Plot with only nitrifiers (heat map or bar graph)?

[jessicaday]

Christian - would it be helpful to make a figure with just the composition of nitrosomonas, nitrobacter, and nitrospira versus everything else for all 6 tanks and all timepoints? To show the % composition (since it's so low compared to what people would expect) and we can compare this to other papers?

[cdiener]

So for the counts it looks like that:

That's on the log10 scale so 1 means 10 reads and 2 means 100 reads.

As percentages you don't see too much because it is usually less than 0.1% going to ~1% for sample T1B4.

[cdiener]

Kind of weird that they are more abundant in the aquaponics inoculum where the plants grow worse.

[jessicaday]

That is strange. Is there a way to show (on a heatmap or elsewhere) that although it looks highly enriched, it is only ever ~1% max of the sample? Also - correct me if I'm wrong, but just because it's low in abundance doesn't necessarily mean they aren't a significant part of some process that's occurring, right?

[cdiener]

Here is the same image with percentages:

Only goes up to about 0.8% maximum. So I agree that it is hard to say whether that might not have any effect but the catalytic capacity is probably dependent on biomass for those species. If you have very little Nitrosomonas it can only convert so much Ammonia. I would expect to see more if they would have an impact on the system...