Reply on RC2

RC2 – 8: Line 20 – 21: Change sentence to “Elevated organic matter (OM) concentrations are found in hadal surface sediments relative to the surrounding abyssal seabed. However, the origin of the biological material remains elusive. RC2 – 9: From here on replace all instances of the term “organic matter” with the acronym “OM”. RC2 – 10: Line 22: Replace “cell” with “cellular” and “in” with “extracted from surface sediments”. RC2 – 11: Line 23: replace “depths” with “margin”. Response to RC2 8-11: We will include these suggestions. RC2 – 12: Line 26 – 28: Unclear, please rewrite. Response RC2 – 12: We will modify this in the revised manuscript. RC2 – 13: Line 29: Delete labile – all IPLs are labile lipid structures with some head group classes being more resilient than others. Response RC2 – 13: We will include this suggestion. RC2 – 14: Line 29 – 30: Does not fall out as to how that is necessarily so based on what is written. Response RC2 – 14: We will modify this in the revised version. RC2 – 15: Line 35: End sentence at ecosystem. Begin the next sentence with Furthermore, they also... Response RC2 – 15: We will include this suggestion. RC2 – 16: The abstract does little to reconstruct the microbial diversity based on the recovered lipidomes as extensively discussed in the text. Response RC2 – 16: We will modify this in the revised version.

Response RC2 -1: Thank you for the overall positive review of our work.
RC2 -2: Although, I am in favor of publication, I do not yet necessarily agree with the interpretation or rationalization of the described lipidome. From the paper's title to its conclusion is a focus of IPLs largely representing (or acting as) tracers or proxies of particulate organic matter (POM). While a component of IPLs may find its way into POM, these compounds say little about what POM is, how it comes to be preserved, or how it is transported through the water column. The OM instead comprised of all sorts of detritus (i.e. extracellular polysaccharides, fecal material, animal kills and falls, etc.).
Response RC2 -2: Thank you for this remark and for the opportunity to clarify the scope of our work. We are aware of the complex composition of POM, its transformation along its transit through the water column, and the fact that IPLs only represent a fraction of it. We will highlight this aspect more explicitly in the revised version of the manuscript. Given the labile nature of ester-bond IPLs RC2 -3: Furthermore, the authors explain the similarities between the bathyal and hadal lipidomes as products of mass sediment transport, what they term as being lateral transport. First the term lateral transport is confusing as this could easily also mean transport across on latitudinal position within the base of the trough to another point at the base of the trough. Instead, I think the authors are referring to down slope sedimentation. Second, the basis for a lateral transport does not to me make sense based on the data that have been collected. Down-slope mass wasting events are episodic in space and time (even the V-shaped basins vary in slope from 8-10deg). The sediment depths to which the samples were collect are at the very surface layers (0-1cm deep and no more than 3 cm deep). So, if the kinetics show that upper water column inputs do not survive their direct transport to the seafloor, then how does an IPL survey as a sediment particle moving step-wise down the trench slope? What sedimentary evidence do the authors have that the upper 3 cm of sediment at all of the sampled stations represents debris flows, turbidite, or mass wasting events? What is the slopes adjacent to all AT core sites? Can a model be made to show what the decent time would be for a bathyl sediment to reach the bottom of the trench? Response RC2 -3: We thank the reviewer for this excellent point and for the opportunity to clarify this aspect. First, we agree that the term "lateral transport" is confusing, and that "downslope transport" is more appropriate to explain the potential transfer of sediment from the bathyal to the hadal region. Second, we also agree that we are not able to distinguish between lateral transport within the Atacama Trench from downslope transport from the bathyal region. Third, the lack of sedimentological and geochemical data, in addition to the spatial and temporal limitations of our study, a sediment transport model for the study area is far beyond the scope of our study and warrants further investigation. Thus, given the main focus of our study and the lability of IPLs, we will reduce the role of these mechanisms in our revised manuscript to a hypothesis to be tested by future studies.
Our revised discussion will include the role of tectonic processes, including recently published and/or ongoing work that we were not aware of before the submission of our manuscript. Recent work in the Japan trench indicates that down deposits arise from earthquake-driven remobilization of surface sediments from the continental shelves (Schwestermann et al., 2021). We are now also aware of similar studies currently in preparation for the Atacama and Kermadec trenches (Stewart et al., in prep.; Chen et al., in prep.; Zabel et al., submitted), which we plan to mention. While we lack sedimentological/geochemical data to discriminate if the top 3 cm of our hadal stations A4, A5 and A10, represent debris flows, turbidite, or mass wasting events, a study currently under review addresses this question (Oguri et al., submitted). These authors use 210 Pb ex measurements to indicate that stations A4 and A5 exhibited mono exponential declines in the 210 Pb ex from the sediment surface until depths were they reach low background levels, suggesting no mixing or mass wasting at both sites in the past ~160-180 years. Similarly, other sites of the Atacama Trench indicate that surface sediments consist of continuous hemipelagic sedimentation, except for Station A10, which seems to have been formed by a recent turbidity layer. We plan to place our results within this sedimentological framework to draw revised discussion and conclusions sections.
RC2 -4: More likely is that the microbial communities of the sea floor are not sensitive to the change in hydrostatic pressure and all things the same, thrive on a low nutrient supply from the upper water column -creating its own selective mechanism. As such the paper would be better served focusing on the important conclusions that it does resolve well. These are: This is an environmental baseline survey of bacterial and eukaryotic sourced IPLs. The most abundant ester-based IPL are phospholipids. Most of these have yet to be described. Bathyal and Hadal sediments have very similar compositions of ester-bound IPLs and therefore may indicate that these environments are host to the same microbial surface communities. Most IPLs that would be common to the upper water column appear to get almost entirely degraded during their descent to the hadal seafloor suggesting the highly labile lipids are derived from ocean floor microbial communities.
Response RC2 -4: We thank the reviewer for this valuable comment. We plan to rewrite the conclusions section to more effectively summarize the key findings of our study following the draft below.
Bacterial and eukaryotic sourced IPLs in surface hadal sediments from the deepest points of the Atacama Trench share characteristics with those in bathyal sediments and differ from those found in suspended particles from the upper 750 m of the water column, including the oxygen minimum zone. This indicates that: a) most IPLs abounding the upper water column are almost entirely degraded during their descent to the hadal seafloor, and b) IPLs found in hadal sediments are predominantly derived from in situ microbial communities. The most dominant ester-bound IPL structures found in bathyal and hadal sediments show a great variety of phospholipids with varying degrees of unsaturation, most of them yet to be described, that are likely bacterial and/or fungal in origin. Hadal sediments also exhibit unique glycolipid structures, such as SQDG-42:11, SQDG-23:0, DGDG-35:1, DGDG-35:2 and DGDG-37:1, that have not yet, to the best of our knowledge, been reported in other environments. However, these lipids are present in low abundance and represent a small fraction (~0.00012%) of the total IPL pool. Elevated ratios of unsaturated/saturated fatty acids in hadal sediments are likely indicative of homeoviscous adaptation to the high pressure and low temperatures characteristic of this extreme deep-sea environment. An improved understanding of the phylogenetic, ecological, and metabolic association of IPLs present in the Atacama Trench could be achieved in future studies by the pairing of lipidomics with genomic techniques (e.g., microbial community composition, functional groups, lipid biosynthesis) in addition to a detailed sedimentological and biogeochemical characterization of sediments.
RC2 -5: Lastly, I would suggest that some of the eukaryotic IPLs may represent fungi or metazoan type detritivor. That would be a interesting use of IPLs if this link could be constrained.
Response RC2 -5: We thank the reviewer for this suggestion. We will add a discussion about potential fungal and/or metazoan sources, including information from the recent publications listed below.
Gao, Y., Du, X. Xu, W., Fan, R., Zhang, X., Yang, S., Chen, X., Lv, J., Luo, Z. Fungal diversity in deep sea sediments from east yap trench and their denitrification potential. Geomicrobiol. J., 1-11, 2020. RC2 -36: Line 107: It is a mischaracterization to consider IPLS as a proxy of OM loading to sediments. Microbes may hitch-hike on other forms of detritus (fecal material, extracellular polysaccharides, clay minerals, etc.), but they easily represent (and most commonly and simply do represent) what is the living or very recently deceases microbial components in the sediment. The very nature of applying a modified Bligh and Dyer extraction to get IPLs insinuates that these compounds are still attached as complete or partially degraded cellular membranes. If OM provenance is to be assessed from IPLs it must be done in combination with traditional techniques, be they hydrocarbon biomarker analyses, bulk rock sediment parametrization (TOC, HI, and OI) and/or FT-ICRMS POM studies.
Response RC2 -36: We agree with the reviewer that other biomarkers/analyses are necessary to evaluate the origin of organic matter in more detail, which is beyond the specific scope of our study, but part of planned investigations. We will modify the text and be more explicit about our interpretation of IPL signatures in sediments. In a nutshell, and as explained above, we use them as indicators of in situ microbial production and to demonstrate that IPLs produced in surface waters degrade through their transit to the seafloor.

Materials and Methods
RC2 -37: Line 120: Indicate that this is bacterial and eukaryote IPLs.
Response RC2 -37: We will add this.
Response RC2 -38: We will modify this in the revised version.
RC2 -39: Line 144: It is unclear why on three very shallow sediment samples (up to 3 cmbsf) were analyzed within a 60 cm core.
Response RC2 -39: Given the lability of IPLs, we focused on the top 3 cm of the sediment column to facilitate their comparison with surface sediment samples from the bathyal region as well as with POM from surface waters. We will provide an expanded justification for this rationale in the revised version of the manuscript.
RC2 -40: Section 2.2.1 Lipid extraction -Comment: Presumably the samples were immediately sectioned and frozen when removed from the multicorer? No details provided on this stage of sample collection and processing.
Response RC2 -40: Yes, they were. We will add more details about the sampling, processing, and storing of samples.