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Investigation of New Actinobacteria for the Biodesulphurisation of Diesel Fuel

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Investigation of New Actinobacteria for the Biodesulphurisation of Diesel Fuel Investigation of new actinobacteria for the biodesulphurisation of diesel fuel Selva Manikandan Athi Narayanan A thesis submitted in partial fulfilment of the requirements of Edinburgh Napier University, for the award of Doctor of Philosophy May 2020 Abstract Biodesulphurisation (BDS) is an emerging technology that utilises microorganisms for the removal of sulphur from fossil fuels. Commercial-scale BDS needs the development of highly active bacterial strains which allow easier downstream processing. In this research, a collection of actinobacteria that originated from oil-contaminated soils in Russia were investigated to establish their phylogenetic positions and biodesulphurisation capabilities. The eleven test strains were confirmed as members of the genus Rhodococcus based on 16S rRNA and gyrB gene sequence analysis. Two organisms namely strain F and IEGM 248, confirmed as members of the species R. qingshengii and R. opacus, respectively based on the whole- genome sequence based OrthoANIu values, exhibited robust biodesulphurisation of dibenzothiophene (DBT) and benzothiophene (BT), respectively. R. qingshengii strain F was found to convert DBT to hydroxybiphenyl (2-HBP) with DBTO and DBTO2 as intermediates. The DBT desulphurisation genes of strain F occur as a cluster and share high sequence similarity with the dsz operon of R. erythropolis IGTS8. Rhodococcus opacus IEGM 248 could convert BT into benzofuran. The BDS reaction of both strains follows the well-known 4S pathway of desulphurisation of DBT and BT. When cultured directly in a biphasic growth medium containing 10% (v/v) oil (n-hexadecane or diesel) containing 300 ppm sulphur, strain F formed a stable oil-liquid emulsion, making it unsuitable for direct industrial application despite the strong desulphurisation activity. Whereas the strain 248 formed distinct oil, biomass and aqueous phases which enabled easy extraction of the desulphurised oil with more than 80% reduction in total sulphur content, making it a potential candidate strain for the development of a robust BDS biocatalyst to upgrade crude oils and refinery streams at industrial scale. Whole-genome analysis of these strains also revealed the presence of a high copy number of various monooxygenases and sulphur metabolism related genes that occurred in clusters. These genes offer potential target sites for future mutation strategies to forestall sulphate induced repression of the desulphurisation genes which warrants future investigation. i Declaration I declare that this thesis is a result of my own independent work and all the work presented in it was undertaken and written by me. I also declare that no part of this work has been submitted for any other degree or professional qualification. Selva Manikandan Athi Narayanan Date 25/05/2020 ii Dedication To my beloved parents and my dear brother who funded my research and have been supportive of all my experiments with life, seeing me through successes and failures iii Acknowledgement I thank my Director of Studies, Dr Fiona M Stainsby for her comments, criticisms and guidance for the entirety of the research work and for steering me through university regulatory aspects regarding the course. Her profound feedback on my thesis chapters was hugely helpful in structuring the thesis to its form. I would like to thank my co-supervisor Prof Nick Christofi, Recircle Ltd, who has a key role in conceiving the idea for this project, providing the bacteria and persistent guidance throughout the project in terms of the research activities and great moral support. My sincere thanks to Ms Patricia Gonzalez-Iglesias and her team at the Microbiology Laboratory, School of Applied Science for their daily support and timely services during my laboratory-ridden days. I thank Ms Sadie Kemp for providing consultation regarding PCR techniques and the use of the thermal cycler. I thank Dr Sonja Rueckert for demystifying the procedures related to gene sequencing. I thank Mr Chris Edmans for putting up with my standard and at times strange purchase requests and especially for his patience and cooperation while dealing with sequencing related results that were sometimes sent to his inbox. The little succours from these helpful colleagues made me feel positive and reassured while trying out those techniques for the first time. I am immensely thankful to Ms Tatyana Peshkur and Ms Mara Knapp at the University of Strathclyde, for their role in providing consultation and demonstration of the analytical techniques used in this research. I thank Mr Chris Gould and Ms Louise MacNicol at Petroineos Refining, Grangemouth, UK for providing with HDS stream gas oil used in this research. I am very grateful to my lovely wife, Mrs Divyapradeepa, for the sacrifices she made, the love she showered, the care and support she offered during my long student life. iv Contents Chapter 1 Literature Review ............................................................................. 1 1.1 Overview of sulphur compounds present in crude oil ............................ 2 1.2 Impact of sulphoxide emission ............................................................... 4 1.3 Standard sulphur limits in fuel ................................................................ 5 1.4 Technologies for desulphurisation of crude oil-derived fuels ................ 6 1.4.1 Hydrodesulphurisation (HDS) .......................................................... 7 1.4.2 Other desulphurisation techniques ................................................ 10 1.5 Biodesulphurisation (BDS) ................................................................... 12 1.6 Bacterial BDS Pathways ....................................................................... 14 1.6.1 The Kodama pathway .................................................................... 14 1.6.2 The 4S pathway ............................................................................. 16 1.6.3 Pathways of BT desulphurisation .................................................. 20 1.7 Avenues for the improvement of BDS technology ............................... 21 1.8 Scope of the thesis ............................................................................... 27 Chapter 2 Phylogenetic study of putative rhodococci isolated from hydrocarbon-contaminated environments...................................................... 29 2.1 Introduction ........................................................................................... 30 2.1.1 Biology of Rhodococcus ................................................................ 30 2.1.2 Role of polyphasic approaches in resolving rhodococcal systematics ................................................................................................................. 32 2.1.3 Use of genomic sequences in resolving rhodococcal taxonomy .. 32 2.1.4 Current phylogenetic structure of the genus Rhodococcus .......... 41 2.1.5 Background information about the identity of the test strains ....... 42 2.1.6 Aim .................................................................................................. 45 2.2 Materials and Methods ......................................................................... 46 2.2.1 Test strains ..................................................................................... 46 v 2.2.2 Cultivation, maintenance and preservation of test strains ............ 46 2.2.3 Colony and micromorphology characteristics ............................... 50 2.2.4 Chemotaxonomy ............................................................................ 50 2.2.5 Genomic DNA extraction and purification ..................................... 52 2.2.6 PCR amplification of the 16S rRNA gene and gyrB gene ............ 53 2.2.7 Detection of DNA and integrity check ............................................ 56 2.2.8 Sequencing of purified 16S rRNA and gyrB gene......................... 57 2.2.9 Consolidation of sequencing data ................................................. 59 2.2.10 Construction of phylogenetic trees .............................................. 59 2.3 Results .................................................................................................. 61 2.3.1 Mycolic acid profile of the test strains ............................................ 61 2.3.2 Phylogeny of the strains based on 16S rRNA gene and gyrB gene sequence analyses .................................................................................. 63 2.3.3 Identification of strains 208, 488 and 508 ..................................... 75 2.3.4 Identification of strains 20, 213, 505 and F ................................... 80 2.3.5 Identification of strains 87 and 369 ................................................ 86 2.3.6 Species identification of strain 60 .................................................. 91 2.3.7 Identification of strain 248 .............................................................. 95 2.4 Discussion ............................................................................................. 99 Chapter 3 Biodesulphurisation of benzothiophene and dibenzothiophene present in aqueous medium and diesel oil by new rhodococci strains ....... 105 3.1 Introduction ......................................................................................... 106 3.1.1 Development of bacterial catalysts for BDS ................................ 106 3.1.2 Gibbs assay .................................................................................. 114 3.1.3 Adaptation of Gibbs reaction for the development
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