Understanding (senesced) leaf lignin

[hrlai]

Goal

Hi, I would like to better understand how leaf lignin operates in VE, in order to better address ImperialCollegeLondon/ve_data_science#78 (comment) and thereafter. I'm parameterising the litter chemistry and decay model; the last hurdle is to make sure we have the right data for leaf lignin content in [g C in lignin per g C in litter].

What I did specifically in virtual_ecosystem

I searched for the term lignin in the repo to first know where it is used; the plant and litter models are the main places as expected, plus some animal waste.

Then I saw senesced_leaf_lignin in the plant model. This is my main question. I had thought that leaf lignin in the plant model is about fresh leaves. If it updates senesced_leaf_lignin, can I use it for the litter model too @jacobcook1995 ? Is this what you obtained in ve_data_science @arne-exe , i.e., senesced not fresh leaf stoichiometry? I am careful about whether the plant model's variables can be reused in the litter model because one is about fresh matter and the other dead. This is why the litter model has lignin_above_structural that is separated from the plant model?

Thanks!

[hrlai]

Ah digging deeper, it seems that the litter model takes senesced_leaf_lignin from the plant model into the argument of turnover_chemical_proportion in the function merge_input_chemical_proportions?

[arne-exe]

@hrlai I've been wanting to ask about this too, as there seems to be quite a bit of overlap between plant and litter model when it comes to this, especially considering available data.

Then I saw senesced_leaf_lignin in the plant model. This is my main question. I had thought that leaf lignin in the plant model is about fresh leaves. If it updates senesced_leaf_lignin, can I use it for the litter model too?

So, the way I understood it is that we have "foliage" and "senesced leaves".
Senesced leaves are leaves post nutrient resorption (so their nutrient content should be lower).
It's unclear to me if senesced leaves still contribute to foliage mass, I would assume so.
If so, does that mean we need some ratio representing the amount of foliage that is senesced.
Feedback on this by @davidorme and @sallymatson would be much appreciated.

I'm not sure if lignin content of senesced leaves also needs to change (it's less mobile than N/P), but on a dry weight basis lignin content should change. However, since we're working on a carbon mass basis (not dry weight), I think accounting for this in the model will be challenging, not even speaking about the data needed to calibrate these differences at PFT level.
So, I expect that senesced leaves in the model have lower nutrient content than foliage, but the same lignin content.

It is unclear for how long senesced leaves stay within the tree, in other words, do they become litter the same iteration?
On second thought, maybe the model doesn't need ratio for senesced leaves, and instead just assigns all leaf turnover within a time-step as senesced leaves (then calculates the amount of nutrient resorbed) and then passes these senesced leaves as leaf litter.
@davidorme and @sallymatson can you please explain how the model handles this?

Once senesced leaves have been passed as leaf litter, I think leaf litter should have the same nutrient and lignin content as senesced leaves.

Is this what you obtained in ve_data_science, i.e., senesced not fresh leaf stoichiometry? I am careful about whether the plant model's variables can be reused in the litter model because one is about fresh matter and the other dead.

At the moment, I have one set of values for leaf stoichiometry, which actually are derived from chemical analysis on leaf litter.
The reason for this is that most leaf nutrient content for our forests of interest are derived this way (instead of from fresh leaf chemical analysis).
We have several options here:
-Use these values for senesced leaves/leaf litter, and correct foliage (i.e., fresh leaves) using some average ratio that represents the nutrient resorption during senescence.
-Use fresh leaf chemical analysis data (unlikely to be SAFE data) for foliage, and use the same values for senesced leaves/leaf litter as above. This means that the nutrient resorption ratio will unlikely be correct (as the datasets will not match).
-Use the values derived from leaf litter for fresh leaves, senesced leaves, and leaf litter. This means that there would be no nutrient resorption. I think this option is the most basic one, but would work right now, until we decide to go for a different option, or find additional datasets with fresh leaf chemical analysis.
Any thoughts?

This is why the litter model has lignin_above_structural that is separated from the plant model?

I cannot comment on this.

[jacobcook1995]

Ah digging deeper, it seems that the litter model takes senesced_leaf_lignin from the plant model into the argument of turnover_chemical_proportion in the function merge_input_chemical_proportions?

So the reason that merge_input_chemical_proportions exists because there are two streams of litter to the litter model, tissue senescence and herbivory waste (i.e. because herbivory inevitably leads to dropped plant matter). The reason why we distinguish these streams is that the senesced tissues will differ stoichiometrically as plants can draw back nutrients in the process of senescing tissues but not when they are consumed by herbivores. As @arne-exe says above this probably makes less sense for lignin, so this might be something to get rid of (i.e. by combining "herbivory_waste_leaf_lignin" and "senesced_leaf_lignin" into a single variable).

(There will actually be a third stream of litter from tree mortality #982, but this will follow essentially the same logic as the herbivory case)

This is why the litter model has lignin_above_structural that is separated from the plant model?

It's one reason (as discussed above much more relevant to the nutrients). The other is time lags, i.e. when the properties of the plant community change the litter stocks and chemistries shouldn't instantaneously change. This won't matter as much for the high turnover rate pools, but for the deadwood pools you still expect to see large accumulations of deadwood years after a logging event

[sallymatson]

It's unclear to me if senesced leaves still contribute to foliage mass, I would assume so.

Senesced leaves do not contribute to foliage mass for CNP. The use of senesced leaves in the plants model is solely to calculate how many nutrients are reclaimed by the plant, and how many nutrients are thus passed into litter.

I can't really speak to lignin as I haven't done much with this yet.

Hope this helps please let me know if you need further clarification!

[arne-exe]

Thank you @sallymatson, your clarification in #943 (comment) was also very helpful.

[hrlai]

Thanks all for the discussion. Closing this now as it does not require any PR.