| 10 Mar 2026
Different paths, same destination: similar functional outcomes in nitrogen cycling within artificialized coastal habitat
Abstract. Human activities are increasingly affecting coastal ecosystems, with shoreline stabilization structures becoming a prevalent response to sea-level rise and extreme climatic events. While these structures aim to protect coastal communities and infrastructures, their effects on ecosystem functioning, and particularly nitrogen cycling and fixed-nitrogen loss processes such as denitrification, remain poorly understood. To assess the ecological impacts of breakwater construction, we employed a space-for-time substitution approach to examine changes in sediment biogeochemistry, macrobenthic community structure, and nitrogen cycling in an intertidal salt marsh in the St. Lawrence Estuary, Canada. We measured benthic fluxes, denitrification rates, and macrofaunal assemblages at five locations: two landward of the breakwater (impacted sites), one situated immediately seaward of the breakwater (intermediate site) and two reference sites (one vegetated and one unvegetated). Landward sites exhibited finer sediment with higher organic carbon content and supported distinct macrobenthic communities dominated by opportunistic Oligochaetes while reference sites were dominated by Molluscs and Crustaceans. The intermediate seaward site closely resembled the unvegetated reference site in both sediment characteristics and oxygen dynamics. Surprisingly, despite these substantial physical and biological changes, dark total benthic oxygen uptake, NO3−, NH4+ benthic fluxes and benthic denitrification rates showed no significant differences between impacted and reference sites. This functional similarity suggests a degree of ecosystem plasticity, where different combinations of abiotic and biotic factors can maintain similar ecosystem function. However, such functional plasticity might not apply to all ecosystem services offered by natural salt marshes, emphasizing the importance of careful consideration in coastal management decisions.
The manuscript “Different paths, same destination: similar functional outcomes in nitrogen cycling within artificialized coastal habitat” by Pascal et al. investigates how man-made structures aimed at mitigating coastal erosion, such as breakwaters, shape the natural coastal ecosystem, particularly the benthic habitat and its nitrogen-cycle. Method wise, they look at porewater geochemistry, flux measurements, denitrification process rates and macrofauna at both impacted and non-impacted coastal sites. Interestingly, while there are clear differences in benthic biogeochemistry and fauna between the impacted and non-impacted sites, denitrification rates do not follow this pattern but show high and low rates at both impacted and non-impacted sites. This leads the authors to the conclusion that there is no impact of the breakwater structure on the benthic nitrogen-cycle. This is an interesting and important study, and I had pleasure reading it. Because of climate change, man-made structures to protect the coastline are of increasing societal and infrastructural importance, and it is nice to read that this does not necessarily come at the cost of ecosystem functioning. Particularly the nitrogen-cycle is important in a coastal setting, given that coastal eutrophication is pre-dominantly driven by nitrogen.
Specific comments:
However, I do have a couple of concerns, the major one being the lack of explanation for the variation in denitrification rates, from which then the conclusion was derived that there is no general/concise effect of the breakwater on the nitrogen-cycle (as the variation was in both impacted and non-impacted sites). The impacted sites had much higher organic matter and organic carbon content, different macrofauna, and a lower OPD / higher DOU than the non-impacted sites, while nitrate concentration in surface sediments were about similar between all sites. Nevertheless, given the higher organic carbon content, which was seemingly of labile composition given the higher DOU, it could have been expected that denitrification rates would have been higher than at the non-impacted sites. Instead, the highest rates were found at an impacted and a non-impacted site, and the main explanation offered is “functional plasticity”- which, I feel, is too vague and a bit unsatisfying (l. 436). I would like to encourage the authors to look more thoroughly into their biogeochemical data and use them for their conclusions. Referring to the title, this means to describe in more detail what the “different path” is. Overall, for a manuscript that focusses on the nitrogen-cycle, the nitrogen data are too little discussed, esp. the results of the denitrification rate measurements. Furthermore, dissimilatory nitrate reduction to ammonium (DNRA) is not mentioned in the introduction but suddenly pops up in materials & methods (l. 192) and results, whereas anaerobic ammonium oxidation (anammox) is mentioned in the introduction, but not in the materials & methods and results; neither of them is mentioned in the discussion.
Another issue that needs clarification is the sampling in two years: 2021 and 2022 (l. 125). However, it is not mentioned whether this means (i) that some sites were sampled in 2021 and others in 2022, or (ii) that all sites were sampled repeatedly over two years? Maybe I missed it, but I couldn’t find this information. If the sites were sampled in different years, it would add potential interannual variability to the data and maybe that could be a reason for the variation in results (particularly the nitrogen results). Please clarify that point.
L. 168: I would be cautious with the porewater data taken in 0.5 cm resolution; commonly the “catchment area” of rhizons is assumed to be 1 cm (Seeberg-Elverfeldt et al. (2005) Rhizon sampling of porewaters near the sediment water interface of aquatic systems. Limnol Oceanogr Methods 3: 361−371); hence, when sampled in smaller resolution you likely draw water from “wrong / overlapping layers”.
L. 178: did you account for the different nutrient concentration of the replacement water in your flux calculation (given that during the flux incubation nutrients will either accumulate or deplete, different to the replacement water)?
L. 185: how did you decide for the pre-incubation time of 3 h, was it calculated? Given the OPD of max. 1.3 mm, the silty sediment with a porosity of 0.65-0.83 and a temperature of 9°C, you should have reached a 90% steady state denitrification within less than 15 min (see e.g. Dalsgaard et al 2000, NICE handbook).
L. 189: did the replacement water during the 15N-incubation also contain the tracer?
L. 190: did you also take a sample for denitrification after mixing the porewater with the overlying water? Commonly, a lot of the produced 29N2 and 30N2 sits in the porewater, rather than diffuses out into the water phase; hence, if you do not sample the porewater, you likely miss a portion of 29N2 and 30N2.
L. 190: did you treat the slurry sample with KCl to desorb the 15N-NH4 that might be attached to the grains? The particle-bound portion of NH4 can be significant, so if no KCl was applied or a correction factor used, DNRA rates can be potentially underestimated.
L. 200-201: checking 28N2 vs 15N-concentration relates to the potential occurrence of anammox, which should be mentioned here. Further, did you also check for the linear increase of D15 with 15N-concentration, needed to assure nitrate-limitation of sediment and functioning of the method / reliability of calculated rates (see Risgaard-Petersen et al. 2003, page 69)?
L. 423: I am skeptical of the argument that higher denitrification rates at LBWS than at LBWN are due to higher density of macrofauna at LBWS, as the reference site VS had similarly high denitrification rates as LBWS but also similarly low macrofauna as LBWN.
Technical comments:
L. 14: nitrogen removal is part of nitrogen-cycling, so maybe reformulate to something like “particularly nitrogen-cycling and its removal processes denitrification and anammox” or similar.
L. 19: maybe add some location to the reference sites, such as “reference sites outside the breakwater system”.
L. 20: “higher organic carbon content” compared to what? Please add.
L. 23: “NO3, NH4” needs a prior abbreviation or write in full.
L. 29: “benefits” or maybe “services”?
L. 36-38: could you add the difference between the two structures? They sound very similar, but I guess bulkheads might be typically a bit smaller (?).
L. 39: “they” don’t refer to the waves (as I guess you wanted to) but rather the structures; please edit.
L. 51: coastal eutrophication is predominantly driven by nitrogen-enrichment, which I would put here into focus to also justify why you specifically look at the nitrogen-cycle (rather than the phosphorous-cycle); this also makes your next sentence “understanding nitrogen removal is crucial..” a bit smoother.
L. 57: “microbially-mediated” is redundant as you already said that it is a microbial process.
L. 59: this is a matter of taste, but in the context of denitrification I would argue that the release of N2O is more important that that of CO2; N2O has a higher warming potential than CO2 (due to a longer lifetime in the atmosphere) and denitrification can be a significant source of it under certain circumstances; whereas a portion of CO2 is always emitted and kind of part of the process, as it relates to OC oxidation.
L. 59 ff: anammox is often not too common in coastal systems, which can be organic-rich, thus putting (autotrophic) anammox at a disadvantage compared to (heterotrophic) denitrification, see e.g. Dalsgaard et al. 2005. However, it of course can appear. Maybe reformulate, e.g. either talk about “sediment systems” (rather than “coastal systems”, line 56) or add some info to anammox.
L. 71: please add a “that” after “showed”.
L. 71 ff: do you mean here that the areal nitrogen removal rates would decrease (due to a shrinkage of the area) while the process rates itself would stay constant? Please reformulate for clarity.
L. 73: could this be simplified to “when built with sufficient vertical distance between...”
L. 93: “adaptation” or “structure”?
L. 93 ff: this sentence seems a bit out of place; is this not exactly what you first want to find out?
Fig. 1: maybe a slightly stupid question: is all the green in Figure 1C the saltmarsh?
L. 102: what is the trophic status of the bay, resp. what is the nutrient load of the river / does it carry a significant nutrient load into the bay? This might not be essential for your study, but it gives some background understanding, especially as you mention coastal eutrophication in your introduction.
L. 118-119: maybe one time “intertidal” is enough.
L. 129: the sediment cores were 15 cm long but the acrylic liners were 30 cm long- was the leftover 15 cm then overlaying water or air? Please clarify.
L. 141 ff: you say that sediment characteristics were analyzed from the small cores taken at each location, but in the following sentences you specify to “analyzed in one sediment core”- this is a bit confusing (also, which core was chosen?), but as you have a separate chapter dealing with your replicates, maybe you could reformulate the sentence here a bit and refer to the other chapter?
L. 144: could you add a small description after LOI like you did for porosity, i.e. “weight loss after combustion”?
L. 148: do you mean “natural” rather than “stable”? While it’s both, it’s commonly called natural δ13C abundance.
L. 162: please add the meaning of the variables.
L. 233: I feel this chapter is not needed but the given information could be integrated in the previous chapters, such as line 237 ff would fit better after l. 190. Also, the information from l. 239 should come earlier, as the result (no DNRA) was already given in l. 202.
L. 241: hypobromite iodine?
L. 286 ff: was the difference statistically significant?
L. 288: “TS” probably means “TN”
L. 301 ff: three times “notable / notably” in three consecutive sentences is a bit too much.
L. 365: what “remains limited”: the effect of artificial structures on ecosystems or the amount of studies dealing with that? Please reformulate.
L. 383: Please reformulate this sentence, as coupled nitrification-denitrification cannot have been enhanced by rhizone oxidation, as you used different cores for rate measurements and porewater sampling.
L. 387: the impacted sites had also higher organic matter, so it makes sense that they have higher NH4 accumulations in porewaters.
L. 390 ff: I slightly disagree with the argument / conclusion here, as earlier you suggested that nitrogen-cycling was not largely affected by the change in sediment biogeochemistry.