should isoprene emissions move to traits?

teixeirak commented 2 years ago

@NidhiVinod and @tyeentaylor , Sorry to re-open an old debate, but now that we've reorganized the traits section by category rather than intraspecific- interspecific, I think it might make more sense to put isoprene emissions back in traits. The orphan blob on isoprenes seems strange.

What do you think?

NidhiVinod commented 2 years ago

@tyeentaylor, what do you think? I don't mind moving it to traits

tyeentaylor commented 2 years ago

I support the consolidation of isoprene in traits! I can take a look at it early Monday, UK time.

On Fri, Feb 11, 2022 at 10:34 PM Nidhi Vinod @.***> wrote:

@tyeentaylor https://github.com/tyeentaylor, what do you think? I don't mind moving it to traits

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teixeirak commented 2 years ago

Okay, I just did the macro move in the document. Still to be done:

[x] merge text previously in traits with that previously in metabolism (I'll work on this now)
[x] move isoprenes to table 1 (@NidhiVinod )
[x] move isoprenes on Fig. 1 (@NidhiVinod )

NidhiVinod commented 2 years ago

I'll work on Fig 1 and Table

NidhiVinod commented 2 years ago

Okay isoprene in the trait table now

teixeirak commented 2 years ago

@NidhiVinod , wondering if the isoprenes are quite right in the traits table? Specifically, are we trying to represent (1) rate of emission within emitting species (my interpretation of what's currently there), (2) fraction of species/ individuals with emission capability, or (3) a mix of the two? I think it's (3), but not sure. I've left these highlighted until we're sure.

teixeirak commented 2 years ago

I guess the same question applies to monoterpenoids.

NidhiVinod commented 2 years ago

@teixeirak, yes, it's 3) please correct me if I'm wrong @tyeentaylor .

teixeirak commented 2 years ago

Okay, so let's create another category for those (e.g., "isoprene emissions capability"). The units we have now imply that what's listed is a rate. We need to make sure these all have the right label/units.

NidhiVinod commented 2 years ago

@krista, I had isoprene emission ability actually above VOC section which is emission capability. Yeah, you're right, i should remove the units there and maybe change the name to "capability", and move it below VOC?

teixeirak commented 2 years ago

Oh, I missed that. In that case, we can just delete the VOC production header.

teixeirak commented 2 years ago

@NidhiVinod , I did this-- table is fine now.

BUT... Do refs 49 (@tyeentaylor 's) and 63 (Simpraga et al. 2013) really examine height AND light gradients?

NidhiVinod commented 2 years ago

@krista, thank you, I'm still working on optical properties. Yes, 63 does. I'm double checking if 49 (Ty's does) where they do mention VOC responses to dynamic light conditions as in mid-canopy, but I don't see direct response to light itself (@tyeentaylor, please correct me if i'm wrong)?

teixeirak commented 2 years ago

@NidhiVinod , if we're looking at a height gradient, we should list it just as height. The implication/ assumption is that light also varies, whether or not it is measured. My definition of a light gradient would be leaves collected near ground level from sun and shade conditions.

NidhiVinod commented 2 years ago

@teixeirak, oh okay, I see, then in that case I might have to remove light variables for the two: isoprene and MT. And maybe I'll also double check if the light gradient definition matches the citations in the tables. That's what i had in mind while working on it but maybe i have a few that might not belong in the light gradient section.

tyeentaylor commented 2 years ago

Hi all.

In the table, suggest changing "isoprene emission ability" with "relative abundance of isoprene emitting species". Or shorter versions "abundance isoprene emitting species" or "proportion isoprene emitting trees" or "proportion isoprene emitters" or "abundance isoprene emitters" (I think I'd vote for the last one, but see which you think is clearest).
Change "monoterpenoid" to "monoterpene" (both are correct, but monoterpene is more common, and is what is used the main text).
You're correct that I only hypothesize about light effects on emission rates in my methods paper. My next paper will show the light data.
I don't see the merged VOCs text in the google doc. Tag me when ready if you want me to check it.

On Sun, Feb 13, 2022 at 6:47 PM Nidhi Vinod @.***> wrote:

@teixeirak https://github.com/teixeirak, oh okay, I see, then in that case I might have to remove light variables for the two: isoprene and MT. And maybe I'll also double check if the light gradient definition matches the citations in the tables. That's what i had in mind while working on it but maybe i have a few that might not belong in the light gradient section.

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teixeirak commented 2 years ago

@NidhiVinod and @tyeentaylor , I've made the changes to Table 1 that you mentioned: -removed light rows for isoprenes and monoterpenes

changed wording as suggested by Ty

teixeirak commented 2 years ago

@tyeentaylor , we're not keeping the google doc up to date. I will email you the latest. Note submission deadline today (so it's only worth commenting if you can do it right away).

And I'll close this issue-- everything here is resolved, unless Ty has wording changes.

tyeentaylor commented 2 years ago

Please just check the edits I made on this google doc https://mail.google.com/mail/u/0?ui=2&ik=f10edf24ab&attid=0.1&permmsgid=msg-f:1724742689506098120&th=17ef845688f67bc8&view=att&disp=inline that Krista sent about an hour ago. Only in the VOCs paragraphs.

On Mon, Feb 14, 2022 at 1:26 PM Kristina Anderson-Teixeira < @.***> wrote:

@tyeentaylor https://github.com/tyeentaylor , we're not keeping the google doc up to date. I will email you the latest. Note submission deadline today (so it's only worth commenting if you can do it right away).

And I'll close this issue-- everything here is resolved, unless Ty has wording changes.

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teixeirak commented 2 years ago

I'm getting a "temporary" error when I try to access this (but it seems to be persisting). @NidhiVinod , can you see it?

NidhiVinod commented 2 years ago

@teixeirak and @tyeentaylor, no, I cannot access it either, not sure why

tyeentaylor commented 2 years ago

I can't see it anymore either. I can make the edits again if you can send me another doc.

On Mon, Feb 14, 2022 at 4:56 PM Nidhi Vinod @.***> wrote:

@teixeirak https://github.com/teixeirak and @tyeentaylor https://github.com/tyeentaylor, no, I cannot access it either, not sure why

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NidhiVinod commented 2 years ago

@tyeentaylor: here is the .rmd, if you are able to knit it, it will the most updated version:

https://github.com/EcoClimLab/vertical-thermal-review/blob/master/vertical-thermal-review.Rmd

Also here is the document that is updated: https://github.com/EcoClimLab/vertical-thermal-review/blob/master/vertical-thermal-review.docx

tyeentaylor commented 2 years ago

Sorry, I'm not able to do that. If you want to just paste those two VOC paragraphs into the chat here, I can make my edits again and send it back.

On Mon, Feb 14, 2022 at 5:53 PM Nidhi Vinod @.***> wrote:

@tyeentaylor https://github.com/tyeentaylor: here is the .rmd, if you are able to knit it, it will the most updated version:

https://github.com/EcoClimLab/vertical-thermal-review/blob/master/vertical-thermal-review.Rmd

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teixeirak commented 2 years ago

Capacity for heat-sensitive, light-dependent (photosynthetically linked) emissions of volatile organic compounds (VOCs), including isoprene and monoterpenes, enhances photosynthetic thermal tolerance by regulating antioxidant defenses and other metabolic processes [@sharkeyIsopreneEmissionPlants2008; @taylorCapacityEmitIsoprene2019; @monsonLeafIsopreneEmission2021; @vickersUnifiedMechanismAction2009; @copoloviciCapacityThermalProtection2005; @riedlmeierMonoterpenesSupportSystemic2017]. In contrast to VOCs stored in oils that are released passively by heat and wounding, such as the monoterpenes responsible for pine scent, light-dependent emissions are linked to photosynthetic substrate supply and are dynamically tuned to environmental and metabolic conditions as a component of metabolic regulatory processes [@monsonLeafIsopreneEmission2021; @laothawornkitkulBiogenicVolatileOrganic2009; @lantzIsopreneNewInsights2019; @riedlmeierMonoterpenesSupportSystemic2017]. Due to its much higher emission rates and relative ease of detectability, isoprene has received far more study in the field, though both isoprene and monoterpenes are expressed by a wide diversity of angiosperms and gymnosperms across all biomes of the globe [see @taylorNewFieldInstrument2021 and references therein].

Less than half of tree species express significant light-dependent isoprene emissions [@kesselmeierBiogenicVolatileOrganic; @taylorIsopreneEmissionStructures2018], such that variation in emissions across the vertical profile is influenced both by vertical variation in species compositions and plasticity in emission rate capacities [@taylorNewFieldInstrument2021]. Within species, isoprene emission rates tend to increase toward brighter and hotter microenvironments [@niinemetsPhotosynthesisResourceDistribution2007], and across landscapes, emitting species increase in relative abundance toward hotter climates, exceeding half of trees in warm tropical forests [@taylorIsopreneEmissionStructures2018]. However, a recent study found a contrasting interspecific vertical structuring of emission capacities, with more emitting species and higher species-maximum emission rates in the mid-canopy region of an Amazonian forest [Table r table_leaf_traits, @taylorNewFieldInstrument2021]. Similarly, within tree crowns of European beech, monoterpene emissions were found to be highest in semi-shaded leaves beneath the canopy surface [Table r table_leaf_traits, @simpragaVerticalCanopyGradient2013]. This pattern may indicate the importance of temporal variability in thermal conditions as distinct from the long-term average. Temperature sensitive VOC emissions have been hypothesized to enable real-time acclimation to rapidly changing leaf thermal environments typical of the mid-canopy region [see section 1, @sharkeyIsopreneEmissionPlants2008]. Future work seeking to understand how temporal dynamics of leaf heating [see @leighInfluenceLeafSize2017] with height and influence leaf function will be important for resolving the role of VOCs in forest thermal sensitivity across the vertical gradient. Given current understanding, we may hypothesize that light-dependent VOC emissions are important for mid-canopy thermal responses, while other traits play the same role in sun-exposed canopy leaves.

tyeentaylor commented 2 years ago

See my tracked change edits to the two paragraphs here https://docs.google.com/document/d/1cFuYVBX9O454e8wwCrOrlJqsTbrXH82gxfhGKE6qFyU/edit?usp=sharing .

On Mon, Feb 14, 2022 at 6:13 PM Kristina Anderson-Teixeira < @.***> wrote:

Capacity for heat-sensitive, light-dependent (photosynthetically linked) emissions of volatile organic compounds (VOCs), including isoprene and monoterpenes, enhances photosynthetic thermal tolerance by regulating antioxidant defenses and other metabolic processes @.; @taylorCapacityEmitIsoprene2019; @monsonLeafIsopreneEmission2021; @vickersUnifiedMechanismAction2009; @copoloviciCapacityThermalProtection2005; @riedlmeierMonoterpenesSupportSystemic2017]. In contrast to VOCs stored in oils that are released passively by heat and wounding, such as the monoterpenes responsible for pine scent, light-dependent emissions are linked to photosynthetic substrate supply and are dynamically tuned to environmental and metabolic conditions as a component of metabolic regulatory processes @.; @laothawornkitkulBiogenicVolatileOrganic2009; @lantzIsopreneNewInsights2019; @riedlmeierMonoterpenesSupportSystemic2017]. Due to its much higher emission rates and relative ease of detectability, isoprene has received far more study in the field, though both isoprene and monoterpenes are expressed by a wide diversity of angiosperms and gymnosperms across all biomes of the globe [see @taylorNewFieldInstrument2021 and references therein].

Less than half of tree species express significant light-dependent isoprene emissions @.; @taylorIsopreneEmissionStructures2018], such that variation in emissions across the vertical profile is influenced both by vertical variation in species compositions and plasticity in emission rate capacities @.. Within species, isoprene emission rates tend to increase toward brighter and hotter microenvironments @., and across landscapes, emitting species increase in relative abundance toward hotter climates, exceeding half of trees in warm tropical forests @.. However, a recent study found a contrasting interspecific vertical structuring of emission capacities, with more emitting species and higher species-maximum emission rates in the mid-canopy region of an Amazonian forest [Table r table_leaf_traits, @taylorNewFieldInstrument2021]. Similarly, within tree crowns of European beech, monoterpene emissions were found to be highest in semi-shaded leaves beneath the canopy surface [Table r table_leaf_traits, @simpragaVerticalCanopyGradient2013]. This pattern may indicate the importance of temporal variability in thermal conditions as distinct from the long-term average. Temperature sensitive VOC emissions have been hypothesized to enable real-time acclimation to rapidly changing leaf thermal environments typical of the mid-canopy region [see section 1, @sharkeyIsopreneEmissionPlants2008]. Future work seeking to understand how temporal dynamics of leaf heating [see @leighInfluenceLeafSize2017] with height and influence leaf function will be important for resolving the role of VOCs in forest thermal sensitivity across the vertical gradient. Given current understanding, we may hypothesize that light-dependent VOC emissions are important for mid-canopy thermal responses, while other traits play the same role in sun-exposed canopy leaves.

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teixeirak commented 2 years ago

Hmmm... I don't see any track changes. I copied and pasted what I saw, and it is identical to the original text (with the exception of removing necessary ` symbols).

FYI, we got an extension on the re submission until next Tuesday, so we have time to get these in.

tyeentaylor commented 2 years ago

I had the link set to "anyone with the link can view", but maybe that still doesn't allow people to see tracked changes? I gave Nidhi full access now anyways. Hopefully that will work!

On Mon, Feb 14, 2022 at 10:43 PM Kristina Anderson-Teixeira < @.***> wrote:

Hmmm... I don't see any track changes. I copied and pasted what I saw, and it is identical to the original text (with the exception of removing necessary ` symbols).

FYI, we got an extension on the re submission until next Tuesday, so we have time to get these in.

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NidhiVinod commented 2 years ago

@tyeentaylor, I can see track changes now. Thank you

EcoClimLab / vertical-thermal-review

should isoprene emissions move to traits? #104