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Molecular Tools for Microbial Diversity Analysis
Published in Maulin P. Shah, Wastewater Treatment, 2022
Ekta Saini, Pooja Rohilla, Sakshi Papneja, Sudipto Adhikary, Sourish Bhattacharya
DGGE is a technique that is able to produce “barcodes and fingerprint” data of any microbial community. In this method fragments are amplified in PCR by using denaturing agents, urea and formamide, and are identified by electrophoresis. Often, temperature is used as a denaturing agent, the so-called temperature gradient gel electrophoresis (TGGE). The temperature is in increasing order and the urea and formamide concentration is constantly higher (Ercolini, 2004; Sigler et al., 2004). In DGGE, the temperature (almost 60°C) and polyacrylamide gel are constant, and the concentration of urea and formamide increases the gradient. When the amplified DNA fragment domains run in electrophoresis, some fragments are denatured by chemical and thermal denaturing agents at favorable condition, which is called the melting domain. At a certain temperature there is a complete denaturation of these domains. Also, there are changes in conformation and molecule migration ceases in the gel, acquiring a specific position (Figure 14.4).
Glossary of scientific and technical terms in bioengineering and biological engineering
Published in Megh R. Goyal, Scientific and Technical Terms in Bioengineering and Biological Engineering, 2018
TGGE is an abbreviation for thermal gel gradient electrophoresis. TGGE and Denaturing Gradient Gel Electrophoresis (DGGE) are forms of electrophoresis which use either a temperature or chemical gradient to denature the sample as it moves across an acrylamide gel. TGGE and DGGE can be applied to nucleic acids such as DNA and RNA, and (less commonly) proteins. TGGE relies on temperature dependent changes in structure to separate nucleic acids. DGGE was the original technique, and TGGE a refinement of it.
Investigation of biogas for enhancing oil recovery with indigenous microorganism in high salinity oil field
Published in Petroleum Science and Technology, 2023
Jun Wang, Xiaopeng Cao, Zhigang Sun, Hongxin Zhang
However, the oil field is endowed with some characteristics such as high pressure and salinity; the actual condition of microbial can’t be fully reflected by traditional culture. In order to promote the development of MEOR quickly, more attentions are increased to the application of molecular analysis which can not only study the microbial community diversity to provide a novel and effective method for the study of viable but non-culture or uncultured microbes, but can analyze the predominant species and main functional bacteria for MEOR. Now, there have been some studies of microbial community with molecular analysis. DGGE (Denaturing gradient gel electrophoresis method), TGGE (temperature gradient gel electrophoresis) and T-RFLP (Terminal Restriction Fragment Length Polymorphism) were used to analyze the indigenous microorganism of injection plant in Shengli oil field, water injection well and an oil well in Dagang oil field, and the microbial community of transition zone in a Daqing petroleum reservoir, respectively (Cheng et al. 2005; She et al. 2005; Wu et al. 2009; Wang 2016).
Effects of Petroleum Hydrocarbon Contamination on Soil Bacterial Diversity in the Permafrost Region of the Qinghai-Tibetan Plateau
Published in Soil and Sediment Contamination: An International Journal, 2020
Zhi-Long Dong, Bao-Shan Wang, Jie Li
Microorganisms, being in intimate contact with the soil environment, are considered to be the best indicators of soil pollution (Andreoni et al. 2004). The soil microbial community is relatively diverse under natural conditions, and the highest level of prokaryotic diversity is arguably found in the soil (Ferguson et al. 2004). The development of modern molecular biology techniques, such as polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (Scherr et al. 2011; Scollo et al. 2016), temperature gradient gel electrophoresis (García, Rendueles, and Díaz 2019), and high-throughput sequencing (Zhang et al. 2012), has bridged the knowledge gap regarding responses of the soil microbial community to soil oil pollution, beyond the limits of traditional microbial culture techniques, which provides new possibilities for estimating soil microbial diversities. Nutrients, organic materials, environmental temperature, and the Redfield ratio are the main driving factors that control microbial metabolic processes, which cause differences in the soil ecosystem (Zhou et al. 2019). Lassalle et al. found that the presence of PHs alters the soil physicochemical properties, including the soil moisture content, porosity ratio, C/N ratio, C/P ratio, and environmental pH (Lassalle et al. 2019). As a result, oil contamination affects microbial distributions in the vertical and horizontal dimensions, which results in the development of rare species in soil and to relatively homogenous populations of microorganisms in soil (Ribeiro et al. 2013). Peng et al. proposed that oil-polluted soils could support the growth of more diverse bacterial communities than uncontaminated soils (Peng, Zi, and Wang 2015). The above-mentioned studies presented a clear academic gap in understanding changes of microbial diversity (bacterial and fungal) occurring in response to oil contamination. Most studies have focused mainly on developing restoration technology for use after oil pollution occurs, improving oil degradation, and identifying functional microflora that thrive during oil degradation (Shintani et al. 2019). Crucially, exploring the microbial diversity and differences occurring at various oil-contamination sites is considered key for effective bioremediation and will provide the comprehensive information for future ecological restorations and environmental-sustainability assessments.