Talk:WikiJournal of Science/Bioclogging
WikiJournal of Science
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It was adapted from the Wikipedia page Bioclogging and contains some or all of that page's content licensed under a CC BY-SA license. Post-publication review comments or direct edits can be left at the version as it appears on Wikipedia.
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DOI: 10.15347/WJS/2024.002
QID: Q116782181
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Katsutoshi Seki (14 February 2024). "Bioclogging". WikiJournal of Science 7 (1): 1. doi:10.15347/WJS/2024.002. Wikidata Q116782181. ISSN 2470-6345. https://upload.wikimedia.org/wikiversity/en/a/aa/Bioclogging.pdf.
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Wikipedia: This work is adapted from the Wikipedia article Bioclogging (CC BY-SA). Content has also subsequently been used to update that same Wikipedia article Bioclogging.
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This is an open access article distributed under the Creative Commons Attribution ShareAlike License, which permits unrestricted use, distribution, and reproduction, provided the original author and source are credited.
Andrew Leung 
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Edwin Saavedra Cifuentes
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Article information
Peer review 1
reviewer-annotated pdf
Review by Edwin Saavedra C 
, PhD Candidate, Northwestern University
These assessment comments were submitted on , and refer to this previous version of the article
This preprint is a fine introduction to the topic of bioclogging, framed as the loss of permeability in porous media due microbial growth. It gives a clear definition of the term, and then expands in the description section. The "Field observation" section touches on multiple examples of bioclogging in natural and constructed environments, and it is a great list with the potential to be expanded by the community in the wiki. Overall, the article is succinct and informative, and I believe it should be accepted after the attached comments are addressed.
- I would like to express my gratitude for your valuable comments on the manuscript. In response, I have revised the manuscript in accordance with your suggestions. Below, you will find my detailed responses to each of your individual comments.
- Abstract
- [E1]: (Comment) The examples cover constructed systems, but bioclogging also occurs in natural systems like riverbeds and soils.
- (Reply) Following your suggestion, description of "natural systems such as riverbeds and soils" was added.
- [E2]: Or to enhance soil mechanic properties.
- The description of "or to enhance soil mechanic properties" was added.
- [E3R2]: Possible relevant source: doi:10.1007/s11157-007-9126-3
- The reference was added in the "Field observation" section.
- [E1]: (Comment) The examples cover constructed systems, but bioclogging also occurs in natural systems like riverbeds and soils.
- General description
- [E4]: I recommend not putting these times as they are highly dependent on the system conditions: nutrient and electro acceptor availability, microbes biofilm formation proneness, initial conditions, etc.
- The description is based on Allison's work, which is based on various experiments at the time. However, as Allison's work was cited at the previous sentence, it was not clear. I modified the sentence to make this point clear. I added Allison's desctiption "After initiating field or laboratory tests, the permeability decreases to a minimum. On highly permeable soils this initial decrease is small, or nonexistent, but for relatively impermeable soils, permeability decreases for 10 to 20 days" to show that this stage may not be present in all condition. I also added a desctiption "This description is based on an experiment conducted at that time, and the actual process of bioclogging depends on system conditions, such as nutrient and electron acceptor availability, microbial biofilm formation propensity, initial conditions, etc."
- [E5]: These are separate processes that are not covered by bioclogging. I think it would be better to keep the Bioclogging article focused on that topic, and just redirect to other resources about physical and chemical clogging, which can be whole topics on their own.
- Following your suggestion, I focused on the description of bioclogging. Physical and chemical causes are only briefly described now.
- [E4]: I recommend not putting these times as they are highly dependent on the system conditions: nutrient and electro acceptor availability, microbes biofilm formation proneness, initial conditions, etc.
- Field observation
- [E6]: This could be expanded. Bioclogging not only affects aquifer recharge, but plays an interesting role in the dynamics of surface water and groundwater connection.
- To be replied with the next suggestion.
- [E7R6]: Here is a relevant source on the topic that could be mentioned: doi:10.1029/2019WR024826
- This is an interesting aspect that I was not aware of. I added the reference and discussed it.
- [E8]: It would be worth expanding this idea. Bioclogging does not only modify soil hydraulic properties (like permeability) but also mechanical properties, like cohesion and resistance.
- In the original manuscript I did not mention biocementing, but as it is a closely related phenomena, I described biocementing at the last paragraph.
- [E6]: This could be expanded. Bioclogging not only affects aquifer recharge, but plays an interesting role in the dynamics of surface water and groundwater connection.
- Katsutoshi Seki (discuss • contribs) 09:03, 14 January 2024 (UTC)
Peer review 2
reviewer-annotated pdf
Review by researcher in the field of microclimate, ecosystem function and nature conservation ,
These assessment comments were submitted on , and refer to this previous version of the article
- I would like to express my gratitude for your valuable comments on the manuscript. In response, I have revised the manuscript in accordance with your suggestions. Below, you will find my detailed responses to each of your individual comments.
- Abstract
- [m2]: (Comment) This is not well connected to the rest. A context is needed.
- (Reply) I have revised the sentence to clarify the context in which bioclogging can be beneficial.
- [m2]: (Comment) This is not well connected to the rest. A context is needed.
- General description
- [m3]: Not only, if there is less water available it will also lead to reduced rates. Please be more specific.
- As it is a "ponded infiltration", it is clear that we are talking about infiltration in saturated condition, where the infiltration rate depends on saturated hydraulic conductivity, not on the water content.
- [m4]: I think that this sentence is about the history of studying bioclogging? If so it should be formulated accordingly.
- The description is based on Allison's work, which is based on various experiments at the time. However, as Allison's work was cited at the previous sentence, it was not clear. I modified the sentence to make this point clear.
- [m5]: Please add since when…
- The description of the 1st stage was expanded based on Allison's work.
- [m6]: Why talk now about clogging which is more general than bioclogging? I would suggest a general statement of few sentence about clogging in the section that could be view as “history of Biolclogging” and removing this section below. Ot just focusing on item 3 in the list.
- In the revised manuscript, I focused on item 3 in the list, and only briefly mentioned other causes of clogging.
- [m3]: Not only, if there is less water available it will also lead to reduced rates. Please be more specific.
- Field observation
- [m7]: Of what?
- It is a section about "Field observations of bioclogging". As it is an article about bioclogging, I think it can be ommitted.
- [m8]: Is this needed for the structure of the article?
- The section of "Under ponded infiltration" and "Horizontal flow" were removed and merged.
- [m9]: This sentence does not connect well to the previous sentence.
- The sentence was removed because it does not give much insight without proper description of specific field condition.
- [m10]: “The organic material causing bioclogging is sometimes…”
- The sentence was modified according to your suggestion.
- [m11]: This is too short to stand alone. Please unite all 3 subsections here under “field problems and countermeasures” to what coherent paragraph. The aspect of countermeasures is very weak. Please extend.
- In response to your feedback, I have integrated the "Field observation" section into "Field problems and countermeasures" and "Benefits" sections. This restructuring, as referenced in [m16], [m17], and [m18], allows for a clearer and more comprehensive overview of the issues and their respective solutions. Additionally, I expanded the content on countermeasures, drawing upon insights from Song et al. (2020). While the information about river systems presented a categorization challenge, I opted to include it in the "problems" subsection, ensuring that it contributes to the overall context without standing in isolation. This approach maintains the focus on field-related issues and their respective solutions, while also highlighting the benefits observed in various scenarios.
- [m12]: On what?
- Clarified as "influence hydrological process".
- [m13]: Reducing water loss?
- "for reducing water loss" was added.
- [m14]: To what purpose?
- I added description about several properties related to geotechnical engineering; porosity, hydraulic conductivity and shear strength, which is mentioned in the reference.
- [m15]: In what way? This statement is unclear.
- By the modification with the next point [m16], the sentence comparing the vertical flow was removed.
- [m16]: This section is unclear. Why not merging it with the benefits section above?
- The section of "Horizontal flow" was removed and the description of the constructed wetlands was moved to "benefit" section.
- [m17]: Perhaps move it to problems above? I understand that the author wishes to partition the water movement direction into section of different relevance but there is too little material to support this structure in my opinion.
- The section of "Water withdrawal from the well" was moved to "Field problems and countermeasures" section.
- [m18]: I would have moved it to benefits. Also contamination was already addressed earlier – another reason to merge.
- The section of "Oil recovery" was moved to "Benefits" section.
- [m7]: Of what?
- Katsutoshi Seki (discuss • contribs) 09:04, 14 January 2024 (UTC)
Review by researcher in the field of microclimate, ecosystem function and nature conservation ,
These assessment comments were submitted on , and refer to this previous version of the article
"The change in permeability with time is observed in various field situations. Depending on the field condition, there are various causes for the change in the hydraulic conductivity, physical (suspended solids, disintegration of aggregate structure, etc), chemical (dispersion and swelling of clay particles), and biological causes. Biological causes are listed as follows. Usually bioclogging means the first of the following, while bioclogging in a broader sense means all of the following."
Where I would suggest instead:
"The change in permeability with time is dependent on the field condition and there are various causes for the change in the hydraulic conductivity, including physical (suspended solids, disintegration of aggregate structure, etc), chemical (dispersion and swelling of clay particles), and biological causes (as listed above). Usually bioclogging means the first of the following, while bioclogging in a broader sense means all of the following: "
"Field Observations"
In " Field Observations" sections I feel that two lists would be more suitable with a general sentence followed by items 1 - 4... Right now it is too fragmented.
Thank you for your comments. I revised the manuscript as suggested; "as listed above" was modified to "as listed below".
Plagiarism check
Pass. Report from WMF copyvios tool detected stock phrase overlap such as "microbial cells", "disintegration of aggregate structure", "microbial enhanced oil recovery" and "extracellular polymeric substance (EPS)" that are relevant to the topic presented. OhanaUnitedTalk page 04:43, 6 January 2024 (UTC)