Overall analysis:

The manuscript by Cutmore et al., offers a thorough and well-rounded analysis of nitrogen cycle dynamics in the Black Sea, covering the period from deglaciation through the Holocene. The use of diverse biomarker proxies and geochemical data provides a solid foundation for the study’s conclusions. The work is valuable not only for understanding past biogeochemical processes but also for its implications on how similar changes could unfold in modern marine environments facing deoxygenation and stratification. The integration of isotopic, lipid biomarker, and microbial evidence is particularly strong, and the study effectively links these proxies to long-term environmental changes. 

What I particularly found the strength points of the manuscript include: 

Comprehensive approach: The use of multiple lines of evidence (e.g., isotopes, biomarkers, and microbial data) results in a robust dataset, allowing for a detailed reconstruction of changes in the N-cycle across key transitions.

Long-Term perspective: By covering a wide temporal range, the study provides valuable insights into the resilience and shifts in the N-cycle across significant climatic events, including the shift to an anoxic marine basin at 7.2 ka.

Relevance to modern changes: The findings are timely and relevant, as they offer a useful analogy for understanding how current and future shifts in marine stratification and deoxygenation might affect nitrogen cycling.

Strong microbial ecology component: The discussion linking microbial processes (e.g., anammox and Thaumarchaeota activity) with geochemical changes helps bridge paleoclimate research and microbial ecology, making the study multidisciplinary and compelling.

Despite the strong evidence for a stable subsurface N-cycle throughout the Holocene and deglaciation periods, the manuscript does not delve deeply enough into why this stability persisted, despite significant hydrological and climatic changes. The authors convincingly show that the subsurface N-cycle was resilient, but the mechanisms behind this resilience are not explored in detail. For example, it would be useful to discuss the potential roles of microbial community structure, nutrient buffering, or physical mixing processes that might explain this stability? in this regard I would like if the authors could address the following questions: 

1. The observed stability of the subsurface N-cycle is a key finding, but there is little discussion on what processes could have maintained this stability. The authors could consider elaborating on potential factors, such as community dynamics or nutrient availability, that might have contributed?

2. The use of hexose glycosides (HG) as indicators of cyanobacterial activity is somewhat speculative, especially given the shifts in salinity and environmental conditions throughout the study period. A more critical evaluation of this proxy’s reliability would strengthen the interpretation. I suggest providing a more critical assessment of the assumption underlying biomarkers proxies, especially HGs. 

3. The temporal resolution during critical transitions, particularly around 7.2 ka, may not be high enough to capture rapid or short-term variations in N-cycle dynamics. Acknowledging this limitation and its potentiaal impact on the findings would be helpful

4. The reliance on modern analogues for interpreting past microbial and biogeochemical processes introduces uncertainties, especially given that past environmental conditions co uld differ significantly from present-day scenarios. This should be addressed more explicitly. For instance, the authors could expand the discussion a little bit to include a more nuanced view, highlighting the uncertainties of extrapolating modern findings to past conditions. 

Detailed comments: 

Line 30: remove "our", in "the global oceans" sounds more scientific

Line 35: The term Anammox was used in the abstract without introduction, and this is the first time it is introduced, I would add the complete term in abstract as well.

Line 120-121: I would avoid using "with" twice, perhaps you can change with heated electrospray ionization to "using heated..."

Line 216: Clarify if "C32 triol pentose that are specific to cyanobacteria symbiotic with diatoms" mean a marine source or the earlier mentioned freshwater/brackish environments?

Figure comments:

I have one major comment regarding the use of figures in the manuscript. As a general rule, figures that are referenced more than twice should be included in the main text. Figures S2, S3, S4, and S5 are mentioned more than five times each, indicating that they will be of significant interest to the audience. Including them in the supplements makes it more difficult for readers to refer to them easily. I recommend moving at least Figure S2 into the main text. Supplements should be only for figures/material that are "supplementary" to understanding of the manuscript. 

Cutmore et al. present a detailed study using new organic biomarker data (e.g., heterocyte glycolipids, crenarchaeol, bacteriohopanetetrol) and d15N records from the Black Sea to investigate nitrogen cycle changes over the past 20,000 years. Similar to previous studies of Black Sea history, this study documents the transition of the Black Sea from an oxygenated lacustrine basin to an anoxic marine environment. Significant shifts in the nitrogen cycle are identified between 9.7 and 7.2 ka as the basin reconnected to the global ocean, leading to stratification and anoxic conditions. These changes include increased nitrogen fixation and anammox activity, as well as reduced nitrification by Thaumarchaeota.

The biomarker data are compelling and align well with the broader understanding of Black Sea evolution since the early Holocene. The interpretations are generally logical and provide valuable insights into aquatic nitrogen cycle dynamics. However, there are several key areas where the manuscript could be improved to strengthen its clarity.

Major Comments

1. Implications for future ocean deoxygenation: While the study provides valuable insights into the aquatic nitrogen cycle, it is highly unlikely that future ocean deoxygenation might lead to euxinic conditions similar to the Black Sea. There is no evidence of sulfidic waters in the modern global ocean, even in the most oxygen-depleted zones, such as the eastern tropical Pacific, which still contain significant nitrate concentrations. Furthermore, no model projections suggest that oxygen-deficient zones will evolve toward euxinia under global warming scenarios. The authors should conduct a thorough literature review and clarify this point to avoid potential confusion.
2. Stratification-induced nitrogen fixation: The authors conclude that stratification led to increased nitrogen fixation since 7.2 ka and suggest that future ocean stratification could similarly enhance nitrogen fixation. This extrapolation from the Black Sea to the global ocean is problematic. Stratification alone does not directly enhance nitrogen fixation. Rather, nitrogen fixation is more directly influenced by nitrogen limitation relative to phosphorus. In the modern Black Sea, intense nitrogen limitation, driven by anammox-induced nitrogen loss in the subsurface, is the key driver of surface nitrogen fixation. Enhanced stratification slows the upward supply of ammonium and promotes fixed nitrogen loss through anammox, indirectly increasing surface nitrogen limitation. A more detailed discussion connecting these paleo-data to modern Black Sea and global ocean observations is essential to contextualize these findings.
3. Riverine nitrogen input: Previous studies have suggested that riverine nitrogen input is a major source of fixed nitrogen in the modern Black Sea. The authors should discuss how riverine nitrogen input might influence their paleo-records and whether it impacts their interpretations of nitrogen cycle dynamics.
4. Comparison with existing d15N records: The study presents a new d15N record, but comparisons with existing records (e.g., Fulton et al., 2012) are limited. A direct comparison of these d15N records, ideally plotted together, would highlight potential consistencies or discrepancies and strengthen the study. In addition, as the authors point out, bulk sedimentary d15N is well-known to reflect mixed signals; and its limitations should be discussed thoroughly.
5. Diagenesis and preservation bias: Bulk sedimentary d15N and biomarkers such as BHT-x and crenarchaeol are prone to diagenesis and preservation biases, which could complicate interpretations of microbial population dynamics. The authors should discuss how such biases may affect their results and the reliability of their conclusions.

Minor Comments

1. Line 23-24: As mentioned above, specify the mechanisms by which salinity and stratification affect cyanobacterial nitrogen fixation. 
2. Adding a figure showing modern water column chemical data (e.g., oxygen, nitrate, and ammonium profiles) would provide essential context for readers unfamiliar with the Black Sea.
3. Table 1: Table 1 is not directly referenced in the discussion and could be moved to the supplementary materials. In contrast, I found that supplementary figures such as S1, S2, S5, and S6 are highly informative and should be included in the main manuscript for accessibility.
4. Figure 1: Add descriptions of depth contours.