Bacterial Communities in Informal Dump Sites: A Rich Source of Unique Diversity and Functional Potential for Bioremediation Applications
, Henry Ogola 1, Chimdi M. Kalu 1, Timothy Sibanda 3 and Chinedu Obize 4
Round 1
Reviewer 1 Report
Some of the minor queries are 1. What is the novelty of this work. 2. Statistical analysis is missing. 3. References are too many for a research article.
Author Response
Some of the minor queries are
- What is the novelty of this work.
To our knowledge, this is the first study to investigate functional genes from informal dumpsites, whereas many studies have been reported in active or abandoned landfills that have been matured for many years and results showed unique bacterial diversity and functional potential for bioremediation applications
It is important to note that the chemical profiles cannot be compared to those of long-term landfills because the samples studied were not taken from a landfill that has been operational for decades. It is our view, however, that the chemical and biological profiles of soils near these informal dumps are still influenced significantly.
Intriguingly, Nocardioides a significant genus in the Actinomycetes, was present in all samples used in this study suggesting the idea that this genus could serve as a potential biomarker for pollution in landfills.
- Statistical analysis is missing.
Given that this is the first study to use informal dumpsites, we used composite samples. Although samples were collected in triplicate, all samples were thoroughly mixed to obtain an overall picture of the physicochemical and bacterial composition. We did, however, use statistical analysis to compare the sites. In addition, we will take the advice of a reviewer for future studies.
- References are too many for a research article
To make clear, this study never used landfill samples and instead relied on samples from newly formed informal dumpsites. The results showed unique and diverse bacterial members from various samples, and discussion of important genera required more number of studies from the previous literature.
Reviewer 2 Report
The manuscript describes the study of the microbial diversity evaluation on five different informal dumpsites, microbial diversity was evaluated through metagenomic approaches using high throughput sequencing technologies, the metabolic capabilities and bioremediation potential applications of the microbial communities in dumpsites was evaluated using Biolog Ecoplate tests. A result the five dumpsites showed significant differences in microbial diversity due to the differential physicochemical parameters, nutrients availability and heavy metals presence among dumpsites, in the control site (free litter) main microbial phylum was Proteobacteria, while in the dumpsites Actinobacteria followed by Firmicutes were the most representative phylum. Microbial genera with bioremediation potential were identified in dumpsites. The fallowing minor commentaries must be addressed prior accepting the manuscript for publication in Applied Sciences.
Commentaries
In title, line 2, eliminate the word “an”
Line 41, eliminate extra period next to references [2,3]
Line 91, “clue” may be “clues”
Line 106, add a space between “land” and [26]
Line 110, “roadside dump 1 (ID4)”, must be “roadside dump 1 (ID5)”
Line 115-115, in “an area of 2 m x 2 m”, may be “2 x 2 m”
Line 121, correct centigrade symbol
Line 128, add period in “et al”
Line 192, correct centigrade symbol
Lines 194-200, indicate the used wavelength, define if use Absorbance (Abs)or Optical density (OD) is more adequate for the determination.
Line 201, define the “EC” acronym
Line 216, “afew”, may be “ a few”
Line 218, if sems that some information is missing in “World Health Organization (WHO)”
Line 227, aliminate extra space in “96 %”
Line 238, check the ID2 Shannon diversity magnitude value
Line 310, use italics for “p”
Line 317, use italics for “Acidimicrobiia”
Line 341, use italics for “in-situ”
Line 344, “carbon source” may be “carbon sources”
Line 377, eliminate extra space in “94 %”
Line 396, define THE “HMs” acronym
Line 429, check, heavy metal could not be degraded
Author Response
Commentaries
- In title, line 2, eliminate the word “an”
Removed “an” as suggested.
- Line 41, eliminate extra period next to references [2,3]
Eliminated.
- Line 91, “clue” may be “clues”
Changed from clue to clues.
- Line 106, add a space between “land” and [26]
Added.
- Line 110, “roadside dump 1 (ID4)”, must be “roadside dump 1 (ID5)”
Changed from ID4 to ID5.
- Line 115-115, in “an area of 2 m x 2 m”, may be “2 x 2 m”
Modified as advised.
- Line 121, correct centigrade symbol
Corrected
- Line 128, add period in “et al”
Added
- Line 192, correct centigrade symbol
corrected
- Lines 194-200, indicate the used wavelength, define if use Absorbance (Abs)or Optical density (OD) is more adequate for the determination.
Defined as advised.
- Line 201, define the “EC” acronym
It is defined in the materials and method section Line no 122.
- Line 216, “afew”, may be “a few”
Corrected
- Line 218, if sems that some information is missing in “World Health Organization (WHO)”
Modified as “within the recommended limits for soil by World Health Organization (WHO)” in line 218.
- Line 227, eliminate extra space in “96 %”
Eliminated
- Line 238, check the ID2 Shannon diversity magnitude value
Modified the correct number.
- Line 310, use italics for “p”
Italicized
- Line 317, use italics for “Acidimicrobiia”
Italicized
- Line 341, use italics for “in-situ”
Italicized
- Line 344, “carbon source” may be “carbon sources”
Modified
- Line 377, eliminate extra space in “94 %”
Eliminated
- Line 396, define THE “HMs” acronym
Heavy metals (HMs) defined in the Table 1.
- Line 429, check, heavy metal could not be degraded
Modified into “play a pivotal role in the degradation and assimilation of both organic and inorganic substances respectively, including heavy metal contaminants”.
Reviewer 3 Report
After careful reading, I consider that the structure, logical flow, literature review, and statistics used in this manuscript are up to the standards but need to improve.
Authors made frequent mistakes throughout the MS. The authors would do well to refer to other peer-reviewed publications for guidelines on what is most appropriate in tables, results, and figures, and what is better placed in an appendix.
Although I am aware that there is a great effort behind the manuscript, there still are several difficult parts for publication.
Please double-check ALL references (both citations and bibliography)
Throughout the whole paper, please double check ALL proper nouns/abbreviation+full names, etc., are correctly spelled (including being italic or not)
Specific suggestions are in the attached word file.
Comments for author File: 
Comments.pdf
Author Response
Line 38: Keywords should arrange in alphabetical order
Keywords arranged in alphabetical order in Line 30-31.
Line 69-70: Cubic meter should correct as m3
Not applicable
Line 99: It’s better to use CO2 instead of Carbon dioxide
Modified
Line 140-144: Rewrite the objectives. Don’t use the following words to mention objectives. "First objective and secondly"
According to this article, the objectives never used the term as mentioned by the reviewer, our aim was given as stated “ The aim of this research is to determine the taxonomic and functional diversity of bac-terial communities that have been impacted by pollution caused by a variety of an-thropogenic activities at a number of different illegal dumping sites. Furthermore, the carbon substrate utilization ability of the soil bacterial communities in illegal dumping sites was also determined using Biolog EcoplatesTM based CLPP analysis to shed light on the bacterial metabolic activities in relation to various pollutants”.
Line 173, 182: Use one style to mention land size in whole text (ha or hectare)
Not applicable
Line 309-315: It’s better to mention what is the used version of SPSS
We never used the SPSS statistical software in this study, but we did mention all the statistical software tools we used, including their versions.
Line 414: Mention figure number in main text
Mentioned as advised.
Line 434-462: It is unclear. It’s better to use two column table to mention these equations
Not applicable.
Line 585-586: It’s better to use the word “other option” instead of the word second option
We never used such word in this article.
General:
Keep a space between the value and the percentage mark. In some places, it is can be visible and in some places, it is not
Modified
All formulas should be written in formula mode
Not applicable, we never addressed any formula in the article.
Rearrange all tables and figures. There are few format errors.
Arranged.
