Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) Profile of Bacterial Community from Agricultural Soils in Bauchi, North-East Nigeria

Abstract

The population dynamics of bacterial community was investigated in three Agricultural soils, designated as Loamy sand (A), Peaty coarse (B) and Loamy coarse sand (C) in North-East, Nigeria. The soil chemical properties were characterized to fully understand their nature. Metagenomic approach was used to extract soil DNA using the fast DNA Spin Kit extraction technique. The PCR-electrophoresed DNA bands were excised and subjected to a full scale Denaturing Gradient Gel Electrophoresis (DGGE) analysis. DGGE fingerprinting for the PCR-16S rDNA product revealed a diverse profile of complex population of bacterial community in the study area. The study shows that more bacterial community can be fully investigated using molecular techniques rather than traditional culture method. The implication of the results obtained is discussed.

Sub-Lethal Effects of Pesticides on the DNA of Soil Organisms as Early Ecotoxicological Biomarkers

“…The critical analysis of the papers examined can help registration authorities to derive ecotoxicological parameters useful for a high-tier risk assessment. Regarding microbial communities, soil microorganisms play key roles in significant ecological processes such as bioremediation, recycling of elements, soil structure establishment, and degradation of organic matter and chemical xenobiotics (Umar et al, 2017;Walvekar et al, 2017). Among them, pesticides are the most common contaminants in the agricultural field (Wołejko et al, 2020), and their persistence in the soil can alter the physico-chemical structure and microbiota composition causing a negative impact on soil biodiversity (Diez et al, 2017).…”

“…The use of biopesticides, differently from synthetic ones, does not affect the microbial community reversibly (Reali and Fiuza, 2016;Umar et al, 2017). In this respect, several studies have shown that the pesticide-induced microbial changes are mainly transient and the structure of the microbial population can improve gradually (Gao et al, 2012;Chen et al, 2013).…”

“…Specific examples of direct molecular monitoring approaches in soil microbiology are represented by DGGE, temperature gradient gel electrophoresis (TGGE) (Heuer and Smalla, 1997;Muyzer and Smalla, 1998), terminal restriction fragment length polymorphism (T-RFLP) (Kuske et al, 2002), single-strand conformational polymorphism (SSCP) (Schwieger and Tebbe, 1998), ribosomal internal spacer analysis (RISA) (Ranjard et al, 2000), and length heterogeneity-PCR (LH-PCR) (Ritchie et al, 2000). Among culture-independent fingerprinting methods, the DGGE, firstly theoretically described in the early 80s by Fischer and Lerman (1979), has been widely applied (Hoshino and Matsumoto, 2007;Coppola et al, 2011;Umar et al, 2017). To obtain optimal results in DGGE analysis, the first practical aspect concerns the high-quality extraction of total DNA from samples and then the control of amplification via PCR selecting universal primers targeting part of the 16S or 18S rRNA sequences for bacteria and fungi, respectively.…”

“…Nevertheless, DGGE is still commonly employed for soil microbial ecology studies in order to monitor population structure and dynamics during that time, especially because of its ability to provide a representative profile of the dominant microbial diversity from specific environments such as soils (Ercolini, 2004;Munaut et al, 2011). In particular, DGGE is a useful tool for the rapid evaluation of microbial profiles in complex ecosystems (Kurtzman et al, 2011;Ng et al, 2014;Di Lenola et al, 2017;Zhang C. et al, 2017), allowing a rapid and efficient separation of the DNA fragments (Umar et al, 2017).…”

“…The shift in the composition was thus only transitory and, at the end of the trial the populations, returned to their initial robustness. Umar et al (2017) recently applied DGGE fingerprinting of 16S rDNA to study the bacterial profile of Nigerian agricultural soil. This study confirmed the complex nature of this matrix, and the PCR-DGGE approach gave the advantage of not requiring previous knowledge on this habitat, providing an immediate picture of specific microbial population constituents in both a qualitative and a semi-quantitative way.…”