Tiny soil microbes turn detective to uncover the timeline of oil spill contamination

Scientists in Belfast and Nigeria have developed a diagnostic tool that deploys microbes to uncover the timeline of crude oil contamination in soils.

The collaborative project is led by researchers from Queenʼs University Belfast and partners in Nigeria and is outlined in the study ʽ’Developing a Molecular Tool for Evaluating the Status of Petrochemical-Contaminated Soils Using functional Gene Ratio Strategy’, which appears in Letters in Applied Microbiology, an Applied Microbiology International publication.

The international team developed and validated a novel molecular diagnostic tool that uses functional gene ratios to assess the status and apparent age of crude oil contamination in soils, said corresponding author Dr Aliyu Ibrahim Dabai.

“Focusing on the chronically polluted Niger Delta in Nigeria, we demonstrated that microbial gene abundance patterns, mainly the ratio of aerobic to anaerobic hydrocarbon-degrading genes, can serve as reliable biomarkers for the severity and timeline of petrochemical pollution,” he said. 

Widespread environmental crisis

Petrochemical contamination from oil spills is a widespread environmental crisis, especially in the Niger Delta, where decades of unregulated extraction have left soils severely degraded. Existing methods rely heavily on chemical analysis, which quantifies pollutants but fails to capture how microbial communities, natureʼs primary agents of biodegradation respond over time. 

The goal in this project was to develop a biologically informed method that could both assess current contamination and infer the duration since a spill occurred, thereby offering a tool for better remediation strategy and environmental forensics.

The team collected 90 soil samples from known contaminated sites across Bayelsa and Rivers States, differentiating between new and old pollution. Using gas chromatography (GC-MS and GCxGC-FID), they quantified hydrocarbon pollutants including using kerosene as reference standard. 

They then applied quantitative PCR and metagenomic analysis to quantify three key genes: PAH-RHDα (from Gram-negative and Gram-positive bacteria) involved in aerobic degradation, and bamA, a marker of anaerobic breakdown of aromatic hydrocarbons. The 16S gene was quantified for the purpose of deducing the % microbial population with the functional genes to the total microbial population.

Core discovery

“Our core discovery was that the ratio of PAH-RHDα to bamA genes correlates both with pollutant concentration and the inferred age of contamination,” Dr Dabai said. 

“Freshly polluted soils showed elevated Gram-negative dioxygenase gene levels and detectable kerosene, while older sites had depleted kerosene but retained anaerobic bamA signatures and sesquiterpane biomarkers. In silico gene mining confirmed these ratios, validating the method independently of PCR bias.

What was striking was the diagnostic clarity provided by the gene ratios, Dr Dabai said. 

“Despite environmental complexity and potential PCR inhibitors, the consistency between qPCR and metagenomic data revealed a robust biological signal underpinning contamination history. Moreover, the ability to distinguish old from new pollution through microbial markers - something that can be missed with chemical tests alone - was unexpectedly precise.”

Evidence-based approach

This tool has profound implications for environmental monitoring, remediation planning, and legal accountability. In regions like the Niger Delta, where oil contamination is persistent but often poorly documented, a gene ratio-based method allows rapid, field-deployable assessment of site condition and pollution age. 

It offers regulators, NGOs, and industry stakeholders an evidence-based approach to prioritise clean-up efforts, evaluate bioremediation efficacy and ensure environmental accountability.

“Future work should extend this approach to a broader range of hydrocarbons (e.g., diesel, bitumen) and diverse soil types across tropical and temperate zones,” Dr Dabai said.

“Integration with portable qPCR platforms or Loop-mediated isothermal amplification (LAMP) based approach could yield a rapid diagnostic kit for field use. Longitudinal studies tracking gene ratio shifts over time will enhance our understanding of natural attenuation processes and microbial succession during remediation.

The study was conceptualised and led by Dr. Aliyu Ibrahim Dabai and Prof. Christopher C. R. Allen, with significant contributions from Raghavendra Juluri Rao, Anna Kulakov, Shamsudeen Umar Dandare, Rory Doherty and Mathew Boyd. Funding was provided by the Petroleum Technology Development Fund (PTDF) Nigeria and the QUESTOR Centre. Technical assistance was supported by Leonid Kulakov, and sequencing services were provided by the University of Cambridge.

ʽ’Developing a Molecular Tool for Evaluating the Status of Petrochemical-Contaminated Soils Using functional Gene Ratio Strategy’, is published in Letters in Applied Microbiology.

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