Canada
  • NRC (Algal Biofuels)
• PhD in Biological Oceanography, MIT/WHOI (2011-2016)
• Postdocs:
  • CUHK (2017)
  • USC (2018 - present)

Why study microbial ecology?

• Like astronomy, it gives us a sense of perspective...
• ...and helps us look back in time to how life evolved

Undergraduate research at StFX

• Microbes are everywhere, yet poorly described:
  • Cultivation / surveys
  • Native Microbiota
• Huge amount of 'omics data:
  • "Data science"
• Tools have yet to be perfected:
  • Methods development