Dear Mr. Gagliano

Thank you for submitting the revised manuscript to BGD. Your manuscript has been reviewed with two external experts, both of whom raised major concerns for publications. Although these comments have been addressed, I have reviewed your ms and feel that the presentation of your results is not sufficiently clear for readers to follow.

The major concerns are following:
1. The title does not reflect what you have done in this study. The title suggested that this study deal with both methane oxidation and bacterial diversity. However, the majority of your data is about methane oxidation, but not bacterial diversity (only one TTGE figure). In fact, the authors have no any idea about taxonomic identities of microbial communities in these soils. I therefore suggest that the title be rephrased and TTGE could be deleted or placed into suppl.
2. The presentation of results is not well organized. It can be done as follows:
(1) Introduce the geological settings and relevant sampling information (Fig. 1).
(2) Present soil physical-chemical properties (New Table 1 by combining original Table 1 and original Table 3. Note: methane oxidation activity could be removed from Table 1, while the information about pmoA could be kept)
(3) Show methane oxidation activity (New Fig.2 ). This figure could be made by data from Table 1 and original figure 2.
(4) The effort to isolate methanotrophs that are likely responsible for in situ methane oxidation (New Fig. 3). However, the methanotrophic isolate appeared not exactly what the authors had expected for. This implied that there existed bias during cultivation. Therefore, molecular approaches were employed to investigated diversity of methanotrophic communities by phylogenetic tree.
(5) The genetic diversity of pmoA genes (New Fig. 4)
(6) In discussion. The authors need to discuss how relevant the isolate Pan1 to in situ methane oxidation activity and the implication of pmoA genes from culture-independent techniques.

Specific comments.
(1) Page 1 Line 21 to Line 25. Please delete bacterial diversity and focus this study on microbial methane oxidation. It is a bit abrupt that TTGE was included, and indeed the authors showed no more information of bacterial diversity other than a TTGE fingerprint. This part must be removed in this manuscript, or placed as a very minor section for bacterial diversity in supplementary materials.
(2) I agree with the reply that it is very hard to manipulate soil pH and investigate its effect on methane oxidation activity. But, please discuss the possibility of methane oxidation under low pH conditions. In addition, please discuss the possibility of better cultivation strategy for methanotrophs by addition of rare earth metals. (Pol et al., 2014 EM)
(3) The geological settings could be placed as a subsection within the Material and method.
(4) In table 1. Please put the a,b,c,d as the not at the bottom of the table, but not in the main message of Table 1. In addition, primer information could be specified in the note, without reference to Table 2.
(5) I side with reviewers for scientific units. In table 1, please change ng g hour-1 to nmol g hour-1; in addition, Please change methane flux unit as nmol methane per gram soil throughout the manuscript.
(6) Table 2 could be placed as supplementary table or simply deleted, because 16S rRNA gene diversity was not main theme in this study (341F/534R pair and fD1/rD1 pair could then be removed; and M13F and M13R could be briefly described in the materials and methods section
(7) Table 3. It is not common to define ppm by using umol mol-1 because it usually refers to volume/volume. Therefore, it could be revised asµL L-1 throughout the manuscript. In addition, It seems that the authors can simply use percentage. For example, oxygen concentration was actually 14.38%, 4.10% and 2.45% (FAV1 site) at depths of 13cm, 25cm and 50 cm, respectively.
(8) Table 1 and Table 3 can be combined. However, methane consumption data could be shown as a figure (Fig. 2a) and placed side by side with Fig. 2 (original figure 2 could be termed fig. 2b).
(9) Figure 3 can be deleted or moved to supplementary part.
(10) Figure 4 should be placed after Figure 5. And please specify Methylocystis sp. strain Pan1. in growth curve refers to isolate Pan1 in phylogenetic tree. One of the reasons is that the pmoA gene from culture (Fig.5) was shown in Fig.4 phylogenetic tree. Generally speaking, the figure or table must appear at the first place where it is described.

Yours sincerely

Zhongjun Jia

Dear Mr. Gagliano

Thank you for submitting the revised manuscript to BGD. The manuscript has been improved and I still have few minor concerns before publication.

1. About the ppm unit. The authors stated that “In geochemical studies it is widely diffused to express ppm by VOLUME as µmol mol-1 and ppm by weight as µg g-1 or g kg-1, which are unequivocal SI units. …. . Nevertheless, to avoid large numbers we expressed the gas concentration in table 3 in mmol mol-1.
Please note “Mole” is a base unit referring to the amount of substance containing as many elementary entities, and is widely used to describe a practical quantity of material and is the link between the microscopic and macroscopic worlds. Therefore, ppm by VOLUME should not have been mol mol-1.
2. Table 2 could be moved into supplementary table. Methane oxidation activity was determined in surface soil, but not the deep soils in table 2. Table 2 in the ms was mentioned only once. These data are important evidence in support of the statement ‘geothermal soil’. But it is not very necessary to make a separate table. The authors could indeed briefly mention the higher temperature in deeper soils as the note at the bottom of the Table 1, while moving table 2 to supplementary part.
3. All Data could be rounded to three significant figures throughout the ms

Yours sincerely

Zhongjun Jia