Our research
Research Areas
Can we treat living systems like ‘Lego’ ? Or is the whole greater than the sum of the parts?
We are increasingly taking a SynBio approach to studying various research questions in the lab; this approach is based on themes such as modularity, abstraction, modelling, and standardisation. This work is typically open-source, sharing standard DNA parts and data with other labs. We have applied SynBio methods to bioremediation, biocatalysis, biosensors, medical biotech, and to design of new cloning vectors.
How do microbes ‘learn’ to metabolise xenobiotic chemicals that are new to the environment? How can we harness the capabilities of microbes to enable cleanup of contaminated sites?
We are working on finding answers to these questions, with a special focus on organochlorine and nitroaromatic pollutants, including solvents and pesticides. We are interested in finding novel microbes, genes and enzymes capable of attacking these compounds, elucidating the metabolic pathways, and understanding the physiology and ecology of the organisms – this knowledge is essential for effective use of these microbes for bioremediation.
Which industrial chemical reactions can be replaced with biochemical reactions? How can we exploit microbes and enzymes to make useful products?
We are especially interested in the reactions of monooxygenases – these enzymes add oxygen to specific locations in organic molecules, yielding alcohols and epoxides. Some monooxygenases act in a highly selective fashion, e.g. making nearly pure single enantiomers of epoxides, which are valuable for pharmaceutical synthesis. Our favourite enzyme is the ethene monooxygenase of Mycobacterium spp, which we are trying to express in more industrially-friendly hosts (e.g. E.coli).
What are the ecological roles of mycobacteria? How can we use them for biotechnology?
The ‘fast-growing’ species of mycobacteria are common in many environments, and known to be important for biodegradation of pollutants. We suspect that these bugs also have important roles in soils, such as influencing plant growth. We are using a mix of ecological, molecular and genomic methods to study these bacteria and developing new genetic tools to help understand mycobacterial gene functions.
How do MGEs work, and how do they impact bacterial evolution? How can we detect and manipulate MGEs to minimise negative effects (e.g. antibiotic resistance) and enhance positive effects (e.g. pollutant degradation)?
MGEs are incredibly powerful tools both for bacteria and for biotechnologists. We are interested in all aspects of these tricky little beasts, but especially in developing new methods for detecting their activities in environmental contexts, and in using them to develop tools for bacteria that currently lack effective genetic manipulation systems. Our favourite MGEs are integrons and catabolic plasmids.
Publications
Publications by Nicholas V. Coleman
- Impacts of Domestication and Veterinary Treatment on Mobile Genetic Elements and Resistance Genes in Equine Fecal Bacteria March 29, 2023Antimicrobial resistance in bacteria is a threat to both human and animal health. We aimed to understand the impact of domestication and antimicrobial treatment on the types and numbers of resistant bacteria, antibiotic resistance genes (ARGs), and class 1 integrons (C1I) in the equine gut microbiome. Antibiotic-resistant fecal bacteria were isolated from wild horses, healthy […]
- Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review January 27, 2022Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases […]
- The equine hindgut as a reservoir of mobile genetic elements and antimicrobial resistance genes April 26, 2021Antibiotic resistance in bacterial pathogens is a growing problem for both human and veterinary medicine. Mobile genetic elements (MGEs) such as plasmids, transposons, and integrons enable the spread of antibiotic resistance genes (ARGs) among bacteria, and the overuse of antibiotics drives this process by providing the selection pressure for resistance genes to establish and persist […]
- Biodegradation and Abiotic Degradation of Trifluralin: A Commonly Used Herbicide with a Poorly Understood Environmental Fate August 14, 2020Trifluralin is a widely used dinitroaniline herbicide, which can persist in the environment and has substantial ecotoxicity, especially to aquatic organisms. Trifluralin is very insoluble in water (0.22 mg/L at 20 °C) and highly volatile (vapor pressure of 6.7 mPa at 20 °C); these physicochemical properties determine a large part of its environmental fate, which […]
- Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes August 9, 2020The evolutionary processes that drive variation in genome size across the tree of life remain unresolved. Effective population size (N(e)) is thought to play an important role in shaping genome size [1-3]-a key example being the reduced genomes of insect endosymbionts, which undergo population bottlenecks during transmission [4]. However, the existence of reduced genomes in […]
- Metabolic Engineering of the MEP Pathway in <em>Bacillus subtilis</em> for Increased Biosynthesis of Menaquinone-7 June 29, 2019Vitamin K is essential for blood coagulation and plays important roles in bone and cardiovascular health. Menaquinone-7 (MK-7) is one form of vitamin K that is especially useful due to its long half-life in the circulation. MK-7 is difficult to make via organic synthesis, and is thus commonly produced by fermentation. This study aimed to […]
- Microcosm experiments and kinetic modeling of glyphosate biodegradation in soils and sediments December 21, 2018Glyphosate (GLP) is one of the most widely-used herbicides globally and its toxicity to humans and the environment is controversial. GLP is biodegradable, but little is known about the importance of site exposure history and other environmental variables on the rate and pathway of biodegradation. Here, GLP was added to microcosms of soils and sediments […]
- Glyphosate dispersion, degradation, and aquifer contamination in vineyards and wheat fields in the Po Valley, Italy September 18, 2018Biodegradation of glyphosate (GLP) and its metabolite aminomethylphosphonic acid (AMPA) was numerically assessed for a vineyard and a wheat field in the Po Valley, Italy. Calculation of the Hazard Quotient suggested that GLP and AMPA can pose a risk of aquifer contamination in the top 1.5 m depth within 50 years of GLP use. Numerical […]
- Heterologous Expression of Mycobacterium Alkene Monooxygenases in Gram-Positive and Gram-Negative Bacterial Hosts May 27, 2018Alkene monooxygenases (MOs) are soluble di-iron-containing enzymes found in bacteria that grow on alkenes. Here, we report improved heterologous expression systems for the propene MO (PmoABCD) and ethene MO (EtnABCD) from Mycobacterium chubuense strain NBB4. Strong functional expression of PmoABCD and EtnABCD was achieved in Mycobacterium smegmatis mc²155, yielding epoxidation activities (62 and 27 nmol/min/mg […]
- Author Correction: Seasonal total methane depletion in limestone caves April 13, 2018A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
- Co-occurrence of genes for aerobic and anaerobic biodegradation of dichloroethane in organochlorine-contaminated groundwater October 18, 20171,2-Dichloroethane (DCA) is a problematic groundwater pollutant. Factors influencing the distribution and activities of DCA-degrading bacteria are not well understood, which has hampered their application for bioremediation. Here, we used quantitative PCR to investigate the distribution of putative DCA-dehalogenating bacteria at a DCA-impacted site in Sydney (Australia). The dehalogenase genes dhlA, tceA and bvcA were […]
- Seasonal total methane depletion in limestone caves August 18, 2017Methane concentration in caves is commonly much lower than the external atmosphere, yet the cave CH(4) depletion causal mechanism is contested and dynamic links to external diurnal and seasonal temperature cycles unknown. Here, we report a continuous 3-year record of cave methane and other trace gases in Jenolan Caves, Australia which shows a seasonal cycle […]
- The influence of the ethane-1,2-diamine ligand on the activity of a monofunctional platinum complex August 10, 2017The continued use of platinum-based chemotherapeutic drugs in the clinic mandates the need for further investigation of the biological activity of structural analogues of the clinically approved complexes. Of interest are monofunctional platinum(II) complexes, which bear only one labile ligand, for which it is believed that each complex binds to DNA only once. Pyriplatin ([PtCl(NH(3))(2)(py)]^(+)) […]
- Bacterial communities associated with apical periodontitis and dental implant failure November 12, 2016CONCLUSION: Increased abundances of Prevotella, Fusobacterium and TG5 (Synergistetes) were associated with apical periodontitis and a failed implant. A larger sample set is needed to confirm these trends and to better define the processes of bacterial pathogenesis in implant failure and apical periodontitis. The application of combined culture-based, microscopic and molecular technique-based approaches is suggested […]
- A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site June 26, 20161,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was […]
- Biochemical and biophysical characterisation of haloalkane dehalogenases DmrA and DmrB in Mycobacterium strain JS60 and their role in growth on haloalkanes April 23, 2015Haloalkane dehalogenases (HLDs) catalyse the hydrolysis of haloalkanes to alcohols, offering a biological solution for toxic haloalkane industrial wastes. Hundreds of putative HLD genes have been identified in bacterial genomes, but relatively few enzymes have been characterised. We identified two novel HLDs in the genome of Mycobacterium rhodesiae strain JS60, an isolate from an organochlorine-contaminated […]
- SmoXYB1C1Z of Mycobacterium sp. strain NBB4: a soluble methane monooxygenase (sMMO)-like enzyme, active on C2 to C4 alkanes and alkenes July 13, 2014Monooxygenase (MO) enzymes initiate the aerobic oxidation of alkanes and alkenes in bacteria. A cluster of MO genes (smoXYB1C1Z) of thus-far-unknown function was found previously in the genomes of two Mycobacterium strains (NBB3 and NBB4) which grow on hydrocarbons. The predicted Smo enzymes have only moderate amino acid identity (30 to 60%) to their closest […]
- Mutagenesis of the hydrocarbon monooxygenase indicates a metal centre in subunit-C, and not subunit-B, is essential for copper-containing membrane monooxygenase activity April 1, 2014The hydrocarbon monooxygenase (HMO) of Mycobacterium NBB4 is a member of the copper-containing membrane monooxygenase (CuMMO) superfamily, which also contains particulate methane monooxygenases (pMMOs) and ammonia monooxygenases (AMOs). CuMMOs have broad applications due to their ability to catalyse the oxidation of difficult substrates of environmental and industrial relevance. Most of our understanding of CuMMO biochemistry […]
- Insertion sequence ISPst4 activates pUC plasmid replication in Pseudomonas stutzeri March 11, 2014Insertion sequences (IS) are important drivers of bacterial evolution. Here, we report a previously undescribed IS element (ISPst4) in Pseudomonas stutzeri, and its unusual interaction with plasmids introduced into this species. Transformation of the pUC19 derivative plasmid pUS23 into P. stutzeri yielded ampicillin-resistant transformants in P. stutzeri, but these grew very poorly. Plasmids recovered from […]
- Adaptation of a membrane bioreactor to 1,2-dichloroethane revealed by 16S rDNA pyrosequencing and dhlA qPCR November 2, 2013A pilot-scale membrane bioreactor (MBR) was tested for bioremediation of 1,2-dichloroethane (DCA) in groundwater. Pyrosequencing of 16S rDNA was used to study changes in the microbiology of the MBR over 137 days, including a 67 day initial adaptation phase of increasing DCA concentration. The bacterial community in the MBR was distinct from those in soil […]