One of the two reviewer have doubts regarding the acceptance of this manuscript in this Special Issue, but I think it is relevant to the aim of the Special Issue and I recommend the publication here.
Besides, there were a lot of revisions suggested by both the referees, but authors made the necessary changes, and the paper is now acceptable for publication.
Best regards,
Silvia

Dear author,
despite the positive recommendations by the handling editor and one reviewer, I regret to inform you that I cannot accept the publication of your manuscript in Biogeosciences in its current form. Beyond the fact that the written text requires quite some editing (attached please find suggestions from p. 1 to p.9, where I decided to stop), the manuscript presents the fundamental scientific issue that nowhere in the data and analysis it presents robust evidence of biphasic kinetics. This is in contrast to previously cited work such as Tholosan et al. (1999; with the use of Lineweaver-Burk plots) as well as Unanue et al. (1999) where results are also confirmed by the use of statistical tests as well as the standard errors presented (which in the case of your manuscript are also too large to corroborate the existence of two enzymatic systems). Further, if enzymes operate at different range of concentrations, it is contradictory to use the whole data range for the estimates of the low affinity system. Should you wish to revise your manuscript accordingly I, however, believe the data presented to be of value and appropriate for this issue, and would accept a revised version.
Sincerely,
Christine Klaas

Dear author,
the revised manuscript has tackled most of the main comments from previous versions in a convincing manner. There are still a few minor issues that need addressing. See comments below and annotated manuscript. The annotated manuscript also contains suggestion for improvement of the text which needs a thorough revision. I would urge you to take these comments into consideration (this has not always been the case in the last submitted version).
Sincerely,
Christine Klaas


Comments (further comments are given in the annotated manuscript):

Line 381-382: referring to figure 4, which only shows one example for the argument is not sufficient. Similarly, in the following statements (whole paragraph, lines 382-388) you discuss the individual model parameters and their se, but in Table S2 present average values for each layer over several stations instead of the values discussed. Please show the actual data discussed here. I suggest that in supplement Table S2, instead of statistical data on average parameters for each layer, which is already partially shown in Table 2, you provide the individual Km1, Vm1, Km50, Vm50 and Kmall, Vmall with their uncertainties as estimated for each station and layer. I have the same comment for the next paragraph (lines 389-400), please show the individual values for the biphasic indicator in a figure or in the supplement Table 2.

p.16 includes a detailed discussion on Vm ratios between different enzymes, yet the data is presented nowhere. It would be helpful to include a figure similar to Fig. 9.

Discussion lines 729-731 and Fig 11: It seems odd when you have BP data measured directly to include a 10% convertion efficiency factor. The BP is the actual carbon demand. The 10% factor would only make sense if you want to concert BP into growth rates or biomass accumulation. This needs to be corrected.

in Figures 2, 5-8 and 10-11 please use capital to indicate layers (SURF, DCM, LIW, MDW) as in the text.

Figure 5b: x axis legends are missing

Figure 9: in plot legends replace "per cell Vmall etc..." with "specific" or "cell specific Vmall " or Vm1, respectively. Or find a different abbreviation for cell specific Vm. (see annotated manuscript).

Supplement Table S1: replace ld with "
Change legend Supplement Figure S2 to: "Nonlinear least squares regression fits of Michaelis-Menten kinetics for different and incremental ranges of substrate concentrations from 0.25 corresponding to a 0.025-0.25µM substrate concentration set to 50 corresponding to a 0.025-50µM substrate concentration set for a) LAP, b) GLU and c) AP. Red dots correspond to the field measurements. The dataset is the same as in Figure 3 (DCM at station FAST). d, e f : corresponding distribution of the Vm and Km parameters calculated according to the different concentrations ranges tested."

Supplement Figure S2: It would be helpful if the colors for the dataset used in panels a, b, c (0.25,05, 1 etc...) were used for the corresponding Vm and Km values in panels d,e,f.

Dear author,
the revised manuscript has tackled most of the main comments from previous versions in a convincing manner. There are still a few minor issues that need addressing. See comments below and annotated manuscript. The annotated manuscript also contains suggestion for improvement of the text which needs a thorough revision. I would urge you to take these comments into consideration (this has not always been the case in the last submitted version).
Sincerely,
Christine Klaas


Comments (further comments are given in the annotated manuscript):

Line 381-382: referring to figure 4, which only shows one example for the argument is not sufficient. Similarly, in the following statements (whole paragraph, lines 382-388) you discuss the individual model parameters and their se, but in Table S2 present average values for each layer over several stations instead of the values discussed. Please show the actual data discussed here. I suggest that in supplement Table S2, instead of statistical data on average parameters for each layer, which is already partially shown in Table 2, you provide the individual Km1, Vm1, Km50, Vm50 and Kmall, Vmall with their uncertainties as estimated for each station and layer. I have the same comment for the next paragraph (lines 389-400), please show the individual values for the biphasic indicator in a figure or in the supplement Table 2.

p.16 includes a detailed discussion on Vm ratios between different enzymes, yet the data is presented nowhere. It would be helpful to include a figure similar to Fig. 9.

Discussion lines 729-731 and Fig 11: It seems odd when you have BP data measured directly to include a 10% convertion efficiency factor. The BP is the actual carbon demand. The 10% factor would only make sense if you want to concert BP into growth rates or biomass accumulation. This needs to be corrected.

in Figures 2, 5-8 and 10-11 please use capital to indicate layers (SURF, DCM, LIW, MDW) as in the text.

Figure 5b: x axis legends are missing

Figure 9: in plot legends replace "per cell Vmall etc..." with "specific" or "cell specific Vmall " or Vm1, respectively. Or find a different abbreviation for cell specific Vm. (see annotated manuscript).

Supplement Table S1: replace ld with "
Change legend Supplement Figure S2 to: "Nonlinear least squares regression fits of Michaelis-Menten kinetics for different and incremental ranges of substrate concentrations from 0.25 corresponding to a 0.025-0.25µM substrate concentration set to 50 corresponding to a 0.025-50µM substrate concentration set for a) LAP, b) GLU and c) AP. Red dots correspond to the field measurements. The dataset is the same as in Figure 3 (DCM at station FAST). d, e f : corresponding distribution of the Vm and Km parameters calculated according to the different concentrations ranges tested."

Supplement Figure S2: It would be helpful if the colors for the dataset used in panels a, b, c (0.25,05, 1 etc...) were used for the corresponding Vm and Km values in panels d,e,f.