Aquatic microbial ecology at DPES

DPES, University of Toronto-Scarborough (Feb 8th, 2022)

Jesse McNichol (he/him) : PhD, Biological Oceanography

Postdoctoral Scholar, University of Southern California

How do aquatic microbial communities* influence the Earth System**, and vice-versa***?

*whole community methods

**primary productivity, elemental cycling

***effect of anthropogenic pressure on aquatic ecosystems

Microbe art: @claudia_traboni

Core research question

Microbiology

Environmental science

Bioinformatics

Evolution, population genetics

Ecosystem modelling, global change biology

Microbial ecology, biogeochemistry

3 "pillars"

Microbiology

Bioinformatics

How do aquatic microbial communities influence the Earth System, and vice-versa?

Pillars support core research question

Environmental science

In silico

Laboratory

Field work

Holistic ecosystem knowledge

Reductionist (multiple entry points)

Interdisciplinary opportunities

Entry points, interconnections

Outline

1. Current work

2. HK/Taiwan work

3. PhD work

1. Current work

Outline

Ecology & environmental science

Bioinformatics

Research questions

An in silico global phytoplankton model (DARWIN project, MIT)

  • How robust are model predictions?
    • Need "ground truth" biogeographic distribution data
  • What is the function of  microbial "black box"?
  • Can models and data help predict consequences of climate change?
  • Goal: measure abundance of microbial life across space / time in global oceans using PCR "barcodes"
    • Comprehensive (515Y / 926R primers target all cellular life)
    • Sensitive with deep sequencing
    • Specific with "denoising" algorithms

Microbe art: @claudia_traboni

Assembling "ground truth" data

Accomplishments & novelty

1. Led in silico method optimization

Universal primers for barcoding work almost* perfectly across global oceans

 2. Developed collaborations and generated data

Global metagenomes

Over 800 globally-distributed barcode samples allow model-data intercomparison

Craig Carlson, UCSB

Current & future collaborations

Ecological niche differentiation

Taxon abundance across depth

Current & future collaborations

Model-data intercomparison

Taxon abundance across Pacific Ocean transect

Yubin Raut, USC

Current & future collaborations

Mathematical framework for comparing ASVs to other data types

x axis = Synechococcus flow cytometry counts (cells/mL)

y axis = Calculated Synechococcus cell density (cells/mL)

Enrico Ser-Giacomi, MIT

Current & future collaborations

Building models of marine microheterotroph function

Bacterial / archaeal abundance and diversity across Pacific Ocean transect

Emily Zakem, Carnegie/USC

Microbial biogeography & modelling at DPES

  • Short term: Set up bioinformatic infrastructure, develop "bite-size" biogeographic projects:
    • Analysis and interpretation to support CBIOMES
  • Med. term - apply for grants:
    • NSERC Discovery Grant
    • CBIOMES /Simons Foundation Young Investigator awards
    • CFI to set up microbiome sequencing facility
  • Long term:
    • Develop local / pan-Canadian collaborations to apply these techniques to diverse ecosystems (+ "eDNA"?)

In silico

  • Collaboration with modellers

Laboratory

  • Method optimization / intercalibration

Field work

  • New data collection

Pathways for mentees

1. Current work

Outline

Ecology & environmental science

Bioinformatics

2. HK/Taiwan work

Outline

Bioinformatics

Microbiology

Research questions

  • What bio(geo)chemical processes do microbes catalyze?
  • How does speciation/evolution affect biogeochemistry?
  • What are the specific proteins/pathways responsible and their properties?

DNA sequencing is now low-cost...

...allowing us to sequence environmental "microbiomes"

Methods

1. Cultures or environmental genomes

Plot made with anvi'o

2. (Pan)genomic analysis with anvi'o

3. Diversity, evolution, biogeochemistry

Accomplishments

  • Developed novel, high-throughput, isolation methods
  • Assembled collection of isolates with full genomes

Heterotrophs (marine sediments)

Chemoautotrophs (shallow-water vents)

New genus

Xiaoyuan Feng, CUHK

Genomics to biogeochemical insights

Plot made with anvi'o

Clade 1:

+ denit, + N2'ase

N source & sink

Clade 2:

- denit, + N2'ase

N source

Diagram = Li et al., 2018.

N2

In silico

  • Study evolution and explore new genomes

Laboratory

  • Describe novel taxa, study their physiology

Field work

  • Explore new ecosystems

Pathways for mentees

Annie Wing-Yi Lo, CUHK

  • Set up equipment for O2-sensitive microbes
  • Retrieve cultures / samples / data
  • Train students in cultivation, genomic analysis
  • Medium term: Develop methods to identify essential genes (Tn-Seq)
  • Long term:  Conduct isolation campaigns in model systems, do biochemical assays

Cultivation and genomics at DPES

Microbial evolution at DPES

  • Campylobacteria likely originated in Earth's "middle ages", but timing uncertain
  • Genomic analysis can place their evolution in Earth Systems context
    • A long-term, collaborative project (proposal ready)
       

?

2. HK/Taiwan work

Outline

Bioinformatics

Microbiology

3. PhD work

Outline

Ecology & environmental science

Microbiology

Bioinformatics

Research questions

  • What is the effect of subsurface productivity on the deep sea?
  • How do physicochemical factors affect ecology and productivity?

Deep-sea hydrothermal vents: Oases fueled by geochemical energy

  • Developed novel high-pressure incubations
  • Quantified bulk and single-cell CO2 fixation (NanoSIMS)

Methods

FISH

SIP

Impact - biogeochemistry

Subsurface C production > 10 - 10,000x photic zone export

Subsurface C production rivals chemosynthetic symbioses

Impact - ecology

O2 caused major shift in community over ~ 24 h

Have single-cell genomes - good student project

Biochemical underpinnings of this response?

O2 reduced the efficiency of carbon fixation

Process studies = holistic research

Holistic, process studies require a "model system"

Ecology & environmental science

Microbiology

Bioinformatics

  • Set up lab (FISH, isotope-labeling)
  • Medium term:
    • Continue hydrothermal vent work
    • Investigate new model systems
  • Long term:
    • Study the effect of climate change on global aquatic ecosystems

Process studies at DPES

What I would bring to your department

Microbiology

Ecology & environmental science

Bioinformatics

  • > 10 years experience in marine microbial ecology
  • Can train mentees in lab, computational, field techniques
  • Diverse interests: oceanography, modelling, analytical method development, natural history, evolution
  • Passionate about integrating cutting-edge "microbiome" research techniques into my teaching (CURE)
  • Track record of successful interdisciplinary collaborations, and excited to build connections at DPES / UofT

Mentoring philosophy & DEI

Instrumental

  • Real data, skills
  • Student-driven research
  • Important questions, diverse collaborations

Psychosocial

Evidence-based approaches

  • Building "soft skills"
  • Foster emotional belonging
  • Student-centered mentoring philosophy
  • Modern pedagogy
  • Scaffolding approaches
  • Culturally-aware mentoring

Microbe art: @claudia_traboni

Core motivation

Earth Systems Science more important than ever

  • Would bring unique perspective and passion to Global Environmental Change program

Acknowledgements

 

WHOI / UFZ: Stefan Sievert, Jeff Seewald, François Thomas, Niculina Musat, Craig Taylor

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

USC/MIT/UCSB/Dalhousie/Carnegie: Jed Fuhrman, Yubin Raut, Enrico Ser-Giacomi, Paul Berube, Steven Biller, Mick Follows, Stephanie Dutkiewicz, Craig Carlson, Zoe Finkel, Emily Zakem

Sources

 

Images used in presentation were adapted from:
Line diagram (slide 9): J. A. Fuhrman, J. A. Cram, D. M. Needham, Marine microbial community dynamics and their ecological interpretation. Nature Reviews Microbiology 13, 133–146 (2015).

Metagenome image (slide 19):  V.A. Iverson et al., Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science, 335(6068): 587-590 (2012).

Anvi'o used to make image on slide 20: https://merenlab.org/software/anvio/; https://peerj.com/articles/1319/

Shallow-water vent image (slides 20, 22): Y. Li et al., Coupled Carbon, Sulfur, and Nitrogen Cycles Mediated by Microorganisms in the Water Column of a Shallow-Water Hydrothermal Ecosystem. Frontiers in Microbiology. 9:2718 (2018).

Speciation image (slides 20, 22): R. Stepanauskas et al., Gene exchange networks define species-like units in marine prokaryotes. bioRxiv, 2020.09.10.291518 (2020).

Oxygen diagram (slide 25): L.R. Kump, The Rise of Atmospheric Oxygen. Nature, 451(7176): 277-8 (2008).

Water column image on slide 30 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).

Unless otherwise noted, other images are either my own (un)published work, ⓒWHOI, or public domain images from Wikimedia Commons

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