the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 18 Jul 2024
Ancient clays support contemporary biogeochemical activity in the Critical Zone
Abstract. Late Cretaceous clays exposed at sites located on the north shore of Long Island, New York, USA were sampled to explore questions about how contemporary factors and processes interact with ancient geological materials. Chemically and biologically catalyzed weathering processes have produced multi-colored clays belonging to the kaolin group with inclusions of hematite, limonite, and pyrite nodules. We sampled exposed clays at three sites to address three questions: 1) Do these exposed clays support significant amounts of microbial biomass and activity, i.e., are they alive? 2) Do these clays support significant amounts of nitrogen (N) cycle activity? 3) Are these clays a potential source of N pollution in the contemporary landscape? Samples were analyzed for total carbon (C) and N content, microbial biomass C and N content, microbial respiration, organic matter (OM) content, potential net N mineralization and nitrification, soil nitrate (NO3-) and ammonium (NH4+) content, and denitrification potential. Results strongly support the idea that ancient geologic materials play a role in contemporary N and C cycling in the Critical Zone. Respiration was detectable in all samples and was strongly correlated to OM, indicating a living microbial community on the clays. There was evidence of an active N cycle. Higher levels of denitrification potential compared to both potential net nitrification and potential net N mineralization indicate that these clays act more as a sink rather than as a source of N pollution in the landscape.
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RC1: 'Comment on egusphere-2024-1165', Anonymous Referee #1, 11 Nov 2024
The article “Ancient Clays Support Contemporary Biogeochemical Activity in the Critical Zone” by Alfonso et al. examines the interaction of Late Cretaceous clays on Long Island, NY, with modern biogeochemical processes, aiming to answer three central questions: whether these clays support microbial life, their role in nitrogen (N) cycling, and whether they function as sources or sinks of nitrogen pollution. The authors report that these clays support active microbial communities involved in carbon (C) and nitrogen (N) cycling, with findings suggesting they act more as N sinks than sources in the current landscape.
While these clay outcrops are an interesting research system, this manuscript contains several key issues that impact its clarity and effectiveness. First, it seems that there is confusion between the role of nitrogen in clays (which are part of the soil) and geologic, lithified clays (sedimentary rock). One of the main conclusions these authors present is that the nitrogen in their samples was of geologic origin. This could be true if their study system was lithified clays (sedimentary rock), but it seems that the authors sampled soil clay that is exposed to the atmosphere and biosphere. For this reason, it is more plausible that this nitrogen originates from biological inputs, such as organic debris or nitrogen-fixing bacteria. Emphasizing this point would enhance the clarity and scientific accuracy of the findings.
Second, there seems to be a misalignment between the research questions and the analyses. While the study addresses relevant biogeochemical questions, some analyses—such as comparisons between clay color groups—appear to lack a strong initial hypothesis or rationale. If differences in clay color and texture are central to understanding microbial and nitrogen dynamics, introducing these factors within the research questions, along with hypotheses on their significance, would clarify the study’s objectives and improve reader engagement.
Further, some clay color differences are likely indicative of oxidative or reducing conditions (e.g., red-yellow-brown clays indicating oxidative conditions, dark gray-light gray-white clays suggesting reducing conditions). These environments have significant implications for microbial activity, organic matter decomposition, and nitrogen cycling. Including a discussion of these environmental differences in the context of microbial and nitrogen dynamics would enrich the interpretation of results.
This manuscript would also be improved by reframing the question of N pollution. While the study explores whether clays may act as sources of N pollution, pollution often implies anthropogenic contamination. Reframing this question as “Are these clays sources or sinks of reactive nitrogen?” would allow for a more relevant exploration of nitrogen fluxes without presupposing anthropogenic contamination.
Major comments:
Background: The background section provides some useful information but could be condensed for clarity. For instance, the detailed descriptions of clay mineralogy and their role in biogeochemical cycling could be distilled into a few key sentences relevant to the study's objectives. Simplifying this section would help maintain focus on the study’s aims. Throughout the manuscript, the authors may consider cutting down on more textbook-like definitions.
Introduction: Key points from the background could be integrated here to streamline the manuscript. Additionally, a brief summary of the research approach at the end of the introduction would provide readers with a helpful roadmap. Most importantly, the authors should provide the rationale and motivation for their analytic approach.
Methods: This section is well-detailed but would benefit from visual aids (e.g., images of the clays in situ) to help readers visualize the sampling locations and types of clays. Including sample numbers, sample sizes per site and clay type, and explanations of the statistical methods would enhance reproducibility and interpretability. Specific points include:
- Clarify sample numbers, types, and reasoning behind using one-way ANOVAs over two-way ANOVAs.
- Explain the rationale behind grouping clays by color and texture, and clarify whether color/texture was hypothesized to impact microbial and nitrogen dynamics.
- The statistical methods would be clearer if directly tied to the research questions. Including R² values for correlations would allow readers to gauge model strength and clarify interpretations. For the pairwise correlations, it seems that most of these data are log-distributed, so log transformations would be appropriate. Log transformations are typical of these types of data.
- What is the sample size? How many samples were retrieved from each site, of each color, and of each texture?
- Without a clear description of the research questions, it is difficult to provide feedback on the choices made in the statistical analysis. For example – why one-way ANOVAs and not two-way ANOVAs? Why is there no test for interactive effects of site, color, or texture?
- What was the motivation for fitting linear correlations between response variables? What research questions and/or hypotheses are addressed here?
Results: Structure the results around mechanistic hypotheses rather than descriptive correlations. Rather than listing observed correlations, frame findings in terms of initial hypotheses about microbial activity and nitrogen cycling within oxidative and reducing conditions.
Effect Sizes and Interpretation: Including effect sizes along with significance testing will give readers a clearer understanding of the practical implications of differences. Emphasize interpretation, especially where findings may contrast or align with known behaviors in similar environmental settings.
Discussion:
Relevance of N in Sedimentary Rock (Section 5.1): While the discussion on sedimentary rock N is informative, it could be more focused on the study's core material—clays—rather than extending to other geologic nitrogen sources.
Interpretation of Oxidative/Reducing Conditions: Discuss the potential implications of Fe and organic matter for microbial activity, and consider that the high OM content in dark gray clays could be due to reducing conditions that inhibit decomposition. This hypothesis could explain the enhanced microbial activity in certain clays and provide a more cohesive interpretation.
Nitrogen Source (Line 526): The study cannot conclusively determine that the N in clays is of geological origin; it’s more plausible that organic matter adsorbed onto clay particles contributes to the nitrogen pool. Acknowledging this distinction would align the study with current understanding.
Comparisons with Other Studies (Lines 410–425): The relevance of comparing these results to agricultural, forest, and grassland soils is unclear without a stronger argument for its relevance. The authors should provide context for this comparison, explaining why it is included and what conclusions they hope to draw from it. Without a clear rationale, including an entire table of results from the Hubbard Brook soils study seems tangential.
Summary of Results (Lines 455–465): Some portions of this section simply summarize results without interpretation. Offering an interpretation of the findings (e.g., the significance of high OM content in dark gray clays due to potential reducing environments) would provide more depth.
Minor comments:
Lines 45-48: Rephrase Morford et al. (2011) as an influential study rather than recent. Additionally, clarify whether the study examined soil or lithified clays.
Line 118: If both clay and shale are being sampled, clearly differentiate between these materials as they may interact differently with microbial processes.
Lines 125-134 Seem to belong in the discussion section? Also, please describe what pXRF is. E.g. “Analysis by a portable X-ray fluorescence device (pXRF) revealed…”
Line 140 – It says here there are four types of clays, but the next line reads that 5 types of clays were sampled. Clarification?
Line 149 –Particle size distribution? Was this measured in this study or previously? If this is from previous research, it should be cited. If this is from this present study’s analysis, these are results and should be in the results section.
Line 183: Replace “ignited” with “combusted” in describing the LOI process.
Line 201: Provide a citation or rationale for using the proportionality constant of 0.41 in microbial biomass calculations.
Line 205 – Was nitrate and ammonium extracted with KCl before and after the incubation time? If so, this needs to be stated.
Line 209 – What mass of sample did you use? What volume of nitrate solution, glucose, and chloramphenicol did you use?
Line 230 – Meaning unclear.
Line 246: For pXRF analysis, define “semi-quantitative” and specify the elements of interest, along with their relevance to the research questions. Including the purpose of investigating pairwise correlations would improve focus.
Line 272 – It would be helpful to discuss the magnitude and direction of the differences between groups, not just that the differences were significant.
Table 1 – Sample size? Standard deviations?
Figure 1 – Use a consistent color palette to represent sites.
Line 304 –Magnitudes and directions of these differences?
Line 311 - Note that, while correlations are significant, small R² values suggest weak relationships. Consider tempering strong interpretations.
Lines 373-380: Suggesting black carbon as the primary source of organic C may not be fully supported unless a history of fire is known for the study site. The authors here cite a study on prairie soil carbon, which is more likely fire-derived. Acknowledging that local plant material may also contribute to organic C would provide a more balanced interpretation.
Lines 450-454: This section presents textbook-like information that could be simplified or distilled. Emphasize relevance to the study’s aims.
Citation: https://doi.org/10.5194/egusphere-2024-1165-RC1 -
RC2: 'Comment on egusphere-2024-1165', Anonymous Referee #2, 08 Dec 2024
I read with interest the manuscript by Alfonso et al. on the role of ancient clays on biogeochemistry.
The questions posed on the abstract hit a bit abruptly. Just because the parent material is older why might there not be microbial activity? The questions regarding N pollution were more interesting but without context made it difficult to ascertain its importance (is there the notion that these soils are contributing to excess N on Long Island? Will this be addressed later?)
Along these lines the arguments in the paragraph ending line 49 strike me as a bit incomplete. Is there something unique about these parent materials other than age that might make them unique, biogeochemically? Is there evidence from other older and/or not exposed (or exposed) clays that would lead one to believe that their biogeochemical cycling is different? I'm personally interested in most things biogeochemical and find value in such studies in and of themselves, but for a more general audience what should be expected to be found given previous results, and what might one learn? Reading on to the background section, it may help to merge the background and introduction to give people context first before going into the details; I find that the exposition does not funnel well from broader importance to particular study. The Background section itself doesn't necessarily flow with the introduction; it could almost be a supplement or a sidebar. The geological history is critical of course, but restructuring is required and after reading it a couple of times it needs a re-write (if pathways is the noun, progresses shouldn't be the verb).
(Mason should be capitalized because it is a formal name of the founder of this type of jar.)
The typesetters will likely catch this but the digital quality of figures 2 & 3, actually most figures, should be improved.
The importance of the analysis by color of clay really needs to be described sooner. Of course these clays are different, but for a reader who is not an expert in clays, what should one expect to find and how does this study build on that knowledge?
292: avoid using 'marginally correlated'. Pick a significance level and stick with it. This can also help streamline the results section.
Note in the figures that p can't technically be '0.000'. Use either < 0.05 or less than some other small value
For context, in case I'm seeming obtuse, using statements like 'For contemporary ecosystem processes, it is generally assumed that geologic materials are not an important source of N (Schlesinger, 2013)' in the introduction rather than the discussion can really help people understand why this work is important and novel.
I found the comparison against different soils rather interesting. The pollution section was less well-developed and without more context on its importance this section might best be removed.
Citation: https://doi.org/10.5194/egusphere-2024-1165-RC2
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