A comprehensive analysis of chemical and biological pollutants (natural and anthropogenic origin) of soil and dandelion (Taraxacum officinale) samples

Mieczysława Irena Boguś; Anna Katarzyna Wrońska; Agata Kaczmarek; Mikołaj Drozdowski; Zdzisław Laskowski; Anna Myczka; Aleksandra Cybulska; Marek Gołębiowski; Adrianna Chwir-Gołębiowska; Lena Siecińska; Ewelina Mokijewska

doi:10.1371/journal.pone.0280810

Peer Review History

Original SubmissionApril 29, 2022
31 Oct 2022 Decision Letter - Estibaliz Sansinenea, Editor Transfer Alert This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present. PONE-D-22-12598A comprehensive analysis of chemical and biological pollutants (natural and anthropogenic origin) of soil and dandelion (Taraxacum officinale) samples - pathogenic microorganisms and parasites pose a greater threatPLOS ONE Dear Dr. Boguś, 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 Dec 15 2022 11:59PM. 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Kind regards, Estibaliz Sansinenea Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. In your Methods section, please provide additional information regarding the permits you obtained to collect samples for the present study. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. Thank you for stating in your Funding Statement: “This work was supported by the Marshal’s Office of the Mazowieckie Voivodeship grant RPMA.01.02.00-14-5626/16 to the Biomibo company. There was no additional external funding received for this study. Biomibo covered the cost of the salaries of its employees (MIB, AC-G, LS, EM), provided support in the purchase of chemicals, and made laboratory equipment available for all authors. The specific roles of the authors are articulated in the ‘author contributions’ section. The funder did not has any additional role in the study design, data collection, analysis and interpretation, decision to publish, or preparation of the manuscript.” Please provide an amended statement that declares all the funding or sources of support (whether external or internal to your organization) received during this study, as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now. Please also include the statement “There was no additional external funding received for this study.” in your updated Funding Statement. Please include your amended Funding Statement within your cover letter. We will change the online submission form on your behalf. Additional Editor Comments (if provided): The reviewers have commented about several issues that need to be attended. I recommend a major revision of this MS. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. 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 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: No 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: A comprehensive analysis of chemical and biological pollutants (natural and anthropogenic origin) of soil and dandelion (Taraxacum officinale) samples - pathogenic microorganisms and parasites pose a greater threat Although the title and purpose of this manuscript is very interesting, I think that in some cases the correct scientific method was not used. Laboratory methods used for microorganisms are not very clear. Meanwhile, organisms like Francisella grow in specific medium and microaerophilic conditions. Reviewer #2: The present work is a good effort to detect chemical and biological contaminations in soil and dandelion samples using a wide range of analytical methods (GC-MS, LC-MS, voltammetry, 505 microbiological and microscopic techniques, PCR). I agree with its publication. However, herewith I have few suggestions for its improvement • Revise the title for clarity • Make abstract and introduction short • Discussion section needs improvement with more relevant latest articles • Avoid use of pronouns (e.g. we, our etc.,) in the text • Most of the headings are too lengthy. It would be better to shorten headings • Increase visibility of the figures for clarity • Supplementary data has captions while captions of main figures are missing ****** 6. 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Revision 1
8 Jan 2023 Author Response Response to Reviewers Comments to the Author 1. 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 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: No Answer: After addition two supplementary tables (Supplementary Table 6 and 7) containing raw measurements all data underlying the findings presented in the manuscript are fully available. 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: A comprehensive analysis of chemical and biological pollutants (natural and anthropogenic origin) of soil and dandelion (Taraxacum officinale) samples - pathogenic microorganisms and parasites pose a greater threat Although the title and purpose of this manuscript is very interesting, I think that in some cases the correct scientific method was not used. Laboratory methods used for microorganisms are not very clear. Meanwhile, organisms like Francisella grow in specific medium and microaerophilic conditions. Answer: It is difficult to respond to such a general comment because Reviewer #1 did not mention any specific methodological errors that he believed we had made. In this work, very diverse methods were used, from voltammetric determinations of heavy metals through gas and liquid chromatography coupled with mass spectroscopy (GC-MS and LC-MS), microbiological methods and PCR. All these methods are described in detail in the Materials and Methods section. We expect Reviewer #1 to present specific objections to the methods used by us. In microbiological studies, we used classical inoculation methods on commercially available media: Columbia Agar plates with 5% sheep blood (CASB) and Sabouraud Glucose Selective Agar plates (SGSA), both from Becton Dickinson. Half of the inoculated CASB plates were kept aerobically, while the second half was kept anaerobically using the anaerobic jar (Roth) and AnaeroGen ™ sachets (Thermo Scientific). All CASB plates were incubated at 37oC for 24 hours. Following this, the number of colony forming units (CFU) was determined using a SCAN 500 automatic bacterial colony counter (Interscience). The bacteria were Gram stained (Gram Stain Kit, Thermo Scientific) and examined under a microscope to distinguish gram-positive and gram-negative colonies and bacterial morphology as this was a prerequisite for strain identification using an automated Vitek-2 system (Biomerieux). Homogeneous bacterial colonies were applied to correctly-selected Vitek-2 disposable cards. The modern, Vitek-2 automated microbiology system is validated and widely used in clinical microbiology to identify various bacterial strains in diagnostic laboratories and hospitals around the world (https://www.biomerieux-usa.com/vitek-2; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC254354/ ). The composition of the growing media used in the Vitek-2 system cards dedicated various groups of microorganisms is a manufacturer's secret. Francisella tularensis might be grown in defined media such as Chamberlains or in non-selective media such as Mueller-Hinton broth and a modified Brain Heart Infusion (BHI) broth enhances the growth of this microbe (Morris BJ, Buse HY, Adcock NJ, Rice EW. A novel broth medium for enhanced growth of Francisella tularensis. Lett Appl Microbiol. 2017 Jun;64(6):394-400. doi: 10.1111/lam.12725). We do not know which medium is used in the Biomerieux cards for Francisella tularensis identification (manufacturer secret). Reviewer #2: The present work is a good effort to detect chemical and biological contaminations in soil and dandelion samples using a wide range of analytical methods (GC-MS, LC-MS, voltammetry, 505 microbiological and microscopic techniques, PCR). I agree with its publication. However, herewith I have few suggestions for its improvement • Revise the title for clarity Answer: Revised title: “A comprehensive analysis of chemical and biological pollutants (natural and anthropogenic origin) of soil and dandelion (Taraxacum officinale) samples.” • Make abstract and introduction short Answer: The abstract is only 268 words long and is written in a very concise manner. Attempts to shorten it result in a loss of clarity. The Introduction has been shortened in such a way as not to lose important information and clarity of the message, as well as the justification why the research described in this work was carried out. • Discussion section needs improvement with more relevant latest articles Answer: Done • Avoid use of pronouns (e.g. we, our etc.,) in the text Answer: Done • Most of the headings are too lengthy. It would be better to shorten headings Answer: Where possible, subsection titles have been made shorten. • Increase visibility of the figures for clarity Answer: Unfortunately, improving the quality of the Figure 2 and Supplementary Figure 1 is not possible for technical reasons. The quality of the chromatograms depends on the factory software of the GC-MS and LC-MS chromatographs (Shimadzu). The quality of Figures 1, 3, 4 and 5 seems technically satisfactory. • Supplementary data has captions while captions of main figures are missing Answer: The titles of the main figures are placed in the main text according to the editorial requirements of PlosOne i.e. Figure 1 lines 130-134, Figure 2 lines 222-224, Figure 3 lines 249-250, Figure 4 lines 301-302, Figure 5 lines 319-329, respectively. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0280810.r002
10 Jan 2023 Decision Letter - Estibaliz Sansinenea, Editor A comprehensive analysis of chemical and biological pollutants (natural and anthropogenic origin) of soil and dandelion (Taraxacum officinale) samples PONE-D-22-12598R1 Dear Dr. Boguś, 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, Estibaliz Sansinenea Academic Editor PLOS ONE Additional Editor Comments (optional): The authors have followed all.comments improving MS therefore it can be accepted in the current form. Reviewers' comments: https://doi.org/10.1371/journal.pone.0280810.r003
Formally Accepted
11 Jan 2023 Acceptance Letter - Estibaliz Sansinenea, Editor PONE-D-22-12598R1 A comprehensive analysis of chemical and biological pollutants (natural and anthropogenic origin) of soil and dandelion (Taraxacum officinale) samples. Dear Dr. Boguś: 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. Estibaliz Sansinenea Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0280810.r004

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