scholarly journals Bioinformatic approaches for analysis of coral-associated bacteria using R programming language

2021 ◽  
Vol 18 (4) ◽  
pp. 733-743
Author(s):  
Doan Thi Nhung ◽  
Bui Van Ngoc
Keyword(s):  
Programming Language ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Metagenomic Data ◽  
Rrna Gene ◽  
Marine Microorganisms ◽  
Taxonomic Assignment ◽  
Associated Bacteria ◽  
R Programming Language ◽  
R Programming

Recent advances in metagenomics and bioinformatics allow the robust analysis of the composition and abundance of microbial communities, functional genes, and their metabolic pathways. So far, there has been a variety of computational/statistical tools or software for analyzing microbiome, the common problems that occurred in its implementation are, however, the lack of synchronization and compatibility of output/input data formats between such software. To overcome these challenges, in this study context, we aim to apply the DADA2 pipeline (written in R programming language) instead of using a set of different bioinformatics tools to create our own workflow for microbial community analysis in a continuous and synchronous manner. For the first effort, we tried to investigate the composition and abundance of coral-associated bacteria using their 16S rRNA gene amplicon sequences. The workflow or framework includes the following steps: data processing, sequence clustering, taxonomic assignment, and data visualization. Moreover, we also like to catch readers’ attention to the information about bacterial communities living in the ocean as most marine microorganisms are unculturable, especially residing in coral reefs, namely, bacteria are associated with the coral Acropora tenuis in this case. The outcomes obtained in this study suggest that the DADA2 pipeline written in R programming language is one of the potential bioinformatics approaches in the context of microbiome analysis other than using various software. Besides, our modifications for the workflow execution help researchers to illustrate metagenomic data more easily and systematically, elucidate the composition, abundance, diversity, and relationship between microorganism communities as well as to develop other bioinformatic tools more effectively.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

Microbial Community Analysis inside a Biooxidation Heap for Gold Recovery in Equador

2017 ◽  
Vol 262 ◽  
pp. 135-138 ◽  
Author(s):  
Carlos L. Aspiazu ◽  
Paulina Aguirre ◽  
Sabrina Hedrich ◽  
Axel Schippers
Keyword(s):  
Microbial Community ◽  
Fine Fraction ◽  
Community Analysis ◽  
Gold Recovery ◽  
Microbial Community Analysis ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Probable Number ◽  
Cell Numbers ◽  
Cell Counts

In a mine owned by the company Orenas S.A. (Equador), a biooxidation process for gold recovery has been developed. Refractory gold ore was crushed, milled and 500 ton of flotation concentrate was agglomerated by coating a support rock. This was piled up on a liner and the biooxidation process in the heap of 35x25x6 m3 was run for approximately 150 days. The oxidized material was subsequently removed for further processing. An outcrop allowed for depth dependent sampling of altogether 36 samples at three sites over the complete depth of 6 m. The fine fraction was removed from the host rock and sent to the laboratory for analysis of the microbial community. The pH ranged between 2.2 and 2.9. Total cell counts determined via counting under a fluorescence microscope after SYBR Green staining indicated a high microbial colonialization of the heap in all depths between 106 to 109 cells per g concentrate, however the highest cell numbers were mainly found in the upper 50 cm. Most-probable-number determination of living, acidophilic iron (II)-oxidizers for one site also revealed a decrease of cell numbers with depth (between 104 to 108 cells per g concentrate). Further molecular analyses of the community composition based on extracted DNA and 16S rRNA gene analyses by TRFLP and qPCR revealed a complex archaeal and bacterial community within the heap. It can be stated that an active community of acidophiles runs the biooxidation process in all sampled parts of the heap.

scholarly journals Developing codes for validation of PM10, PM2.5, and O3 datasets using R programming language

2019 ◽  
Author(s):  
Ramin Nabizadeh ◽  
Mostafa Hadei
Keyword(s):  
Air Pollution ◽  
Programming Language ◽  
Assessment Method ◽  
Daily Maximum ◽  
Data Handling ◽  
R Programming Language ◽  
Wide Range ◽  
Us Epa ◽  
R Programming ◽  
Pm 10

Introduction: The wide range of studies on air pollution requires accurate and reliable datasets. However, due to many reasons, the measured concentra-tions may be incomplete or biased. The development of an easy-to-use and reproducible exposure assessment method is required for researchers. There-fore, in this article, we describe and present a series of codes written in R Programming Language for data handling, validating and averaging of PM10, PM2.5, and O3 datasets.   Findings: These codes can be used in any types of air pollution studies that seek for PM and ozone concentrations that are indicator of real concentra-tions. We used and combined criteria from several guidelines proposed by US EPA and APHEKOM project to obtain an acceptable methodology. Separate   .csv files for PM 10, PM 2.5 and O3 should be prepared as input file. After the file was imported to the R Programming software, first, negative and zero values of concentrations within all the dataset will be removed. Then, only monitors will be selected that have at least 75% of hourly concentrations. Then, 24-h averages and daily maximum of 8-h moving averages will be calculated for PM and ozone, respectively. For output, the codes create two different sets of data. One contains the hourly concentrations of the interest pollutant (PM10, PM2.5, or O3) in valid stations and their average at city level. Another is the   final 24-h averages of city for PM10 and PM2.5 or the final daily maximum 8-h averages of city for O3. Conclusion: These validated codes use a reliable and valid methodology, and eliminate the possibility of wrong or mistaken data handling and averaging. The use of these codes are free and without any limitation, only after the cita-tion to this article.

scholarly journals Spatial variation of physicochemical parameters in a constructed wetland for wastewater treatment: An example of the use of the R programming language

2021 ◽  
Vol 13 (1) ◽  
pp. 15
Author(s):  
Junior Pastor Pérez-Molina ◽  
Carola Scholz ◽  
Roy Pérez-Salazar ◽  
Carolina Alfaro-Chinchilla ◽  
Ana Abarca Méndez ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Spatial Variation ◽  
Water Flow ◽  
Programming Language ◽  
Constructed Wetland ◽  
Physicochemical Parameters ◽  
Preferential Flow ◽  
Oxygen Demand ◽  
R Programming Language ◽  
R Programming

Introduction: The implementation of wastewater treatment systems such as constructed wetlands has a growing interest in the last decade due to its low cost and high effectiveness in treating industrial and residential wastewater. Objective: To evaluate the spatial variation of physicochemical parameters in a constructed wetland system of sub-superficial flow of Pennisetum alopecuroides (Pennisetum) and a Control (unplanted). The purpose is to provide an analysis of spatial dynamic of physicochemical parameters using R programming language. Methods: Each of the cells (Pennisetum and Control) had 12 piezometers, organized in three columns and four rows with a separation distance of 3,25m and 4,35m, respectively. The turbidity, biochemical oxygen demand (BOD), chemical oxygen demand (COD), total Kjeldahl nitrogen (TKN), ammoniacal nitrogen (N-NH4), organic nitrogen (N-org.) and phosphorous (P-PO4-3) were measured in water under in-flow and out-flow of both conditions Control and Pennisetum (n= 8). Additionally, the oxidation-reduction potential (ORP), dissolved oxygen (DO), conductivity, pH and water temperature, were measured (n= 167) in the piezometers. Results: No statistically significant differences between cells for TKN, N-NH4, conductivity, turbidity, BOD, and COD were found; but both Control and Pennisetum cells showed a significant reduction in these parameters (P<0,05). Overall, TKN and N-NH4 removal were from 65,8 to 84,1% and 67,5 to 90,8%, respectively; and decrease in turbidity, conductivity, BOD, and COD, were between 95,1-95,4%; 15-22,4%; 65,2-77,9% and 57,4-60,3% respectively. Both cells showed ORP increasing gradient along the water-flow direction, contrary to conductivity (p<0,05). However, OD, pH and temperature were inconsistent in the direction of the water flow in both cells. Conclusions: Pennisetum demonstrated pollutant removal efficiency, but presented results similar to the control cells, therefore, remains unclear if it is a superior option or not. Spatial variation analysis did not reflect any obstruction of flow along the CWs; but some preferential flow paths can be distinguished. An open-source repository of R was provided. 

scholarly journals Community Structure of Subsurface Biofilms in the Thermal Sulfidic Caves of Acquasanta Terme, Italy

2010 ◽  
Vol 76 (17) ◽  
pp. 5902-5910 ◽  
Author(s):  
D. S. Jones ◽  
D. J. Tobler ◽  
I. Schaperdoth ◽  
M. Mainiero ◽  
J. L. Macalady
Keyword(s):  
Community Structure ◽  
16S Rrna ◽  
Specific Conductivity ◽  
Ground Surface ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Ecological Success ◽  
Cave Waters

ABSTRACT We performed a microbial community analysis of biofilms inhabiting thermal (35 to 50°C) waters more than 60 m below the ground surface near Acquasanta Terme, Italy. The groundwater hosting the biofilms has 400 to 830 μM sulfide, <10 μM O2, pH of 6.3 to 6.7, and specific conductivity of 8,500 to 10,500 μS/cm. Based on the results of 16S rRNA gene cloning and fluorescent in situ hybridization (FISH), the biofilms have low species richness, and lithoautotrophic (or possibly mixotrophic) Gamma- and Epsilonproteobacteria are the principle biofilm architects. Deltaproteobacteria sequences retrieved from the biofilms have <90% 16S rRNA similarity to their closest relatives in public databases and may represent novel sulfate-reducing bacteria. The Acquasanta biofilms share few species in common with Frasassi cave biofilms (13°C, 80 km distant) but have a similar community structure, with representatives in the same major clades. The ecological success of Sulfurovumales-group Epsilonproteobacteria in the Acquasanta biofilms is consistent with previous observations of their dominance in sulfidic cave waters with turbulent water flow and high dissolved sulfide/oxygen ratios.

scholarly journals Population Abundance of Potentially Pathogenic Organisms in Intestinal Microbiome of Jungle Crow (Corvus macrorhynchos) Shown with 16S rRNA Gene-Based Microbial Community Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Isamu Maeda ◽  
Mohammad Shohel Rana Siddiki ◽  
Tsutomu Nozawa-Takeda ◽  
Naoki Tsukahara ◽  
Yuri Tani ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Pathogenic Bacteria ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Jungle Crow ◽  
Corvus Macrorhynchos

Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous toEimeriasp., which belongs to the protozoan phylumApicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the generaCampylobacterandBrachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.

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