Bioremediation of Diesel Contaminated Marine Water by Bacteria: A Review and Bibliometric Analysis

Round 1

Reviewer 1 Report

General comments:

The manuscript entitled “Role of bacteria in bioremediation of diesel contaminated marine water: A review and bibliometric analysis” represents an updated review on oil spill and bioremediations related to diesel oil. I think the review paper is interesting and may be beneficial to the potential readers. The manuscript may be acceptable but there are some concerns which need to be justified before it can be published.

The first and main concern is that the review focused only on potential effectiveness of remediation technique, but no limitations or drawbacks of the method was described. I would recommend that the authors consider describing the factors affecting bioremediation and/or their limitations.

Apart from that, the authors also tend to cross-reference between general statements of “oil spill” with “diesel” type spills. For instance, the authors described the component compositions of diesel but provided large oil spill examples that were not related to diesel oil (lines 96-100). Cross-references should be prevented throughout the whole manuscript.

I would recommend that the figures for physical and chemical properties of BTEX and PAHs should be presented in the supplementary information. Because these are well-known compounds related to oil spills, they may be redundant in the body of the manuscript.

Specific comments:

I have listed some examples of grammatical errors which may need attention, but I would recommend the authors to consider re-checking the manuscript for grammatical errors.

I recommend that the first word in the abstract “Diesel” be changed to “Oil”.

The authors mentioned “completely mineralized” but also mention “other less toxic compounds” which is controversial to each other.

Lines 34-35: Therefore, high salinity bacteria are the remarkable microbes… The “the” here should be removed.

Lines 42-43: The contamination of water with diesel hydrocarbons… “water” should be “water bodies” and “diesel hydrocarbons” should be “petroleum hydrocarbons” or just “diesel oil”.

Lines 43-44: This does not only increase concerns toward ecosystems and human health, but also on other organisms particularly aquatics life. I think it would be more accurate to mention “human health” first followed by “the ecosystem”. Also, aquatic life is considered as part of the ecosystem. Try re-phrasing this sentence.

Lines 67-68: In recent years, halophiles have gotten spotlight… consider changing the word “gotten” to “received the”.

Author Response

General comments

Comment 1: The manuscript entitled “Role of bacteria in bioremediation of diesel contaminated marine water: A review and bibliometric analysis” represents an updated review on oil spill and bioremediations related to diesel oil. I think the review paper is interesting and may be beneficial to the potential readers. The manuscript may be acceptable but there are some concerns which need to be justified before it can be published.

Answer: Noted on the concerns which need to be justified before can be published.

Comment 2: The first and main concern is that the review focused only on potential effectiveness of remediation technique, but no limitations or drawbacks of the method was described. I would recommend that the authors consider describing the factors affecting bioremediation and/or their limitations.

Answer: The factors affecting biodegradation have been added in lines 199-202 (Subtopic 5).

Comment 3: Apart from that, the authors also tend to cross-reference between general statements of “oil spill” with “diesel” type spills. For instance, the authors described the component compositions of diesel but provided large oil spill examples that were not related to diesel oil (lines 96-100). Cross-references should be prevented throughout the whole manuscript.

Answer: 1) oil spill examples in line 96-100 (Subtopic 3) has been deleted to prevent cross references and 2) the sentence of diesel composition in lines 95-97 has been reorganised (Subtopic 3) 

Comment 4: I would recommend that the figures for physical and chemical properties of BTEX and PAHs should be presented in the supplementary information. Because these are well-known compounds related to oil spills, they may be redundant in the body of the manuscript.

Answer: All figures in the table have been discarded  to avoid redundant in the body of manuscript (Table 2 and table 3).

Specific comments:

Comment 1: I have listed some examples of grammatical errors which may need attention, but I would recommend the authors to consider re-checking the manuscript for grammatical errors.

Answer: Noted on the grammatical errors in the manuscript.

Comment 2: I recommend that the first word in the abstract “Diesel” be changed to “Oil”.

Answer: The first word diesel has been changed to oil as recommended (Abstract, line 20)

Comment 3: The authors mentioned “completely mineralized” but also mention “other less toxic compounds” which is controversial to each other.

Answer: Correction has been done. Word ‘completely’ has been discarded in line 25 (abstract).

Comment 4: Lines 34-35: Therefore, high salinity bacteria are the remarkable microbes… The “the” here should be removed.

Answer: Correction has been done. Word ‘the’ has been removed from line 34-35 (abstract)

Comment 5: Lines 42-43: The contamination of water with diesel hydrocarbons… “water” should be “water bodies” and “diesel hydrocarbons” should be “petroleum hydrocarbons” or just “diesel oil”.

Answer: Correction has been done. Word water has been changed to water bodies and diesel hydrocarbons has been change to petroleum hydrocarbons in line 41 (introduction)

Comment 6: Lines 43-44: This does not only increase concerns toward ecosystems and human health, but also on other organisms particularly aquatics life. I think it would be more accurate to mention “human health” first followed by “the ecosystem”. Also, aquatic life is considered as part of the ecosystem. Try re-phrasing this sentence.

Answer: Sentence in line 42-43 has been rephrased as suggested.

Comment 7: Lines 67-68: In recent years, halophiles have gotten spotlight… consider changing the word “gotten” to “received the”.

Answer: The word ‘gotten’ has been changed to ‘received the’ in line 66 (Introduction).

Author Response File: Author Response.pdf

Reviewer 2 Report

This review calls “Role of Bacteria in Bioremediation of Diesel Contaminated Marine Water: A Review and Bibliometric Analysis”. I liked the bibliometric part and approaches for literature analysis. The results are presented in a rather unusual way that sets this review apart from others. However, regarding the review on the topic of bioremediation  seawater from diesel pollution, this part leaves much to be desired. For example, in the introduction, the authors mentioned several major crude oil spills and accidents. One of them is on the Deepwater Horizon platform in 2010 in the Gulf of Mexico. For bioremediation, a large number of biopreparations have been used and many articles have been published on this topic. Nevertheless, this part of the research remained practically outside the scope of the article. Moreover, the authors performed a search for the word "diesel", but the composition of the diesel is very diverse, even depending on the manufacturer. What do the authors mean by the definition of "diesel oil"? What is different from "diesel"? And why do they stop at the decomposition data for BTEX and PAH in their review? Where is the data on diesel components such as paraffins?

If the authors devoted almost half of the review to data on the decomposition of BTEX, then a search for these words (BTEX and water; BTEX and Marine water) will give a large number of additional articles. E.g., Analysis of Dissolved BTEX and PAHs in Seawater Following an Oil Spill: Development of Sensitive, Operational Methods for Rapid Diagnosis. In Proceeding of the International oil spill conference (IOSC), Portland, 23-26 May 2011. May 2011 Conference: International oil spill conference (IOSC), Portland, 23-26 May 2011 Anne-Laure Balcon, Rami Kanan, Sophie Vanganse, Julien Guyomarch, ; BTEX compounds in water – future trends and directions for water treatment OM Fayemiwo1, MO Daramola2 and K Moothi1* http://dx.doi.org/10.4314/wsa.v43i4.08. Available on website http://www.wrc.org.za ISSN 1816-7950 (Online) = Water SA Vol. 43 No. 4 October 2017. By the way, the last one is the  good review.

Another confusion in concepts concerns biodiesel, which is mentioned in fig. 1.  "Biodiesel", obtained microbially from vegetable oil and animal fats, has nothing to do with oil diesel. Also in Table 4 – soybean biodiesel.

Lines 231-233. The phrase "To date, the specific microbial species and their functions for diesel pollutant removal from water are not fully discovered yet [68]", in my opinion, does not quite correspond to the subsequent material outlined by the authors. First, later in the article, the authors provide many examples of the potential use of bacteria to clean diesel contamination. Secondly, if we proceed from the data that at the moment not 10% of all bacteria have been isolated into a pure culture and studied, but a large role in the biodegradation processes is played by uncultivated microorganisms, then this phrase is appropriate for the biodegradation processes of any compounds. Or to none.

Section 7 is referred to as “Potential Role of High Salinity Bacteria as Bioremediatory Agent”, but it provides, among other things, data on bacteria that degrade PAHs at lower salt concentrations. Thus, lines 261-265 show examples of bacteria that decompose PAHs at 4% sodium chloride. This is a low concentration and does not fit into the High Concentration section. I would recommend to modify the title of the section. Or move all data that does not describe diesel degradation at high salt concentrations to another section.

Lines 268-270. An arthrobacter capable of degrading PAHs is given as an example. There are some remarks:

1. Reference 79 does not describe the bacteria of the genus Arthrobacter and should be moved to the part where the consortium of bacteria is described.
2. There is no evidence that Arthrobacter spp. from refs 86, 87 degrade PAHs at high salt concentrations, so these two references should be removed from the section on "High Salinity Bacteria" or cite the data that these bacteria degrade diesel in high salinity conditions.
3. since we are talking about different representatives of the genus Arthrobacter, it is more logical to use the plural rather than the singular when describing the abilities of these bacteria.

Lines 326 – please, give citations.

Lines 330 – ortho and meta should be in italic.

there are small typos: lines 128, 166 (n- italic), 266

In general, the article is interesting, but it requires either a rephrasing of the title or an additional literature search.

Author Response

Comment 1:

This review calls “Role of Bacteria in Bioremediation of Diesel Contaminated Marine Water: A Review and Bibliometric Analysis”. I liked the bibliometric part and approaches for literature analysis. The results are presented in a rather unusual way that sets this review apart from others. However, regarding the review on the topic of bioremediation seawater from diesel pollution, this part leaves much to be desired. For example, in the introduction, the authors mentioned several major crude oil spills and accidents. One of them is on the Deepwater Horizon platform in 2010 in the Gulf of Mexico. For bioremediation, a large number of biopreparations have been used and many articles have been published on this topic. Nevertheless, this part of the research remained practically outside the scope of the article. Moreover, the authors performed a search for the word "diesel", but the composition of the diesel is very diverse, even depending on the manufacturer. What do the authors mean by the definition of "diesel oil"? What is different from "diesel"? And why do they stop at the decomposition data for BTEX and PAH in their review? Where is the data on diesel components such as paraffins?

Answer: 

Diesel are also called diesel oil. In my point of view, both are the same. The word diesel oil used for definition has been changed to diesel in line 84 (Subtopic 3). Paraffins = alkane. Alkane degradation pathway included in the review. Most of the aliphatics are well known, the compounds are not tabulated to prevent unimportant data in the review paper. Data on degradation of alkane by halophilic microorganism has been added in table 5 – reference 101 (subtopic 7).

Comment 2:

If the authors devoted almost half of the review to data on the decomposition of BTEX, then a search for these words (BTEX and water; BTEX and Marine water) will give a large number of additional articles. E.g., Analysis of Dissolved BTEX and PAHs in Seawater Following an Oil Spill: Development of Sensitive, Operational Methods for Rapid Diagnosis. In Proceeding of the International oil spill conference (IOSC), Portland, 23-26 May 2011. May 2011 Conference: International oil spill conference (IOSC), Portland, 23-26 May 2011 Anne-Laure Balcon, Rami Kanan, Sophie Vanganse, Julien Guyomarch, ; BTEX compounds in water – future trends and directions for water treatment OM Fayemiwo1, MO Daramola2 and K Moothi1* http://dx.doi.org/10.4314/wsa.v43i4.08. Available on website http://www.wrc.org.za ISSN 1816-7950 (Online) = Water SA Vol. 43 No. 4 October 2017. By the way, the last one is the good review.

Answer:

As this paper does not solely discuss on the composition of diesel, the keywords “diesel” and “water pollution” or “marine pollution” were searched, limit to article-type document only to minimise false-positive result from duplication in conference paper. The choice of word search for bibliometric analysis was determined to provide a big picture of the trend in the diesel pollution research specifically in marine water. The query search should be inclusive, which includes a wide range of related research focus such as the occurrence of diesel pollution, composition of diesel (i.e., BTEX, PAH), the remediation techniques, and future prospect. It shall provide enough coverage of relevance topic with the extensive search of selected keywords through the abstract, title and keyword from the database.

Comment 3:

Another confusion in concepts concerns biodiesel, which is mentioned in fig. 1.  "Biodiesel", obtained microbially from vegetable oil and animal fats, has nothing to do with oil diesel. Also, in Table 4 – soybean biodiesel.

Answer:

Content in Table 4 was generated from the bibliometric analysis, showing the trend of research topics over the decade. It is not advised to remove the keyword “biodiesel” even it has nothing to do with oil diesel to avoid bias. The keyword might not be directly associated with diesel and marine pollution but were frequently used by the authors in the publication throughout the year of 2016.

Comment 4:

Lines 231-233. The phrase "To date, the specific microbial species and their functions for diesel pollutant removal from water are not fully discovered yet [68]", in my opinion, does not quite correspond to the subsequent material outlined by the authors. First, later in the article, the authors provide many examples of the potential use of bacteria to clean diesel contamination. Secondly, if we proceed from the data that at the moment not 10% of all bacteria have been isolated into a pure culture and studied, but a large role in the biodegradation processes is played by uncultivated microorganisms, then this phrase is appropriate for the biodegradation processes of any compounds. Or to none.

Answer:

Lines 231-233 has been deleted as it does not quite correspond to the subsequent materials mentioned earlier (currently line 199-200) subtopic 5.

Comment 5:

Section 7 is referred to as “Potential Role of High Salinity Bacteria as Bioremediatory Agent”, but it provides, among other things, data on bacteria that degrade PAHs at lower salt concentrations. Thus, lines 261-265 show examples of bacteria that decompose PAHs at 4% sodium chloride. This is a low concentration and does not fit into the High Concentration section. I would recommend modifying the title of the section. Or move all data that does not describe diesel degradation at high salt concentrations to another section.

Answer: 

Title of the section has been modified to potential role of halophilic bacteria as bioremediatory agent (line 243). The reason is to suit the data for alkane which has low salinity percentage (subtopic 7). Most data found below 4%. Below 4% is consider as weak halophile.  Additional data on degradation by high salinity bacteria was barely found, mostly has been included in the review (above 5%).

Comment 6:

Lines 268-270. An Arthrobacter capable of degrading PAHs is given as an example. There are some remarks:

Reference 79 does not describe the bacteria of the genus Arthrobacter and should be moved to the part where the consortium of bacteria is described.

There is no evidence that Arthrobacter spp. from refs 86, 87 degrade PAHs at high salt concentrations, so these two references should be removed from the section on "High Salinity Bacteria" or cite the data that these bacteria degrade diesel in high salinity conditions.

since we are talking about different representatives of the genus Arthrobacter, it is more logical to use the plural rather than the singular when describing the abilities of these bacteria.

Answer:

Reference 79 has been removed as it does not describe the mentioned bacteria.

Reference 86 and 87 have been removed as no evidence of Arthrobacter spp. Degrades PAHs at high salt concentration (lines 266-268) (subtopic 7)

Reference number re-organized.

Comment 7:

Lines 326 – please, give citations

Answer:

Citation has been added to sentence in line 324. Reference number [118] (subtopic 8)

Comment 8:

Lines 330 – ortho and meta should be in italic.

Answer: 

Ortho and meta in line 328 have been italicised.

Comment 9: 

there are small typos: lines 128, 166 (n- italic), 266

Answer: 

All typos in line 124 from [ to ], Line 162 italicised n-, andLine 264 from ; to : has been corrected.

Comment 10:

In general, the article is interesting, but it requires either a rephrasing of the title or an additional literature search.

Answer: 

Title of review paper has been rephrased to "Bioremediation of Diesel Contaminated Marine Water by bacteria: A Review and Bibliometric Analysis"

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

The authors have made some corrections to the article.
In my opinion, fundamental questions remained unchanged, keywords and, as a result, a limited number of cited publications, precisely because many details remained outside the search. However, if the authors are convinced of their correctness, let the manuscript to be published in this limited version.