IAP2-22-428

Towards the design of a digital twin for biopile remediation of hydrocarbon contaminated soils.

Industrialisation has left behind a legacy of pollution that presents a risk to human health and the environment. Newly developed sustainable and safe remediation approaches include bioremediation through stimulation of the local microbial ecology. Biopiles is a type of bioremediation technology in which excavated soils are formed into piles, enclosed and mixed with amendments such as moisture, nutrients or air. In the pile the contaminants are mineralised or converted into contaminants of lower toxicity. They are successful in remediating low and mid-level petroleum contaminated soils; like many environmental biotechnologies they are still mostly “black boxes”. Moving to the design of smart and efficient biopiles, possibly for more concentrated or recalcitrant contaminants, requires extracting from the exhaustive knowledge on the degradation of complex samples the information that will enable enhancement of the degradation of listed contaminants.
Nucleic acid sequencing has enabled the high-resolution characterisation of microbial communities in contaminated soils; metataxogenomic and metagenomic approaches have shown that pollution triggers a reduction in species richness and enriches the soil microbial population with species that are adapted to hydrocarbon degradation. Consequently, the microbial ecology of a soil candidate for biopile contains information on its potential for hydrocarbon degradation . However, without high resolution information on the exhaustive contamination profile, this information will not be sufficient for the design of an efficient site-specific bioremediation. Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) has allowed the near comprehensive characterisation of semi-volatile organic carbons (SVOCs) in tars and contaminated soils from former manufactured gasworks (FMGs). Integration of metataxogenomics and GC × GC-MS analysis has the potential to unveil information on the interactions between the complex mixtures of environmental contaminants and site-specific microbial ecology never accessed before. In this project, the student will investigate lab-scale biodegradation of coal tar contaminated soils from different origins; they will study the role of various amendments in affecting the bioremediation process. By integrating chemical and molecular biology results through existing pipelines uniquely designed by the supervisors and approaches developed during the PhD, the student will be able to produce a first example of a digital twin of biopiles, i.e. a virtual representation of the biopile system.

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Integration of non targeted hydrocarbon analysis and metataxagenomics

Methodology

Lab-scale biopile remediation of coal-tar contaminated soil will be run in the Environmental Laboratories in the Water and Environmental Group at the University of Glasgow. The group is specialised in environmental biotechnology and the labs are ideally equipped for both microcosms and mesocosms experiments. Bioremediation will be carried out on soil from various origin and different level of contamination. The effect of various amendments such as air supply, moisture and nutrients (nitrogen and phosphorus) will be investigated. For each biopile system, times series data will be collected for 1) comprehensive hydrocarbon characterisation (non-targeted analysis) using extraction and analytical methods that includes GC x GC-MS already available in Gauchotte-Lindsay’s research group and 2) metataxogenomics using 16S rRNA sequencing which is established in Gutierrez and Ijaz’s groups. For non-targeted hydrocarbon data, existing and novel data workflow for time series will be used to describe the yield of degradation as a whole (rather than on individual compounds), to cluster compounds that have similar kinetics and possibly establish precursor and product compounds. This will allow generating a high-level kinetics study of the biodegradation of samples as a whole. For the multi omics data generated through this project, we will utilise the R packages and workflows already established at Ijaz’s lab The metataxogenomics dataset will recover Amplicon Sequencing Variants (ASVs), their taxonomic resolution, and phylogenetic tree of relatedness for the sequencing data generated. Network interference approaches will also be used to find relationships between microbial species through recently developed approaches in Ijaz’s lab. Both approaches remain untested for the above contamination dataset and will be extended by the PhD student. Integrative Omics Approaches will find reduced feature sets that will discriminate between multiple conditions. Conversely, we will model bacterial abundances based on commonly used distributions and will regress these against environmental covariates using generalised linear latent variable model to identify outcomes that associate positively/negatively for a single feature (microbes).
Timeline – Year 1*
In Year 1, the student will carry out a thorough literature review on biopiles as a remediation biotechnology, the development and use of digital twins in biotechnologies and the integration of molecular biology to other complex data. The student will be trained in the necessary analytical chemistry and molecular biology lab skills. An initial lab-scale experiment will be designed, looking at the two soils we have already characterised in detail with a unique set of amendment condition. This will establish the template for future mesocosms and enable to establish and validate sample and data workflows.

Project Timeline

Year 1

In Year 1, the student will carry out a thorough literature review on biopiles as a remediation biotechnology, the development and use of digital twins in biotechnologies and the integration of molecular biology to other complex data. The student will be trained in the necessary analytical chemistry and molecular biology lab skills. An initial lab-scale experiment will be designed, looking at the two soils we have already characterised in detail with a unique set of amendment condition. This will establish the template for future mesocosms and enable to establish and validate sample and data workflows.

Year 2

In Year 2, the student will continue to develop and test workflows for the processing, cleaning and analysis of the data produced by the first lab-scale experiment. They will present the initial approach for the characterisation of degradation kinetics for a whole sample and investigate correlation with the microbial ecology. This should lead to the design of several new lab-scale biopiles experiments, using a new soils and various types of amendments- prioritising aeration and nutrients. The kinetics and the time series change of the microbial communities will be characterised and compared, for example, using temporal spline based and timeOmics approaches.

Year 3

In Year 3, the student will carry out statistical integration of the data and work on prediction models. This will lead to an initial design of a digital twin model. The model will be tested on a lab-scale and a field-scale biopile of the same soil, working with our industrial partner ERS. The soil will be characterised, comprehensively analysed for chemical composition and microbial ecology; the same set of amendments will be reproduced in both tests. The capacity of the twin to predict and help optimised bioremediation of hydrocarbons in biopiles will be evaluated.

Year 3.5

This is expected to be time spent by the student to finish writing the thesis.

Training
& Skills

The student will receive a unique set of multidisciplinary training in environmental engineering, analytical chemistry, molecular biology and chemo and bioinformatics. This will happen in an interdisciplinary supervisory team and research groups. Between them, the supervisory team have world-leading expertise in environmental engineering, analytical chemistry, microbiology and data science and are able to fully support all aspects of the scholar’s research programme This is an exciting interdisciplinary project addressing real and topical issues in environmental sciences with a true potential for significant long-term impact on current practices working closely with stakeholders. It will transform the student into a highly employable individual with a unique set of skills and a transdisciplinary approach to science and engineering that will set them apart from traditionally trained postgraduate students.

References & further reading

The projects builds on a strong collaborative network between Gauchotte Lindsay, Ijaz, and Guitierrez on understanding microbially mediated biodegradation and bioremediation, with past publications as:
Gauchotte-Lindsay et al. Faradays Discussion, 2019. DOI: 10.1039/C9FD00020H
Nikolova et al. Microbiome, 2021. DOI: 10.1186/s40168-021-01143-5
Nikolova et al. Ecology and Evolution, 2021. DOI: 10.1002/ece3.8091
culminating in the joint press-release: Phys.org – Oil industry should invest in bio solutions for oil spills
Trego et al. Microorganisms, 2022; DOI: 10.3390/microorganisms10101961).

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