|The paper has been significantly improved, however I believe this resubmission still has significant issues and recommend some restructuring of the paper to highlight its goal and main contributions. |
-The definition of the process measured has to clearly defined, in some parts of the text it is named as nutrient removal and others a denitrification.
- There is a lack of discussion/introduction of the method used in groundwater. Since as indicated in the manuscript the HPFM is an adaptation from passive methods it would be informative to explain which aspects of the groundwater passive meter are to be adapted to be able to use them in the hyporheic zone. At first sight, there should be no problem to apply groundwater methods to the hyporheic zone, and thus needs to be clearly indicated in the manuscript.
- The introduction has improved but the message and goals are still unclear; they should be clearly stated to make the delivery stronger. I suggest re-organizing the introduction with to follow an structure similar to the following one, in order to get the reader to the final goal of the work:
1. Significance of the hyporheic zone. Include the significance of denitritication right here, so the all the examples can be easily understood from this perspective, there is lack of knowledge on any flux, nitrogen is just an example easily used to test the HPFM.
2. Limitations imposed in the hyporheic zone to measure fluxes and rates: Two aspects have to be measured and combined in order to measure fluxes: flow and concentration.
3: Limitations of the commonly used methods to asses both components of the fluxes (including methods such as gels or peeper methods to determine pore water concentrations, which are like the primitives HPFM).
4. From a groundwater perspective, passive meter are being used to assess fluxes.
6. What is needed to apply those ground water methods to the hyporheic zone.
7. Goal of the manuscript.
- Some estimations of the applicability of the HPFMs would complete the interesting results and help future research, and would strengthen the message.
P1, L28: Although the HPFMs can be certainly used to assess denitrification, the setup presented can only provide information on N-NO3 uptake, this uptake could result in denitrification (reduction of NO3 to N2) or in biomass production, use of N to build proteins, DNA... however this cannot be estimated from NO3 changes in concentration without additional N2 measurements or using isotopes like 15N.
P1, L31-33: Move the sentence to line 29 to have a more coherent abstract.
Methods and Results
To ease the reading, organize the methods and results section in a similar way, Laboratory tests and field tests. As well, use the same headings for the subsections that are present in both sections, for example subsection 3.2.2. should be named as 2.6.5, the first one is the direct results of the latter one.
P5, L20: If all the values are provided in those units, it would be more adequate and simple to use the terminology NO3--N or SRP –P so the reader does not need to remember that information. It is not indicated whether the PO4 values are expressed as PO4-P or PO4. Additionally, SRP is “only” P there is no need to indicate it, by contrast with NO3 measurements that provide the mass of the molecule NO3.
P5, L21: “The experiments described in this chapter were accomplished on triplicate samples” It would be more informative to indicate the number of replicated when explaining the design of the experiment. For example in P2, L30, “... analyzing NO3- and PO4- from each resin (n = 3)”.
P8, L1: Does this section refer to the field installation described in more detail on section 2.6? If yes, for the logic reading of the manuscript section 2.5 should be placed after section 2.6.
P11, L33-37: It is unclear the reason to assess the diurnal variation of with MLS within the scope of the manuscript. It is already indicated in the introduction that such sampling methods are highly influenced by spatio-temporal variability. Since the HPFMs were not used at that small temporal scale, it is needed to clarify the reasons behind those results. For example those results could support that the comparison between MLS and HPFMs result in higher values provided by MLS compared to HPFMs, since the latter one integrate those temporal oscillations. It would be of help to include a short sentence in the methods indicating that to assess the short term variability in nutrient fluxes...
P12, L13: I suggest rewriting the title of the section to something like: Estimation of nitrate turnover with HPFMs
P14, L9-10: As written, the sentence belongs to the discussion section, it might be better to merge it directly with the previous sentence and write, indicating low groundwater influence. If the significance of the measurements has to be clearly indicated, it might be better explained in the methods.
P14, L25-27: The reference to the study performed by Layton (2015) is a bit rough and the following sentences do not clarify the sentence. That Layton applied a similar method to assess contaminants does not mean that study performed is of less value. Instead, it would be better to explain how does the present work complements Layton work and which are the actual differences with Layton´s work, for instance, did he used resins or AC? Did Layton also measured darcy velocities? In which type of hyporheic zone did Layton work, more permeable, less? A more detailed comparison will provide more information and will strengthen the message of the findings of the manuscript.
P14, L19-21: The following sentence is not clear from the results why “... biofilm growth only started after the loading capacity of the tracer was exhausted”. Biofilm growth starts as soon as the substrate is placed in the stream. Please, indicate clearly which results support that affirmation.
P15, L31-36: This section is slightly speculative; no data provided proofs that the device did not create preferential flowpaths. The manuscript would gain strength if the disturbance caused is acknowledged, but at the same time indicating that compared with other implementations the present method could cause lower disturbance.
P15-16, L29-58, L1-9: What about the impact caused the presence of material of different permeability in the hyporheic zone? Were the permeability or porosity of the resin and AC similar to the conditions found in the stream? Structures of different permeability of the surroundings influence hyporheic flows (Ward et al., 2011). Not only the mesh, but the properties of the resin could influence the results, and create preferential flows.
P16, L5: It would be interesting to provide an estimation of the minimum time of exposition for the HPFMs, although it would of course depend on nutrient concentration and fluxes. Would it be possible to estimate it using for example the interstitial velocities measured by Angermann et al. (2013)?
Angermann, L.; Krause, S.; Lewandowski, J., Application of heat pulse injections for investigating shallow hyporheic flow in a lowland river. Water Resources Research 2012, 48, W00P02.
P16, L5-9: Would it be possible to provide an estimation of maximum and minimum permeabilities where the HPFMs could be implemented? For example too different permeabilities compared with surrounding sediment will in overestimated or underestimated fluxes (see Ward et al., 2011). Are there limitations of porosity imposed by the resin or AC producers? Additionally, at very high porosities, the time of exposure might be lower than for lower porosities. While time would highly depend on the nutrient concentrations, it would more limiting water fluxes. Such practical approximations would be of great help for potential users of the HPFMs.
Ward, A. S.; Gooseff, M. N.; Johnson, P. A., How can subsurface modifications to hydraulic conductivity be designed as stream restoration structures? Analysis of Vaux’s conceptual models to enhance hyporheic exchange. Water Resources Research 2011, 47, W08512.
P16, L19-20: Heterotrophic respiration occurs in all sediments, the rates vary partly as a function of mass transfer of nutrients. Diurnal oscillations due to benthic primary production can of course favour night denitrification, since the limit oxic layer would oscillate.
P16, L20: Denitrification is not the only process affecting the NO3 concentrations; also NO3 uptake for biomass production can influence concentrations.
P17, L29-30: Flowpath length can be defined as the distance travelled by the water before leaving the hyporheic zone (see Findaly, 1995), in that case the flowpath length cannot be “derived from the residence time of water and solutes in the hyporheic zone HZ and the horizontal Darcy velocity”. Instead, the flowpath velocity can be assessed. However, flowpath can also be used as the distance travelled by a solute before being uptaken into the microbial community, something similar to the uptake length in nutrient cycling. Please indicate clearly which term is used.
Findlay, S., Importance of Surface-Subsurface Exchange in Stream Ecosystems - the Hyporheic Zone. Limnology and Oceanography 1995, 40 (1), 159–164.
P17, L33: I am not sure if the difference “difference between the theoretically transported NO3- mass MNO3-HZ theor, which is the product of QHZ and CNO3-SW and the measured mass flux MNO3-HZ real” can be defined as denitrification. Denitrification is the reduction of nitrate to N2, however since no N2 was measured the calculations cannot distinguish between denitrificaiton and nitrate uptake to build biomass.
P18, L18-19: The limitation of nutrient removal by mass transfer is always the case, in very low permeable sediments mass transfer limits nutrient removal independently of the human activities tacking place in the stream or catchment. I propose another view of this section and for the significance of the HPFMS: knowing how mass transfer influences nutrient removal is crucial to manage streams and rivers, especially in the light of the worldwide increase in morphological alterations (Borchardt and Pusch, 2009), eutrophication (Ingendahl et al., 2009) and sediment loading (Hartwig and Borchardt, 2015).
P18, L20: The term “horizontal fluxes” is a bit confusing, since many of the results presented in the manuscript are compared with the surface water concentrations. Horizontal fluxes in the hyporheic zone are flowpaths, which are kind of vertically started in the surface or groundwater. Therefore the direction of the fluxes does not seem relevant, although it is true that the manuscript does not represent all the potential fluxes, the HPFMs could be simply oriented differently to gain information of different directions.
P18, L28: Based on the definition of denitrification provided in the introduction (P2, L13) this manuscript does not report denitrification rates since the measurements are based on changes in NO3 concentrations without additional measurements of N2.
Figure 5: It might be interesting to include the values of SW during the MLS sampling.
P2, L23: If the acronym DEA is not used anywhere in the text, it is not necessary.
P12, L23: Replace “average concentration observed in the HPFM” with “average concentrations measured with the HPFM”
Results: the standard deviations are presented in an uncommon way; it might be easier to read when the values are presented as for example (P13, L15) 4.2 ± 0.1 mg NO3- m² d-1.
P13, L28: In the tables dissolved oxygen is named as O2, please keep uniform terms throughout the text.
P13, L30: Add (MLS) to the heading as in the methods section.
P13, L37: Minima and maxima are the plural or minimum and maximum, however concentration is written in singular.
P17, L15: replace degrease with decrease.
P19, Table 1: Use the same format (italics, subscript for Rd) in the table and in the caption.