Round 1

Reviewer 1 Report

In the present manuscript, the authors review the body of literature that has been published regarding the archaeal and bacterial diversity associated with shallow submarine hydrothermal vents near the Eolian islands of Italy. The authors conduct a pretty comprehensive review of the research that has been conducted at these sites, from the perspective of microbial diversity analyses, inclusive of both culture independent and dependent works. I have a few minor comments/suggestions included below. In addition, I would suggest that the authors try to contextualize the importance of conducting this review somewhere in the introduction. It is never quite made clear what the impetus, or need, for such a review is, and I think that motivating this type of discussion would go a long way towards making readers understand why such a review is needed. Further, a few suggestions regarding organization of the text are indicated below. 

General Comments:

I would suggest breaking the first section up into smaller subsections. As it is, the latter half of the introduction reads like a list of information rather than a cohesive section. Perhaps including another section about the diversity of known physiological characteristics of cultivated Archaea would help, and/or in addition to a subsection describing the currently known diversity of Archaea. 

At the beginning of the conclusions, the authors provide a handful of reasons as to why SHS sites are important to investigate (e.g., ocean acidification, global change, etc). However, these topics are never really addressed in the text. If the impetus for further work on these systems hinges on these ideas, and the impetus behind the review, I would suggest motivating how these connections exist, somewhere in the introduction. Or otherwise provide more context as to how SHS sites can help inform our understanding of these processes. As it is, they seem to be an afterthought, but paradoxically an important reason for studying these sites. 

Specific Comments:

Abstract, Line 13: What is meant by "unusual chemical conditions" in the context of SHS? In the broad sense, I do not see evidence in the text that these sites are unusual among hydrothermal vents or hydrothermal environments in general. Not to say that they aren't "unusual" but describing why would be useful. Such a discussion in the main text would actually add an interesting dimension as to why these environments are of particular interest. 

Typos: Line50: interpret; 266: gradient; 380: together; 394: hyperthermophily; 

Line61: I'm not sure if this list is meant to be exhaustive, but there are a number of important archaeal taxa that have been discovered outside of what's described here. The DPANN group for instance warrants discussion as a major archaeal group (Rinke et al 2013), as do the Bathyarchaeota and Verstraetearchaeota (Evans et al 2015; Vanwontergheim et al 2017), just to name a few that are probably quite important for global biogeochemical cycling and other processes. Several recent reviews are good starting points (Adam et al 2017; Borrel et al 2019). 

Line 67: I realize that the earlier reports that the authors cite here call these organisms Crenarchaeota, but its widely known now that they are actually Thaumarchaeota. I would suggest the authors revise this statement to that effect. 

Line 78: There's other isolates besides N. equitans for this group. Nanoclepta for instance (john et al 2019). Nanopussillus, etc. 

Line 109 and elsewhere: What is meant by 'primordial conditions'? This term is used several times, but it's not clear how those conditions are present at these sites, a discussion of why such a term is used to describe SHS is warranted if the term is to be used. 

Line 139: To my knowledge, elemental sulfur is only yellow - although when in minerals with other compounds, can be different colors - such as orpiment or other arsenic sulfides. The authors may want to better describe their reasoning here. 

Line 239: Would suggest a different word choice than "unpredictable" - if the intent is just to say it's high diversity, than I would suggest just saying that. 

Line 240 - is there a reference for the statement that archaeal communities at vents are generally lower than those of Bacteria? There likely should be one associated with this statement, as I don't know that all of the present data about vents confirms this. 

Line 256: Why is DGGE considered the most reliable tool for microbial diversity studies? I would argue that next generation sequencing with a low error rate technology like Illumina would probably be the most reliable. 

Line 309: Could these differences in archaeal relative abundances be due to PCR primer bias? A brief discussion of this may be warranted. If hte primers used were standard archaeal + bacterial primers (e.g., 515F-806R) - these are known to very significantly bias bacterial amplification over Archaea (see Edwards et al 2015) including of nearly all of the taxa present in hydrothermal systems. In my experience with such primers, these biases are very significant and cause dramatic underrepresentation of Archaea in hydrothermal environments. 

Line 339: It seems as though this statement is incomplete. Is this supposed to indicate that Crenarchaeota dominated at the hottest site? 

Line 440: References missing for statements about Korarchaeota distribution. 

Reviewer 2 Report

This review reports about archaeal and bacterial diversity in shallow hydrothermal systems around the Eolian Islands (Italy). The authors generalise the materials presented in recent studies.

Detailed comments:

In Table 2 not understand what is reference site, there is not decoding - bdl, nd and there gaps. For example, for sample PV there is no information on CO2 and H2S.

In Table 4 there is phylum, class, but there are species in top table.

In Table 5 discusses the results of the DGGE analysis, but sample type was appears (water or sediments). Why in table 3 is absence separation of samples on type (water or sediment)?

Why only representatives of three phyla were detected in the studied communities? In the text there is no discussion of it.

Figure 4 and 5. What does BPF27, BPF74 differ from BP27 and BP74? In paper not information about samples BPF27 and BPF74. 

Page 12, 381 - in table 3 pH values are 4.5-4.7 for samples of Hot Lake.

Not information about salinity OTUs and other for Vulcano, Hot Lake, Black Point, and Kueishan in Table 7.

Page 14, 464 ddep-sea?

Conclusions are deneral and do not provide specific information about cmmunity in shallow hydrothermal systems. 

Page 14, 451-455 There ara no refers on papers.

In Table 7 change HT on HL (Hot Lake=HT)

Page 10,  330 A high number of archaeal sequences ... How sequences?

Page 6, 189-190 In Table 3 only the highest temperature and the lowest pH (3.3) have site BP27 where T=27 and pH=2.4

In summary, in paper contains a lot of information about sites and samples which need systematised.  

Reviewer 3 Report

Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter” https://doi.org/10.1007/s0079

Multi-omics analysis provides insight to the Ignicoccus hospitalis-Nanoarchaeum equitans association https://doi.org/10.1016/j.bbagen.2017.06.001

https://doi.org/10.1371/journal.pone.0148675