the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 07 Oct 2024
Sedimentary ancient DNA insights into foraminiferal diversity near the grounding line in the western Ross Sea, Antarctica
Abstract. Foraminifera are important marine environmental indicators widely used in paleoceanography and paleoclimate studies. They are a dominant component of meiobenthic communities around the Antarctic continental shelf, including rarely studied locations below the ice shelves, close to the grounding line. In this study, we use high-throughput sequencing of sedimentary ancient DNA (sedaDNA) targeting foraminifera with two molecular markers, including the ultra-short one newly designed for this study, in five cores from the western Ross Sea, containing sediments up to thirty thousand years old. No foraminiferal DNA is detected in the tills, suggesting a lack of preservation of sedaDNA during glacially induced sediment reworking and transport. We reconstruct diverse foraminiferal communities in the open marine settings and significantly less diverse communities in sediments from the slopes of the grounding zone wedges, deposited proximal to the grounding line. Both assemblages are rich in soft-walled monothalamids not preserved in the fossil record and complement the results of earlier micropaleontological studies, allowing a more complete reconstruction of past biodiversity. The newly designed mini-barcode provides higher foraminiferal diversity in surface and subsurface samples than the standard barcode and allows better differentiation between foraminiferal communities in different sediment types. It appears to have great potential for future paleoenvironmental studies, although its taxonomic resolution needs to be evaluated.
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RC1: 'Comment on egusphere-2024-2824', Anonymous Referee #1, 10 Nov 2024
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General Comments
This study explores the diversity and composition of foraminiferal communities in the Western Ross Sea, Antarctica, particularly near paleo-grounding lines—areas that are critical for understanding past Antarctic ice sheet dynamics. Using sedimentary ancient DNA (sedaDNA) sequencing, the researchers examined foraminiferal DNA from five sediment cores, dated to as far back as 30,000 years, collected from both glacier-proximal and open marine environments. This innovative approach allowed the detection of both calcareous foraminifera and soft-walled monothalamids, a group rarely preserved in fossil records due to their fragile structure. The study reveals notable differences in foraminiferal diversity across sediment types, with open marine sediments exhibiting substantially higher diversity than those near glacier-proximal settings, where community composition was more limited. Notably, the researchers designed a new mini-barcode to improve the detection of monothalamid foraminifera, enabling the identification of species previously undetectable by fossil-based methods. This mini-barcode improved taxonomic resolution between foraminiferal communities in different sediment types and holds promise for broader application in future paleoenvironmental studies, though it may require further refinement for enhanced accuracy. One major finding was the lack of foraminiferal DNA in glacial tills, indicating that sedimentary DNA may not preserve well in reworked glacial sediments. This finding implies that stable, open marine environments may be more conducive to DNA preservation, offering more reliable records in such settings. Overall, the study underscores the potential of sedaDNA for reconstructing past biodiversity, especially in environments where fossil records are incomplete or absent, thereby contributing new perspectives on the ecological history of Antarctic grounding line environments. This work offers valuable insights into Antarctic marine biodiversity, and the findings, particularly concerning the use of sedaDNA to identify previously undetected monothalamid foraminifera, could significantly enhance paleoenvironmental reconstructions in glacimarine settings. However, there are several areas where the manuscript could be improved for greater clarity, coherence, and scientific rigor. (I recommend major revisions primarily focused on restructuring the manuscript and clarifying the text, rather than on redoing analyses.)Specific Comments
Firstly, the manuscript would benefit from a more refined structure, as the introduction does not fully explain the rationale for certain methodological choices—specifically, the need for a shorter barcode, which later becomes a focus of the discussion. This omission creates a somewhat fragmented flow and shifts the balance of the manuscript, as significant introductory material about sedaDNA methodologies and barcode design only appears later in the discussion section. A more focused introduction that fully describes the study’s objectives would establish a clearer narrative, reinforcing the purpose of the methods and findings. In brief, it’s essential to introduce the main findings that are later discussed (and even appear in the abstract).
While the results section is accompanied by effective figures, the text itself relies heavily on subjective descriptions and lacks specific quantitative data. Terms like “somewhere in between” (L. 207) and “very small” (L. 237) are subjective and would be improved with precise values, enabling a clearer interpretation of findings. A more quantitative approach to presenting results would better support the study’s conclusions. Furthermore, the statistical methods, while mentioned in figure captions, are not adequately explained within the main text. Including detailed explanations of each statistical test, the conditions under which they were applied, and whether they were one- or two-sided, would enhance the transparency and reproducibility of the study’s analytical approach.
The methods section is generally well-constructed, but further elaboration on statistical analyses would strengthen the scientific rigor. Clear descriptions of each test and a justification for their selection would improve the robustness of the analysis. Expanding this section would also improve reproducibility, allowing future researchers to better follow the study’s procedures.
Lastly, the manuscript would benefit from a thorough proofreading by a native English speaker. At times, certain phrasing or wording makes it difficult to discern the authors' intended meaning. While such a review could be completed following major revisions, it would greatly improve the manuscript’s readability.
Technical Corrections
L30-31: The connection between Arctic warming and Antarctic ice sheets is not clearly articulated. It feels abrupt, with no clear link.
L37: "More advanced" is too vague—does it imply previous techniques were not advanced? Being from the sedaDNA field myself, I understand that you might mean “recently developed” or “innovative” but you need more care with your wording choice.
L49-51: Monothalamids are hard to track in fossil records, and sedaDNA provides an alternative means, but what role do monothalamids play in the ecosystem? Why are they of interest? A brief introduction to their ecological significance would provide context.
L61-63: There is no clear mention of the need for a new mini-barcode, which is emphasized in the abstract as a major result. Why was a shorter barcode necessary?
L65-68: I find this sentence difficult to follow. Consider rephrasing for clarity.
L70-73: The stated goals don’t mention developing a shorter marker, yet this is presented as a significant outcome in the abstract and discussion. Clarify if this is a primary aim or a secondary result.
L151: Unusual spacing between “and” and “3uL.”
L169: A fixed 90% coverage threshold affects the markers differently, as the shorter marker would allow more mismatches. Please clarify this point.
L195: The notation “135 80” is unclear—is this 13,580, 13 580, or two separate values?
L195-196: The sentence is unclear regarding replicates for all samples except those at 200 and 280 cm. Please clarify.
L207: “As significantly as” may suggest a statistical difference. Please ensure accurate wording to avoid misinterpretation.
L216: Does “they” refer to datasets or patterns? Clarify what is being described as “more scattered.”
L218: “Slightly different” is subjective. Aim for a more precise description (other instances of subjective terms were noted throughout the results but not all listed here—please review for accuracy).
L222: “Tend to form”—do all samples follow this pattern, or only some? Provide specific values.
L237: “Very small numbers” is vague—specify.
L260: "Highly irregular"—what is considered regular in this context? Constant over time or without variation?
L260-275: The description of SH and ST detection of OTUs is difficult to follow within this paragraph. Consider restructuring for clarity.
L280-304: This section lacks discussion or interpretation of results and instead offers a lengthy introduction to sedaDNA preservation.
L286: Unusual spacing between “sediments.” and “To determine.”
L310: When discussing sediment mixing and dilution, does this imply mechanical damage to DNA fragments or dilution due to sedimentation rate? Clarify.
L321: Could you report DNA concentrations post-extraction or gel bands after PCR amplification?
L323-326: Shotgun sequencing could confirm DNA preservation. Even without sequencing, a Bioanalyzer or TapeStation could verify fragment distribution, which may confirm the need for a shorter marker.
L377-409: This key discussion point about shorter markers was not introduced earlier—consider integrating into the introduction.
L378-382: The rationale for a shorter marker should appear in the introduction.
L404-405: Have you checked databases for potential sequence overlaps? Your taxonomic assignments should follow the Last Common Ancestor (LCA) principle. Therefore, the use of a shorter fragment would lead to potential lower taxonomic resolution (i.e., the inability to differentiate between two species) rather than misassignment. If all species within Borelis and Planoperculina are exclusively tropical and show no sequence overlap with the ST marker what are the closest relatives present in the databases?
L453: Unusual spacing between “(2023).” and “(1).”
L454-473: Conclusions should reflect the study's aims, with better alignment between introduction and final conclusions.Figures:
The figures are generally clear. You may wish to consider scaling the y-axis with depth, allowing for easier identification of core coverage. Also, note that only two dating points are provided for the entire record, which may limit chronological confidence.Citation: https://doi.org/10.5194/egusphere-2024-2824-RC1 -
AC1: 'Reply on RC1', Wojciech Majewski, 20 Nov 2024
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Thank you for your comments! We will incorporate them into the revised manuscript, following further guidance from the editor.
Citation: https://doi.org/10.5194/egusphere-2024-2824-AC1
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AC1: 'Reply on RC1', Wojciech Majewski, 20 Nov 2024
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