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

PCR-based quantification of 16S & 18S SSU rRNA

"Phylogenetic stains" with DNA probes & (stable) isotope tracers

  • Culture-based genomics        
  • Single-cell genomics
  • Shotgun metagenomics
  • Microoxic/anoxic cultivation
  • Physiological measurements
  • Analytical chemistry assays

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

Pure cultures or environmental genomes

(Pan)genomic analysis

Understanding of speciation

Plot made with anvi'o

Cultivation & physiology

  • Develop and test hypotheses about biochemical basis of ecological niches

Specific hypotheses that can be used to guide future work ('omics / biochemistry)

Cultivation @ StFX

  • Set up equipment for O2-sensitive microbes
  • Retrieve cultures / samples from WHOI, CUHK
  • Train students in isolation, cultivation
  • Medium term: develop 'omics methods for cultures
  • Long term:  Targeted isolation campaigns, biochemistry

Barcoding surveys

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

Microbe art: @claudia_traboni

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)

Oxygen caused major shift in community structure over ~ 24 h

FISH

SIP

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**

*HTS=High throughput sequencing

**tinyurl.com/mgprimereval

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)

 

Slide Citation
1 (tree image) A. Spang, T. J. G. Ettema, Microbial diversity: The tree of life comes of age. Nat Microbiol 1, 16056 (2016).
2 (ocean diagram) M. Hügler, S. M. Sievert, Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean. Annu. Rev. Marine. Sci. 3, 261–289 (2011).
8 (speciation diagram) R. Stepanauskas, et al., Gene exchange networks define species-like units in marine prokaryotes. bioRxiv, 2020.09.10.291518 (2020).
9 (protein image) J. McNichol, S. M. Sievert, Reconciling a Model of Core Metabolism with Growth Yield Predicts Biochemical Mechanisms and Efficiency for a Versatile Chemoautotroph. bioRxiv, 717884 (2019).
10 (abundance plot) J. A. Fuhrman, J. A. Cram, D. M. Needham, Marine microbial community dynamics and their ecological interpretation. Nature Reviews Microbiology 13, 133–146 (2015).
13 (incubation plot) J. McNichol, et al., Assessing microbial processes in deep-sea hydrothermal systems by incubation at in situ temperature and pressure. Deep-Sea Res. Pt. I 115, 221–232 (2016).
12 (FISH + SIP diagram) J. McNichol, et al., Primary productivity below the seafloor at deep-sea hot springs. PNAS 115, 6756–6761 (2018).
15 (Water column diagram) P. M. Strain, P. A. Yeats, The Chemical Oceanography of the Bras D’Or Lakes. Proc NSIS 42, 37–64 (2002).
17 (book image) B. D. Dyer, A Field Guide to Bacteria, Illustrated edition (Comstock Publishing Associates, 2003).

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

Woese's tree

Haeckel's tree

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