Evaluation of crude oil biodegradation using mixed fungal cultures

Abeer R. M. Abd El-Aziz; Monira R. Al-Othman; Sameh M. Hisham; Shereen M. Shehata

doi:10.1371/journal.pone.0256376

Peer Review History

Original SubmissionJune 4, 2021
2 Jul 2021 Decision Letter - Sagheer Atta, Editor PONE-D-21-18480 Evaluation of crude oil biodegradation using mixed fungal cultures. PLOS ONE Dear Dr. Abdelaziz, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Aug 16 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: # L11 The mixed flora of the four isolates has significant biodegradation efficiency up to 73.6%. From this sentence I can imagine that the authors did some attempts, with different yields, mixing the 4 strains…but the sentence, as it is, is not clear. Please rework it. #L16 normal alkanes. Did you mean that the aliphatic carbon chain is open? If so, please change to “straight-chained alkanes” #L27 consists of a sticky liquid structure is a mix of different simple and complex hydrocarbons. Please change to …consist of a sticky liquid where simple and complex hydrocarbons are mixed #L27-28 .it is… There is an exceeding full stop…you should perform little changes to join this sentence to the previous one. #L28-29 Crude oil is an incredibly harmful cancer-causing, exceptionally mutagenic, and comprises of complex teratogenic mixes. The sentence should be reworked. Incredibly and exceptionally are not appropriate because the risks associated with crude oil are well known. So, I suggest synthesizing the concept as follows: Crude oil has recognized carcinogenic, mutagenic and teratogenic effects. #L30-31 It is viewed as a critical risk to ecosystems, and after a spill, it takes numerous years or a longer time to recuperate from the ensuing natural issues [3]. Rework the sentence, please. #L32 This requires the utilization of ideal strategy, such as bioremediation methods, that are environmentally friendly – bioremediation methods are by definition “environmentally friendly” #L40 Fungal, bacterial, and yeast consortia … Yeast are fungi. so that, the sentence sounds redundant #L43-46 In these consortia, three strategies of biodegradation are represented: (1) The target hydrocarbon compound is used as a carbon source by fungi; (2) the target hydrocarbon compound is enzymatically attacked but is not used as a carbon source (cometabolism); (3) the target compound is not metabolized at all but is absorbed and accumulated within the fungi (bioaccumulation). biodegradation should be changed to bioremediation; the capital letter is not necessary #L58-63 the work’s aims should be reported synthetically as a bullets list. I mean in this section you must give information on what is the current know-how, what you want to achieve and very fast how….in these lines you what you did but not why. #L78 (Victoria, Australia). You missed the supplier name and the spectrophotometer model #L79 the same idea was applied …you are not applying an idea but a method #L82 you are not preparing a suspension, you are preparing the inoculum. So, please change this title accordingly #L85 100 rev. Did you mean 100 rpm? #L105 Are there replicates for each enzyme measured? #L110 Cellulase activity (Cx) was determined [20]; cellulose activity (Cx) was measured as a reduction in sugar. Please check there is an exceeding cellulase activity. Reviewer #2: I have suggested some corrections which are necessary to make this manuscript more fashionable and easy to understand for readers. This suggested corrections are highlighted in original submission file. Authors should revise their manuscript as per my recommendation and also cite some fresh references for this study. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: PONE-D-21-18480.pdf https://doi.org/10.1371/journal.pone.0256376.r001
Revision 1
27 Jul 2021 Author Response Responses to reviewer 1 # L11 the mixed flora of the four isolates has significant biodegradation efficiency up to 73.6%. From this sentence I can imagine that the authors did some attempts, with different yields, mixing the 4 strains…but the sentence, as it is, is not clear. Please rework it. Response: I correct sentence into “The mixed fungal of the four isolates have a powerful tool for biodegradation up to 73.6% of crude oil (1%, w/v) in 14 days” #L16 normal alkanes. Did you mean that the aliphatic carbon chain is open? If so, please change to “straight-chained alkanes” Response: No, i mean all normal alkanes compound not straight-chained alkanes #L27 consists of a sticky liquid structure is a mix of different simple and complex hydrocarbons. Please change to …consist of a sticky liquid where simple and complex hydrocarbons are mixed Response: I do #L27-28 it is… There is an exceeding full stop…you should perform little changes to join this sentence to the previous one. Response: I merge between two sentences #L28-29 Crude oil is an incredibly harmful cancer-causing, exceptionally mutagenic, and comprises of complex teratogenic mixes. The sentence should be reworked. Incredibly and exceptionally are not appropriate because the risks associated with crude oil are well known. So, I suggest synthesizing the concept as follows: Crude oil has recognized carcinogenic, mutagenic and teratogenic effects. Response: I change into “Crude oil has recognized carcinogenic, mutagenic and teratogenic effects” #L30-31 It is viewed as a critical risk to ecosystems, and after a spill, it takes numerous years or a longer time to recuperate from the ensuing natural issues [3]. Rework the sentence, please. Response: I rework of sentence “It is regarded as a significant threat to ecosystems, and after a spill, it will take several years to recover from the environmental issues that result” #L32 This requires the utilization of ideal strategy, such as bioremediation methods, that are environmentally friendly – bioremediation methods are by definition “environmentally friendly” Response: I change sentence #L40 Fungal, bacterial, and yeast consortia … Yeast are fungi. so that, the sentence sounds redundant Response: I remove Yeast #L43-46 In these consortia, three strategies of biodegradation are represented: (1) The target hydrocarbon compound is used as a carbon source by fungi; (2) the target hydrocarbon compound is enzymatically attacked but is not used as a carbon source (cometabolism); (3) the target compound is not metabolized at all but is absorbed and accumulated within the fungi (bioaccumulation). biodegradation should be changed to bioremediation; the capital letter is not necessary Response: I change the word #L58-63 the work’s aims should be reported synthetically as a bullets list. I mean in this section you must give information on what is the current know-how, what you want to achieve and very fast how….in these lines you what you did but not why. Response: The work aims (1) evaluated four fungal isolates which were isolated from date palm soil, individually and in various combinations to biodegrade crude oil, (2) effects of a variety of environmental factors containing crude oil concentration, incubation temperature, initial pH, biodegradation time, and salinity, on the biodegradation of crude oil, (3) we investigated the performance of the best fungal consortium on the biodegradation of normal alkanes (n-alkanes) and polycyclic aromatic hydrocarbons (PAHs) by GC–MS. I write about the current know-how between line 38-48. #L77 exceeding full stop Response: I remove it #L78 (Victoria, Australia). You missed the supplier name and the spectrophotometer model Response: I write (Biochrom Libra S22, Victoria, Australia) #L79 the same idea was applied …you are not applying an idea but a method Response: I change word #L82 you are not preparing a suspension, you are preparing the inoculum. So, please change this title accordingly Response: I change word #L85 100 rev. Did you mean 100 rpm? Response: Yes, rpm L88 For all crude oil biodegradation tests, the fungal suspension was used as a biodegrade agent. This sentence is not necessary, please discard Response: Yes, I discard #L92 The combinations were divided into four groups: The first group contained individual isolate. As stated previously, you perform the first run of experiments using a single isolate each, then you performed the test in combination. So that the sentence above has a contradiction: combination vs individual isolate the same as in table 1 where the author's purpose consortium 1-4 a single strain. It cannot be, it is a contradiction in terms! Response: No, contradiction my sentence is “The combinations were divided into four groups: The first group contained individual isolate, the second group contained two isolates, the third group contained three isolates, and the fourth group contained all four isolates”. It is clear #L105 Are there replicates for each enzyme measured? Response: Yes #L110 Cellulase activity (Cx) was determined [20]; cellulose activity (Cx) was measured as a reduction in sugar. Please check there is an exceeding cellulase activity. Response: Yes, I correct it to cellulase activity (Cx) Responses to reviewer 2 # L26-28 “crude oil, important fossil fuel and non-renewable energy…. petrochemical industry” Re-write it. As it looks confusing. Response: I re-write sentence to be “Crude oil, important fossil fuel and non-renewable energy source. It consists of a sticky liquid where simple and complex hydrocarbons are mixed. It is a source of various types of fuels and chemical feedstock for the petrochemical industry” #L40-45 “many researchers are improving fungal consortia for…… hydrocarbons as sole carbon sources” is this only single method? Response: No, this is summary of three basic strategies of bioremediation #L46-53 Fungi can provide powerful and unique of biodegrading…… hydrocarbon biodegradation ability” Re-write this sentence. citation should be according to journal style.? Response: Ok, I re-write this sentence according to journal style #L69-75 “A conical flask inoculated by one…… from blue to colorless” Any citation for this methodology. Response: Yes, the citation is [15] at the end of paragraph #L92 “was completed in compliance with [18]” old citation. Response: I update citation to Chen et al., 1017. #L145 “Molecular Identification” How you identify these fungal species? Response: I mention the method at 2.1. Fungal Isolates identification (materials and methods), i repeat it in 3.1. Molecular identification based on internal transcribed spacer (ITS) regions #L159 “crude oil biodegradation trial by DCPIP” Which marker was used? Response: I mention the marker at 2.2. Crude oil biodegradation, the marker is DCPIP (2,6-dichlorophenol indophenol #L191-200 “biodegradation mechanism depends……..enzymatic biodegradation” Revise this sentence. It looks repeated. Response: No, repeat From 191- 195 the paragraph mentions the mechanisms of fungi to attack low and high molecular-weight of hydrocarbon From 195-200 the paragraph mentions the classification of hydrocarbon compounds attack by fungi #L217-220 “the application of microbial mixed cultures ……. other mixed cultures” What you want to say in this sentence. looks confusing for readers. Response: We have two kinds of mixed cultures (MC) first one mixed of fungal isolates (FMC) or mixed of bacterial isolates (BMC), the second is mixed of fungal and bacterial (FBMC) and the last one has the powerful potential for a biodegradation #L324-338 “Table 13 presents the variation in……… with a biodegradation of more than 50.00% of PAHs” These section doesn't show the results explanation. Properly explain your results and then discuss it with others. Response: I think this section showed results and make discuss by two references #L364-373 “In this study, four oil-degrading………………. clear high than that of PAHs (56.8%)” Is this conclusion? If not, then add conclusion. Response: Yes, It is conclusion Attachments Attachment Submitted filename: Responses to reviewer 1 and 2.docx https://doi.org/10.1371/journal.pone.0256376.r002
5 Aug 2021 Decision Letter - Sagheer Atta, Editor Evaluation of crude oil biodegradation using mixed fungal cultures. PONE-D-21-18480R1 Dear Dr. Abdelaziz We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Sagheer Atta, Ph.D Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: (No Response) Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: (No Response) Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: (No Response) Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: (No Response) Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: (No Response) Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: (No Response) Reviewer #2: (No Response) ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No https://doi.org/10.1371/journal.pone.0256376.r003
Formally Accepted
16 Aug 2021 Acceptance Letter - Sagheer Atta, Editor PONE-D-21-18480R1 Evaluation of crude oil biodegradation using mixed fungal cultures Dear Dr. El-Aziz : I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Sagheer Atta Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0256376.r004

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