This manuscript investigates microbial communities in surface and subsurface snow as well as the geochemistry of these snow zones in the Swiss Alps. The study presents seasonal data from ~1800-2600 m a.s.l. The study of subsurface and surface snow in relation to seasonal changes addresses key uncertainties in snow microbial ecology and biogeochemical cycling. Few studies have investigated surface and subsurface snow, particularly in this altitude range, seasonally. Differences between snow layers are a key variable that is difficult to constrain across locations (even those in close proximity) and seasons. 

Some broader comments:

I am curious about the use of “layers” throughout. It appears that you sampled at specific depths regardless of any apparent structure in the snow. But snow layers have a specific definition — they are distinct horizons in the snow based on water events. And typically have characteristics specific to a snowfall event. Please update the manuscript accordingly to either specifically state how you identified layers in the snow pack or update the wording to better reflect that you sampled specific depths regardless of snow layers or structure. I have similar comments below about “surface” vs. “bulk” snow. Both samples are “bulk”. 

Standard reporting of geochemical analsyes would include supplying a table of the actual data. I would encourage the results and discussion sections to more explicitly address the concentrations. As such, the reader has no context for how these samples might compare to other snow and ice studies. The results and discussion address only patterns and do not integrate with other studies on snow chemistry, limiting the potential utility of the data set. 

The surface layer may be quite different, physically, from surface snow. Water content, physical properties of the snow, and potential abundance of particles (and particle-associated microbes). Particles also carry nutrients. Was this investigated as part of the study, or what is the justification for only focusing on aqueous measurements? The surface particles likely control the chemistry below, and the findings that Ca2+ is important or related to community structure strongly point to the need to assess the full chemistry of the snow, which would include dust, sediments, and other surface constituents. 

Do you have any evidence that these microbial communities are active in either location? And how much movement of cells is expected? Presumably, more water later in a melt season could move cells (dead or alive) into the subsurface — this would not be evidence that those microbes are important to active processes, merely that their biomass is mobile. The study would be strengthened by microscopy to visualize intact cells (and by a biomass measure to relate recovered DNA and 16S rRNA sequences). Indeed, the discussion invokes movement of solutes — cells too I assume. In reviewing the paper, it isn’t clear if the point is cell movement through the snow or distinct communities expected throughout the snowpack. 

If allowed by The Cryosphere, I suggest combining the results and discussion. The Discussion is short and not well integrated with the data presented. For example, deposition could be discussed when the observed patterns are discussed (along with a section on what the actual concentrations are and how they relate to other studies). I mentioned this above, but there is no justification or context provided for the different valleys but this is also part of the discussion. 

Line 9: Particles that are transported in the atmosphere. Semantic, maybe, but these do not originate in the atmosphere. 

Line 20: Putative? Or is spore formation monophyletic in these groups?

Line 21-23: These aren’t really enriched (you did not add nutrients). Perhaps link these observations to what you did measure - N and Ca concentrations. 

Line 65: Is it necessary to say “In contrast to previous studies”? Please cite them if so and be specific about how this study differs. 

Line 70: According to the methods, you sample the 10-15 cm zone. Please update.

Line 74: specific gradients of chemistry in the snow? I would not know what chemical snow is let alone gradients in this. 

Line 85: How long were samples stored? What impact did freeze-thaw have on downstream chemical analyses? Also provide specific methods for how samples were collected. And pictures of the field samples that could be included? How did you choose sites to sample? What was visible on the snow surface?

Line 88: Please discuss detection limits and field blanks. 

Line 94: Any negative controls to discuss? Low DNA concentrations? Did you assess the amount of biomass in each sample type to see if that might impact the recovered sequences? Similarlly, presumably smaller volumes were sampled for the snow surface? Or did you collect the same volume and if so, how do account for that potential bias? How much snow was filtered? How were samples store, etc etc. Many methods missing here. 

Line 144: Please provide the actual concentration data in a table. 

Figure 2: The PCA is too small to read. This figure also includes regions or valleys that were not introduced anywhere before this figure. Please provide sample site context and relate this to the data if that is a key part of the study. Here you also use bulk and surface to describe the snow samples. Is surface not also a “bulk” sample? I’m not understanding how these labels are informative. 

Figure 3: Why are the valleys denoted with a different color palette than in Figure 2? This is very confusing. It’s also nearly impossible to discern between the shades. 

Lines 187-194: Is this a Core analysis? Or an abundance analysis? Where are the methods and justification for these cutoffs? 

Line 191: Ecological adaptations of individual microbes cannot be investigated with 16S rRNA gene sequences.

Line 196: were not significant

Figure 3: What are the color codes on the x-axis of e for? Is the reader supposed to know these models? I guess we get them in the text but looking at the figure and then back to the text is quite confusing. 

Figure 3e and Table 2 are the same data? Is there a reason to have both?

Line 240: I’m struggling to see these as gradients. They are distinct samples.

Line 280: What are the actual concentrations? How do these relate to deposition rates, or marine sources, etc. Please provide specific details as well as the actual data. 

This study explores the chemical characteristics, bacterial diversity, and composition of snow in the Swiss Alps, comparing these features across three sampling sites and two distinct snow layers: surface snow and bulk snow (15 cm depth). The results indicate that these layers differ in both chemical properties and bacterial diversity and composition, with surface snow exhibiting greater diversity than bulk snow. In surface snow, Total Inorganic Nitrogen (TIN) concentrations were higher than in bulk snow, whereas organic acids, Ca²⁺, PO₄³⁻, Mg²⁺, Na⁺, and K⁺ were more abundant in the bulk layer. Regarding potential relationships between environmental variables and bacterial genera, the authors report a positive and statistically significant correlation between various spore-forming genera and TIN concentrations in surface snow, as well as between cold-adapted bacteria and calcium concentrations in bulk snow.

General comments:

This study involves a substantial number of snow samples, and the effort is commendable. However, certain aspects, particularly the introduction and discussion, could be improved.

The introduction places considerable emphasis on the role of airborne bacterial dispersal and post-depositional processes in microbial selection. While this is a relevant aspect of snow microbial ecology, it does not align well with the study objectives outlined therein. For instance, the authors highlight topographic differences as a key feature of their study, given the sampling of three distinct Swiss Alpine valleys. The introduction would benefit from incorporating more background on how topography may influence snow microbial composition and chemical characteristics, thereby providing better context to frame the study. Furthermore, the altitudinal gradient is mentioned but barely developed, with no substantial relevant results presented.

In the Materials and Methods section, the rationale for selecting the snow sampling depths (surface vs. 15 cm) is not specified, despite its apparent relevance to the paper's framing. The authors propose that the sampled snow originated from two distinct snowfall events (three days and one day prior to collection), yet they provide no justification for these depth choices or assurance that the deeper snow layer corresponds to the earlier event, which they discuss later. Moreover, most comparisons in the results focus on snow depth rather than topographic variables, which misaligns with the initially stated objectives of investigating topography. Reframing the Materials and Methods to better address the introduction's questions would strengthen the study.

The results provide detailed descriptions of differences between snow layers but fail to present findings for comparisons between sampling sites or emphasize the altitudinal gradient. This applies to both chemical and bacterial composition analyses. Most comparisons focus on depth rather than topography, overlooking these initial objectives.

In the discussion, the data presented are interesting but challenging to interpret meaningfully, as the methodological details and linkage to the introduction are insufficiently explained. Consequently, drawing robust conclusions is difficult.

I suggest that the authors reconsider the paper's objectives as presented in the introduction, potentially shifting focus to snow layers, and provide stronger justification. Specifically, what criteria determined the depth cutoff? Were differences observed in snow characteristics, and how were they assessed? Adding site comparison results or reframing the introduction, methods, and discussion to ensure coherence would greatly strengthen the manuscript.

Specific comments:

Line 83: specify the volume of snow collected.

Line 89: specify the volume of melted snow filtered for chemical analyses

Line 109: There appears to be an error here, referring to ASV instead of OTUs.

Line 143: Please provide a table with the results of the chemical characterization.

Lines 166-170: This result contributes little to the study and is not discussed further. Additionally, no context is provided to justify its inclusion.

Line 187: The rationale for conducting the core microorganisms analysis is not contextualized.