the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Down in the dungeons: microbial redox reactions and geochemical transformations define the biogeochemistry of an estuarine sediment column
Thibault Duteil
Raphaël Bourillot
Olivier Braissant
Adrien Henry
Michel Franceschi
Marie-Joelle Olivier
Nathalie Le Roy
Benjamin Brigaud
Eric Portier
Pieter T. Visscher
Abstract. The surface of intertidal estuarine sediments is typically covered with a photosynthetic biofilm. A large fraction of the carbon that is fixed is in the form of exopolymeric substances (EPS), providing the biofilm matrix. The consumption of organic carbon within the sediment column by heterotrophs bacteria is stratified according to the availability of electron acceptors used for organic matter degradation. This sequential use of electron acceptors strongly impacts geochemical gradients and early diagenetic processes within the sediment. In most studies, the distribution and role of the predominant microbial metabolisms is deduced from porewater chemistry and restricted to the upper decimeters of the sediment column, but rarely from direct measurements of microbial activity, potentially leading to erroneous conclusions of biogeochemical processes.
We measured geochemical gradients in three estuarine sediment cores to a depth of 6 meters. Geochemical analyses of porewater and sediment were combined with measurements of microbial activity. In situ microelectrode measurements were performed for pH, oxygen and sulfide. Porewater was extracted and analyzed for major elements using Ion Chromatography, Inductively-Coupled-Plasma, and colorimetric assays for iron speciation. Porewater chemistry was compared to measurements of microbial activity including isothermal calorimetry and metabolic assays (triphenyltetrazolium chloride (TTC) and fluorescein diacetate (FDA)) and concentrations of EPS (sugars, proteins) measured in a previous study on the same cores. Finally, sediment composition was characterized through X-Ray Fluorescence core scanning.
Results show that: (i) aerobic respiration occurred between 0 and 1 cm, (ii) nitrate reduction between 6 and 16 cm, (iii) sulfate reduction between 10 and 50 cm, (iv) manganese oxide reduction between 2–6 and 35–50 cm and (v) iron oxide reduction between 16–18, 24–26 and 35–45 cm. This is concomitant with the area where the microbial activity is the highest. In contrast to the literature, we conclude that some reactions, for example sulfate and nitrate reduction, were locally coupled or at least occurred concomitantly.
Impacts of microbial metabolism on early diagenesis have been modeled via PhreeQc and predicted potential precipitation of metastable iron and/or sulfides. This is confirmed by iron and sulfur increases in sediments characterized through XRF. All these observations have been used to propose a biogeochemical model linking microbial metabolisms and early diagenesis that can be used as a basis for the study of other geochemical profiles in the future.
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Thibault Duteil et al.
Status: final response (author comments only)
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RC1: 'Comment on bg-2023-62', Dirk de Beer, 27 Apr 2023
The paper describes a biogeochemical study towards activities in deep estuarine sediments. A broad suite of methods is used, mostly in a correct way. Concluded is that also deep in sediments, below several meters significant activities occur. The discussion lacks depth, not all strange results are recognized, sedimentation time is not considered, nor transport phenomena.
The paper is written in good English, but poor style, making it hard to read. The text in the result section consists of summation of numbers of the plots and table. The text should rather describe the figures and point to the remarkable features, give a first interpretation, that later may be discussed. It is exceptionally difficult reading and not informative. The figures require some basic interpretation for readability, that is missing. The authors should tell us a story, not provide a list of dry facts. Unfortunately, this section must be completely rewritten to make a fluent and readable text.
The summary is good and invites to further reading. The introduction is acceptable but a bit short, focusing on the well-known redox cascade. However, the essential introduction to transport processes in coastal sediments is missing. The rational for the sample location should be described. The location is not ideal, with many complicating influences. The methods is detailed, can be improved at some minor points. The result section is described above. Also in the discussion deep advection, that is often essential for understanding of deep biosphere activities and certainly for close to coast permeable sediments, is missing.
Understanding of transport phenomena, especially in such ‘difficult’ sites is crucial. The site is very difficult, as it is a freshwater site with some marine influence, in a flowing river and very likely with lateral groundwater input. On top of that, the location is in a river bend, with irregular sedimentation.
The figures are made with care, but on several places the letters and numbers must be made larger.
Some details:
From Figure 1 we cannot understand where the 3 cores are taken. Firstly, the 2 maps in 1A should be aligned so that North is on top. Indicated is the location of the box and short core, not of the long core. It is probably not the same spot as the geochemistries are different. The drawings are nice, but the text should be much larger. The depth axes labels are invisibly tiny and of poor quality. I recommend to make more space for the plots. Explain what is a mud pebble and a mud drape. What is the meaning of the letters at the bottom right?
All cores have the label BXN, better remove that as it does not help keeping them apart.
How are the blanks, so the killed controls, treated for the metabolic assays by TTC and FDA?
In Fig 2 the letters and numbers are far too small. Instead of repeating these plots in numbers in the text, describe what we see and what is remarkable. What I find remarkable is the multiple peaks in the sulfate, Fe and Mn plots. Very strange is the high nitrate peak in the sulfidic zone. These observations are important as it is impossible in a 1D interpretation: they can only be result of lateral transport through permeable layers. Thus best is to align these plots with porosity plot or at least the geological info in Fig 1 (mud, sand etc).
In Fig 3 we see again peaks, and nitrate and sulfate correlate: lateral input. Fe2+ is absent where nitrate peaks, nice. The FeIII plots shows impossible concentrations, the method cannot be correct. FeIII does not dissolve well, certainly not to µM levels. Very strange is to have high nitrate levels down to 1.3 m depth. Must be advection and low conversion. Is the land next to the river cultivated and fertilized intensively?
The concentrations of sulfate and Fe differ strongly between the long and short cores. Why?
The paragraph on microbial activities has almost more numbers than text. Unreadable. The hydrolytic activity seems to be hardly decreasing with depth, that is possible, but unlikely. Did you correct for killed controls? Same for the TCC release. Both do not relate with the peak in metabolic activity measured by calorimetry (Table 1). What do you actually measure with TCC release?
The metabolic activity peaks at 50 cm depth, according to table 1. Explain what drives this high rate.
Also the description of the XRF data is sedative. The plots show that the distributions of metals and S correlate. Compare again with the sedimentary log of Fig 1.
The discussion lacks depth. It is a summary of possible microbial conversions. Transport is missing.
L 504 accumulation of nitrate by sulfide is nonsense. Many bacteria oxidise sulfide by nitrate.
L 509 MnO2 driving ammonium oxidiation has been mentioned before, indeed. Interesting, but it does show in the Mn distributions.
L521 Sulfate reduction is very important bit only in the marine realm where sulfate is 28 mM. Here we have very low levels in the order of 100 µM. That is even for rivers very low!
L644 the conceptual model is 1D, right? In the discussion and the model lateral transport is entirely missing. Please check with literature from the waddensea, e.g. by Engelen, Cypionka and Beck on deep biosphere activities in the shallow intertidal flats. See also the review from Joye on transport phenomena and the activities at 20 m depth (doi.org/10.1016/B978-0-444-63893-9.00012-5).
Citation: https://doi.org/10.5194/bg-2023-62-RC1 -
RC2: 'Comment on bg-2023-62', Anonymous Referee #2, 15 May 2023
Duteil et al. conducted a series of geochemical and microbiological analyses on sediment cores from the Garonne estuarine channel. Based on porewater and solid-phase geochemical profiles, the authors define the biogeochemical zonation of the sediment cores. Good spatial resolution is achieved in the upper 25 cm, whereas low-resolution profiles of deeper sediments hinder the discussion on certain processes. Microbial activity data are used to facilitate the discussion on biogeochemical processes, but they are not specific to certain processes, which limits their further application. Nevertheless, I found some of the conclusions are justified by the observation and the utilization of metabolic assays and isothermal calorimetry are novel in this type of work. I have several concerns about the interpretation of porewater geochemical profiles as detailed below.
Line 35-37. Given the low resolution of geochemical profiles in the subsurface, I would suggest avoiding defining certain biogeochemical processes to occur at exact depth intervals. For example, it seems to me that iron reduction occurs below 16 cm and manganese reduction occurs below 2 cm to the lower part of the short core. In addition, metal reduction can well be due to abiotic processes involving sulfide oxidation, as the authors mentioned later in the discussion. Therefore, I would suggest interpreting their significance more carefully when discussing their presence in the context of microbial metabolism.
Line 25. “Restricted to the upper decimeters of the sediment column” and “rarely from direct measurements of microbial activity” are not accurate. Porewater geochemical profiles and rates of sulfate reduction and methanogenesis have been frequently measured in both surface and subsurface marine sediments.
Line 96-97. “Potential links between microbial metabolisms and early diagenesis” has been widely studied not only to depths of around 20 cm but also in meter- or kilometer-long sediment cores.
Line 148. The methodology for the analysis of sulfate concentrations and its detection limit is not described. In Figure 3B, the sulfate concentrations are all lower than 12 μM, which is often the detection limit of ion chromatography.
Line 535. Given the extremely low concentrations of sulfate in the subsurface and the low resolution of the sulfate profile below 25 cm, I am not convinced that sulfate reduction occurs below 25 cm in the short core or throughout the long core. My concern is supported by the sulfide profile, in which the sulfide concentrations only increase with depth in the upper 20 cm.
Line 572. Following the comment above, I would instead suggest that methanogenesis occurs from shallow depth (e.g., 25 cm or 1 m) to the deep subsurface. Discrete methanogenic zones are not commonly observed in natural environments.
Citation: https://doi.org/10.5194/bg-2023-62-RC2
Thibault Duteil et al.
Thibault Duteil et al.
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