Nitrate or not nitrate. That is the question
Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits
The article by Legay et al.  addresses two main issues: the links between belowground and aboveground plant traits and the links between plant strategies (as defined by these traits) and the capacity to absorb nitrate and ammonium. I recommend this work because these are important and current issues. The literature on plant traits is extremely rich and the existence of a leaf economic spectrum linked to a gradient between conservative and acquisitive plants is now extremely well established [2-3]. Many teams are now working on belowground traits and possible links with the aboveground gradients [4-5]. It seems indeed that there is a root economic spectrum but this spectrum is apparently less pronounced than the leaf economic spectrum. The existence of links between the two spectrums are still controversial and are likely not universal as suggested by discrepant results and after all a plant could have a conservative strategy aboveground and an acquisitive strategy belowground (or vice-versa) because, indeed, constraints are different belowground and aboveground (for example because in given ecosystem/vegetation type light may be abundant but not water or mineral nutrients). The various results obtained also suggest that we do not full understand the diversity of belowground strategies, what is at stake with these strategies, and the links with root characteristics.
Each time I give a conference on the work we are carrying out on African grasses that likely absorb ammonium preferentially because they inhibit nitrification [6-7], somebody asks me a question about the fact that plant essentially absorb nitrate because ammonium is toxic and nitrate more available in the soil. The present article confirms that this is not the case and that, though there are currently some teams working on the subject, we do not really know for the moment whether plants absorb nitrate or ammonium, in which proportion, how plastic this proportion is within individuals and within species. This subject seems to me crucial because it is linked to (1) the capacity of ecosystems to conserve nitrogen , because nitrate, much more than ammonium, goes out of ecosystems through leaching and denitrification, (2) to carbon cycling and plant energy budget because absorbing nitrate requires spending mucho more energy than absorbing ammonium because nitrate must be reduced before being incorporated in plant biomass, which is very energy costly. These two issues are naturally very relevant to develop efficient cropping systems in terms of carbon and nitrogen.
Interestingly, the present article, comparing three grass species in different sites, suggests that there is no trade-off between the absorption of nitrate and ammonium: more acquisitive individuals tend to absorb more ammonium and nitrate. This is contrary to hypotheses we made to predict the outcome of competition between plants absorbing nitrate and ammonium in different proportions  but should be tested in the future comparing many different types of plants. The results also suggest that more conservative plants absorb relatively more ammonium, which makes sense because this allows them to spare the energy necessary to reduce nitrate. This leads to the question of the effect of these strategies on nitrogen retention within the ecosystem. If nitrification is high (low), absorbing ammonium is not efficient and likely leads to high (low) nitrogen losses. This should be tested in the future. Moreover, the authors have measured the absorption of nitrate and ammonium through measurements at the root scale on cut roots. This should be complemented by measurements at the whole plant scale.
 Legay, N., Grassein, F., Arnoldi, C., Segura, R., Laîné, P., Lavorel, S. and Clément, J.-C. (2020). Studies of NH4+ and NO3- uptake ability of subalpine plants and resource-use strategy identified by their functional traits. bioRxiv, 372235, ver. 4 peer-reviewed and recommended by PCI Ecology. doi: 10.1101/372235
 Shipley, B., Lechowicz, M.J., Wright, I. & Reich, P.B. (2006) Fundamental trade-offs generating the worldwide leaf economics spectrum. Ecology, 87, 535-541. doi: 10.1890/05-1051
 Reich, P.B. (2014) The world-wide ‘fast-slow’ plant economics spectrum: a traits manifesto. J. Ecol., 102, 275-301. doi: 10.1111/1365-2745.12211
 Maire, V., Gross, N., Pontes, L.D.S., Picon-Cochard, C. & Soussana, J.F. (2009) Trade-off between root nitrogen acquisition and shoot nitrogen utilization across 13 co-occurring pasture grass species. Func. Ecol., 23, 668-679. doi: 10.1111/j.1365-2435.2009.01557.x
 Roumet, C., Birouste, M., Picon-Cochard, C., Ghestem, M., Osman, N., Vrignon-Brenas, S., Cao, K.F. & Stokes, A. (2016) Root structure-function relationships in 74 species: evidence of a root economics spectrum related to carbon economy. New. Phytol., 210, 815-826. doi: 10.1111/nph.13828
 Lata, J.-C., Degrange, V., Raynaud, X., Maron, P.-A., Lensi, R. & Abbadie, L. (2004) Grass populations control nitrification in savanna soils. Funct. Ecol., 18, 605-611. doi: 10.1111/j.0269-8463.2004.00880.x
 Srikanthasamy, T., Leloup, J., N’Dri, A.B., Barot, S., Gervaix, J., Koné, A.W., Koffi, K.F., Le Roux, X., Raynaud, X. & Lata, J.-C. (2018) Contrasting effects of grasses and trees on microbial N-cycling in an African humid savanna. Soil Biol. Biochem., 117, 153-163. doi: 10.1016/j.soilbio.2017.11.016
 Boudsocq, S., Lata, J.C., Mathieu, J., Abbadie, L. & Barot, S. (2009) Modelling approach to analyze the effects of nitrification inhibition on primary production. Func. Ecol., 23, 220-230. doi: 10.1111/j.1365-2435.2008.01476.x
 Boudsocq, S., Niboyet, A., Lata, J.-C., Raynaud, X., Loeuille, N., Mathieu, J., Blouin, M., Abbadie, L. & Barot, S. (2012) Plant preference for ammonium versus nitrate: a neglected determinant of ecosystem functioning? Am. Nat., 180, 60-69. doi: 10.1086/665997
Sébastien Barot (2019) Nitrate or not nitrate. That is the question. Peer Community in Ecology, 100038. 10.24072/pci.ecology.100038
Evaluation round #2
DOI or URL of the preprint: https://doi.org/10.1101/372235
Version of the preprint: V2
Author's Reply, None
Decision by Sébastien Barot, 15 Dec 2019
I am satisfied with the way the manuscript has been improved and the reviewers’ comments addressed. I would be ready to recommend the manuscript but have a few more comments.
The abstract could mention the fact that the preference for ammonium vs. nitrate is different between species and higher for conservative species.
I like the discussion however:
1) It should explicitly mention the fact that the interpretation is limited by the fact that only three species are studies.
2) I think the way nitrate and ammonium uptake rates are measured is very useful but I think the discussion/conclusion should mention that it would also be interesting to measure the absorption of nitrate and ammonium at the whole plant scale. For example, through 15N pulses. This could give a different image of N uptake.
3) I like the discussion about the differences between the relative nitrate and ammonium rates and the link with the plant strategy. However, I am surprised it is never mentioned that assimilating ammonium is less costly than assimilating nitrate (that has to be reduced). This could be in line with a more conservative strategy? Similarly the influence, of the ammonium vs. nitrate preference likely has consequences on ecosystem functioning and the N budget of the ecosystem (because nitrate is more prone to losses) (see Boudsocq 2009 and 2012, OK I am co-author of these articles).
4) Ammonium is more absorbed during autumn. Could that just be due to the fact that ammonium is less mobile than nitrate within the soil so that it requires more humid soils to be absorbed?
There are still some writing glitches. I have listed some of them (see below) but the manuscript should be carefully proofread.
Line 55. It is awkward to start the sentence with “And”. I think the “plant ecology, ” should be deleted
Line 60. I suggest “the significance of root traits is less understood than the one of leaf traits”
Line 66. “is both influenced by anatomical …. and by physiological adjustments such as …“
Line 69. “Nitrogen is one of the best studied mineral nutrients and its uptake by plants under both the ammonium and nitrate forms is influential for plant and ecosystem functioning”
Line 72 “some information” à la place de “supports”
Line 100. Could the first hypothesis be expressed more precisely? What does that mean “contributing to the economic spectrum”? Does that mean that there is a root economic spectrum fully correlated (positively) to the leaf spectrum?
Line 105. I do not understand the “both in quantity and quality”
Line 130. “managements”
Line 146. “during the day”
Line 151 “kept in ice”?
Line 152 “5.6 mm mesh”
Line 164 “living young roots”
Line 174 “root 15N natural”
Line 183 “at the cost of losing relevant ecological information“
Line 210 “Hanes’s relations were used” or ‘’Hanes’s relation was used”
Line 269 I do not understand this sentence because obviously the paragraph is comparing different sites
Line 287 I find that “resource use “ is too vague and not related enough to the previous sentence
Line 288 “despite relatively weak relationships”
Line 289 “different selective pressures” “specializations”
Line 304 “indeed” seems to me inappropriate here
Line 326 “opposite response” is for me to vague. Response to what? Response of what?
Line 359 “could depend on”
Line 364 The sentence is in my opinion awkward. Should the plural be used? Not clear whether this is a result of the manuscript or a general thought coming from the reference.
Line 379 “remain”
Line 397 “grassland N cycling rate”
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/372235
Author's Reply, None
Decision by Sébastien Barot, 16 Oct 2018
Dear authors Your manuscript is interesting. However, the two reviews are pointing at potential problems that should be addressed before any final decision is made. I am looking forward reading a new version of the manuscript together with answers to the reviewers. I apologize for delay in sending my decision. It has indeed been difficult to find reviewers during the summer period.