This manuscript raises interesting points, among which the impact of root topology and maturity on plant water status and root water uptake dynamics. The text is well structured and figures and tables are clear.
The improvements of the manuscript as compared to the previous version are significant, among which:
- The differentiation of the existing concept of “hydraulic isolation” (i.e. with increasing axial resistance, less water is absorbed in the distal part of a root) and the newly introduced concept of “axial limitation” (i.e. root hydraulic resistance would increase with root length at some point).
- General definitions of the newly introduced indexes “effort” and “water yield”.
- The clarification that effort is not a measure of plant hydraulic resistance, even though it is sensitive to it.
- Variables are also clearly declared with their units.
However, the theoretical background is definitely subject to the artefact mentioned in the first part of the reviewing process. I believe that it is misleading and should be removed from the manuscript. The study on (un-)branched roots is seemingly still slightly affected by the artefact for young roots, but especially the absence of vertical soil water flow coupled to the non-equilibrium initial soil water condition might be responsible for the increased effort for longer roots. If not, it should be clarified whether or not the increased effort actually results from an increased (absolute) xylem water potential.
RC1, P4, L14: Lobet et al.  and Lobet and Draye  also did excellent work on the subject recently.
RC2, P4, L24: Doussan et al.  does not appear in the bibliography. Isn’t it 2006?
RC3, P6, L2: Here it is mentioned that the soil water potential is initially homogeneous. However it is further explained that the initial water content is initially homogeneous. Was it first meant that the soil matric potential is initially homogeneous? Is the gravitational potential accounted for? This point is important for what follows (RC13).
RC4, P6-7, L24-11: Equation (1) corresponds to the case of a root composed of a single segment. As demonstrated by Referee #1 of the first reviewing process and by the authors in the supplemental figure S1(a), the estimation of total root resistance (Rtot) using a single long segment is inaccurate and leads to overestimated absolute values of collar water potential.
About Eqs. (2-5), an aggregated radial resistance is valid if xylem potentials are uniform (assumed on short distances -> short segments), while an aggregated axial resistance makes sense if no radial conductances generate parallel pathways in the circuit.
Equations (6-7) and the predicted minima are thus incorrect for hydraulic architectures with significant axial resistances and radial conductances.
RC5, P7, L23: The term nicely does not sound very scientific…
RC6, P7, L25-27: Here is explained that the indices account for both root and soil hydraulics. The indexes are indeed sensitive to both root and soil hydraulic resistances (as long as both are present). However, only root hydraulic resistances are accounted for in most of this study (all of it except simulations with aRoot).
RC7, P9, L4-6: The supplementary mentioned here demonstrates that for a mature root, a discretization of 100 segments is largely enough to avoid any significant artefact on the estimated total root resistance for a mature root. However, this was not demonstrated for young roots, which are more sensitive to the artefact due to their limited axial conductance. In the lower-left subplot of the attached figure, it is visible that an error of a few percents remains for long young roots. However this small error alone probably does not explain the significant change of effort visible in Fig. 3 of the manuscript (other possible reasons are discussed in RC13). Actually, a simple way to avoid the artefact of “increasing root resistance with root length” is to model growth by adding root segments of constant size instead of elongating existing segments (see low-right subplot of the attached figure).
RC8, P9, L18-20: I agree with the authors, the simplifying assumptions chosen in this part of the manuscript are good as long as they do not lead to misleading conclusions. Their goal is to emphasize how simple root topologies and hydraulic properties affect the newly introduced indices, before testing these two indices on more complex hydraulic architectures.
RC9, P13-15, L20-8: Here the authors provide clear definitions of water yield and effort, which I think was very important in order to correctly interpret the results. The following minor suggestions are rather a matter of taste:
In the definition of water yield, the authors selectively exclude water transpired during water stress. This justifies the fact that water yield does not change once water stress was reached in the simulations with constant Tpot, and that it continues to evolve in simulations with day-night fluctuations of Tpot. I found it counter-intuitive that water transpired during stress events is not part of the yield; after all, the index including stressed transpiration would discriminate fully transpiring plants from plants under water stress anyway (even though not as much). It might actually be problematic for the application of the index on real plants, for which it is not always easy to delimit when stress begins and ends, while for a plant in pot the measure of total cumulative transpiration by weighing (not discounting stressed transpiration) is easy.
Water yield and effort are said to represent the benefit and cost in the quantification of root water uptake efficiency. I easily see cumulative transpiration as a benefit (as it can be translated in terms of cumulative photosynthesis product) and leaf energy level and root length as costs (as a very low xylem water potential implies consequences that might be bad for the plant, while building roots involves a cost in terms of carbon and other elements). However the fact that water yield has root length (a cost) as denominator does not make the classification in terms of cost and benefit as straightforward. As is, water yield represents some kind of average benefit per root length, which does not make it as clear whether it is beneficial for the plant to build more roots. Actually increasing the root length might very well delay water stress (beneficial) but decrease water yield. Also, in effort, the energy cost is divided by the cumulated transpiration, the latter being a benefit. I believe that both indices are efficiency-related, but should not be categorized in terms of cost and benefit since they both represent the division of a cost by a benefit or vice-versa.
RC10, P14, L14: I think that the verb is “to take up”, and the noun “the uptake”.
RC11, P14, L17: The symbol “V_H2O” is the same as in Eq. (15) while its definition differs, which might be confusing for the reader.
RC12, P15, L24-25: I searched for references to the index “water yield” in the articles of Javaux et al.  and Schneider et al. , but only noticed that both display transpiration rate versus time, or mean water content, from which the cumulated transpiration rate at the onset of water stress could be estimated. Dividing this value by the total root length would provide water yield. Mentioning that these authors used the index “water yield” thus does not seem really accurate, and I believe that, under its current form, this index should be recognized as newly introduced (unless other literature would refer to it).
RC13, major comments about the interpretation of the index effort: Here I would like to discuss several points about the interpretation of the index effort.
Firstly, in the definition of effort, it is said that the value of effort (w~) is taken at the onset of water stress. Let’s consider two root systems with constant Tpot, one reaching early water stress with its (absolute) leaf xylem water potential increasing in a concave way, the other reaches water stress later with its leaf water potential increasing in a convex way and always lower than the other plant’s water potential. If effort is saved at the onset of water stress (a different time for the two plants), effort might very well be higher for the plant that permanently had the lower leaf water potential. With its current definition, and in the graphics displayed in the manuscript, low effort is thus not tantamount of low xylem water potential (in opposition to the statement at page 16, L7). I believe this is a big weakness in the definition of effort that might lead to misinterpretations in the results of this study. A simple way to dodge this weakness would be to save effort at the same time for all hydraulic architectures. Then a permanently lower (absolute) xylem water potential would always have for consequence a lower effort. This could also be applied to water yield by not excluding “stressed” transpiration rate and estimating water yield at a uniform time.
Secondly, only the root hydraulic architecture is supposed to change when studying the impact of root length and topology on effort. However, if the gravitational potential was accounted for, and the soil matric potential initially uniform with depth, the initial total soil water potential must have been initially different in simulations having different root depths. Particularly, soil water potential around the extremity of long roots was up to 500 hPa lower than around the extremity of short roots. The initial plant-sensed water potential was thus initially more negative for long roots. Such situation may have participated to the increase of effort for longer roots. An initial hydrostatic equilibrium would probably result in significantly different results (particularly no increased effort for longer roots) and be in better agreement with the assumption of neglecting vertical soil water flow (soil water flow is null at hydrostatic equilibrium while drainage occurs for a uniform soil matric potential). Actually, even using an initially constant soil matric potential and accounting for vertical water flow would progressively tend to equilibrate soil water potential in the root zone and below, thus draining water away from shorter roots, and would probably also result in the absence of increase of effort for longer roots.
These two points and RC7, make it possible that the chosen simplifications were responsible for the observation that effort increases with root length. In order to clarify the situation, I would advise the authors to repeat the simulations with (i) short and constant root segment lengths, (ii) an initial hydrostatic equilibrium, and (iii) to calculate effort at a uniform time for all hydraulic architectures, or to demonstrate that the increase of effort was a consequence of an increased (absolute) xylem water potential.
Javaux, M., Schroder, T., Vanderborght, J., and Vereecken, H. (2008), Use of a three-dimensional detailed modeling approach for predicting root water uptake, Vadose Zone J., 7, 1079-1088.
Lobet, G., Pagès, L., and Draye, X. (2011), A novel image-analysis toolbox enabling quantitative analysis of root system architecture, Plant Physiol., 157, 29-39.
Lobet, G., and Draye, X. (2013), Novel scanning procedure enabling the vectorization of entire rhizotron-grown root systems, Plant Methods, 9, 10.1186/1746-4811-9-1.
Schneider, C. L., Attinger, S., Delfs, J. O., and Hildebrandt, A. (2010), Implementing small scale processes at the soil-plant interface - The role of root architectures for calculating root water uptake profiles, Hydrol. Earth Syst. Sc., 14, 279-289.