Metagenomic profiling for assessing microbial diversity and microbial adaptation to degradation of hydrocarbons in two South African petroleum-contaminated water aquifers

Leonard Kachienga,Keshri Jitendra,Maggy Momba

doi:10.1038/s41598-018-25961-0

Leonard Kachienga, Keshri Jitendra + Show 1 more

Open Access

https://doi.org/10.1038/s41598-018-25961-0

Copy DOI

Abstract

Biodegradation of hydrocarbons by indigenous populations of microorganisms found in petroleum-contaminated water sources represents one of the primary mechanisms by which petroleum and other hydrocarbon pollutants are eliminated from the aquatic environment. The identification of these microorganisms, which have capabilities to convert the majority of toxic hydrocarbons into compounds that are less harmful for end-users, is therefore crucial for bioremediation purposes. The aim of this study was to profile the microbial diversity of two South African petroleum-contaminated water aquifer sites and to determine the microbial adaptation to hydrocarbon degradation using a metagenomics approach. The sequenced samples revealed that protozoa (62.04%) were found to be the most dominant group, followed by fungi (24.49%), unknown (12.87%), and finally other sequences such as Animalia and plantae which were <(0.10%) domains in the first oil-polluted aquifer site. In the second site, protozoa (61.90%), unknown (16.51%), fungi (11.41%) in that order. According to the classification at the genus level, the dominant group was Naegleria (15.21%), followed by Vorticella (6.67%) as the only ciliated protozoan genus, other species such as Arabidopsis (2.97%), Asarum (1.84%) Populus (1.04%) were significantly low and drastically lower in the first site. Regarding the second site, the dominant group was Naegleria (18.29%) followed by Colpoda (9.86%) with the remainder of the genera representing <2%. Overall results demonstrated the ability of various groups of microorganisms to adapt and survive in petroleum oil-polluted water sites regardless of their respective distributions and this can be explored further for their role in bioremediation and environmental management.

Highlights

Continuous pollution of the existing freshwater sites across the globe by hydrocarbons of petroleum and their by-products has disastrous consequences for the end-users such as animals, humans, plants and microorganisms
Results of the present study have demonstrated that the microbial community of the petroleum oil-polluted water aquifers of the two different sites in Pretoria/South Africa consisted of various microbial domains with the protozoa were the most dominant groups, followed by fungi and archaea which were present in low numbers in both oil-polluted aquifer sites, which were present in low numbers in both oil-polluted aquifer sites
Based on the metagenomic data analysis, the two petroleum-contaminated sites were inhabited by a diverse array of eukaryotic organisms were the predominant groups, followed by fungi and other domain such as plantae which were found to be present in relatively low numbers in both sites

Summary

Introduction

Continuous pollution of the existing freshwater sites across the globe by hydrocarbons of petroleum and their by-products has disastrous consequences for the end-users such as animals, humans, plants and microorganisms. Microbial diversity involved in bioremediation is always considered as a form of natural degradation of hydrocarbons in various water sources[3]. According to Gong et al.[11], most of the metagenomic analysis tools have opened new windows of opportunities for researchers to analyse the microbial community as a whole (whole-genome sequencing) and the genetic diversity, which facilitates active metabolic pathways in any given environment. There is always a well-established direct correlation between microbial diversity and the presence of hydrocarbons in any oil-contaminated sites. These studies have reported microbial species richness and diversity in different geographical locations. Metagenomic studies provide excellent opportunities for finding new microbial strains and genes involved in bioremediation of hydrocarbon contaminants. The aim of this study was to assess the taxonomic profile of the metagenome and the microbial adaptations in two different petroleum-contaminated sites using a metagenomics approach

Objectives

Methods

Results

Discussion

Conclusion