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
Wide phylogenetic diversity
Key questions
- Distribution of phytoplankton taxa
- Polar vs. temperate vs. tropical
- Coastal vs. Pelagic
- Surface vs Chlorophyll maximum
- Polar vs. temperate vs. tropical
- Seasonnal cycles
- Effect of global change
- Change in community structure
- Indicator species
Microscopy data
Large datasets
Plankton response to global change
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)
Assignment
Reference database
- Genbank
- Taxonomy very bad
- Silva
- OK for prokaryotes
- Eukaryotes bad
- OK for prokaryotes
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)
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
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 ?
The green lineage
- Streptophyta
- Land plants
- Chlorophyta
- Core chlorophytes
- “Prasinophytes”
- Mamiellophyceae
- Chloropicophyceae
The green lineage represents 25% of coastal phytoplankton
Data from OSD
But up to 94%…
Which are the most important classes ?
Are all classes uniformly distributed?
Coastal waters (OSD)
Are all classes equally prevalent?
Coastal waters (OSD)
Community structure?
Coastal waters (OSD)
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
Micromonas
OSD data set
Nine clades/species
- M. pusilla
- M. commoda
- A1-A2
- A1-A2
- M. bravo
- B1-B2
- M. polaris
- clades B3-B5
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
Take home messages
- Understand distribution of (phyto)plankton
- Latitude
- Temperature, nutrients, depths…
- Metabarcoding is critical tool
- Need however databases
- Example of green phytoplankton
- Micromonas