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Importance of Genetically Engineered Microbes (GEMs) in Bioremediation of Environmental Pollutants
Published in Vineet Kumar, Vinod Kumar Garg, Sunil Kumar, Jayanta Kumar Biswas, Omics for Environmental Engineering and Microbiology Systems, 2023
Wilgince Apollon, Héctor Flores-Breceda, Gerardo Méndez-Zamora, Juan Florencio Gómez-Leyva, Alejandro Isabel Luna-Maldonado, Sathish-Kumar Kamaraj
Table 10.1 shows previous studies related to recombinant DNA technology (gene modification) using laboratory techniques. Here, it can be seen that GEMs have been applied in biodegradation processes for some time. Figure 10.1 illustrates the schematic representation of the mechanism for GEM creation in a laboratory. Genes modified by DNA techniques were used to evolve both monooxygenases and dioxygenases in all bioremediation processes (Leungsakul et al., 2005). Furthermore, RNA technology has also been developed for the elimination of toxic elements in the environment (Poretsky et al., 2005). RNA technology allows not only the acquisition of nitrogen (N) and assimilation of Cl compounds, but also the oxidation of sulphur (S) as an abundant element in the Earth’s crust. With this technology, 16S rRNA genes are used that have a high capacity to allow the characterization of microorganisms, which can then be exploited for the bioremediation of polluted areas (Stewart et al., 2010).
Diagnosing Microbiologically Influenced Corrosion
Published in Torben Lund Skovhus, Dennis Enning, Jason S. Lee, Microbiologically Influenced Corrosion in the Upstream Oil and Gas Industry, 2017
Jason S. Lee, Brenda J. Little
MMM have been used to detect causative microorganisms in MIC. For example, Lutterbach et al. (2011) used qPCR on dsrAB to detect SRB in fuel storage tanks. Larsen et al. (2013) used the average number of RNA molecules per cell determined by reverse transcription quantitative PCR as a measure of activity of methanogens and sulfate-reducing prokaryotes within biofilms. Pipelines with more activity were judged to be at higher risk for MIC. Lopez et al. (2006) used clone libraries of PCR-amplified 16S rRNA gene fragments to identify bacteria in a corrosive biofilm in a steel pipeline that was used to inject water into an oilfield in the Gulf of Mexico. They found members belonging to different genera within the Gammaproteobacteria (96.66%), Bacilli (2.67%), and Alphaproteobacteria (0.67%) but, significantly, no SRB. Almahamedh et al. (2011) identified both metal and sulfate-reducing bacteria in oilfield water using 16S rRNA gene sequence analysis for bacteria, archaea, and eucaryotes using database comparisons.
Development and Composition of the Human Microbiome from Birth
Published in Nwadiuto (Diuto) Esiobu, James Chukwuma Ogbonna, Charles Oluwaseun Adetunji, Olawole O. Obembe, Ifeoma Maureen Ezeonu, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Microbiomes and Emerging Applications, 2022
Toochukwu E. Ogbulie, Nwadiuto (Diuto) Esiobu, Muinah Fowora
Furthermore, the human skin microbiota consists of bacteria, eukaryotes and viruses most of which are located in the superficial layers of the epidermis, gland tracts and hair follicles. The composition of the human skin microbiome was made known previously with culture-dependent methods where culture media were used to isolate possible microbiota. But due to the diverse nature of microorganisms and possible presence of culture-independent organisms that may possibly not grow on solid media to form colonies for identification, culture-independent approaches have been found to be more reliable and accurate in determining the true consortium of microbes present in given sample. Many culture-independent methods rely on the polymerase chain reaction (PCR). Highly conserved genes across different taxa, such as the 16S/18S ribosomal RNA (rRNA) gene and certain housekeeping genes such as the rpoB gene and the cpn60 gene as respectively reported by Khamis et al. in 2004 and Chaban et al. in 2009, are often amplified by PCR and used to identify the microbial composition of the microbiota. Denaturing gradient gel electrophoresis (DGGE) was often used in the past to examine microbial diversity based on varied band profiles. When next-generation techniques as such as amplicon, transcriptome and shortgun sequencing are employed, identification of the microorganisms can be made based on the sequence similarity of the sequenced conserved genes to known sequences. 16S rRNA gene sequencing is the method most used in identifying bacterial and archaeal composition in microbial communities. Several 16S rRNA gene databases have been developed and are commonly used in microbiome studies, including RDP, SILVA and Green genes.
Biodegradation and detoxification study of triphenylmethane dye (Brilliant green) in a recirculating packed-bed bioreactor by bacterial consortium
Published in Environmental Technology, 2022
Himanshu Tiwari, Ravi Kumar Sonwani, Ram Sharan Singh
Microbial species identification, classification, and quantification are frequently accomplished using the sequencing of the 16S rRNA gene sequencing. 16S rRNA sequencing is commonly utilised in the identification of bacteria and phylogenetic research because the 16S rRNA gene is conserved in bacteria and contains hypervariable areas that can offer species-specific signature sequences. High precision, low cost, and quick sequencing of the 16S rRNA are its main advantages. The molecular characterisation of isolated potential bacterial species was carried out in Bioraj Laboratories, Pune, India. The AxyPrep Bacterial Genomic DNA Miniprep kit was used to extract and purify genomic DNA from bacterial species, and Nanodrop was used to ensure purity and quantification. In the amplification, universal 16S rRNA PCR (polymerase chain reaction) forward primer (27F-5′ AGAGTTTGATCMTGGCTCAG3′) and reverse primer (1492R-5′ AAGGAGGTGWTCCARCC3′) were used [18]. PCR reaction was performed in a thermal cycler (Bio-rad) using the following conditions: initial denaturation of 5 min at 94°C, followed by 35 cycles consisting of 30 s at 94°C (denaturation), 20 s at 58°C (annealing), and 1 min 30 s at 72°C (extension) and final extension was 15 min at 72°C. The PCR products were analysed by 1.2% agarose gel electrophoresis, amplified products in the gel were cut by a clean scalpel, purified by Quigen quick PCR purification kit and DNA was sequenced. The obtained 16S rRNA sequences were further subjected to the BLAST programme (http://www.ncbi.nlm.nih.gov/) to confirm the organisms.
Silver decorated green nanocolloids as potent antibacterial and antibiofilm agent against antibiotic resistant organisms isolated from tannery effluent
Published in Inorganic and Nano-Metal Chemistry, 2021
Ranjani S., Faridha Begum I., Tasneem I. K., Senthil Kumar N., Hemalatha S.
Antibiotic resistant strains were chosen, and identification of bacterial strains was performed through amplification of 16S ribosomal RNA using 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1392R (5′-ACGGCTACCTTGTTACGACTT-3′) targeting conserved regions of eubacterial 16S rRNA gene. Polymerase chain reaction was performed under the following conditions: 35 cycles of denaturation at 94 °C for 60 seconds, annealing temperature at 50 °C for 45 seconds and extension at 72 °C for 1 minute with an initial denaturation and final extension for 5 min at 94 °C and 72 °C, respectively. The amplified PCR product was used for sequencing using 27 F forward primer. The nucleotide sequence was used for construction of phylogenetic tree using MEGA-X, based on Maximum Likelihood algorithm. The phylogenetic tree was used to identify the relationship between the isolated bacteria and closely related organisms retrieved from NCBI. After identifying and constructing the phylogenetic tree, bacterial sequence was submitted to NCBI Genbank.[12]
Irritable bowel syndrome and the gut microbiota
Published in Journal of the Royal Society of New Zealand, 2020
Phoebe E. Heenan, Jacqueline I. Keenan, Simone Bayer, Myrthe Simon, Richard B. Gearry
The gut microbiota is believed to be one of the main contributors to the aetiology of IBS. However, past and current research has been unable to determine exactly what components of the microbiota play a part in IBS development. An early study found that IBS patients had a greater proportion of facultative anaerobes cultured from stool samples compared to healthy controls (Bayliss et al. 1984). More recently, a systematic review and meta-analysis of IBS studies using culturing techniques found consistent reductions in Bifidobacterium and Lactobacillus in IBS patients compared to healthy controls (Zhuang et al. 2017). However, anaerobic culturing techniques are no longer considered appropriate for studying the complex ecology of the gut microbiota. Instead genetic sequencing techniques are now widely used, particularly 16S rRNA sequencing, which allows the investigation of complex microbial communities by amplifying the evolutionarily conserved 16S rRNA gene (Larsen et al. 1993). This sequencing technique is able to identify bacterial colonies that grow poorly in culture as well as detect species of bacteria previously uncultured. Subsequent analyses comparing culture and sequencing techniques found that 60%–80% of bacteria present in human stool are unculturable and only 24% of the sequencing results identify species that corresponded to previously described organisms (Suau et al. 1999). Despite these advances studies investigating differences in the gut microbiota in IBS populations are still contradictory.