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

Ahmed Faruk Umar,Fatimah Tahir,Ediga Bede Agbo

doi:10.4236/aim.2017.76037

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.

Highlights

Microorganisms are key players in important ecological processes such as soil structure formation, decomposition of organic matter and xenobiotic, recycling of essential elements [1]
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
Denaturing Gradient Gel Electrophoresis (DGGE) fingerprinting for the Polymerase Chain Reaction (PCR)-16S rDNA product revealed a diverse profile of complex population of bacterial community in the study area

Summary

Introduction

Microorganisms are key players in important ecological processes such as soil structure formation, decomposition of organic matter and xenobiotic, recycling of essential elements (e.g. carbon, nitrogen, phosphorous and sulphur) [1]. The need to understand the microbial community that channel soil affair is quite imperative These will pave way in knowing their activities and mechanistic role to the sustenance of ecosystem (e.g. energy flow, biogeochemical cycling, and ecological resilience). This study intends to use the science of metagenomics to bring fore the nature of the bacterial community in three agricultural soils in Bauchi State North-Eastern Nigeria. It will involve the use of Polymerase Chain ReactionDenaturing Gradient Gel Electrophoresis (PCR-DGGE) fingerprinting as a whole community analysis method. PCR-DGGE is flexible that allows a unique combination of different approaches for a more accurate identification of functional genes present in particular bacterial population by using hybridization or species-specific probes

Sampling and Study Area

Characterization of Soil Samples

Results and Discussion