Crude oil hydrocarbons' effect on soil microbial metagenome from Niger Delta polluted soils

Introduction

Successful microbial remediation of polluted environments depends largely on the prevailing baseline physicochemical parameters, ecological conditions, available microbial community structure and their numbers and how the pollutant influences the interaction of these factors. For this study crude oil polluted soils were monitored prior to a microbial remediation project. Crude oil is a major pollutant of environmental concern. At certain concentrations it is toxic to microorganisms and other life forms within the receiving environmental compartment. It contains compounds like the polycyclic aromatic hydrocarbons (PAHs) which are priority chemicals of concern according to the United States Environmental Protection Agency (USEPA). PAHs are reported to be toxic, mutagenic, teratogenic to mammals. They bioaccumulate along the food chain and can persist in the environment. Crude oil hydrocarbons also alter the physicochemical parameters like pH, oxygen tension, and nutrient composition of receiving environment thereby affecting microbial activities within the impacted site. The Niger Delta region of Nigeria has a high incidence of crude oil pollution due to the heightened oil and gas industry activities within the region (Nwilo & Badejo, 2005). Most polluted environments within the region exceed both the regulatory intervention value of 40 mg/kg of soil or 70 μg/L for ground waters of PAHs and total petroleum hydrocarbons (TPH) concentration of 5000 mg/kg of soil or 600 μg/L for groundwater as contained in the Environmental Guidelines and Standards for the Petroleum Industry in Nigeria (EGASPIN) (Okafor et al., 2021; UNEP, 2011).

The data collected were to address the specific objectives of the study which were to:

Methods

The data were collected from two polluted sites in Rivers State, Nigeria, namely Bodo community (N4.620134, 7.282998E) and Ngia-Ama Tombia Community (N4.9816667; 7.0608333E) within the Niger Delta region of Nigeria. The Ngia-Ama Tombia site is a moderate low land in close proximity to mangroves and creeks whereas Bodo is an upland environment. Eight (8) samples per 1000 sqm of soil at the depth of 0-30 cm were collected from each site and used for this study. The eight samples were collected, four (4) from points around the pollution point and another four (4) samples about 200m away from the point source. The samples were pooled and homogenized into duplicates per site according to proximity before analysis. The physical properties of the polluted soil were analyzed according to regulatory recommended test methods for physicochemical parameters as contained in (APPENDIX VIII-E1, EGASPIN) (Resources, 2018). Sieve analysis and hydrometer method were used to determine the proportion of sand, salt, clay and sand using the standard test methods for particle-size distribution of both soils and fine-grained soils (ASTM, 2017b; ASTM, 2021a). The soil density, specific gravity and water content by gravimetric method, were also determined to project pollutant movement within the soil. Other parameters within the polluted soil were determined and these physicochemical parameters included pH of the soil, soil conductivity, soil nutrients (nitrates and phosphate concentration) of the polluted soil. pH was analyzed according to the United States Environmental Protection Agency (USEPA, 2004) using the pH meter (Hanna multimeter reader), soil conductivity was by a modification of the APHA 145 method, whereas the nutrients, nitrates and phosphates were determined using the spectrophotometer method (PG, T60) and nutrient pillows from HACH^®. The concentration of extractable total petroleum hydrocarbon (eTPH) in the soil was determined using the GC-FID protocol. The residual petroleum hydrocarbons were extracted from the samples by hexane (for slightly contaminated soils) or chloroform (for heavily contaminated soils) and the extract cleaned in activated charcoal column prior to spectrophotometry. Agilent 1760 spectrophotometer with flame ionizing radiation was used for TPH concentration determination. GC-MS protocol was used in the determination of the PAHs concentration in the soil samples after sample clean-up (ASTM, 2017a). Heavy metals analysis was done using the ASTM-D8404-21 method (ASTM, 2021b). The practice covered drying, homogenization, ammonium bifluoride-nitric acid digestion of soil samples and associated quality control (QC) samples for the determination of metals and metalloids using laboratory flame atomic absorption spectrometry (FAAS).

For microbial community analysis, shotgun metagenomic sequencing was used to determine the composition, diversity, spread and functional profile of extant microbial population within the polluted environment. The samples were processed and analyzed with the ZymoBIOMICS^® Shotgun Metagenomic Sequencing Service for Microbiome Analysis (Zymo Research, Irvine, CA). Sample processing included DNA extraction, library preparation, and metagenomic DNA sequencing.

Data availability

The results obtained are deposited with the European Nucleotide Archive (ENA) of the European Molecular Biology Laboratory (EMBL) repository.

European Nucleotide Archive: Crude oil hydrocarbon polluted soil metagenomes. Accession number: PRJEB53529 (Okafor et al., 2022).

This project contains the following underlying data:

Data are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).