the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 29 Nov 2021
Linking sediment biodegradability with its origin in shallow coastal environments
Abstract. In coastal areas and estuaries, such as those encountered in the western part of France (Brittany region), the recycling of carbon and nutrients from sediments can participate in the development of micro and macro-algal blooms with harmful consequences for these ecosystems. One of the main processes controlling this recycling is the microbial mineralization of sedimentary organic matter (SOM). Mineralization is controlled by the origin, quantity and accessibility of the SOM, three factors whose relative importance remain, however, poorly quantified, mainly due to the great diversity of OM sources in coastal areas. The first objective of the present work was to assess the variability of the SOM origin at the regional scale representative of the complexity of the sources likely to be involved. The second objective was to determine the link between the SOM origin and its biodegradability, and how the OM sources can drive nutrient dynamics at the sediment-water interface. To this end, a broad sediment sampling campaign was carried out on Brittany mudflats, particularly affected by the eutrophication, during the spring period. A total of 200 samples were collected at 45 sites. They were characterized by their porosity and grain-size, as well as their chemical composition through elemental, isotopic and molecular biomarker analysis. A wide range of OM sources were identified in the sediments, including both natural (bacteria, algae, macrophytes, terrestrial plants), and anthropogenic (combustion products, crude oil, petroleum products – e.g. from the processing of crude oil at refineries- and fecal matter) sources. Sediment slurry incubations were carried out to determine the spatial variability of potential mineralization rates under oxic conditions. In addition, the measurements of NH4+ and PO4 fluxes at the sediment-water interface were made from sediment core incubations under realistic redox conditions of sediment. The physical and chemical sedimentary characteristics explained 58 % of the variability of mineralization rates under oxic conditions, with a negligible independent effect of the SOM origin (3 %). Conversely, under insitu redox conditions, the prevalent role of SOM origin over quantity/accessibility on the sediment biodegradability was highlighted with a significant effect 5 and 1.5 fold higher on the PO4 and NH4+ fluxes respectively. The anthropogenic inputs from the watershed to the coastal sediment, through agricultural runoff and/or sewages discharge, seem to significantly drive the nutrient dynamics at the sediment-water interface. Higher values of NH4+ and PO4 fluxes were measured for the sediment with a chemical composition impacted by human activities.
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Interactive discussion
Status: closed
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RC1: 'Comment on bg-2021-318', Wytze Lenstra, 07 Dec 2021
“Linking sediment biodegradability with its origin in shallow coastal environments” by Louis et al.,. In this current manuscript the authors evaluate the effect of different types of organic matter on the degradability of the organic matter and use different types of measurements to evaluate the sources of the organic matter. To quantify the biodegradability of the sediment incubations are carried out under oxic conditions and benthic flux measurements of PO4 and NH4 were done. With this manuscript I have two main comments (1) the link between the measured fluxes and biodegradability of the sediment is made in a too simplified way in my opinion. There are many factors that can control the benthic release of PO4 and NH4 from the sediment such as macrofaunal activity and bottom water redox conditions. These factors are discussed in a few sentences in the discussion but I think that these should also be introduced in the introduction. (2) I found it difficult to find the comparison of the measured fluxes and the measured rates of the incubations. Do these match with each other? The way I understood the manuscript these are both used to quantify the degradability of the sediment so I think a comparison between these parameters should at least be made in that case. See my detailed comments below:
L16: "controlled by the origin, quantity and accessibility". There are also other factors controlling the mineralization such as for example temperature or the presence of electron acceptors. In my opinion this is written in a too absolute way.
L27: "the eutrophication" remove "the"
L24: can you already mention what kind of samples were taken here in the abstract. All surface sediment?
L28: "oxic conditions" will this not lead to strongly enhanced mineralization of organic matter? In that case should "potential" not be replaced by "maximum"?
L30: " The physical and chemical sedimentary characteristics ". Can you already give examples here in the abstract? ..such as...
L28:" 5 and 1.5 fold higher on the PO4 and NH4+ fluxes respectively". Does this mean compared to the oxic incubations? In that case the degradability cannot be quantified/compared by using fluxes of PO4 and NH4. In oxic conditions PO4 will be affected by the presence of Fe oxides (i.e. lower benthic flux) and NH4 will be remove via nitrification for example.
L36: Is this corrected in any way for the bottom water redox conditions?
The introduction is in general well written and has a clear flow. The only thing I miss in the introduction is information on geochemical processes that control NH4 and PO4 mobilization in the sediment and their benthic release. There is at this point no information about different pathways for PO4 mobilization for example. While NH4 (and CO2) mobilization can be coupled to (anaerobic) organic matter degradation for PO4 this is more difficult because release of P bound to Fe oxides is often a important source of P in sediments. Also P cycling in sediments is strongly affected by mineral precipitation in the sediment such as for example vivianite and apatite and adsorption onto Fe oxides (mostly in oxidized sediments near the sediment water interface for the latter). This means that even at sites where the OM degradation is high the benthic flux of P can be limited. Also if benthic fluxes are presented, the effect of macrofaunal activity on these fluxes should in my opinion also be explained a bit more (i.e. bioturbation and bioirrigation).
L42: "at the sediment water interface" microbial degradation of organic matter does not only occurs at the SWI and continues when the OM is buried. Especially when linking this to the benthic fluxes of CO2, ammonium and phosphate the deeper sediments are very important as well in the degradation of organic matter and production of porewater CO2, ammonium and phosphate.
L46: Mn oxides occur also as Mn(III) or combinations of Mn(IV) and Mn(III) birnessite or manganite for example. I would just call this "Mn oxides" and in that case also "Fe oxides".
L50: "e.g. oxic conditions)" why is this text included here? Do you mean "redox conditions"?
L53: so the other factors mentioned earlier in this paragraph are ignored?
L83: remove "phenomena"
L102:"ii) to use this variability to go back to the variability of OM sources" is it not easier to just quantify the OM variability of the different OM types at the source? I do not understand the importance of this point.
L107:"(NH4+ and PO4)" why not CO2 in this case? That was also introduced earlier in the introduction.
L112: It would be nice to end this introduction with the most important finding of this study.
L120: what is the depth interval of this surface sediment?
L145: can you add the original reference for this method in this sentence.
Section 2.5. Are there also quality controls to discard a flux when the R2 of the measurements is not high enough?
L184: Can you add how many samples are taken in time? Is the water that is removed during sampling replaced with new artificial seawater?
L187: how are these oxic conditions maintained and controlled? What is the reason these where carried out under oxic conditions? Oxygen often only penetrates a few mm in the sediment and therefore these oxic conditions might be artificial and alter geochemical processes that control the degradation of the sediment.
L232:"(response variables), " what does this mean.
L261:"Over all sediment samples, " for me it is unknown which depth interval is used. This is key information given the strong gradients often observed in the parameters discussed below.
Table 2: are bottom water redox conditions also measured for all the sites? If yes can this information be added somewhere in the paper because it is highly relevant for the benthic release of NH4 and PO4.
L365: add space before "The"
Caption Fig. 7 is not correct. "Boxplot of the benthic NH4+ (A) and PO4 flux (B) (μmol.m-2.h-1) " (A) = (C) and (B) = (D)
L376: It would be good to have some information of the quality of the measurements of these fluxes. I also cannot find this in the original paper (i.e. Louis et al., 2021). What are the changes in concentrations during the measurements? This could be added to the supplements as a figure or a table. Concentrations of solutes during the incubation can vary quite a bit in time and increases (effluxes) are not always linear. At this point it is not clear to me how many samples there were taken in time. In the case of only two samples (beginning and end) this has to be stated somewhere and also the uncertainty should be mentioned in my opinion.
Caption figure 9: Change (A) in the caption to (a), also for b,c and d.
L536:"oxic conditions" are the oxygen concentrations monitored during the incubations? How do the authors know O2 is not depleted at some point in the bottles?
L453:" The mineralization process...". Do the authors mean that because these incubations are carried out under oxic conditions the quality of the OM is not very important anymore because it will be degraded with O2 anyway? This statement is not very clear to me. If this is the case I'm not sure if this statement is valid on the timescales of these incubations.
L552: typo in y-1
L564:"realtistic". What does this mean? Are the incubations carried out under the in-situ redox conditions or at redox conditions the authors find realistic? I would like to see the bottom water redox conditions for the different sites somewhere in this manuscript or in the supplements.
567:"Under these redox....". I agree that the lability is important in this case however the presence of electron acceptors or the presence of macrofauna is also very important. I think only mentioning the lability of the OM is too much of a simplification in this case. The authors should in my opinion also discuss other controlling mechanisms or at least mention them.
L569: "We thus suggest...". I agree that the origin plays a role but just ignoring other main controlling mechanisms such as bottom water O2 is not possible in my opinion. Especially for PO4 bottom water redox conditions are very important.
L573:"All parameters...". Can you mention which ones are the most important.
L596: "...assuming that this results from an increase in sediment biodegradability. " Why assuming in this case. Can the authors not compare this with the incubations they did to quantify this biodegradability? In this paragraph I miss the comparison between the measured fluxes and the degradation rates that were presented earlier. Do they match?
L617:"remains unexplained here" Can the authors elaborate a bit more on which mechanisms might be responsible for these variations? i.e. bottom water O2, mineral formation etc.
L625: "link with sediment potential biodegradability and nutrient release". I actually miss the comparison between the incubations and the measured fluxes in this manuscript.
Wytze Lenstra
Citation: https://doi.org/10.5194/bg-2021-318-RC1 -
AC1: 'Reply on RC1', Justine Louis, 18 Jan 2022
Dear Wytze Lenstra,
We thank you for your constructive comments and corrections that we took into consideration to improve our revised manuscript.
Please find our answers to your main comments below.
- The other factors that can control the benthic release of PO4 and NH4+, such as macrofaunal/microbial activities, should be more discussed
As stated in the introduction (lines 44-47), the SOM biodegradability and nutrient release also depend on other factors such as the temperature, the terminal electron acceptor availability, and the microbial and macrofaunal activity and diversity. Nevertheless, the goal of our study was to separate the parameters related to SOM origin (=qualitative parameters) from the other sedimentary characteristics related to the chemical composition (C, N, P) and physical properties (=quantitative parameters) in order to assess their independent effects on the mineralization rates and benthic nutrient fluxes measured during the campaign. In order to link the NH4+ and PO4 release with the sedimentary characteristics and the SOM origin, and to reduce other environmental variables such as temperature, light, overlying water nutrient concentrations, we have decided to conduct the core incubations for all sites under controlled temperature in the dark and by using nutrient-free artificial seawater as overlying water. All core incubations were done under the same ambient conditions. Nevertheless, as mentioned in the manuscript (lines 618 – 622), the microbial abundance/diversity as well as the bioturbation were not determined in our study. We assumed that these biological parameters could be significantly involved in the spatial variability of benthic nutrient fluxes, and therefore correspond to the residual part of the variance partitioning of nutrient fluxes that remains unexplained here. More details about this assumption will be added to the revised manuscript, as you recommend:
- “Through particle reworking and burrow ventilation by benthic macrofauna, a shift in redox conditions, a remobilization of burial OM, and a stimulation of solute exchanges at the interface can occur in the sediment (Graf and Rosenberg, 1997; Welsh, 2003; Kristensen et al., 2012). For example, Nizzoli et al. (2007) has shown a stimulation of NH4+ fluxes from all bioturbed sediment by the polychaete Nereis spp., whereas the bioturbation had site-specific effects on the PO4 fluxes (sediment acts either as a source or sink of PO4) which depends on, among other factors, the sediment composition, the burrow ventilation depth.”
- "We hypothesize that differences in microbial community structure, i.e diversity, may play a role in variations in SOM mineralization and nutrient recycling. Most literature focused on the effect of environmental variables shaping the microbial community structure (Ge et al., 2021 and references therein), but the impact of differences in microbial community composition on the sediment biodegradability of carbon remains little studied and thus speculative (Abell et al., 2013; Li et al., 2015). As Abell et al. (2013) showed, the bacterial community composition is related to the nature of the OM in estuarine systems, and their combination may lead to a shift in benthic nutrient fluxes.
- More technical details about the sediment sampling and the measurements of benthic nutrient fluxes and mineralization rates need to be added, and information about redox conditions in bottom water and sediment is requested
Please find below some technical details that will be added in the revised manuscript to improve its understanding:
Benthic nutrient flux measurements: As described in the Louis et al 2021, two 0.22 µm-filtered water samples were collected in the overlying water after 2h and 4h of incubation and stored at 4°C for less than 3 days until nutrient analysis. Nutrient-free artificial seawater was used for these incubations (lines 179-180). The water sample collected (5 ml) corresponded to 3 % of the total volume of the overlying water (150 ml). This collected volume was not replaced with new artificial seawater during the incubations, and the exact volume (145 ml for T2 and 140 ml for T4) was taken into account for the calculation of benthic nutrient fluxes. The core incubations allowed to preserve the redox conditions of the sediment and thus the term “realistic” mentioned in the manuscript (line 564) corresponds to “in situ”. Generally a low O2 penetration in the sediment of few millimeters is observed in eutrophicated coastal areas. Vertical profiles of O2 in the sediment collected by colleagues in the Trieux estuary, one of our sampling sites, confirm this statement. The sediments were depleted in oxygen below 2 mm vertical depth.
Before sediment sampling, no measurements of in situ bottom water redox conditions were done. The sediment cores of intertidal mudflats were collected at low tide. The core incubations carried out in our work allowed to assess the potential benthic NH4+ and PO4 fluxes mimicking the mudflat submerged during the rising tide by the oxygenated coastal water. The bottom water conditions can be considered oxic (based on temperature, salinity and tidal effect), sediment redox conditions were not determined for the 200 samples.
Surface sediment samples: For the sediment slurry incubation as well as for the characterization of surface sediment (physico-chemical composition, SOM origin), each sample was collected in the upper 5 cm sediment layer. This information will be added to 2.1 section.
Mineralization rate measurements: During the sediment slurry incubations, no measurements of oxygen were carried out. The mineralization rates were calculated from the measurement of CO2 production. We consider that these incubations (time = 4h) were carried out under oxic conditions over the 4 h incubation. These incubations consisted of 5 g of wet sediment mixed with 25 ml of artificial seawater in the glass flask of 145 ml total volume. It can be assumed based on previous work that the mineralization process was not oxygen-limited due to a large reservoir of O2 in the headspace of flask (V ≈ 115 ml) corresponding to 21 % of the air volume.
Under these conditions, we assumed that the presence of oxygen and homogenization of the sediments are optimal for SOM degradation (lines 539-543), and thus we were able to calculate the optimal sediment reactivity, noted k, from the measurements of mineralization rate and TOC content of sediment. A spatial variability of k was observed (0.8 to 11 y-1 for 75 % of data) (lines 552-553). This approach has been used and described by Nicholls and Trimmer (2009) (https://doi.org/10.3354/ame01285).
- A comparison between the benthic nutrient fluxes and mineralization rates is missing
Even though a comparison would be interesting, we thing a direct comparison between the mineralization rates and the benthic nutrient fluxes would be not appropriate as the methodology (slurry versus core incubations) and the redox conditions are different. Such differences can be illustrated by the fraction of their variances explained by the SOM origin: it was interesting to observe that the SOM origin had a significant effect on the NH4+ and PO4 fluxes, which was 1.5 and 5 fold higher than that determined by the other physico-chemical sediment parameters (e.g. porosity, TN and Org-P content), contrary to had been observed for the mineralization rates.
Sincerely yours, on behalf of all authors,
Justine Louis
Citation: https://doi.org/10.5194/bg-2021-318-AC1
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AC1: 'Reply on RC1', Justine Louis, 18 Jan 2022
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RC2: 'Comment on bg-2021-318', Anonymous Referee #2, 21 Dec 2021
“Linking sediment biodegradability with its origin in shallow coastal environments”
The authors aimed in this paper to explain possible factors that drive biodegradability of OM in sediments of Bay and estuaries of Britanny Region. This paper has two parts: the first one, deals with the identification of potential sources of shallow OM through several biomarkers and isotopic signatures.
The second one using short time core’s incubations to assess the export of nutriments ( P04 and NH4) from the sediment and to calculate a mineralization rate that is used to inform about the degradability of the OM. It was difficult to see the continuity between these two parts is done through data analysis (variance partitioning) and show the significant inputs of several human activities in these basins and bring attention to the potential detrimental role of microorganisms that were not analyzed in this study.
General comments:
With regards of the type of chemical analysis that were measured, bacteria could have been assessed with their typical FA markers for instance. One can imagine that full FA profiles are available for each site since other FA were displayed in this study.
Also, North and south parts of Britany have some abiotic differences, in average the climate is much wetter in the north and the tides are higher than in the south. There is a Channel Britanny and an Atlantic Britanny. These differences will have an impact on coastal and intertidal waters/sediments qualities.
Both sides of the region have experienced large oil spills in the past.
When it comes to OM origin, a one-time sampling at a large scale is not sufficient to conclude on which anthropic source is influencing the most of the OM origin. Local inputs need to be verified. There is nothing new in announcing that natural and anthropic sources are both contributing to the OM composition.
Specific comments
Abstract
L19 I am not convinced about the chosen scale is being “representative” of the complexity of such anthropized region.
M&M
My main issue here, is what it seems to me the wrong definition that authors have of some chosen “estuaries”. Two of them are in fact not estuaries = water influenced by both open ocean AND riverine waters. La Rance and Triaux, are Ria with no river influence. Waters in these basins are almost totally under marine influence, “functionally and biologically” they are much close to what happened in a covered bay that in a typical estuary which usually exhibit pronounced salinity gradient.
La Rance is also particular because it bears at its mouth the only and unique hydrothermal barrage of France with the consequence that it controls water entrance and volume (only one tide a day). The local hydrodynamic needs to be well known especially if one need to conclude on its sedimentation rate.
Discussion
L489 It is a fact that parts of the north coast have been impacted by oil spills.
L495-500: to be rephrased, also not clear if finally, the petroleum inputs have an impact in the “south” sediments.
L515- to be discussed with regards of the local knowledge to the Rance hydrodynamic.
L550-556: Biodegradability or of organic sediment and its consequence, releasing nutrient and greenhouses gases is something well known in coastal ecology with the concept of “priming effect”. This priming is indeed triggered by eutrophication (human and animal wastes, included).
L557: More importantly is what leads to increase bacterial activity.
L 619: there an enormous literature of the role of bacteria in the degradation of the OM. Need to be fairly discussed.
L619-622: rather speculative, what about the impact on macrofauna of the induced stress with regards of the short term “in situ” measure ?
To conclude, the two parts of this article are not thoroughly connected, besides, there are shortcomings conclusions in the very descriptive first part: spatiality, potential sources changes, local ecological knowledge...
The second part could stand by itself especially if authors would consider a broader literature.
Citation: https://doi.org/10.5194/bg-2021-318-RC2 -
AC2: 'Reply on RC2', Justine Louis, 18 Jan 2022
Dear reviewer,
We thank you for your comments that we will consider to improve our revised manuscript. The revised manuscript will be corrected by a native English speaker. In the following section we respond to your different comments and questions:
- Why did the methodology (regional scale, one-time sampling) used in the present study was appropriate to study the diversity of SOM origin/composition?
As mentioned in the manuscript, most investigations on the spatial variation of the origin and composition of the SOM have been carried out so far at local scale, within a bay or along an estuary. There are only few studies on the regional scale (lines 79 – 82). Therefore, the first objective of this manuscript was to investigate the spatial variability of the origin and composition of the sedimentary organic matter (SOM) at the regional scale. The chosen study area was Brittany, particularly impacted by eutrophication due to the agricultural intensification and the urbanization of watersheds. We therefore expected to have a diversity of OM sources. This was confirmed in our study by combining bulk elemental, isotopic and chemical biomarkers analysis of surface sediment samples. Our results were from a one-time sampling during the spring, but the broad collection (200 samples on 45 sites) allowed to draw the regional variability of sediment characteristics at this study period. The large number of sediment samples also allowed to correctly run the statistical analysis, in order to link the sedimentary characteristics with the mineralization rates and benthic nutrient fluxes measured in our work.
- A better connection between the two main parts in the discussion section (4.1 and 4.2) is requested
As mentioned in the manuscript (lines 531 – 533), “after characterizing the SOM composition at the regional scale, the objective of this work was to quantify the relative significance of the SOM origin on the sediment reactivity, as well as to identify the SOM sources enabling the sediment to act as a nutrient source for the overlying water”. For a better understanding, we suggest to complete the opening paragraph of the second section 4.2 by reminding that “two statistical analysis were used: i) the variance partitioning to quantify the variance proportion of nutrient fluxes and mineralization rates (response variables) independently explained by both the explanatory variables “SOM origin” and “physico-chemical composition”, and ii) the canonical redundancy analysis (RDA) to assess the linear relationships between the explanatory variables and the response variables. For the nutrient fluxes, with a significant part of variance explained by the SOM origin, the RDA allowed to asses which SOM sources can enhance the PO4 and NH4+ release. This could be illustrated using the spatial diversity of SOM origin previously drawn in the first part the discussion section”.
- More information about anthropogenic inputs is requested
As stated in the manuscript (lines 486 - 487), eutrophicated coastal systems, as Brittany coast, receive anthropogenic matter from urban discharges, agricultural and industrial activities impacting the SOM composition. It was expected to observe a mixture between natural (marine and/or terrestrial) and anthropogenic matter sources in our sediments. By using the δ15N and lipid makers specific to anthropogenic matter (fecal matter, combustion products, oil and by-products), we allowed to assess how the impact of human activities on the surface sediment composition vary at the local and regional scale. We have well observed a discrimination between the north and south of the Brittany coast (lines 487 – 491): the sediment composition in the north sites seems to be more impacted by oils spills than the south sites, characterizing by an enrichment of crude oil markers. This likely results from the biggest oil spill that occurred off the north coast of the Brittany by the Amoco Cadiz (source: CEDRE). Conversely, the sediment composition in the south sites would be more impacted by an enrichment of petroleum products, which include products from the processing of crude oil at refineries. High values of δ15N combined with high proportions of fecal markers in surface sediments allowed to trace sewage discharges and agricultural runoff. It was the case in the Vannes Estuary where our observations were consistent with the proximity of a WWTP (lines 501 – 508).
- The role of the hydrodynamic conditions should be more considered in the discussion
The diversity of the SOM composition results from potential sources of OM (related to algal production, land use, human activities …) and also hydrodynamic conditions as mentioned in your comments. As discussed in the manuscript (lines 511 – 513), the hydrodynamic can control the spatial effect of sewage effluents on sediment composition. The gradient of δ15N in surface sediments, that traced sewage-derived N, can be observed with a variable distance from the WWTP outfall according to coastal system (lines 506 – 511).
The addition of the following text in the discussion section about the potential additional role of hydrodynamic conditions on the SOM composition is proposed:
- In the sediments collected in the Goulven Bay where a significant proportion of macroalgal biomarkers was observed (Figure 4; lines 319 – 325): The sampling area was located in the upper part of the intertidal area of the Goulven Bay, which could be impacted by a high sedimentation rate. Under specific hydrodynamic conditions, a significant deposition of macroalgae could occur and fuel the SOM composition.
- In the sediments collected in the Rance Estuary, where high values of δ15N as well as proportion of fecal markers were observed in the mid estuary of the Rance, which likely result from intensive agricultural activities in the watersheds (lines 515 – 521): The Rance Estuary is particular with the second largest operational tidal power station in the world built at the estuary's mouth (Rajae Rtimi et al., 2021). This could enhance the deposition of fine particles in the estuary, except upstream of the sluice gates and downstream of the turbines. The effect of agricultural activities on the molecular and isotopic signature of sediments could be more significant under these hydrodynamic conditions.
- Is the term “estuary” appropriate to define the Rance and the Trieux?
The sampling sites in our study were macrotidal mudflats located in Brittany bays and estuaries. We used the term “estuary” for the Rance and the Trieux, which is widely given in the scientific literature.
Examples:
- Rajae Rtimi et al. Hydrodynamics of a hyper-tidal estuary influenced by the world's second largest tidal power station (Rance estuary, France). Estuarine, Coastal and Shelf Science, Volume 250, 2021, https://doi.org/10.1016/j.ecss.2020.107143
In the present study, the sampling was done in the marine part of the Rance estuary (Figure 1 in Baron S et al (2017). doi: 10.3389/fmicb.2017.01637).
- Hugues Blanchet et al. Multiscale patterns in the diversity and organization of benthic intertidal fauna among French Atlantic estuaries. Journal of Sea Research, Volume 90, 2014, https://doi.org/10.1016/j.seares.2014.02.014.
In this publication, the authors specify that the Trieux estuary can be considered as a Ria system, and differs from coastal plain estuaries such as the Gironde, Loire.
- The role of bioturbation and microbial abundance/diversity need to be more discussed
In the revised manuscript, we will extent the discussion and add more details about the potential effect of microbial abundance/diversity as well as bioturbation on the benthic nutrient fluxes from the literature, which can involve in the large residual part of the variance analysis of benthic NH4+ and PO4 fluxes (Lines 618 – 622):
- “Through particle reworking and burrow ventilation by benthic macrofauna, a shift in redox conditions, a remobilization of burial OM, and a stimulation of solute exchanges at the interface can occur in the sediment (Graf and Rosenberg, 1997; Welsh, 2003; Kristensen et al., 2012). For example, Nizzoli et al. (2007) has shown a stimulation of NH4+ fluxes from all bioturbed sediment by the polychaete Nereis spp., whereas the bioturbation had site-specific effects on the PO4 fluxes (sediment acts either as a source or sink of PO4) which depends on, among other factors, the sediment composition, the burrow ventilation depth.”
- "We hypothesize that differences in microbial community structure, i.e diversity, may play a role in variations in SOM mineralization and nutrient recycling. Most literature focused on the effect of environmental variables shaping the microbial community structure (Ge et al., 2021 and references therein), but the impact of differences in microbial community composition on the sediment biodegradability remains little studied and thus speculative (Abell et al., 2013; Li et al., 2015). As Abell et al. (2013) showed, the bacterial community composition is related to the nature of the OM in estuarine systems, and their combination may lead to a shift in benthic nutrient fluxes.
- What about the biomarkers specific to bacteria?
Bacterial biomarkers are included in the study. Four fatty acids specific to bacteria were identified: ante iso-pentadecanoic acid (aC15:0), iso-pentadecanoic acid (iC15:0), ante iso-pentadecanoic acid (aC17:0) et iso-pentadecanoic (iC17:0). The proportions and concentrations of these biomarkers were presented in the result section (lines 308 – 309) and the figure S1 in the supplementary material.
Sincerely yours, on behalf of all authors,
Justine Louis
Citation: https://doi.org/10.5194/bg-2021-318-AC2
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AC2: 'Reply on RC2', Justine Louis, 18 Jan 2022
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RC3: 'Comment on bg-2021-318', Anonymous Referee #3, 29 Dec 2021
Review of ”Linking sediment biodegradability with its origin in shallow
coastal environments” submitted to BG by Louis et al. (bg-2021-318)The objectives of the study included assessments of the variability of sedimentary organic matter (SOM) origin at the regional scale, determination of the link between SOM origin and its biodegradability, and how the OM sources can drive nutrient dynamics at the sediment-water interface.
General comments
The mineralization rates were measured under oxic conditions. Since the in situ oxygen penetration depths into these coastal sediments likely only were a few mm, why were the mineralization rates only measured under oxic conditions? Most of the mineralization most probably took place under anoxic conditions. In other words, do the mineralization rates you report really reflect in situ ambient conditions?
The number of sampling sites (45) of this study is impressive.
The authors are not native English speaking people, so it may be hard to produce a linguistically correct text. However, to avoid confusion and misunderstanding, the English text should be checked and improved throughout the manuscript by someone with English as mother language.
There are several typos in the manuscript. Please correct throughout.
Specific comments
Line 41: It is Santschi, not Santshi
Lines 176-184: It is not enough to only refer to a previous paper on how the benthic fluxes were measured. Much more details are needed to be provided in the present paper on these measurements. For example:
How was oxygen concentration in the overlying water measured during these incubations?
How well was oxic conditions maintained in the overlying water? What was the range of oxygen concentration measured during the incubations?
How many samples were withdrawn from the overlying water during the 4 h incubations?
The overlying water was replaced by 150 mL of nutrient-free artificial seawater; this must have created a larger concentration gradient across the sediment-water interface compared to in situ conditions with ambient bottom water not being “nutrient-free”. So, are the measured benthic fluxes artifacts and much higher than in situ fluxes?
What was the difference in salinity between the artificial seawater and the ambient bottom water?
Lines 375-376: What do you mean with potential benthic nutrient fluxes? Please explain.
Lines 564-565: “The realistic redox conditions of the sediment were preserved during the core incubation”. Please explain how you can state this. What grounds and which data can you demonstrate to support this statement? For example, what was the oxygen penetration depth in the sediment during the core incubations and how did that depth compare to the in situ oxygen penetration depth?
Lines 616-617 and Conclusions: …”we must keep in mind that a large part of the variance of benthic NH4+ and PO4 fluxes on the regional scale remains unexplained here (66-67 %)”. To how large extent can this unexplained part be due to the fact that you created artificial conditions during the core flux incubations by having nutrient free overlying water? See also my comment above.
Lines 619-622: “In addition, the bioturbation, mediated by the macrofauna activities, was likely preserved in the sediment core incubations and therefore may be involved in the spatial variability of NH4+ and PO4 fluxes”. Preserved? Do you mean present? Again, please use the correct word in English to avoid confusion and misunderstanding.
Final overall comment
I am not convinced that the results (mineralization rates, fluxes) reported reflect ambient in situ conditions; they may thus be artifacts. If they are, the messages conveyed and the conclusions presented in the manuscript may not be correct. Can the authors please better explain (taking my comments above into consideration) why they think the results of their study reflect ambient in situ conditions?
Recommendation
The manuscript should undergo a major revision based on my comments above followed by a second round of review.
Citation: https://doi.org/10.5194/bg-2021-318-RC3 -
AC3: 'Reply on RC3', Justine Louis, 18 Jan 2022
Dear reviewer,
We thank you for your constructive comments and corrections that we will consider to improve our revised manuscript. As you recommend, we plan to check and improve the manuscript by a native English speaker. Please find below our responses to your main comments:
- More technical details about the measurements of benthic nutrient fluxes are requested
We will add more detailed information regarding the benthic nutrient flux measurements in the revised manuscript as you suggest: Two 0.22 µm-filtered water samples were collected in the overlying water after 2h and 4h of incubation and stored at refrigerator temperature (4°C) for less than 3 days to the nutrient analysis by colorimetric method. The salinity of the artificial seawater used as overlying water for the core incubations was equivalent to that measured in the ambient bottom water collected in the Trieux estuary, one of our sampling sites, (salinity = 33.1) by our colleagues of the University of Bordeaux during the same period (april 2019). No oxygen measurement of the overlying water during the incubation was made, but it was well oxygenated by bubbling (lines 180 – 182). The core incubations carried out in our work allowed to assess the potential benthic NH4+ and PO4 fluxes when the mudflat is submerged during the rising tide by the oxygenated coastal water. In addition, the mixing overlying water by bubbling allowed to prevent the build-up of concentration gradients at the sediment-water interface (lines 180 – 182). No measurement of oxygen penetration was done during the core incubations. Nevertheless, we know the vertical profiles of O2 in the sediments collected in the Trieux estuary by our colleagues of the University of Bordeaux. The sediments were depleted in oxygen below 2 mm vertical depth. This confirms our statement mentioned lines 565 – 567: “In the eutrophicated coastal areas, as is the case in Brittany coast, the sediments are often constrained by the hypoxia, […] a low O2 penetration in the sediment of few millimeters (Middelburg and Levin, 2009)”. Since the core incubations were rapidly carried out after sampling (lines 178 – 180) and during a short time (4h), we suggest that the redox conditions in the sediment cores correspond to that in situ.
- Do the benthic nutrient fluxes reflect ambient in situ conditions?
In order to link the NH4+ and PO4 release with the sedimentary characteristics and the SOM origin, and to reduce other environmental variables such as temperature, light, overlying water nutrient concentrations, we have decided to conduct the core incubations for all sites under controlled temperature in the dark and by using nutrient-free artificial seawater as overlying water. As you specify in your comments, a larger concentration gradient across the sediment-water interface can actually occur by using a nutrient-free overlying water. This is one of the reasons why we used the term “potential” for characterizing benthic nutrient fluxes. Nevertheless, we believe that the nutrient fluxes measured in our study can reflect the in situ fluxes. Firstly, the NH4+ and PO4 concentrations in the coastal bottom water are not expected to be relatively high during the study period. In the Trieux estuary, the NH4+ and PO4 concentrations in the bottom water were 1 and 0.1 µM respectively. Secondly, in the companion paper, we compared our results with previous studies carried out in Brittany and other European intertidal mudflats during the spring period, from either incubation in the dark or porewater nutrient profiles. Two of these were conducted respectively in the mouth of the Penzé river (Morlaix Bay) (Lerat et al., 1990) and in the Auray river (Andrieux et al., 2014), and allowed a direct comparison with our results. For the NH4+ fluxes, we presented values of 162 ± 132 µmol.m-2.h-1 in the Auray river and 25 ± 16 µmol.m-2.h-1 in the mouth of the Penzé river (sites #18 ad 19) against 206 ± 47 µmol.m-2.h-1 and 35 ± 14 µmol.m-2.h-1 respectively in the literature.
- About the large part of the variance of the benthic NH4+ and PO4 fluxes still unexplained: can the artificial conditions during the core incubations contribute to this unexplained part?
Since one of the main objectives of our work was to link the spatial variability of benthic nutrient fluxes with that of sedimentary characteristics and SOM origin, the factors such as temperature and bottom water conditions were not considered here to facilitate comparison across sites. All core incubations were done under the same ambient conditions (see above answer). Therefore, the unexplained part of the variance partitioning of nutrient fluxes is likely not due to the artificial conditions during the core incubations. We assumed that the microbial abundance/diversity as well as the bioturbation would be significantly involved in the spatial variability of benthic nutrient fluxes, and therefore correspond to the residual part of the variance partitioning of nutrient fluxes (lines 618 – 622). More details about this assumption will be added to the revised manuscript:
- “Through particle reworking and burrow ventilation by benthic macrofauna, a shift in redox conditions, a remobilization of burial OM, and a stimulation of solute exchanges at the interface can occur in the sediment (Graf and Rosenberg, 1997; Welsh, 2003; Kristensen et al., 2012). For example, Nizzoli et al. (2007) has shown a stimulation of NH4+ fluxes from all bioturbed sediment by the polychaete Nereis spp., whereas the bioturbation had site-specific effects on the PO4 fluxes (sediment acts either as a source or sink of PO4) which depends on, among other factors, the sediment composition, the burrow ventilation depth.”
- "We hypothesize that differences in microbial community structure, i.e diversity, may play a role in variations in SOM mineralization and nutrient recycling. Most literature focused on the effect of environmental variables shaping the microbial community structure (Ge et al., 2021 and references therein), but the impact of differences in microbial community composition on the sediment biodegradability remains little studied and thus speculative (Abell et al., 2013; Li et al., 2015). As Abell et al. (2013) showed, the bacterial community composition is related to the nature of the OM in estuarine systems, and their combination may lead to a shift in benthic nutrient fluxes.
- Do the mineralization rates reflect ambient in situ conditions?
Mineralization rate measurements were determined from the sediment slurry incubations under oxic conditions, and they were thus not considered here as the in situ mineralization rates. We assumed that the presence of oxygen as well as homogenization are optimal conditions to determine organic matter degradation and thus allowing calculation of the optimal sediment reactivity, noted k, from the measurements of mineralization rate and TOC content of sediment.
Sincerely yours, on behalf of all authors,
Justine Louis
Citation: https://doi.org/10.5194/bg-2021-318-AC3
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AC3: 'Reply on RC3', Justine Louis, 18 Jan 2022
Interactive discussion
Status: closed
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RC1: 'Comment on bg-2021-318', Wytze Lenstra, 07 Dec 2021
“Linking sediment biodegradability with its origin in shallow coastal environments” by Louis et al.,. In this current manuscript the authors evaluate the effect of different types of organic matter on the degradability of the organic matter and use different types of measurements to evaluate the sources of the organic matter. To quantify the biodegradability of the sediment incubations are carried out under oxic conditions and benthic flux measurements of PO4 and NH4 were done. With this manuscript I have two main comments (1) the link between the measured fluxes and biodegradability of the sediment is made in a too simplified way in my opinion. There are many factors that can control the benthic release of PO4 and NH4 from the sediment such as macrofaunal activity and bottom water redox conditions. These factors are discussed in a few sentences in the discussion but I think that these should also be introduced in the introduction. (2) I found it difficult to find the comparison of the measured fluxes and the measured rates of the incubations. Do these match with each other? The way I understood the manuscript these are both used to quantify the degradability of the sediment so I think a comparison between these parameters should at least be made in that case. See my detailed comments below:
L16: "controlled by the origin, quantity and accessibility". There are also other factors controlling the mineralization such as for example temperature or the presence of electron acceptors. In my opinion this is written in a too absolute way.
L27: "the eutrophication" remove "the"
L24: can you already mention what kind of samples were taken here in the abstract. All surface sediment?
L28: "oxic conditions" will this not lead to strongly enhanced mineralization of organic matter? In that case should "potential" not be replaced by "maximum"?
L30: " The physical and chemical sedimentary characteristics ". Can you already give examples here in the abstract? ..such as...
L28:" 5 and 1.5 fold higher on the PO4 and NH4+ fluxes respectively". Does this mean compared to the oxic incubations? In that case the degradability cannot be quantified/compared by using fluxes of PO4 and NH4. In oxic conditions PO4 will be affected by the presence of Fe oxides (i.e. lower benthic flux) and NH4 will be remove via nitrification for example.
L36: Is this corrected in any way for the bottom water redox conditions?
The introduction is in general well written and has a clear flow. The only thing I miss in the introduction is information on geochemical processes that control NH4 and PO4 mobilization in the sediment and their benthic release. There is at this point no information about different pathways for PO4 mobilization for example. While NH4 (and CO2) mobilization can be coupled to (anaerobic) organic matter degradation for PO4 this is more difficult because release of P bound to Fe oxides is often a important source of P in sediments. Also P cycling in sediments is strongly affected by mineral precipitation in the sediment such as for example vivianite and apatite and adsorption onto Fe oxides (mostly in oxidized sediments near the sediment water interface for the latter). This means that even at sites where the OM degradation is high the benthic flux of P can be limited. Also if benthic fluxes are presented, the effect of macrofaunal activity on these fluxes should in my opinion also be explained a bit more (i.e. bioturbation and bioirrigation).
L42: "at the sediment water interface" microbial degradation of organic matter does not only occurs at the SWI and continues when the OM is buried. Especially when linking this to the benthic fluxes of CO2, ammonium and phosphate the deeper sediments are very important as well in the degradation of organic matter and production of porewater CO2, ammonium and phosphate.
L46: Mn oxides occur also as Mn(III) or combinations of Mn(IV) and Mn(III) birnessite or manganite for example. I would just call this "Mn oxides" and in that case also "Fe oxides".
L50: "e.g. oxic conditions)" why is this text included here? Do you mean "redox conditions"?
L53: so the other factors mentioned earlier in this paragraph are ignored?
L83: remove "phenomena"
L102:"ii) to use this variability to go back to the variability of OM sources" is it not easier to just quantify the OM variability of the different OM types at the source? I do not understand the importance of this point.
L107:"(NH4+ and PO4)" why not CO2 in this case? That was also introduced earlier in the introduction.
L112: It would be nice to end this introduction with the most important finding of this study.
L120: what is the depth interval of this surface sediment?
L145: can you add the original reference for this method in this sentence.
Section 2.5. Are there also quality controls to discard a flux when the R2 of the measurements is not high enough?
L184: Can you add how many samples are taken in time? Is the water that is removed during sampling replaced with new artificial seawater?
L187: how are these oxic conditions maintained and controlled? What is the reason these where carried out under oxic conditions? Oxygen often only penetrates a few mm in the sediment and therefore these oxic conditions might be artificial and alter geochemical processes that control the degradation of the sediment.
L232:"(response variables), " what does this mean.
L261:"Over all sediment samples, " for me it is unknown which depth interval is used. This is key information given the strong gradients often observed in the parameters discussed below.
Table 2: are bottom water redox conditions also measured for all the sites? If yes can this information be added somewhere in the paper because it is highly relevant for the benthic release of NH4 and PO4.
L365: add space before "The"
Caption Fig. 7 is not correct. "Boxplot of the benthic NH4+ (A) and PO4 flux (B) (μmol.m-2.h-1) " (A) = (C) and (B) = (D)
L376: It would be good to have some information of the quality of the measurements of these fluxes. I also cannot find this in the original paper (i.e. Louis et al., 2021). What are the changes in concentrations during the measurements? This could be added to the supplements as a figure or a table. Concentrations of solutes during the incubation can vary quite a bit in time and increases (effluxes) are not always linear. At this point it is not clear to me how many samples there were taken in time. In the case of only two samples (beginning and end) this has to be stated somewhere and also the uncertainty should be mentioned in my opinion.
Caption figure 9: Change (A) in the caption to (a), also for b,c and d.
L536:"oxic conditions" are the oxygen concentrations monitored during the incubations? How do the authors know O2 is not depleted at some point in the bottles?
L453:" The mineralization process...". Do the authors mean that because these incubations are carried out under oxic conditions the quality of the OM is not very important anymore because it will be degraded with O2 anyway? This statement is not very clear to me. If this is the case I'm not sure if this statement is valid on the timescales of these incubations.
L552: typo in y-1
L564:"realtistic". What does this mean? Are the incubations carried out under the in-situ redox conditions or at redox conditions the authors find realistic? I would like to see the bottom water redox conditions for the different sites somewhere in this manuscript or in the supplements.
567:"Under these redox....". I agree that the lability is important in this case however the presence of electron acceptors or the presence of macrofauna is also very important. I think only mentioning the lability of the OM is too much of a simplification in this case. The authors should in my opinion also discuss other controlling mechanisms or at least mention them.
L569: "We thus suggest...". I agree that the origin plays a role but just ignoring other main controlling mechanisms such as bottom water O2 is not possible in my opinion. Especially for PO4 bottom water redox conditions are very important.
L573:"All parameters...". Can you mention which ones are the most important.
L596: "...assuming that this results from an increase in sediment biodegradability. " Why assuming in this case. Can the authors not compare this with the incubations they did to quantify this biodegradability? In this paragraph I miss the comparison between the measured fluxes and the degradation rates that were presented earlier. Do they match?
L617:"remains unexplained here" Can the authors elaborate a bit more on which mechanisms might be responsible for these variations? i.e. bottom water O2, mineral formation etc.
L625: "link with sediment potential biodegradability and nutrient release". I actually miss the comparison between the incubations and the measured fluxes in this manuscript.
Wytze Lenstra
Citation: https://doi.org/10.5194/bg-2021-318-RC1 -
AC1: 'Reply on RC1', Justine Louis, 18 Jan 2022
Dear Wytze Lenstra,
We thank you for your constructive comments and corrections that we took into consideration to improve our revised manuscript.
Please find our answers to your main comments below.
- The other factors that can control the benthic release of PO4 and NH4+, such as macrofaunal/microbial activities, should be more discussed
As stated in the introduction (lines 44-47), the SOM biodegradability and nutrient release also depend on other factors such as the temperature, the terminal electron acceptor availability, and the microbial and macrofaunal activity and diversity. Nevertheless, the goal of our study was to separate the parameters related to SOM origin (=qualitative parameters) from the other sedimentary characteristics related to the chemical composition (C, N, P) and physical properties (=quantitative parameters) in order to assess their independent effects on the mineralization rates and benthic nutrient fluxes measured during the campaign. In order to link the NH4+ and PO4 release with the sedimentary characteristics and the SOM origin, and to reduce other environmental variables such as temperature, light, overlying water nutrient concentrations, we have decided to conduct the core incubations for all sites under controlled temperature in the dark and by using nutrient-free artificial seawater as overlying water. All core incubations were done under the same ambient conditions. Nevertheless, as mentioned in the manuscript (lines 618 – 622), the microbial abundance/diversity as well as the bioturbation were not determined in our study. We assumed that these biological parameters could be significantly involved in the spatial variability of benthic nutrient fluxes, and therefore correspond to the residual part of the variance partitioning of nutrient fluxes that remains unexplained here. More details about this assumption will be added to the revised manuscript, as you recommend:
- “Through particle reworking and burrow ventilation by benthic macrofauna, a shift in redox conditions, a remobilization of burial OM, and a stimulation of solute exchanges at the interface can occur in the sediment (Graf and Rosenberg, 1997; Welsh, 2003; Kristensen et al., 2012). For example, Nizzoli et al. (2007) has shown a stimulation of NH4+ fluxes from all bioturbed sediment by the polychaete Nereis spp., whereas the bioturbation had site-specific effects on the PO4 fluxes (sediment acts either as a source or sink of PO4) which depends on, among other factors, the sediment composition, the burrow ventilation depth.”
- "We hypothesize that differences in microbial community structure, i.e diversity, may play a role in variations in SOM mineralization and nutrient recycling. Most literature focused on the effect of environmental variables shaping the microbial community structure (Ge et al., 2021 and references therein), but the impact of differences in microbial community composition on the sediment biodegradability of carbon remains little studied and thus speculative (Abell et al., 2013; Li et al., 2015). As Abell et al. (2013) showed, the bacterial community composition is related to the nature of the OM in estuarine systems, and their combination may lead to a shift in benthic nutrient fluxes.
- More technical details about the sediment sampling and the measurements of benthic nutrient fluxes and mineralization rates need to be added, and information about redox conditions in bottom water and sediment is requested
Please find below some technical details that will be added in the revised manuscript to improve its understanding:
Benthic nutrient flux measurements: As described in the Louis et al 2021, two 0.22 µm-filtered water samples were collected in the overlying water after 2h and 4h of incubation and stored at 4°C for less than 3 days until nutrient analysis. Nutrient-free artificial seawater was used for these incubations (lines 179-180). The water sample collected (5 ml) corresponded to 3 % of the total volume of the overlying water (150 ml). This collected volume was not replaced with new artificial seawater during the incubations, and the exact volume (145 ml for T2 and 140 ml for T4) was taken into account for the calculation of benthic nutrient fluxes. The core incubations allowed to preserve the redox conditions of the sediment and thus the term “realistic” mentioned in the manuscript (line 564) corresponds to “in situ”. Generally a low O2 penetration in the sediment of few millimeters is observed in eutrophicated coastal areas. Vertical profiles of O2 in the sediment collected by colleagues in the Trieux estuary, one of our sampling sites, confirm this statement. The sediments were depleted in oxygen below 2 mm vertical depth.
Before sediment sampling, no measurements of in situ bottom water redox conditions were done. The sediment cores of intertidal mudflats were collected at low tide. The core incubations carried out in our work allowed to assess the potential benthic NH4+ and PO4 fluxes mimicking the mudflat submerged during the rising tide by the oxygenated coastal water. The bottom water conditions can be considered oxic (based on temperature, salinity and tidal effect), sediment redox conditions were not determined for the 200 samples.
Surface sediment samples: For the sediment slurry incubation as well as for the characterization of surface sediment (physico-chemical composition, SOM origin), each sample was collected in the upper 5 cm sediment layer. This information will be added to 2.1 section.
Mineralization rate measurements: During the sediment slurry incubations, no measurements of oxygen were carried out. The mineralization rates were calculated from the measurement of CO2 production. We consider that these incubations (time = 4h) were carried out under oxic conditions over the 4 h incubation. These incubations consisted of 5 g of wet sediment mixed with 25 ml of artificial seawater in the glass flask of 145 ml total volume. It can be assumed based on previous work that the mineralization process was not oxygen-limited due to a large reservoir of O2 in the headspace of flask (V ≈ 115 ml) corresponding to 21 % of the air volume.
Under these conditions, we assumed that the presence of oxygen and homogenization of the sediments are optimal for SOM degradation (lines 539-543), and thus we were able to calculate the optimal sediment reactivity, noted k, from the measurements of mineralization rate and TOC content of sediment. A spatial variability of k was observed (0.8 to 11 y-1 for 75 % of data) (lines 552-553). This approach has been used and described by Nicholls and Trimmer (2009) (https://doi.org/10.3354/ame01285).
- A comparison between the benthic nutrient fluxes and mineralization rates is missing
Even though a comparison would be interesting, we thing a direct comparison between the mineralization rates and the benthic nutrient fluxes would be not appropriate as the methodology (slurry versus core incubations) and the redox conditions are different. Such differences can be illustrated by the fraction of their variances explained by the SOM origin: it was interesting to observe that the SOM origin had a significant effect on the NH4+ and PO4 fluxes, which was 1.5 and 5 fold higher than that determined by the other physico-chemical sediment parameters (e.g. porosity, TN and Org-P content), contrary to had been observed for the mineralization rates.
Sincerely yours, on behalf of all authors,
Justine Louis
Citation: https://doi.org/10.5194/bg-2021-318-AC1
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AC1: 'Reply on RC1', Justine Louis, 18 Jan 2022
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RC2: 'Comment on bg-2021-318', Anonymous Referee #2, 21 Dec 2021
“Linking sediment biodegradability with its origin in shallow coastal environments”
The authors aimed in this paper to explain possible factors that drive biodegradability of OM in sediments of Bay and estuaries of Britanny Region. This paper has two parts: the first one, deals with the identification of potential sources of shallow OM through several biomarkers and isotopic signatures.
The second one using short time core’s incubations to assess the export of nutriments ( P04 and NH4) from the sediment and to calculate a mineralization rate that is used to inform about the degradability of the OM. It was difficult to see the continuity between these two parts is done through data analysis (variance partitioning) and show the significant inputs of several human activities in these basins and bring attention to the potential detrimental role of microorganisms that were not analyzed in this study.
General comments:
With regards of the type of chemical analysis that were measured, bacteria could have been assessed with their typical FA markers for instance. One can imagine that full FA profiles are available for each site since other FA were displayed in this study.
Also, North and south parts of Britany have some abiotic differences, in average the climate is much wetter in the north and the tides are higher than in the south. There is a Channel Britanny and an Atlantic Britanny. These differences will have an impact on coastal and intertidal waters/sediments qualities.
Both sides of the region have experienced large oil spills in the past.
When it comes to OM origin, a one-time sampling at a large scale is not sufficient to conclude on which anthropic source is influencing the most of the OM origin. Local inputs need to be verified. There is nothing new in announcing that natural and anthropic sources are both contributing to the OM composition.
Specific comments
Abstract
L19 I am not convinced about the chosen scale is being “representative” of the complexity of such anthropized region.
M&M
My main issue here, is what it seems to me the wrong definition that authors have of some chosen “estuaries”. Two of them are in fact not estuaries = water influenced by both open ocean AND riverine waters. La Rance and Triaux, are Ria with no river influence. Waters in these basins are almost totally under marine influence, “functionally and biologically” they are much close to what happened in a covered bay that in a typical estuary which usually exhibit pronounced salinity gradient.
La Rance is also particular because it bears at its mouth the only and unique hydrothermal barrage of France with the consequence that it controls water entrance and volume (only one tide a day). The local hydrodynamic needs to be well known especially if one need to conclude on its sedimentation rate.
Discussion
L489 It is a fact that parts of the north coast have been impacted by oil spills.
L495-500: to be rephrased, also not clear if finally, the petroleum inputs have an impact in the “south” sediments.
L515- to be discussed with regards of the local knowledge to the Rance hydrodynamic.
L550-556: Biodegradability or of organic sediment and its consequence, releasing nutrient and greenhouses gases is something well known in coastal ecology with the concept of “priming effect”. This priming is indeed triggered by eutrophication (human and animal wastes, included).
L557: More importantly is what leads to increase bacterial activity.
L 619: there an enormous literature of the role of bacteria in the degradation of the OM. Need to be fairly discussed.
L619-622: rather speculative, what about the impact on macrofauna of the induced stress with regards of the short term “in situ” measure ?
To conclude, the two parts of this article are not thoroughly connected, besides, there are shortcomings conclusions in the very descriptive first part: spatiality, potential sources changes, local ecological knowledge...
The second part could stand by itself especially if authors would consider a broader literature.
Citation: https://doi.org/10.5194/bg-2021-318-RC2 -
AC2: 'Reply on RC2', Justine Louis, 18 Jan 2022
Dear reviewer,
We thank you for your comments that we will consider to improve our revised manuscript. The revised manuscript will be corrected by a native English speaker. In the following section we respond to your different comments and questions:
- Why did the methodology (regional scale, one-time sampling) used in the present study was appropriate to study the diversity of SOM origin/composition?
As mentioned in the manuscript, most investigations on the spatial variation of the origin and composition of the SOM have been carried out so far at local scale, within a bay or along an estuary. There are only few studies on the regional scale (lines 79 – 82). Therefore, the first objective of this manuscript was to investigate the spatial variability of the origin and composition of the sedimentary organic matter (SOM) at the regional scale. The chosen study area was Brittany, particularly impacted by eutrophication due to the agricultural intensification and the urbanization of watersheds. We therefore expected to have a diversity of OM sources. This was confirmed in our study by combining bulk elemental, isotopic and chemical biomarkers analysis of surface sediment samples. Our results were from a one-time sampling during the spring, but the broad collection (200 samples on 45 sites) allowed to draw the regional variability of sediment characteristics at this study period. The large number of sediment samples also allowed to correctly run the statistical analysis, in order to link the sedimentary characteristics with the mineralization rates and benthic nutrient fluxes measured in our work.
- A better connection between the two main parts in the discussion section (4.1 and 4.2) is requested
As mentioned in the manuscript (lines 531 – 533), “after characterizing the SOM composition at the regional scale, the objective of this work was to quantify the relative significance of the SOM origin on the sediment reactivity, as well as to identify the SOM sources enabling the sediment to act as a nutrient source for the overlying water”. For a better understanding, we suggest to complete the opening paragraph of the second section 4.2 by reminding that “two statistical analysis were used: i) the variance partitioning to quantify the variance proportion of nutrient fluxes and mineralization rates (response variables) independently explained by both the explanatory variables “SOM origin” and “physico-chemical composition”, and ii) the canonical redundancy analysis (RDA) to assess the linear relationships between the explanatory variables and the response variables. For the nutrient fluxes, with a significant part of variance explained by the SOM origin, the RDA allowed to asses which SOM sources can enhance the PO4 and NH4+ release. This could be illustrated using the spatial diversity of SOM origin previously drawn in the first part the discussion section”.
- More information about anthropogenic inputs is requested
As stated in the manuscript (lines 486 - 487), eutrophicated coastal systems, as Brittany coast, receive anthropogenic matter from urban discharges, agricultural and industrial activities impacting the SOM composition. It was expected to observe a mixture between natural (marine and/or terrestrial) and anthropogenic matter sources in our sediments. By using the δ15N and lipid makers specific to anthropogenic matter (fecal matter, combustion products, oil and by-products), we allowed to assess how the impact of human activities on the surface sediment composition vary at the local and regional scale. We have well observed a discrimination between the north and south of the Brittany coast (lines 487 – 491): the sediment composition in the north sites seems to be more impacted by oils spills than the south sites, characterizing by an enrichment of crude oil markers. This likely results from the biggest oil spill that occurred off the north coast of the Brittany by the Amoco Cadiz (source: CEDRE). Conversely, the sediment composition in the south sites would be more impacted by an enrichment of petroleum products, which include products from the processing of crude oil at refineries. High values of δ15N combined with high proportions of fecal markers in surface sediments allowed to trace sewage discharges and agricultural runoff. It was the case in the Vannes Estuary where our observations were consistent with the proximity of a WWTP (lines 501 – 508).
- The role of the hydrodynamic conditions should be more considered in the discussion
The diversity of the SOM composition results from potential sources of OM (related to algal production, land use, human activities …) and also hydrodynamic conditions as mentioned in your comments. As discussed in the manuscript (lines 511 – 513), the hydrodynamic can control the spatial effect of sewage effluents on sediment composition. The gradient of δ15N in surface sediments, that traced sewage-derived N, can be observed with a variable distance from the WWTP outfall according to coastal system (lines 506 – 511).
The addition of the following text in the discussion section about the potential additional role of hydrodynamic conditions on the SOM composition is proposed:
- In the sediments collected in the Goulven Bay where a significant proportion of macroalgal biomarkers was observed (Figure 4; lines 319 – 325): The sampling area was located in the upper part of the intertidal area of the Goulven Bay, which could be impacted by a high sedimentation rate. Under specific hydrodynamic conditions, a significant deposition of macroalgae could occur and fuel the SOM composition.
- In the sediments collected in the Rance Estuary, where high values of δ15N as well as proportion of fecal markers were observed in the mid estuary of the Rance, which likely result from intensive agricultural activities in the watersheds (lines 515 – 521): The Rance Estuary is particular with the second largest operational tidal power station in the world built at the estuary's mouth (Rajae Rtimi et al., 2021). This could enhance the deposition of fine particles in the estuary, except upstream of the sluice gates and downstream of the turbines. The effect of agricultural activities on the molecular and isotopic signature of sediments could be more significant under these hydrodynamic conditions.
- Is the term “estuary” appropriate to define the Rance and the Trieux?
The sampling sites in our study were macrotidal mudflats located in Brittany bays and estuaries. We used the term “estuary” for the Rance and the Trieux, which is widely given in the scientific literature.
Examples:
- Rajae Rtimi et al. Hydrodynamics of a hyper-tidal estuary influenced by the world's second largest tidal power station (Rance estuary, France). Estuarine, Coastal and Shelf Science, Volume 250, 2021, https://doi.org/10.1016/j.ecss.2020.107143
In the present study, the sampling was done in the marine part of the Rance estuary (Figure 1 in Baron S et al (2017). doi: 10.3389/fmicb.2017.01637).
- Hugues Blanchet et al. Multiscale patterns in the diversity and organization of benthic intertidal fauna among French Atlantic estuaries. Journal of Sea Research, Volume 90, 2014, https://doi.org/10.1016/j.seares.2014.02.014.
In this publication, the authors specify that the Trieux estuary can be considered as a Ria system, and differs from coastal plain estuaries such as the Gironde, Loire.
- The role of bioturbation and microbial abundance/diversity need to be more discussed
In the revised manuscript, we will extent the discussion and add more details about the potential effect of microbial abundance/diversity as well as bioturbation on the benthic nutrient fluxes from the literature, which can involve in the large residual part of the variance analysis of benthic NH4+ and PO4 fluxes (Lines 618 – 622):
- “Through particle reworking and burrow ventilation by benthic macrofauna, a shift in redox conditions, a remobilization of burial OM, and a stimulation of solute exchanges at the interface can occur in the sediment (Graf and Rosenberg, 1997; Welsh, 2003; Kristensen et al., 2012). For example, Nizzoli et al. (2007) has shown a stimulation of NH4+ fluxes from all bioturbed sediment by the polychaete Nereis spp., whereas the bioturbation had site-specific effects on the PO4 fluxes (sediment acts either as a source or sink of PO4) which depends on, among other factors, the sediment composition, the burrow ventilation depth.”
- "We hypothesize that differences in microbial community structure, i.e diversity, may play a role in variations in SOM mineralization and nutrient recycling. Most literature focused on the effect of environmental variables shaping the microbial community structure (Ge et al., 2021 and references therein), but the impact of differences in microbial community composition on the sediment biodegradability remains little studied and thus speculative (Abell et al., 2013; Li et al., 2015). As Abell et al. (2013) showed, the bacterial community composition is related to the nature of the OM in estuarine systems, and their combination may lead to a shift in benthic nutrient fluxes.
- What about the biomarkers specific to bacteria?
Bacterial biomarkers are included in the study. Four fatty acids specific to bacteria were identified: ante iso-pentadecanoic acid (aC15:0), iso-pentadecanoic acid (iC15:0), ante iso-pentadecanoic acid (aC17:0) et iso-pentadecanoic (iC17:0). The proportions and concentrations of these biomarkers were presented in the result section (lines 308 – 309) and the figure S1 in the supplementary material.
Sincerely yours, on behalf of all authors,
Justine Louis
Citation: https://doi.org/10.5194/bg-2021-318-AC2
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AC2: 'Reply on RC2', Justine Louis, 18 Jan 2022
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RC3: 'Comment on bg-2021-318', Anonymous Referee #3, 29 Dec 2021
Review of ”Linking sediment biodegradability with its origin in shallow
coastal environments” submitted to BG by Louis et al. (bg-2021-318)The objectives of the study included assessments of the variability of sedimentary organic matter (SOM) origin at the regional scale, determination of the link between SOM origin and its biodegradability, and how the OM sources can drive nutrient dynamics at the sediment-water interface.
General comments
The mineralization rates were measured under oxic conditions. Since the in situ oxygen penetration depths into these coastal sediments likely only were a few mm, why were the mineralization rates only measured under oxic conditions? Most of the mineralization most probably took place under anoxic conditions. In other words, do the mineralization rates you report really reflect in situ ambient conditions?
The number of sampling sites (45) of this study is impressive.
The authors are not native English speaking people, so it may be hard to produce a linguistically correct text. However, to avoid confusion and misunderstanding, the English text should be checked and improved throughout the manuscript by someone with English as mother language.
There are several typos in the manuscript. Please correct throughout.
Specific comments
Line 41: It is Santschi, not Santshi
Lines 176-184: It is not enough to only refer to a previous paper on how the benthic fluxes were measured. Much more details are needed to be provided in the present paper on these measurements. For example:
How was oxygen concentration in the overlying water measured during these incubations?
How well was oxic conditions maintained in the overlying water? What was the range of oxygen concentration measured during the incubations?
How many samples were withdrawn from the overlying water during the 4 h incubations?
The overlying water was replaced by 150 mL of nutrient-free artificial seawater; this must have created a larger concentration gradient across the sediment-water interface compared to in situ conditions with ambient bottom water not being “nutrient-free”. So, are the measured benthic fluxes artifacts and much higher than in situ fluxes?
What was the difference in salinity between the artificial seawater and the ambient bottom water?
Lines 375-376: What do you mean with potential benthic nutrient fluxes? Please explain.
Lines 564-565: “The realistic redox conditions of the sediment were preserved during the core incubation”. Please explain how you can state this. What grounds and which data can you demonstrate to support this statement? For example, what was the oxygen penetration depth in the sediment during the core incubations and how did that depth compare to the in situ oxygen penetration depth?
Lines 616-617 and Conclusions: …”we must keep in mind that a large part of the variance of benthic NH4+ and PO4 fluxes on the regional scale remains unexplained here (66-67 %)”. To how large extent can this unexplained part be due to the fact that you created artificial conditions during the core flux incubations by having nutrient free overlying water? See also my comment above.
Lines 619-622: “In addition, the bioturbation, mediated by the macrofauna activities, was likely preserved in the sediment core incubations and therefore may be involved in the spatial variability of NH4+ and PO4 fluxes”. Preserved? Do you mean present? Again, please use the correct word in English to avoid confusion and misunderstanding.
Final overall comment
I am not convinced that the results (mineralization rates, fluxes) reported reflect ambient in situ conditions; they may thus be artifacts. If they are, the messages conveyed and the conclusions presented in the manuscript may not be correct. Can the authors please better explain (taking my comments above into consideration) why they think the results of their study reflect ambient in situ conditions?
Recommendation
The manuscript should undergo a major revision based on my comments above followed by a second round of review.
Citation: https://doi.org/10.5194/bg-2021-318-RC3 -
AC3: 'Reply on RC3', Justine Louis, 18 Jan 2022
Dear reviewer,
We thank you for your constructive comments and corrections that we will consider to improve our revised manuscript. As you recommend, we plan to check and improve the manuscript by a native English speaker. Please find below our responses to your main comments:
- More technical details about the measurements of benthic nutrient fluxes are requested
We will add more detailed information regarding the benthic nutrient flux measurements in the revised manuscript as you suggest: Two 0.22 µm-filtered water samples were collected in the overlying water after 2h and 4h of incubation and stored at refrigerator temperature (4°C) for less than 3 days to the nutrient analysis by colorimetric method. The salinity of the artificial seawater used as overlying water for the core incubations was equivalent to that measured in the ambient bottom water collected in the Trieux estuary, one of our sampling sites, (salinity = 33.1) by our colleagues of the University of Bordeaux during the same period (april 2019). No oxygen measurement of the overlying water during the incubation was made, but it was well oxygenated by bubbling (lines 180 – 182). The core incubations carried out in our work allowed to assess the potential benthic NH4+ and PO4 fluxes when the mudflat is submerged during the rising tide by the oxygenated coastal water. In addition, the mixing overlying water by bubbling allowed to prevent the build-up of concentration gradients at the sediment-water interface (lines 180 – 182). No measurement of oxygen penetration was done during the core incubations. Nevertheless, we know the vertical profiles of O2 in the sediments collected in the Trieux estuary by our colleagues of the University of Bordeaux. The sediments were depleted in oxygen below 2 mm vertical depth. This confirms our statement mentioned lines 565 – 567: “In the eutrophicated coastal areas, as is the case in Brittany coast, the sediments are often constrained by the hypoxia, […] a low O2 penetration in the sediment of few millimeters (Middelburg and Levin, 2009)”. Since the core incubations were rapidly carried out after sampling (lines 178 – 180) and during a short time (4h), we suggest that the redox conditions in the sediment cores correspond to that in situ.
- Do the benthic nutrient fluxes reflect ambient in situ conditions?
In order to link the NH4+ and PO4 release with the sedimentary characteristics and the SOM origin, and to reduce other environmental variables such as temperature, light, overlying water nutrient concentrations, we have decided to conduct the core incubations for all sites under controlled temperature in the dark and by using nutrient-free artificial seawater as overlying water. As you specify in your comments, a larger concentration gradient across the sediment-water interface can actually occur by using a nutrient-free overlying water. This is one of the reasons why we used the term “potential” for characterizing benthic nutrient fluxes. Nevertheless, we believe that the nutrient fluxes measured in our study can reflect the in situ fluxes. Firstly, the NH4+ and PO4 concentrations in the coastal bottom water are not expected to be relatively high during the study period. In the Trieux estuary, the NH4+ and PO4 concentrations in the bottom water were 1 and 0.1 µM respectively. Secondly, in the companion paper, we compared our results with previous studies carried out in Brittany and other European intertidal mudflats during the spring period, from either incubation in the dark or porewater nutrient profiles. Two of these were conducted respectively in the mouth of the Penzé river (Morlaix Bay) (Lerat et al., 1990) and in the Auray river (Andrieux et al., 2014), and allowed a direct comparison with our results. For the NH4+ fluxes, we presented values of 162 ± 132 µmol.m-2.h-1 in the Auray river and 25 ± 16 µmol.m-2.h-1 in the mouth of the Penzé river (sites #18 ad 19) against 206 ± 47 µmol.m-2.h-1 and 35 ± 14 µmol.m-2.h-1 respectively in the literature.
- About the large part of the variance of the benthic NH4+ and PO4 fluxes still unexplained: can the artificial conditions during the core incubations contribute to this unexplained part?
Since one of the main objectives of our work was to link the spatial variability of benthic nutrient fluxes with that of sedimentary characteristics and SOM origin, the factors such as temperature and bottom water conditions were not considered here to facilitate comparison across sites. All core incubations were done under the same ambient conditions (see above answer). Therefore, the unexplained part of the variance partitioning of nutrient fluxes is likely not due to the artificial conditions during the core incubations. We assumed that the microbial abundance/diversity as well as the bioturbation would be significantly involved in the spatial variability of benthic nutrient fluxes, and therefore correspond to the residual part of the variance partitioning of nutrient fluxes (lines 618 – 622). More details about this assumption will be added to the revised manuscript:
- “Through particle reworking and burrow ventilation by benthic macrofauna, a shift in redox conditions, a remobilization of burial OM, and a stimulation of solute exchanges at the interface can occur in the sediment (Graf and Rosenberg, 1997; Welsh, 2003; Kristensen et al., 2012). For example, Nizzoli et al. (2007) has shown a stimulation of NH4+ fluxes from all bioturbed sediment by the polychaete Nereis spp., whereas the bioturbation had site-specific effects on the PO4 fluxes (sediment acts either as a source or sink of PO4) which depends on, among other factors, the sediment composition, the burrow ventilation depth.”
- "We hypothesize that differences in microbial community structure, i.e diversity, may play a role in variations in SOM mineralization and nutrient recycling. Most literature focused on the effect of environmental variables shaping the microbial community structure (Ge et al., 2021 and references therein), but the impact of differences in microbial community composition on the sediment biodegradability remains little studied and thus speculative (Abell et al., 2013; Li et al., 2015). As Abell et al. (2013) showed, the bacterial community composition is related to the nature of the OM in estuarine systems, and their combination may lead to a shift in benthic nutrient fluxes.
- Do the mineralization rates reflect ambient in situ conditions?
Mineralization rate measurements were determined from the sediment slurry incubations under oxic conditions, and they were thus not considered here as the in situ mineralization rates. We assumed that the presence of oxygen as well as homogenization are optimal conditions to determine organic matter degradation and thus allowing calculation of the optimal sediment reactivity, noted k, from the measurements of mineralization rate and TOC content of sediment.
Sincerely yours, on behalf of all authors,
Justine Louis
Citation: https://doi.org/10.5194/bg-2021-318-AC3
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AC3: 'Reply on RC3', Justine Louis, 18 Jan 2022
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Justine Louis
Anniet M. Laverman
Emilie Jardé
Alexandrine Pannard
Marine Liotaud
Françoise Andrieux-Loyer
Gérard Gruau
Florian Caradec
Emilie Rabiller
Nathalie Lebris
Laurent Jeanneau
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