Phytophthora Communities Associated with Agathis australis (kauri) in Te Wao Nui o Tiriwa/Waitākere Ranges, New Zealand

Round 1

Reviewer 1 Report

In general, the paper will be a good addition to the literature on Kauri dieback. A few comments below.

Introduction – enough background information and objectives clearly stated.

Materials/methods – The paragraphs (lines 123-140) about site history could go in the introduction.

Enough detail provided to repeat experiments. In the sections on sequencing provide the approximate length in bp of the regions being sequenced, or put this info in a table.

Results - large number of soil samples for eDNA but relatively low detection of P. spp. compared to other studies mentioned in introduction.

Discussion – mostly addressed questions/problems with data.

Explain or speculate about the bias for P. cinnamomi and how this affects the overall results, such as the low number of species detected compared to other studies (L. 670 paragraph). Is this related to the nested PCR enrichment?

Do you recommend using RPS10 since the number of reads was so low compared to ITS?

L. 619 – in what way will P. cinnamomi have a greater impact with climate change?

L. 624 – how are their mechanisms for dispersal similar?

Supplementary table 2 (labeled S1) for RPS10.

Author Response

1. Introduction – enough background information and objectives clearly stated.

2- Materials/methods – The paragraphs (lines 123-140) about site history could go in the introduction. 

Response: This has been moved. 

3. Enough detail provided to repeat experiments. In the sections on sequencing provide the approximate length in bp of the regions being sequenced, or put this info in a table.

Response: this has been added in the methods 

4. Results - large number of soil samples for eDNA but relatively low detection of P. spp. compared to other studies mentioned in introduction.

5. Discussion – mostly addressed questions/problems with data.

6. Explain or speculate about the bias for P. cinnamomi and how this affects the overall results, such as the low number of species detected compared to other studies (L. 670 paragraph). Is this related to the nested PCR enrichment?

Response: A comment was added on line 637

7. Do you recommend using RPS10 since the number of reads was so low compared to ITS?

Response: I think the sequencing results from the providers we used are an unfair representation of the RPS10 primer set and it has worked well in previous studies. I wouldn't use it again with the same sequencing providers.  

8. Line 619 – in what way will P. cinnamomi have a greater impact with climate change?

Response: The sentence on line 580- 582 was edited for clarity 

9. Line 624 – how are their mechanisms for dispersal similar?

Response: The fact that they are both soil-borne and have resistant resting spores means they would both be moved with any soil movement - therefore, expect correlated distribution.

10. Supplementary table 2 (labeled S1) for RPS10.

Response: This was corrected

Reviewer 2 Report

The paragraph between lines 123 to 140 of the material and methods chapter should be moved to the introduction chapter since it does not correspond to any methodology

Author Response

Comment: The paragraph between lines 123 to 140 of the material and methods chapter should be moved to the introduction chapter since it does not correspond to any methodology.

Response: This has been moved 

Reviewer 3 Report

My comments can be found in the attached MS. 

Comments for author File: Comments.pdf

My comments can be found in the attached MS.

Author Response

Comment 1: move the paragraph starting on line 123 to the introduction.

response: This has been moved. 

Comment 2: italicize "Phytophthora" in the subtitles 3.4 and 3.4.1 

Response: The rest of the subtitle is italicized, so the word Phytophthora should not be 

Comment 3: Make figure 3 larger: 

Response: This should occur during publication by the journal; we will submit a high-quality image that can be downloaded for easier viewing. 

Comment 4: The sentence on line 696 would be best at the beginning of the discussion. 

Response: Agree, thank you. This edit has been made.

Reviewer 4 Report

A partly annotated version is enclosed for revision. The authors must eliminate all the personalization in the manuscript and mention the possibility of association of other pathogen to the described disease since the data presented show that the pathogens studied are also present in asymptomatic plants and the rate between their presence and the disease is not sufficient to establish a close relationship between them.

Comments for author File: Comments.pdf

Minor revisions are suggested in the annotated manuscript mainly to improve clarity.

Author Response

1. Change title

Response: There is a point that the current title narrows the scope and readership, but it is also important not to overstate the scale of the study as this paper is not talking about Phytophthora communities in all NZ kauri forests.

2. Clarify the sentence on line 32 

Response: more details were added 

3. The authors must eliminate all the personalization in the manuscript

Response: This was corrected

4. Comment about remote sensing details on line 141 

Response: more details were added 

5. Comment about the sampling timeframe being inappropriate time for this temperature is too low

Response: While most Phytophthora agathidicida survey work is focussed during autumn and spring to avoid wet conditions that increase the risk of pathogen spread, P. agathidicida is isolated from kauri forests year-round. 

6. Primers used for sequencing must be reported

Response: The details are on lines 194 - 195. 

7. Nested PCR instead of second-round PCR. Line 228

Response. Either is ok, in the Burgess et al. 2022 paper (number 81 in the ref list), they use this terminology 

8. English is not correct revise (lines 250 to 252) 

Response: corrected 

9. Quantitiative instead of real-time. Line 276 

Response: Either is ok, the original paper from which the P. agathidicida primers were designed (Than et al 2013) used 'real-time' 

10. not very clear missed since the area was difference so the infection did not exit the original area? Please clarify line 622 

Response: removed for clarity, not suitable to try and link inoculum loads in rivers with our study. Thanks 

11. The presence of other pathogens could be associated with the dieback? This part must be elucidated better with more explanation in introduction for example and also searching other pathogens such as those insect transmitted and not only soil transmitted. 

Response: The argument was strengthened in the paragraph starting on line 516 and in the discussion and conclusions. Line 103 also notes to not rule out other potential pathogens. 

12: Line 694 in conclusion not well presented in the manuscript please improve this part in the results. 

Response: Edited in results