Changes in Soil Ectomycorrhizal Fungi Community in Oak Forests along the Urban–Rural Gradient
Round 1
Reviewer 1 Report
The manuscript presented for review raises a very interesting topic related to ectomycorrhizal fungi of one of the oak species in China, depending on the place where the oak grew (city-village). Nevertheless, the article contains serious shortcomings, especially the methodology is imprecise, especially with regard to molecular tests. Moreover, the data presented in the publication are not complete. Please see, for example, the publication by Behnke-Borowczyk, J., Kowalkowski, W., Kartawik, N., Baranowska, M. and Barzdajn, W. 2020. Soil fungal communities in nurseries producing Abies alba. Baltic Forestry 26 (1), article id 426. https://0-doi-org.brum.beds.ac.uk/10.46490/BF426 and properly describe the sampling - their size, how was the DNA extracted? what starters were used? what the reaction mixture looked like, etc. Please complete this section. Specific remarks: Summary summary statement (repeated in conclusion): "Overall, these results can provide important base for the protection of ectomycorrhizal fungi diversity and the management of ecological environment along with the urban-rural gradient "- it is incomprehensible. Please elaborate on it. Moreover, you did not discover that soil properties influence the communities of fungi. It is nothing new - the authors of this publication only confirmed this - you write about it in the introduction. The keywords repeat the words contained in the title, please change them. In the introduction, see line 45 - no quotation. Line 57 - oak is not a species, but Genus! And the taxa of the genus Quercus are not only found in China. Practical tips are written for research purposes, but there is no such article at all. There are no research hypotheses in the article. Was the entire community of soil fungi analyzed? Why was only the soil tested? What about fine roots? Since only soil was tested, the title should rather indicate that soil fungi were tested ... On what basis was the taxa found to belong to the ECM? What source was used to verify the mushroom nomenclature? It would be interesting to indicate how the gradient also changes in other groups of fungi, e.g. saprotrophs, pathogens, etc. Why has not the species been identified? How many taxa have been identified at all? Figure 4 is illegible. The post-completion discussion should be rewritten, it is more like recounting the results. The chapter Conclusions rather summarizes the results, and the authors provide very general statements, with no idea how to use the knowledge they have gained in practice, although they refer to practice.
Author Response
Point 1: The manuscript presented for review raises a very interesting topic related to ectomycorrhizal fungi of one of the oak species in China, depending on the place where the oak grew (city-village). Nevertheless, the article contains serious shortcomings, especially the methodology is imprecise, especially with regard to molecular tests.
Response 1: We have added detailed molecular test in lines 138-156, page 3-4 according to the suggestion. Thanks.
Point 2: Moreover, the data presented in the publication are not complete. Please see, for example, the publication by Behnke-Borowczyk, J., Kowalkowski, W., Kartawik, N., Baranowska, M. and Barzdajn, W. 2020. Soil fungal communities in nurseries producing Abies alba. Baltic Forestry 26 (1), article id 426. https://0-doi-org.brum.beds.ac.uk/10.46490/BF426 and properly describe the sampling - their size, how was the DNA extracted? what starters were used? what the reaction mixture looked like, etc. Please complete this section.
Response 2: We have added the reference of the paper “Soil fungal communities in nurseries producing Abies alba” in lines 68-70, page 2. Three independent sample plots were established in the urban, suburban and rural Quercus acutissima forest of Jinan city, respectively. Each plot was 20 × 20 m; and the distances were more than 1000 m each other. We collected the soil samples (four soil cores from the east, west, south and north direction) around the tree with a 3.5 cm-diameter soil auger. We have added the sampling information in line 104 and lines 109-113 of page 3. We have clarified how the DNA was extracted in line 138, page 3, what starters were used in lines 140-143, page 4, and what the reaction mixture looked like in lines 143-145, page 4. Thank you.
Point 3: Specific remarks: Summary summary statement (repeated in conclusion): "Overall, these results can provide important base for the protection of ectomycorrhizal fungi diversity and the management of ecological environment along with the urban-rural gradient "- it is incomprehensible. Please elaborate on it.
Response 3: We have elaborated on the summary. Now it has been revised into “Overall, the differences of composition and diversity in urban-rural gradient forest were driven by the differences of soil physicochemical properties resulted from the forest location.” Please see the revised version in lines 22-24, page 1.
Point 4: Moreover, you did not discover that soil properties influence the communities of fungi. It is nothing new - the authors of this publication only confirmed this - you write about it in the introduction.
Response 4: Yes, we did find the soil properties influence the communities of ECM fungi. It is one of the critical phyla to sustain the tree species health and sustainability. Especially, Quercus Spp. is obligate symbiosis with ECM fungi. It will not survive and establish without ECM. We want to explore how the human activities disturb the forest along with urban-rural gradient and change the ECM fungi. We wrote about influencing factors of ECM fungal diversity in the introduction and found there was little information on ECM fungal communities along with urban-rural gradient. Therefore, in this study, we emphasized the correlation between urban-rural gradient and ECM fungi. We also confirmed that pH, soil organic matter, and ammonium nitrogen were the main driving factors of ECM fungal community composition and diversity in Quercus acutissima forest along with urban-rural gradient. We have supplemented the information on the relationship of Quercus Spp. with ECM fungi in lines 60-62, page 2.
Point 5: The keywords repeat the words contained in the title, please change them. In the introduction, see line 45 - no quotation.
Response 5: We have revised the keywords into “Quercus acutissima forest; soil physicochemical properties; community structure; LEfSe analysis; driving factors”. We have also added the quotations in the introduction line 45, page 1. Thanks for your comments.
Point 6: Line 57 - oak is not a species, but Genus! And the taxa of the genus Quercus are not only found in China.
Response 6: We have changed the sentence into “Oak (Quercus Spp.) is one of the dominant genus in the boreal forest around the world, which has great ecological and economic values in environmental protection, seedling establishment and wood yield” in lines 58-59, page 2.
Point 7: Practical tips are written for research purposes, but there is no such article at all. There are no research hypotheses in the article.
Response 7: Yes. There is actually such article. We have added the study on the rural-urban gradient method in references of 22 and 23. Urban and rural forests are affected by the location because the climate is different in the city and rural areas. The urban forest is one of the important components in the forestry study. The hypotheses we propose are that the soil properties are different due to the location and human disturbance. These differences will change the composition and diversities in the forests. Thus, we provide the study objectives in this study according to our supposal. We presented 2 aims to explore the changes of ECM community and further reveal the effects of soil physicochemical properties on ECM community along with urban-rural gradient in lines 80-83, page 2.
Point 8: Was the entire community of soil fungi analyzed? Why was only the soil tested? What about fine roots?
Response 8: We have analyzed the soil fungi by high-throughput sequencing of fungal ITS sequences of soil samples. In this study, we tested the soil beneath the forest because we want to obtain the distribution of ECM fungi community in the forest soil rather than its association with trees. Thus, we don’t test the fine roots. We will explore the association of ECM fungi with Quercus Spp. in the further study. Thanks for the suggestion.
Point 9: Since only soil was tested, the title should rather indicate that soil fungi were tested ...
Response 9: We have clarified the title and added the “soil” in the title. Now the title is “Changes of soil ectomycorrhizal fungi community in Oak forest along with urban-rural gradient”.
Point 10: On what basis was the taxa found to belong to the ECM? What source was used to verify the mushroom nomenclature?
Response10: We have applied the RDP database and UNITE database (https://unite.ut.ee/) to classify ectomycorrhizal fungi. Please see the detailed content in lines 156-159, page 4.
Point 11: It would be interesting to indicate how the gradient also changes in other groups of fungi, e.g. saprotrophs, pathogens, etc.
Response 11: We agree that it would be interesting to indicate how the gradient also changes in saprotrophs and pathogens. So, we will consider them in the future studies. However, Quercus acutissima is a typical vegetation that can be associated with ectomycorrhizal fungi. Soil ectomycorrhizal fungi are a key component of microbial communities in forest ecosystems, especially as integral constituents of nutrient cycling. Compared with saprotrophic fungi and pathogens, ectomycorrhizal fungi acquire carbohydrates from living host plants and often have a strong ecosystem specificity [1-2]. Soil conditions changes have been reported to strongly influence the ectomycorrhizal fungal abundance, diversity, and activity [3].
References:
- Rosinger, C.; Sandén, H.; Matthews, B.; Mayer, M.; Godbold, D. Patterns in ectomycorrhizal diversity, community composition, and exploration types in European beech, pine, and spruce forests. Forests 2018 9, https://0-doi-org.brum.beds.ac.uk/10.3390/f9080445
- van der Linde, S.; Suz, L.M.; Orme, C.D.L.; Cox, F.; Andreae, H.; Asi, E.; Atkinson, B.; Benham, S.; Carroll, C.; Cools, N.; De Vos, B.; Dietrich, H.P.; Eichhorn, J.; Gehrmann, J.; Grebenc, T.; Gweon, H.S.; Hansen, K.; Jacob, F.; Kristöfel, F.; Lech, P.; Manninger, M.; Martin, J.; Meesenburg, H.; Merilä, P.; Nicolas, M.; Pavlenda, P.; Rautio, P.; Schaub, M.; Schröck, H.W.; Seidling, W.; Šrámek, V.; Thimonier, A.; Thomsen, I.M.; Titeux, H.; Vanguelova, E.; Verstraeten, A.; Vesterdal, L.; Waldner, P.; Wijk, S.; Zhang, Y.; Žlindra, D.; Bidartondo, M.I. Environment and host as large-scale controls of ectomycorrhizal fungi. Nature 2018, 558, 243– https://0-doi-org.brum.beds.ac.uk/10.1038/s41586-018- 0189-9
- He, J.; Tedersoo, L.; Hu, A.; Han, C.; He, D.; Wei, H; Jiao, M.; Anslan, S.; Nie, Y.; Jia, Y.; Zhang, G.; Yu, G.; Liu, S.; Shen, W. Greater diversity of soil fungal communities and distinguishable seasonal variation in temperate deciduous forests compared with subtropical evergreen forests of eastern China. FEMS Microbiol Ecol 2017 93, fix069. https://0-doi-org.brum.beds.ac.uk/10.1093/femsec/fix069
Point 12 Why has not the species been identified? How many taxa have been identified at all? Figure 4 is illegible. Figure 4 is illegible.
Response 12: We have revised the Figure 4 and made it clear now. A total of 282 ECM fungal OTUs were retrieved from ITS sequence of soil samples collected. These ECM fungi distributed in 3 phyla, 5 classes, 11 orders and 26 genera. Moreover, Figure 4 identified 13 key ectomycorrhizal fungi taxa that might explain the differences among the three forests along with urban-rural gradient (LDA > 4, p < 0.05). Especially, Tuber, Russula and Sordariales were the key groups in respond to more pronounced habitats shifts in the urban, suburban and rural Quercus acutissima forests soil, respectively.
Point 13: The post-completion discussion should be rewritten, it is more like recounting the results. The chapter Conclusions rather summarizes the results, and the authors provide very general statements, with no idea how to use the knowledge they have gained in practice, although they refer to practice.
Response 13: We have rewritten the conclusion. The following is the new conclusion. Thanks for the suggestion.
Soil ECM fungi are fundamental components of forest ecosystem. The three Quercus acutissima forests caused a significant shift in ECM fungal communities and diversity in different habitats, suggesting that different forest management strategies may be needed for microbial biodiversity conservation along with urban-rural gradient. Moreover, the distribution of ECM fungi in the oak forest soil imply that the dominance of ECM fungi is different, which depends on the spatial location. Our results could provide a basic information on forest protection and management along with urban-rural gradient in Jinan city. Therefore, more abundant information about the location-specific relationship between environmental factors and microbial community is urgently needed for effective forest soil management.
Reviewer 2 Report
The paper describes the changes of ECM community composition and diversity along with urban-rural gradient in Quercus acutissima forest. This is an interesting study whose topic suits the targeted journal well and that has the potential to attract the appropriate attention of the journal´s readership.
The paper is original and quite well written, clear and easy to read. From the methodological point of view, the experiment was well designed and the collected empirical material was correctly and statistically analyzed so that the results could be adequately evaluated.
I have only a few, rather editorial, comments.
L 76 „jinan city” should be „Jinan city”
The results section should contain only the results, the commentary on them should be placed in the discussion section. Please transfer those sentences which are not results together with the quoted literature to the discussion section: L 169-171, L 205-207, L209-210, L 221-224, L 271-274
Author Response
Point 1: The paper describes the changes of ECM community composition and diversity along with urban-rural gradient in Quercus acutissima forest. This is an interesting study whose topic suits the targeted journal well and that has the potential to attract the appropriate attention of the journal´s readership.
The paper is original and quite well written, clear and easy to read. From the methodological point of view, the experiment was well designed and the collected empirical material was correctly and statistically analyzed so that the results could be adequately evaluated.
Response 1: Thanks for the encouragement.
Point 2: I have only a few, rather editorial, comments. L 76 „jinan city” should be „Jinan city”
Response 2: We have changed the “jinan city” into “Jinan city”in L 80.
Point 3: The results section should contain only the results, the commentary on them should be placed in the discussion section. Please transfer those sentences which are not results together with the quoted literature to the discussion section: L 169-171, L 205-207, L209-210, L 221-224, L 271-274
Response 3: The results section in original L 205-207, L 209-210 only described the figure 3, so we do not change them. We have transfer these sentences in original L 169-171, L 221-224, L 271-274 with the quoted literature to the corresponding discussion section. Please see in L 315-317, L 340-344, L 429-433. Thanks for your comments.
Round 2
Reviewer 1 Report
Thank you for responding to my review and for supplementing the work with the missing information. I believe the manuscript may be published.
