Marine Microbial Ecology at StFX

StFX Biology department, May 19th, 2021

Jesse McNichol, PhD, Biological Oceanography

Postdoctoral Scholar, University of Southern California

Motivation

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

Multicellular

life

My experience

  • PhD work: "Deep dive" into chemoautotrophic* Campylobacteria
  • Postdoc work: Broad "barcoding" surveys across space/time
    • Same motivating questions, different scales

*using reduced inorganic compounds for energy and fixing CO2

My vision for a research program at StFX

  • "Grow" these experiences into a holistic program targeting local ecosystems

My vision for a research program at StFX

  • "Grow" these experiences into a holistic program targeting local ecosystems

My vision for a research program at StFX

  • "Grow" these experiences into a holistic program targeting local ecosystems

Proposed program: 3 pillars

Proposed program: 3 areas

  • Aim = predictive knowledge (niches, traits & environmental impact)
  • Areas interact and inform one another
  • Sequencing & bioinformatics central
  • Interactions
  • Spatial / temporal patterns
  • Abundance
  • Identity
  • Traits
  • Biochemistry
  • Evolution
  • Genomics
  • Ecology
  • Biogeo-chemistry
  • In situ activity / physiology

Proposed program: 3 areas

Proposed program: 3 areas

Proposed program: 3 areas

Proposed program: 3 areas

Proposed program: Methods

  • Different resolution, breadth

Community profiling by amplifying ribosomal RNA or DNA with PCR

Fluorescent "Phylogenetic stains" & isotope tracers

  • Culture-based genomics
  • Single-cell genomics
  • Shotgun metagenomics
  • Low oxygen cultivation
  • Physiological assays
  • Chemical assays  

Previous experience and plans

  1. Cultivation (Campylobacteria):
    • Genomics, physiology
  2. Biogeographic surveys
  3. Process, functional studies

Cultivation of chemoautotrophs

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

Cultivation & genomics

  • Genome sequencing reveals how niche differentiation and speciation occurs

Pure cultures or environmental genomes

Plot made with anvi'o

(Pan)genomic analysis

Understanding of speciation

Cultivation & physiology

  • Test hypotheses about fundamental ecological niches of chemoautotrophic Campylobacteria

Hypotheses guide future 'omics / biochemistry work

Cultivation at 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 : Methods

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

Microbe art: @claudia_traboni

Barcoding surveys: New data

  • Current work : extending marine observations

Barcoding surveys at StFX

  • Set up bioinformatic infrastructure, develop  "bite-size" biogeographic projects:
    • Analysis, interpretation, "data science"
    • Contribute to international collaboration on ecosystem modelling
  • Med. term: Build lab infrastructure (eDNA)
  • Long term: Apply locally (Whycocomagh)

Areas of research

  1. Cultivation (Campylobacteria):
    • Genomics, Physiology
  2. Biogeographic surveys
  3. Process, functional studies

Process study example (PhD work)

  • How active are deep-sea chemoautotrophs?
  • What factors influence their growth?
  • FISH + SIP quantified CO2 fixed at single-cell level
  • Barcoding showed major shift due to oxygen

Process studies (hydrothermal vents)

FISH

SIP

Genomic comparisons can give insight into oxygen tolerance / sensitivity (have data!)

Process studies at StFX: W. Whycocomagh Bay

Open ocean systems

Whycocomagh Bay

  • Set up infrastructure for field work
  • Medium term: Begin sampling local system
    • Diversity of metabolisms within ~1 hour drive
    • Archive DNA / RNA, cells for cultivation / FISH
      • Diverse, iterative projects that build on one another
      • Context for process studies
  • Methods interact and inform 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
    • X-Oceans Outreach
    • Discover new taxa, study sites

*CURE = Course-based undergraduate research experience

Summary

 

  • Samples / data:
    • Global barcoding data
    • Vent strains / samples
    • (meta)genomic data
  • Wet lab skills:
    • HTS* library prep
    • High-throughput, 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

Research plan

 

  • Short term:
    • Cultivation, bioinformatic / modelling projects
  • Medium term:
    • Build infrastructure for barcoding, 'omics, process work
    • Begin sampling Whycocomagh Bay / other systems
    • Establish (inter)departmental collaborations
  • Long term:
    • Conduct process, biochemical, 'omics studies

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 title Citation
Motivation Tree image: A. Spang, T. J. G. Ettema, Microbial diversity: The tree of life comes of age. Nat Microbiol 1, 16056 (2016).
Process studies at StFX: W. Whycocomagh Bay Image adapted from: M. Hügler, S. M. Sievert, Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean. Annu. Rev. Marine. Sci. 3, 261–289 (2011).
Water column data: P. M. Strain, P. A. Yeats, The Chemical Oceanography of the Bras D’Or Lakes. Proc NSIS 42, 37–64 (2002).
Cultivation & Genomics Speciation image: R. Stepanauskas, et al., Gene exchange networks define species-like units in marine prokaryotes. bioRxiv, 2020.09.10.291518 (2020).
Anvi'o: https://merenlab.org/software/anvio/; https://peerj.com/articles/1319/
Cultivation & Physiology 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).
Barcoding surveys: Methods Line diagram: J. A. Fuhrman, J. A. Cram, D. M. Needham, Marine microbial community dynamics and their ecological interpretation. Nature Reviews Microbiology 13, 133–146 (2015).
Process studies example (PhD work) 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).
Process studies (hydrothermal vents) Cell image: J. McNichol, et al., Primary productivity below the seafloor at deep-sea hot springs. PNAS 115, 6756–6761 (2018).
Native Microbiota CURE B. D. Dyer, A Field Guide to Bacteria, Illustrated edition (Comstock Publishing Associates, 2003).

Unless otherwise noted, images are either my own unpublished 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