• Universal metabarcoding measures the abundance of planktonic life across space / time
    • Comprehensive (primers target all cellular life)
    • Sensitive with deep sequencing
    • Specific with "denoising" algorithms

Microbe art: @claudia_traboni

Taxa-specific activity

"Biobank" (collected from time-series sites / field campagins)

Environmental Sample

Viable cells

DNA

RNA

T/S/Chl./Nut.

Fixed cells

Barcoding

Core environmental data

Projects inspired by environmental data

Cultivation

HCR-FISH

'omics

Kalmbach et al. (2017), arXiv:1703.07309v1

  • Taxonomy (CARD/HCR-FISH) / transcription (FISH-TAMB)
  • Respiration, cell viability (RSG); Polyphosphate content (DAPI)

Automatic cell-sorting + environmental databases = taxon-specific activity or genetic potential measurements

Many uses for sorted cells:

  • Taxon-specific isotope uptake
  • Mini-metagenomes with few cells
  • Cell isolation for cultivation

Pjevac et al (2019) 10.1111/1462-2920.14739

Multiple sorting axes now possible

Microbe art: @claudia_traboni

p16S

e16S

18S

  • Comprehensive community data from single PCR assay:
    • p(rokaryotic)16S
    • e(ukaryotic)16S
    • Eukaryotic 18S

3-domain metabarcoding quantifies the whole ecosystem

Microbe art: @claudia_traboni

18S

p16S

e16S

  • Comprehensive community data from single PCR assay:
    • p(rokaryotic)16S
    • e(ukaryotic)16S
    • Eukaryotic 18S

3-domain metabarcoding quantifies the whole ecosystem

Novelty of project:

  • Recover information from legacy datasets
  • Potentially improve ecological resolution of metabarcodes
  • "Rosetta stone" for inter-comparisons, FISH probe design

Dueholm et al. (2020) mBio, e01557-20

Database of full-length 16S rRNA

in silico method optimization

Universal metabarcoding primers work almost perfectly across global oceans

Global metagenomes

plastid

16S

mito 16S

nuclear 18S

Space / time

Abundance

A eukaryotic phytoplankter

"eDNA"

How do microbial communities* influence the Earth System**,

and vice-versa***?

*whole community methods

**primary productivity, elemental cycling

***effect of anthropogenic pressure on ecosystems

Microbe art: @claudia_traboni

My core research question

Microbiology

Bioinformatics

Environmental science

Long term vision: A lab that links microbial diversity & biogeochemical function in the context of global ecosystem change with modern 'omics-enabled techniques

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

Motivated by desire to understand the Earth System

We anticipate that as trait-based biogeography continues to evolve, micro- and macroorganisms will be studied in concert, establishing a science that is informed by and relevant to all domains of life.” -Green, Bohannan, and Whitaker, Science (2008)

Ecosystem-centered teaching & research

Welcome to the lab!

 

The StFX Microbial Ecology Lab studies the interactions between microbes (Bacteria, Archaea, and Eukarya), their physical environment, and the biosphere as a whole. We use a combination of field work, modern DNA sequencing, and classical microbiological approaches to address diverse research questions. Check out stfxmicroeco.ca to learn more!

Lab Contact:

Dr. Jesse McNichol

JBB 419

(902) 867-2386

jmcnicho@stfx.ca

Sebastián & Gasol (2019), 10.1098/rstb.2019.0083 ; McNichol et al (2018) 10.1073/pnas.1804351115 ; Zehr (2015) 10.1126/science.aac9752; Bramucci et al (2021) 10.1038/s43705-021-00079-z

Microscale ecology & biogeochemistry