Add new study: Li_2018

[yangsophieee]

Study investigating variation in key hydraulic and carbon economy traits of 12 woody species in Australia across a broad climatic gradient, using a common garden approach.

Questions for review:

• Unsure what the life_stage is -- they grew plants from seed, seedlings were transplanted in 2016 and then grown and measured until maybe May 2017? So one or two years old. Is it just juvenile?
• Is there a water_potential_12percent_lost_conductivity? I can only find 50 and 88.
• Just checking that Ks is sapwood_specific_conductivity, not stem_specific_conductivity? From text: "Kfinal was normalized by the pressure gradient, sapwood area, and stem length to obtain initial and final xylem-specific hydraulic conductivity (Ks, kg m−1 s−1 MPa−1)."
• Do we have traits for Ψleaf at 50% of maximum stomatal conductance ("Early decline of stomatal conductance; proxy of Ψleaf at which stomata initiate closure") and 10% of maximum stomatal conductance ("Maximum water stress while still maintaining minimal photosynthesis; proxy of complete stomatal closure")?
• What about Cbranch ('Amount of releasable water of living cells as xylem tension increases') and VIGR ('Stem volume index growth rate, a surrogate of plant growth rate')?
• I'm a bit confused with the methods for Amax, it says "Leaf net carbon assimilation rate (An)... were measured by placing the leaf into a 2 × 3 cm cuvette supplied with saturating light (1,500 μmol m−2 s−1) and ambient CO2 concentration (420 μmol mol−1)." If it's ambient CO2 then that's not Amax right? But they say it was for An not Amax. In the section before it says the following but I'm not sure what it means: "During this phase, leaf gas exchange characteristics and corresponding leaf water potential (Ψleaf, MPa) were measured periodically until positive net photosynthesis (Amax, μmol m−2 s−1) was no longer detectable."
• It's unclear to me whether they performed gas exchange measurements on just drought treatment plants or on all of them. "Gas exchange measurements were conducted on recent, fully expanded leaves. During drought stress, the healthiest fully expanded leaf on each individual plant was chosen." I've assumed for replicates that it's all of the plants for now.
• Need to check taxonomic updates
• Will the new names, e.g. sapwood_specific_conductivity to sapwood_specific_hydraulic_conductivity be updated when merged or do we need to do that here?

[codecov-commenter]

Codecov Report

Patch and project coverage have no change.

Comparison is base (a311f6c) 80.20% compared to head (1a0b1b5) 80.20%.

❗ Current head 1a0b1b5 differs from pull request most recent head 3c2a64f. Consider uploading reports for the commit 3c2a64f to get more accurate results

❗ Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the Github App Integration for your organization. Read more.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #719   +/-   ##
========================================
  Coverage    80.20%   80.20%           
========================================
  Files            7        7           
  Lines         1531     1531           
========================================
  Hits          1228     1228           
  Misses         303      303           

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

[ehwenk]

• Just checking that Ks is sapwood_specific_conductivity, not stem_specific_conductivity? From text: "Kfinal was normalized by the pressure gradient, sapwood area, and stem length to obtain initial and final xylem-specific hydraulic conductivity (Ks, kg m−1 s−1 MPa−1)."

yes, correct

[ehwenk]

• Do we have traits for Ψleaf at 50% of maximum stomatal conductance ("Early decline of stomatal conductance; proxy of Ψleaf at which stomata initiate closure") and 10% of maximum stomatal conductance ("Maximum water stress while still maintaining minimal photosynthesis; proxy of complete stomatal closure")?

We don't at this point, but there are several studies with this trait. I'll add it to the additional traits section at the bottom

[ehwenk]

• What about Cbranch ('Amount of releasable water of living cells as xylem tension increases') and VIGR ('Stem volume index growth rate, a surrogate of plant growth rate')?

So... it was just suggested to us that we add capacitance, and I have, but I'm now worried I have the wrong units (lots of options) because my units aren't what they have here. We don't have VIGR

[ehwenk]

• I'm a bit confused with the methods for Amax, it says "Leaf net carbon assimilation rate (An)... were measured by placing the leaf into a 2 × 3 cm cuvette supplied with saturating light (1,500 μmol m−2 s−1) and ambient CO2 concentration (420 μmol mol−1)." If it's ambient CO2 then that's not Amax right? But they say it was for An not Amax. In the section before it says the following but I'm not sure what it means: "During this phase, leaf gas exchange characteristics and corresponding leaf water potential (Ψleaf, MPa) were measured periodically until positive net photosynthesis (Amax, μmol m−2 s−1) was no longer detectable."

I think there are two tricky bits here - it is Asat, not Amax - I'm surprised they call it Amax. Also, if you look at Table 2, they define it as "Maximum carbon assimilation rate under well-watered conditions". So I think that is the mean value they provide.

[ehwenk]

Looks good. I've answered all your questions - and made most of the changes myself.

Just look at some of the replicates.

[yangsophieee]

So... it was just suggested to us that we add capacitance, and I have, but I'm now worried I have the wrong units (lots of options) because my units aren't what they have here.

Looking back at the methods: "Branch RWC (RWCbranch, %) at each measurement period was calculated and plotted against Psi stem. Cbranch was estimated as the slope of the second linear portion of the water release curve, expressed as DeltaRWC/DeltaPsi (RWC MPa-1)."

• Since RWC is in % should the units be 100.g/g/MPa? And if the units don't match with the new trait, what do we do?

[yangsophieee]

Also I used ausflora to check taxonomic updates and I'm wondering if Acmena smithii needs an update to Syzygium smithii?

[ehwenk]

That taxonomic change should be automatic - when I review studies I look at the reports and confirm that all taxa are aligned to species - if the name doesn't automatically update, this wouldn't happen

[yangsophieee]

I think there are two tricky bits here - it is Asat, not Amax - I'm surprised they call it Amax. Also, if you look at Table 2, they define it as "Maximum carbon assimilation rate under well-watered conditions". So I think that is the mean value they provide.

I've changed replicates to 4 because "Four individuals of each species were assigned to a well-watered treatment and were watered daily over the experimental period."