1 To do

2 Methodology

• For assignation with Wang assigner, only ASVs with bootstrap at super group level taked into account
• Metazoa and Fungi not taken into account
• Abundant" OTUs are more than 10% in at least one sample
• Some samples for which the quality of sequencing was bad have been removed (Caroline list)
• Samples have been normalized to the medium number of reads for the group considered (e.g. for all eukaryotes or for all photosynthetic eukaryotes)

3 Environmental data

Figure 3.1: Salinity variation at the different stations with effect of monsoon

4 Basic statistics

• 663 ASVs of which 267 are autotrophs
• 81 samples

5 Taxonomic composition

• Dinoflagellates are dominating followed by diatoms (Figure 5.1)
• Among the key genera/species there are clear differences between Johor and Singapore (Raffles should merged with Singapore probably for this kind of comparison)
  • Dinos (Figure 5.7): Gyrodinium fusiforme (Johor), Gyrodinium gutrula; Woloszeunskia halophila (Johor), Karlodinium veneficum (Singapore)
  • Diatoms (Figure 5.8): Most diatoms are on the Johor side except for Leptocylindrus, Chaetoceros (endosymbiont), Cyclotella (Johor), Carataulina (Johor), Thalassiosira, Shionodiscus
  • Chlorophyta (Figure 5.5, 5.6, 5.4): Nanochloris (Picochlorum, mostly in Johor), Micromonas clade A.ABC.1-2 (M. commoda, mostly Singapore), Micromonas clade lagoons (in fact we call it warm now, mostly Singapore), Ostreococcus clade A (lucimarinus) and tauri
  • Crypto (Figure 5.3): Geminigera (Singapore)

Figure 5.1: Overall euk composition

Figure 5.2: Major species

Figure 5.3: Heatmap for major Eukaryote genera

Figure 5.4: Heatmap for Chlorophyta species

Figure 5.5: Localization of major Chlorophyta genera

Figure 5.6: Localization of major Mamiellophyceae species

Figure 5.7: Localization of major Dinophyceae species

Figure 5.8: Localization of major diatoms species

6 Effect of different factors on eukaryote composition

• Radiolaria, Cryptophyta, Ciliophora, Cercozoa only found in Singapore strait and Raffles (Figure 6.1)
• Monsoon has less effect on the overall composition… (Figure 6.3)

Query: should we do just on the Photosynthetic eukaryotes or all eukaryotes ?

Figure 6.1: Effect of strait on overall eukaryote composition

Figure 6.2: Effect of station on overall eukaryote composition

Figure 6.3: Effect of monsoon on overall eukaryote composition

7 NMDS

• The strait seems to be most discriminant factor (Figure 7.1).
  
• However it is interesting that for eukaryotes (Figure 7.2) Raffles Marina seems to be clustering with Singapore straight rather than Johor most of the time while for prokaryotes (Figure 7.1), Raffles is clearly in between. Probably an interesting point to discuss.

Figure 7.1: NMDS - Prokaryotes

Figure 7.2: NMDS - All eukaryotes

Figure 7.3: NMDS - Photosynthetic eukaryotes

8 Comparison with OSD

• OSD V4 while Singkaryotes amplicon is more upstream. There is no overlap between the two regions so for Mamiellophyceae the comparison is difficult with the new clades defined by Margot (e.g. clade E for Ostreococcus)