Daniel Vaulot

(Phyto)plankton distribution in the ocean

2023-06-23

Outline

• Marine plankton

• Metabarcoding for plankton

• metaPR2: a database of metabarcodes

• Green phytoplankton

Marine plankton

Plankton diversity

• Phytoplankton
• Zooplankton
• Bacteria
• Viruses

Size classes

Phytoplankton

Major groups

Diatoms and dinoflagellates: 20-200 µm

Oceanic deserts

Picoplankton

1982 - John Sieburth - Electron microscopy

Johnson, P.W. & Sieburth, J.M. 1982. J. Phycol. 18:318–27.

Wide phylogenetic diversity

Not, F., Siano, R., Kooistra, W.H.C.F., Simon, N., Vaulot, D. & Probert, I. 2012. In Piganeau, G. [Ed.] Genomic Insights Gained into the Diversity, Biology and Evolution of Microbial Photosynthetic Eukaryotes. Elsevier.

Key questions

• Distribution of phytoplankton taxa
  • Polar vs. temperate vs. tropical
    
  • Coastal vs. Pelagic
  • Surface vs Chlorophyll maximum
• Seasonnal cycles
  
• Effect of global change
  • Change in community structure
  • Indicator species

Microscopy data

Davies et al. 2016. A database of marine phytoplankton abundance, biomass and species composition in Australian waters. Scientific Data

Large datasets

Righetti et al. 2019. Global pattern of phytoplankton diversity driven by temperature and environmental variability. Science Advances

Plankton response to global change

Beaugrand et al. 2009. Rapid biogeographical plankton shifts in the North Atlantic Ocean. Global Change Biology 15:1790–1803

Metabarcoding of Marine plankton

Principle

Target gene

• 18S rRNA

• ITS (Internally Transcribed Spacer)

• 16S plastid

• rbcL

Amplified region

V4

• Long region
• Presence of introns
• Resolutive
• Many reference sequences available

Amplified region

V9

• Short region (cheaper)
• Fewer introns
• Sometimes more resolutive than V4
• Fewer reference sequences available

Primers

Many choices

• V4
• V4 specific
• V9
• Universal (euk+prok)

Vaulot, D., Mahé, F., Bass, D. & Geisen, S. pr2-primer: an 18S rRNA primer database for protists. Molecular Ecology Resources 22, 168–179 (2022).

Assignment

Reference database

• Genbank
  • Taxonomy very bad
• Silva
  • OK for prokaryotes
    
  • Eukaryotes bad

Assignment

The PR2 database

• 221 091 sequences
  • nuclear 18S rRNA
  • plastid 16S rRNA (PhytoRef)
  • bacteria and archaea 16S to check contamination
• Unified taxonomy (9 ranks from kingdom to species)
• Metadata (e.g. coordinates, environment)
• Available as web interface, flat files or as R package
• Latest version: 5.0 (released 05-2023)

Guillou et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41:D597–604. - https://pr2-database.org

metaPR2: a database of metabarcodes

Many metabarcoding studies for eukaryotes

But hard to use…

• Processed with different pipelines
• Different primers
• Different levels of similarity
• Different reference databases
• Metadata lacking

Large datasets

• Ocean Sampling Day

• Tara Oceans

• Malaspina

metaPR2 a database of metabarcodes

Reprocess public data

• Download Genbank (SRA) data
  • Raw sequences
  • Metadata
• Reprocess
  • Amplicon Sequence Variant (dada2)
  • Merge ASVs with same sequence
• Store in MySQL database
• Develop under R
• Web interface and R package
• https://app.metapr2.org

Current status

• Version 2.1
• Datasets: 59
• Samples: 93127
• Barcodes (ASVs): 6202

Vaulot, D. et al. metaPR2: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Molecular Ecology Resources 22, 3188–3201 (2022).

Biogeography

Biogeography of dinoflagellates

Green phytoplankton

Green vs. Red lineages

What is the color of the ocean ?

• Why did the green lineage rapidly decline in ecological importance during the early Mesozoic?

• Why have terrestrial photoautotrophs not followed similar trajectories following the end-Permian extinction?

But maybe the question should be: Is the ocean really red ?

Falkowski et al. 2004. In Thierstein, H. & Young, J. Eds. Coccolithophorids. Springer-Verlag, Berlin, pp. 429–53

The green lineage

• Streptophyta
  • Land plants
• Chlorophyta
  • Core chlorophytes
  • “Prasinophytes”
    • Mamiellophyceae
    • Chloropicophyceae

Leliaert, F., Verbruggen, H. & Zechman, F.W. 2011. Bioessays. 33:683–92.

The green lineage represents 25% of coastal phytoplankton

Data from OSD

But up to 94%…

Tragin, M. & Vaulot, D. 2018. Sci. Rep. 8:14020

Which are the most important classes ?

Lopes dos Santos et al. 2017. ISME J. 11:512–28

Are all classes uniformly distributed?

Coastal waters (OSD)

Tragin, M. & Vaulot, D. 2018. Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset. Sci. Rep. 8:14020.

Are all classes equally prevalent?

Coastal waters (OSD)

Tragin, M. & Vaulot, D. 2018. Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset. Sci. Rep. 8:14020.

Community structure?

Coastal waters (OSD)

Tragin, M. & Vaulot, D. 2018. Green microalgae in marine coastal waters: The Ocean Sampling Day (OSD) dataset. Sci. Rep. 8:14020.

Micromonas

First picoplankton species described in 1952

• M. pusilla (Chromulina pusilla)
• 1.5 µm
• Flagellum

Three more species recently described

• M. commoda
• M. bravo
• M. polaris

Two “candidate” species

• sp. 1
• sp. 2

Butcher, R.W. 1952. J. Mar. Biol. Assoc. U.K. 31:175–91.
Simon, N., Foulon, E., Grulois, D., Six, C., Desdevises, Y., Latimier, M., Le Gall, F. et al. 2017. Protist. 168:612–35.

Micromonas

OSD data set

Nine clades/species

• M. pusilla
• M. commoda
  • A1-A2
    
• M. bravo
  • B1-B2
• M. polaris
• clades B3-B5

Tragin, M. & Vaulot, D. 2019. Novel diversity within marine Mamiellophyceae (Chlorophyta) unveiled by metabarcoding. Sci. Rep. 9:5190

Micromonas

OSD data set

M. polaris only found in polar waters

clade B5 only found in tropical waters

Mantoniella

Two new polar species:

• M. beaufortii
• M. baffinensis

Yau et al.., 2020. Mantoniella beaufortii and Mantoniella baffinensis sp. nov. (Mamiellales, Mamiellophyceae), two new green algal species from the high arctic. Journal of Phycology 56, 37–51

Take home messages

• Understand distribution of (phyto)plankton
  • Latitude
  • Temperature, nutrients, depths…
• Metabarcoding is critical tool
  • Need however databases
• Example of green phytoplankton
  • Micromonas

Questions ?