Articles | Volume 10, issue 2
https://doi.org/10.5194/soil-10-521-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.Improving measurements of microbial growth, death, and turnover by accounting for extracellular DNA in soils
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- Final revised paper (published on 19 Jul 2024)
- Supplement to the final revised paper
- Preprint (discussion started on 10 Nov 2023)
- Supplement to the preprint
Interactive discussion
Status: closed
Comment types: AC – author | RC – referee | CC – community | EC – editor | CEC – chief editor
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RC1: 'Comment on egusphere-2023-2302', Anonymous Referee #1, 15 Dec 2023
- AC2: 'Reply on RC1', Jörg Schnecker, 02 Feb 2024
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RC2: 'Comment on egusphere-2023-2302', Anonymous Referee #2, 05 Jan 2024
- AC1: 'Reply on RC2', Jörg Schnecker, 02 Feb 2024
Peer review completion
AR: Author's response | RR: Referee report | ED: Editor decision | EF: Editorial file upload
ED: Revision (05 Feb 2024) by Ember Morrissey

AR by Jörg Schnecker on behalf of the Authors (10 Mar 2024)
Author's response
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ED: Referee Nomination & Report Request started (11 Mar 2024) by Ember Morrissey
RR by Anonymous Referee #3 (15 May 2024)

ED: Publish subject to minor revisions (review by editor) (16 May 2024) by Ember Morrissey

AR by Jörg Schnecker on behalf of the Authors (16 May 2024)
Author's response
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ED: Publish as is (30 May 2024) by Ember Morrissey

ED: Publish as is (03 Jun 2024) by Jeanette Whitaker (Executive editor)

AR by Jörg Schnecker on behalf of the Authors (03 Jun 2024)
Author's response
Manuscript
This a great paper, I recommend to accept with minor revisions
General comments:
In this study, the authors aimed to assess and compare methods for extracting extracellular DNA (eDNA) in soil samples to better quantify microbial growth, death, and turnover. Two methods, eDNA digestion by DNase and sequential extraction, were tested. The DNase method resulted in a substantial reduction in total DNA (78.2%), and its effectiveness varied across replicates. Sequential extraction, on the other hand, yielded 23.1% less total DNA on average compared to regular DNA extraction. Following these findings, the researchers decided to use sequential extraction for further experiments due to its consistent performance and the potential interference of the DNase method with temperature treatments. Notably, the amounts of eDNA recovered with sequential extraction were found to be 2.4% in agricultural soils and 6.5% in forest soils, contributing novel insights to the field, especially considering the lower end of the range observed in other studies. The study also delved into the temporal dynamics of DNA pools and 18O enrichment during incubation with labeled water. The results suggested that eDNA in agricultural soil might be primarily derived from microbial death, contrasting with the forest soil where eDNA appeared to be actively exuded from the beginning. This observation adds a significant dimension to our understanding of eDNA dynamics in different soil types. In the second part of the study, the researchers explored the temperature response of microbial processes, including biomass, DNA pools, and microbial activity. Notably, they found that the use of 18O incorporation in DNA combined with sequential DNA extraction allowed for a comprehensive analysis. The study revealed temperature-dependent changes in microbial biomass, iDNA, and eDNA contents, providing valuable insights into the ecological implications of temperature variations on microbial communities. Overall, this work presents a thorough investigation into eDNA extraction methods and the temperature effects on microbial processes, introducing new perspectives and highlighting the potential impact of these findings on our understanding of soil ecology. The combination of innovative techniques and insightful results contributes to the novelty and significance of this research. This work is a good starting point for future research to explore more soils with greater replication.
Specific comments:
Introduction
The introduction is clearly written. Below I suggest minor changes.
L53-56 – Run-on sentence consider rephrasing to improve readability.
L64 – Starting a sentence with eDNA is odd.
L76 – Some examples of this application would be nice (either here or later in the discussion)
L82-85 – Sentence could be more concise to improve readability e.g. “Around 30 ℃ is considered the optimal temperature for microbial activity in many soils (Birgander et al., 2018; Nottingham et al., 2019; Rousk et al., 2012) , while 45 ℃ has been demonstrated to reduce microbial process rates compared to temperatures below 30 ℃ (Cruz-Paredes et al., 2021; Rousk et al., 2012).
Methods
Methods are thorough and descriptive, no significant changes requested.
L142 – Shouldn’t this be ‘Dynamics of eDNA and iDNA over time at constant temperature’?
Results and Discussion
I provide the following suggestions in the hopes of improving the understandability of the results: