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Both reviewers are happy with your revision. Therefore, I congratulate you and have recommended acceptance of your work.
[# PeerJ Staff Note - this decision was reviewed and approved by Dezene Huber, a PeerJ Section Editor covering this Section #]
Both reviewers are happy with your revision. Therefore, I congratulate you and have recommended acceptance of your work.
# PeerJ Staff Note: Although the paper is now scientifically acceptable, a final check by Dezene Huber (the Section Editor for this article) has shown that the English language needs further improvement. We request that you revise the English one final time.
#
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The authors have done well in revising the ms and addressing those of my comments on the earlier version of the ms. I would be happy to recommend the acceptance of the revised ms for publication in the journal.
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Please pay attention to the comments from all three reviewers, particularly 2 and 3. They all raised critical concerns for revision. I will be happy to reconsider it after a thorough and careful revision.
[# PeerJ Staff Note: Please ensure that all review comments are addressed in an appropriate rebuttal letter, and please ensure that any edits or clarifications mentioned in the rebuttal letter are also inserted into the revised manuscript (where appropriate). Direction on how to prepare a rebuttal letter can be found at: https://peerj.com/benefits/academic-rebuttal-letters/ #]
The manuscript investigated the soil properties and fungal community composition from different continuous cropping years of alfalfa fields. The authors found significant variations of soil physiochemical properties, fungal community in soil samples less than 10 years and more than 10 years. They also found alfalfa continuous cropping increased the relative abundances of some plant pathogens, and soil total P, available P contents were the important soil factors in affecting the soil fungal community.
The topic is original, and the logic is clear. In general, the manuscript is well written with few grammatical and type errors. However, it seems that several defects are still included in this manuscript.
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Introduction
1. Lines 70-72: “However, a long-term survey showed that the contents of soil organic carbon, total nitrogen, available phosphorus and soil nitrate nitrogen decreased within 10 years of continuous cropping of alfalfa, but then increased after alfalfa grew more than 10 years” Please give a detailed explanation about this phenomenon instead of simply describing the results .
Materials and methods
2. Line 172: “The Chao richness, Shannon diversity, Simpson diversity” Please use the right alpha diversity noun, such as Richness; Shannon Index et al.
3. Lines 183-185: “The fungal OTUs’ taxonomic information was uploaded to FUNGuild (http://www.stbates.org/guilds/app.php) for functional prediction (Nguyen et al., 2016).”, did you only choose the high accuracy of “Highly Probable” and “Probable”?
Results
4. Line 257: “The number of phylotype ranged from 555 to 746,” referred to observed species (Richness)?
5. Lines 263-264: “In addition, other α-diversity indices of Chao1 richness, Shannon’s diversity and Simpson’s diversity also differed among different treatments (Table 2).” Please use the right alpha diversity noun.
Discussion
6. Line 288: “this result is consistent with the report of Jiang et al. (2007)”; Line 293 “this result was basically consistent with the finding of Dong et al. (2016),” Line 298 “this result was also found in a long-term investigation by Fan et al. (2011),” The authors only declared the result was consistent with other peoples’ study, please explain the underlying reasons about the changes of the soil physiochemical properties.
7. Line 310: “this result is basically consistent with the report of Luo et al. (2018),” please explain why?
8. Lines 380-381: “Similarly, Song et al. (2018) found that the soil fungal community composition was significantly affected by the continuous cropping of Coptis chinensis”, please explain the underlying reasons?
Lack of proper control to attribute the observed results due to the continuous cropping.
My biggest concern for this paper is the experimental design. Basically, this paper lack proper control. Authors did not mention the details of the field set up (from line 107-109) and my understanding is each treatment only has one area (more than 900 m2). It will be nice to see how the treatment arrangement. Were these treatment randomly arranged? How much apart between two treatments? Authors did sample 3 samples from each treatment (each sample from ~300 m2). Thus, the replication is not a proper replication. In addition, authors did not include any control (year 0 for each treatment, so the change of soil properties or shift of microbial communities can be attribute to the alfalfa growing, or a nearby soil samples from each treatment at least can give readers the variability of the fields in that area). Assumption of these sites started with same soil properties is not valid.
Regarding figures and tables, authors did not mention what is the data in the tables/figures and what is the error bar. Are they present as mean+/- s.e.? How many reps do they use… How the data from figure 3 comes from? Did the authors simply use mean from 3 samples?
Methods section:
Please provide the detailed field design. I assume alfalfa was monoculture? And no grazing on the site? Line 114, alfalfa was mowed to the soil surface twice in June and August…. Did the material got removed or remained on site? Line 124: the other was dried in the room for soil properties analysis. Did all the soil chemical analysis done using room temperature dried soil (e.g., KCl extraction)?
Fungal MiSeq data: for alpha diversity, authors randomly resampled the sequence depth to the same level. However, other analysis was done by the original sequences. Why not use all re-sampled to the same depth data for all the fungal analysis?
In a number of places, authors indicate continuous cropping affect soil fungal community via changing soil properties (e.g., Line 374-375, 392-393). Is it possible that continuous cropping can have a direct effect on soil fungal communities (e.g., rhizosphere effect) and this effect could also directly shift the soil microbial community overtime. Of course, soil microbial communities can be shifted by the soil properties (and verse vice!). However, authors seem only emphasized on cropping -> soil properties-> microbial community. Fungal activities can indeed influence soil properties as well!
Can authors also explain why they not include bacterial communities here?
Line 255-257: not sure I understand the coverage values here.
Yao et al present a study which investigated the soil properties and fungal community composition from different continuous cropping years of alfalfa fields. The extent of the study is rather impressive and certainly is a current hot topic in soil ecology.I appreciate the study and unanimously find it is well written, , but at the same time I am not sure what is novel about it. I think that the study is nice, but lacks the twist to make it novel enough for Peer J.
The study is sound in design and thorough in execution. I think the analyses are quite solid and informative. With this said, I find some aspects of bioinformatics needing further improvement or clarifications.How long is the sequenced amplicon? How long were the paired end sequences? I am also somewhat concerned about sequence data treatise. If my memory serves, CD-HIT performs suboptimally when the data are not truncated to equal lengths as recommended in the original publication. Thus, the richness estimators >1000 OTUs may be partially driven by the data analyses. However, leaving the data without truncating is a rather common practice and I cannot hold it against the authors. Should the authors confirm this my thinking be correct and find it in their benefit to reassess, I would encourage that.
To some extent, I think the findings from this study is not necessarily ground-breaking. I recommend using Social Network Analysis to further determine the differences among fungal community from different continuous cropping years of alfalfa fields.
I think this is potentially an important paper. However, the sequence data and statistical analysis may need to be partial re-done. If these issues can be adequately addressed in revision, the manuscript may be accepted.
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