Dear authors,

thank you for your detailed and careful considerations of the comments by the two referees. The referees raised concern about the accessibility of the manuscript and how your main messages and implications were outlined. In your revised manuscript these have been improved.

Two parts of the reply still leave some open questions which require clarification in a revised manuscript: (1) where the alteration of the original lignin signal might occur in the environment; (2) how the drip water relates to the speleothem data. These reflect concerns raised by both referees about a lack of clarity on the process of lignin reaching the speleothem, starting from the source vegetation. I don’t think that your reply and revised text completely addresses these points:

(1) in page 2 of the reply, you note in your revised text “Lignin is only produced by vascular plants and therefore has potential as an unambiguous vegetation proxy and to complement other vegetation and climate proxies in speleothems”. Whilst it is true that lignin comes only from the vegetation, it is known that there can be changes to the lignin composition after deposition in soils (e.g. review by Thevenot et al. 2010, Soil Biology and Biochemistry v.42, 1200-1211; and some of the references you cite). Both referees note elsewhere in the manuscript that some of the signals could also reflect changes in the soils – to some extent you address these competing influences on your ‘pure’ vegetation signal (e.g. in your revised abstract, and in the revised text noted in the reply to referee 1 comment 4). However, I would like to see the abstract note *where* you see (or hypothesise) the ‘transport and microbiological effects’. Are these operating in the soil, in the cave, after deposition in the speleothem...? In your reply to referee 1 comment 4 (page 3 of the reply document, and also again on p.9 of the reply document) you do explain a bit more, but the text is still very generic, so that it is still unclear *where* these different processes might operate in the system that you are analysing and what their impact could be. I think this raises several uncertainties for the reader about where in the environment the critical controls over your data may be (see also referee 2 comment 2). A few lines which identify likely places of potential alteration of the original signal along the pathway from vegetation to speleothem are needed (specific to this cave system if you have it, or more general from other studies if that is what is available). Your reply to referee 2 comment 2 for the discussion part (page 5 of the reply) is also still very generic and doesn’t offer much information on what is happening where and how. Although you indicate to referee 2 (comment 4) that “it is not the aim of our publication to discuss all these transformations in detail” you do make statements about vegetation being the main driver when soil transformations or other transport processes, are an important possible source of influence, so I agree with the referees that some more detail on this is required, or that you carefully edit the way that you describe the links to the vegetation.

(2) across pages 3-4 of the reply (reply to referee comment 5) there is a note about the links between the drip water timescale and that of the speleothem. The final statement needs further clarification: “It is important to note that we are looking at the seasonal timescale here. On longer timescales, as recorded in the stalagmite, the release and mobilization of phosphorous from the hostrock can be related to the productivity of the vegetation above the cave since phosphorous serves as a plant nutrient”. Are you saying that on annual timescales you only have direct contributions of phosphorous from the bedrock, but on longer timescales the phosphorous is somehow released ‘upwards’ to the vegetation e.g. through weathering? Would the direct contribution from the bedrock not also contribute at longer timescales? (wetter climate, more flow through bedrock perhaps?) and would availability of phosphorous from weathering not also influence vegetation today? My interpretation of your statement is that you think that because of the longer timescale of weathering making phosphorous available as a nutrient, there would be a better link between vegetation and phosphorous than on a shorter timescale where nutrient availability may vary less but direct access to bedrock by water flow would generate seasonal fluctuations? I may have mis-understood your message, so please consider how to expand this statement to make it more clear what processes you are discussing and how they inter-relate. You use this same example and text in reply to referee comment 6, so I think it is important to ensure that there is no mis-interpretation of your message.


Why is there a question mark in your revised text in answer to referee 2? (page 6 of the reply document, in response to referee pdf comment 3) “Lipid biomarkers, such as fatty acids (?) and...”. It appears in your revised manuscript at the end.

Line 30 p12 of the revised manuscript: remove the “??” (“...only appears in the third principal component (explaining 11.4%), with a high positive contribution, together with positive contributions of P (see table ?? in the SI). This...”

Finally I would recommend a slight change to your title. Although you make quantitative analysis of the LOPs you don’t generate a quantitative vegetation/environment reconstruction. I would recommend something more simple: “Lignin oxidation products as a potential proxy for vegetation and environmental changes in speleothems and cave drip water”.