|I’d like to thank the authors for making substantive improvements to the manuscript. Their responses to the comments I raised in the first review are thorough and thoughtful. This revised version is stronger than the first, but I still see issues with it that need to be addressed to get it into publishable shape. |
First and foremost, the quality of writing is still poor. I made some edits, but stopped once I realized that there is a LOT to edit. Some sentences are barely comprehensible. I trust that with 8 authors, these can be identified and fixed. I list under Other Comments a small handful of issues that stuck out to me.
Second, the data presentation and discussion seem overly complicated. I wonder if the narrative can be simplified to better clarify the take-home messages. Also, the authors toned down on the N story by a lot, but I still find that there is some overreach going on. Here’s my argument:
The benthic chamber data can be interpreted in a more systematic way by comparing to the trend one would expect given the pore water data. For DOC and DON, we expect the values to increase with time. However, this is not always observed; some show no obvious change with time. Setting statistics aside for now, this opens the door for discussion about microbial DOM consumption at the sediment-water interface, or in the bottom water, for Sta. 3 and deeper. (Different matter for Sta. 1 and 2; see below re: Fig. 8.) For aCDOM(325), we also expect values to increase with time, but this is only seen at Sta. 4; elsewhere, values either remain unchanged, or decline. This again points to DOM consumption (or alteration) upon/during export from sediments. Similarly, trends in spectral slope S in the chambers are consistent with overall decline in MW of DOM with time; again pointing to DOM alteration upon/during export from sediments. And with FDOM, one finds that humic-like FDOM increased as expected, but perhaps not when it comes to protein-like FDOM, again pointing to DOM alteration/consumption. In its present state, these take-homes are difficult to grasp, because of too much attention being paid to subtle differences across time and stations (e.g., page 10 line18; p. 11 line 24).
One can then consider the observations that: (1) DON/DOC ratios were much lower in sediments compared to in the chambers, (2) and protein-like FDOM showed muted variability in the chambers, leading to the argument that proteinaceous DOM might have a role in this transformation (as authors discuss on page 11).
I like the idea of Fig. 8, but after reading the manuscript twice, I am finding it a bit disingenuous. Perhaps I am missing something here, but it appears that this figure treats flux data from Sta. 1 and 2 rigorously (statistically speaking), and but not so for the rest of the stations. On page 9, line 14, the authors state that there were no significant differences between diffusive and net DOC fluxes. If that is the case, why is it that data from Sta. 3 – 6 are used to calculate DOM reworking rates, while this is not done for Sta. 1 and 2? In any case, reporting the reworking rates to two significant figures, and attempting to interpret them across a transect seems to be a stretch, given the level of uncertainty involved. We all know how difficult it is to get flux estimates, and that both diffusive and net fluxes are subject to systematic error. I wouldn’t be surprised at all if there is indeed a bottom-water redox effect playing a role here, but whether the data clearly show that is a different matter.
I find the discussion about pLMW-DOM on page 13 far-fetched. Unless the authors can provide a more concrete definition of pLMW-DOM and provide evidence for its existence in their samples, the discussion about unfolding of this material in presence of nitrate in the bottom waters should be omitted (paragraph starting at line 13). pLMW-DOM that is discussed in Burdige and Komada (2015) is largely theoretical, given very limited data on DOM size and composition.
The discussion about DOM removal either at the sediment-water interface, or in the bottom water, needs to be better clarified. The Abstract says sediment-water interface, but there seems to be some waffling going on in the narrative. Also, is anything known about DOM in microbial mats? If they are covering ~40% of the surface, could they be playing a key role here? This point can be better clarified in the discussion.
I believe I mentioned this in my first review, but the sharp spikes in DOC and DON in the pore water profiles and in the chamber time series still bother me. Not because they exist, but that no plausible explanations are given for their occurrence.
The net flux data are buried in Table S1. Upon looking at the numbers, many of the values look indistinguishable from zero. This point is not clear in the narrative (instead, tendency is to read too much into wiggles).
Please report the bottom water values along with t=0 values in the figure showing the chamber data.
P1, L32: “…porewater DOM consists in part of recalcitrant low molecular weight…”
P3, L1: Replace “Oh the other hand” with “At the same time”
P3, L20-25: This section is very difficult to understand, and confuses the reader. Simplify, as you do on P12 L25, and clarify the direction in which absorbance drops.
P3, L25: I do not believe that all FDOM contain aromatic moieties.
P3, L30-31: Example sentence that is barely comprehensible.
P4, L20-21: This comment about nitrate and nitrite is perplexing.
P5: nice addition about syringe filters, including Fig. S4, thank you. But Fig. S4 is presented out of order (in fact, not all figures in the supplement are referenced)
P5, L39: Multicorers (not multiple corers)
P8, L10: Please explain how the range in D was incorporated when determining std deviations of fluxes.
P8, L26-7: Eliminate the statement about vicinity to coast influencing DON distribution. (Or please re-write it, so that it does not sound as if DON concentration of a mud sample on a ship will change as you get closer to the coast.)
P9, top line: what does it mean to “resume the gradient”? This appears again on line 25.
P9, L7-8: What is meant by “near-bottom”? If you are referring to water enclosed in the chamber, say so. Here, DOC concentrations are for averages over time? Unclear.
P9, L13-14: Instead of saying that net fluxes were ‘generally lower’ than diffusive fluxes, state that they were greater at Sta. 1 and 2. Provide plausible explanation. State whether diffusive and net fluxes differed for DON.
P9, L22: replace “absorption” with “absorption coefficient”. I suggest “values of aCDOM(325)” instead of “aCDOM(325)s”
P9, L28: absorption coefficient can increase, but not accumulate. Sta.1 showed greater variance that what is suggested in text.
P9, L30: I would argue that the slope values were higher in the sediments compared to bottom water, but not necessarily increased with depth in sediment.
P10, L12: Fluorescence can intensify, but not accumulate
P10, L31: cite Fig. S1
P11: Top part of this page (and top part of second paragraph) is convoluted, and seems to delve too much into subtleties of the data that may not be significant. I find that it more obfuscating than clarifying.
P12, to paragraph: Is there any methanogenesis going on here?
P12, 4.2 subheading: Please fix this.
P12, L10: replace “classical” with “current”; remove “slow” after “followed by”
P12, L11: “can cause an imbalance in DOM”
P12, L12: “This is in part explained by accumulation of recalcitrant DOM that is thought to be of LMW”
P12, L14-16: sorption and coprecipitation would remove it from DOM
P12, L16-18: “isotope” needs to be identified.
P13, L3: replace Fig. 8 with Fig. 4
P13, L5-6: “However, the previously reported … was generally not observed.”
P13, L10: I am not able to comprehend
P13, L14: Komada et al (2016) should be replaced with (2013).
P13, L20-21: very hard to comprehend
P14, L2-5: The wording is such that DOM data have built-in bias, while POM does not (as in good versus bad). I don’t think the authors mean this; please re-word.
P14, L5 to end of paragraph: This can be shortened. I find it’s obvious that bottom currents will move DOM.
P14, second from bottom line: Should DOM be POM?
P14, last row: the “previous studies” should be cited
P15, L1: “decrease” is a poor choice of word here. “lower compared to”
Fig. 1. “Left: Distribution of … stations (pentagrams).”
Fig. 2. Alpha is used instead of “a” for abs coeff. Please use more distinct colors than black and dark blue. Panels for Sta. 1 should be expanded (or use line breaks) to show high data that aren’t displayed. Also, as done in Fig. S1, will be helpful to indicate which stations are mid-shelf, etc.
Fig. 3. Were any of the data omitted from the regression?
Fig. S1: Y-axis, NO4+ needs to be NH4+
Fig. S3: What are dashed horizontal lines? Replace “near-bottom water” with “BIGO Chamber”
Fig. S4: Very informative, thank you.
Were all figures in supplement referred to?
increase/decrease “in”, not “of”
“sediment-water interface”, not “sediment-water column interface”
Intensity (such as fluorescence) can increase or decrease, but can’t accumulate
Regions of the electromagnetic spectrum (UV, Vis) are ‘ranges’ or ‘regions’, not ‘spectra’