Critical Review: Unraveling the bacterial diversity Cangar Hot Spring, Indonesia by Next Generation Sequencing of 16S rRNA gene
Alonzo Bell
Critical Review Report
Article : Unraveling the bacterial diversity Cangar Hot Spring, Indonesia by Next Generation Sequencing of 16S rRNA gene
Authors : Almando Geraldi, Chia Chay Tay, Ni’Matuzahroh, Fatimah, Wan Nurhayati Wan Hanafi
Journal : Biodiversitas
Comments to the Authors
The paper does a good job of explaining different methods and data to argue the biodiversity and dominance of microorganisms in the Cangar Hot Spring, Indonesia. The authors use rRNa to study the activity of bacteria and archaea in that extreme environment. A great strength in this article is that it compares similar relevant studies and while also distinguishing how their study is unique. The methods and technology used were detailed and correlated with finding biodiversity of bacteria and archaea populations, in these extreme environments of Indonesia. Interestingly, this study uses uncultured Next Generation Sequencing (NGS) rRNA technology to examine and analyze the different genus and phyla present in the hot spring environment of Indonesia. The authors explored the diversity of microbial communities in the extreme Cangar Hot Spring environment, and the study contributes a new method of analyzing the biodiversity of microbes through 16S rRNA sequencing.The writing is intriguing and it would be interesting to the readers who like to study; diverse microbial populations, RNA application in microbiology, extreme environments ecosystems, metabolism processes, respiration processes, photosynthesis process, bioremediation utilizing microbes and many other related science studies. The strength of this paper is that it highlights the most abundant microorganisms in relation to the newly immersing method of rRNA sequencing. Therefore the cohesiveness of the argument is solid and transparent throughout the paper. The results and discussion sections could have been condensed to convey the specific and most significant results related to the study. The degree to which conclusions are supported by data is clear and provides statistics to understand the dynamics of this study. Relative to the new ideas and information introduced; the length is appropriate and proportionate based on the arguments, data and statistical analysis.
General
The authors do a thorough job of explaining in detail how the rRNA sequencing can affect the microbial populations at the Canger Spring. The article explores biodiversity of microbes in the hot spring by using Next Generation Sequencing technology (NGS). It is a new technology emerging which can have great potential for exploring hot and extreme environments, similar to the Cangar Hot Spring. The scientific soundness of this study was sound and influences more people to study hot springs and the associated organisms with those environments. Another strength is that the study wants to further research into these archaea and bacteria to analyze their benefits which they can provide for global use. The article is clear to understand and very organized. The claims are supported through measuring microbial communities and providing data correlating to the main points. The authors are persistent in explaining the dominance of gram negative bacteria in these hot spring environments. The article tells a cohesive story and is tightly supported by showing different graphs and illustrations to display the microbial population. For example, the authors were able to observe 539 different species of microorganisms. Graphs and illustrations directly correlate with the results , in which NGS rRNA can be utilized to detect a myriad of thermophilic microorganisms. The authors have been consistent in the writing and have reported Proteobacteria and Bacteroidetes as being the most abundant microbial populations in the extreme Cangar Hot Spring.
Specific
Presentation
The authors present a cohesive story by explaining the relative abundance of Proteobacteria and Bacteroidetes in these extreme and hot ecosystems. The article argues a few significant points and remains consistent in solidifying those arguments. The author does a detailed job of explaining the conditions of the Cangar Hot Spring environment and other hot spring environments by explaining varying temperatures from 38 degrees celsius - 70 degrees celsius and ranges of pH 2 - pH 8.2. These attributes of the extreme environment affects which type of organisms can thrive in those niches, and the article conveys that information clearly. The abstract, keywords, introduction and conclusion accurately and consistently reflects the major points of the paper. With the breakdown of abundant organisms in combination with the thorough explanation of the Next Generation Sequencing of the prokaryotic 16S rRNA gene; the article consistently draws parallels with the argument, methods and data.
Length
The length was appropriate with proportion to the data, methods and presentation. I think that the paper could have been expanded in regards to going more into depth about the NGS 16S rRNA sequencing, in order to give the reader a better understanding of the process and to reinforce the significance which the the NGS presents in relation to measuring microbial diversity in the Cangar Hot Spring, Indonesia. Besides that, the magnitude of the research in conjunction with data and methods were written in an appropriate manner and proportionate to the main arguments. The author's length of the paper was easy to follow which makes it interesting to study and read.
Methods
Methods are thoroughly detailed and appropriate to help readers understand the process used to determine microbial classification of organisms by sequencing of the 16S rRNA gene. The authors specifically breakdown the NGS process utilizing rRNA by showing the exact base sequencing used to analyze the microorganisms. Primers used in the process are 341F (5’-CCTAYGGGRBGCASCAG-3’) and primer 806R (5’-GGACTACNNGGGTATCTAAT-3’) and these go through an extensive process which allows NGS technology to analyze thermophiles, bacteria and archaea in the Cangar Hot Springs, Indonesia. Methods are described clearly enough that readers with some scientific background and knowledge can understand, but the process is complex and with the proper equipment this work could be repeated by someone else.
Data Presentation
As results are stated in the paper, I can make accurate correlations with the results and the tables and figures. Utilizing the NGS analysis, authors were able to observe 539 different species of microorganisms in Cangar Hot Spring, Indonesia. The authors explained obtaining species diversity results from using Shannon-Wiener which measures ; Index : 5.642, Ciao 1 : 540.615, ACE : 540.629, Good’s coverage estimator : 100% . These results are significant in supporting the main objectives of the article and are clearly labeled and illustrated in Table 1. As bacteria and archaea populations which were observed in the experiment, the authors classified these communities using a krona graph. The krona graph clearly illustrates the relative abundance and distribution of the microbial communities in the Cangar Hot Spring environment. Figure 2 illustrates the highest relative abundance of bacterial phylum ; with Proteobacteria being the greatest (58.05% ) and Bacteroidetes being second greatest (29.58%) which consistently reinforces one of the main points of this study. Figure 3 illustrates the highest relative abundance of the family ; with Flavobacteriaceae being the greatest : (19.11%) and Methylophilaceae (17.97%) which is clearly explained and shown on the graph. Figure 4 illustrates the highest relative abundance of the genus ; with Cloacibacterium being the greatest : (18.64%) and Methylobacillus being the second greatest (17.69%). Results stated in the paper are easy to verify by examining figures and tables. All tables and figures are complex but also easy to understand for the reader. The data is represented transparently through the writing, tables and figures.
Statistical Design and Analysis
Statistical design and analysis is appropriate. The reader can easily correlate results from the study to the figures and tables in the paper. The authors provide descriptive statistics to characterize microbial communities and the effect of NGS 16S rRNA synthesis. These stats are modeled in graphs and broken to analyze the abundance of bacteria and archaea. Significance statements are justified through discussion and results, and it is shown in the writing, tables and figures.
Errors
Some sub headings do not capitalize every word, which can help with the consistency in highlighting important content information. Besides that, there were minimal to no major errors in the paper. Grammar and vocabulary was good and the organization of the paper was planned well and transparent.
Citations
Sources are correctly cited and the use of reference studies were appropriate in regards to thermophilic research in hot springs around the world. Sources were all pertinent, cited correctly and alphabeticalized in order.
Overlap
This paper is unique and original because it reports data and conclusions which have never been published before. This article is the first to analyze microbial populations in the Cangar Hot Spring, Indonesia utilizing Next Generation Sequencing 16S rRNA sequencing to assess the biodiversity of these thermophile populations. There are studies which tend to isolate essential proteins in environments and assess abundance of microbes; in areas similar to the hot spring studied in this article, but they use different measures and culture procedures to achieve their data and conclusions. There are alot of new studies emerging regarding using rRNA to discover microbe diversity in extreme hot springs environments, but this study is unique in providing exact RNA primers used along with the extensive techniques associated in the study.
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