Project highlights

  • Determining how, and to what extent, methylated amines inhibit ammonia oxidising archaea and bacteria in pure cultures 
  • Investigating the uptake and metabolism of methylamines in ammonia oxidisers 
  • Defining the impacts of methylated amines on nitrification in the environment 

Overview

Ammonia oxidation is a key step in the global nitrogen cycle performed by archaea (AOA) and bacteria (AOB), and critically important for climate change and environmental pollution. Although ammonia oxidising archaea are among the most numerous living organisms on Earth, surprisingly little is known about how certain ubiquitous environmental molecules, such as methylated amines, influence their activity and nitrogen turnover. The aim of this studentship is to determine the impact of methylamines on ammonia oxidising microorganisms, and in doing so, reveal previously unsuspected links between the global biogeochemical cycles of nitrogen and carbon. 

Methylated amines are common in the environment and produced from degradation of osmolytes and organic matter. Whilst microbial methylamine metabolism has been studied extensively and methylamine is a known nitrogen source for assimilation, significantly less is known about its participation in, and effects on, other processes in the nitrogen cycle. Methylamine is a structural analogue of ammonia, and an inhibitor of ammonia oxidation and growth in AOB (Figure 1), which have been shown to take up methylamine. Virtually nothing is known about how methylamines interact with AOA, but we have shown that AOA are inhibited by methane at lower thresholds than their bacterial counterparts, and there is every possibility that AOA are also more strongly inhibited by methylamines than AOB. We hypothesise that methylamines are competitive inhibitors of AOA, and like AOB, AOA can take up methylamines. We further predict that in the environment, methylotrophs and other microorganisms will alleviate the inhibitory effects of methylamines on nitrification, and methylamine-derived nitrogen will enter nitrification after degradation (Figure 1).  

This project will use cultivated model AOA, discovered by the lead supervisor, and link mechanistic understanding generated from pure cultures to mixed microbial communities in the environment. By combining cultivation, whole cell enzyme kinetics, proteomics and stable isotope probing, this project will provide exciting novel insights into microbial metabolism, and interactions between microorganisms and biogeochemical cycles. The new knowledge will contribute towards understanding the previously overlooked factors impacting nitrogen cycling and help future predictions of nitrogen turnover and greenhouse gas production in the environment.

A schematic illustrating some of the themes of the project.

Host

University of Warwick

Theme

  • Climate and Environmental Sustainability
  • Organisms and Ecosystems

Supervisors

Project investigator

Co-investigators

How to apply

Methodology

The PhD student will test the mode and thresholds of inhibition by methylated amines (monomethylamine, dimethylamine, trimethylamine) using whole cell kinetics assays previously established by the lead supervisor for pure cultures of AOA and AOB. Nitrification and methylated amine degradation processes will be monitored by colorimetric assays and gas chromatography. Uptake of methylated amines by ammonia oxidisers will be investigated using isotopically labelled compounds and isotope ratio mass spectrometry. The response of ammonia oxidisers to methylated amines will be studied by comparative proteomics in the presence or absence of the compounds, using our recently published approach. To determine the impact of methylated amines on nitrification in the environment, the PhD student will construct soil microcosms with and without methylamine. DNA-Stable Isotope Probing will be performed using 13C- and 15N-labelled compounds to identify the microorganisms actively involved in degradation and uptake of methylamine.  

Training and skills

DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.  

The PhD student will receive advanced research skills training in microbial cultivation, microbial physiology, proteomics, analytical chemistry, molecular techniques and isotopic analyses. The student will present their research findings in lab meetings, seminars and (inter)national conferences, and will be encouraged to participate in scientific outreach and transferable skills training. Supervisory team has very strong track records and expertise in the subject area, and is in an excellent position to support and train the PhD student. This studentship provides an excellent scope for developing critical thinking and data interpretation skills, and will equip the successful applicant with a well-rounded skillset.   

Partners and collaboration

This project will establish new collaborations between the members of the supervisory team, who have highly complementary strengths in the subject area and extensive experience in studying biogeochemical cycling of carbon and nitrogen. Lehtovirta-Morley is an expert in physiology and ecology of ammonia oxidation, Chen in methylated amine metabolism, Mushinski in isotopic analyses and Schäfer in biogeochemical cycling of diverse organic compounds. 

Further details

Applicants are strongly encouraged to contact Laura Lehtovirta-Morley ([email protected]) (www.lehtovirta-morleylab.com) to discuss the project and ask any questions they may have.  

To apply to this project:  

  • You must include a CV with the names of at least two referees (preferably three) who can comment on your academic abilities.  

 Applications must be submitted by 23:59 GMT on Wednesday 8th January 2025.  

Possible timeline

Year 1

Cultivation experiments with AOA and AOB. Using whole cell enzyme kinetics assays with a range of ammonia and methylamine concentrations, the PhD student will determine the inhibitory thresholds and modes of inhibitions in AOA and AOB. 

Year 2

Uptake and metabolic response to methylated amines by ammonia oxidising microorganisms using 13C-labelled methylated amines, isotope ratio mass spectrometry and proteomics. 

Year 3

Stable isotope probing using soil microcosms with methylamine. Microbial communities will be analysed using 16S rRNA amplicon sequencing and clade-specific qPCR assays. 13C- and 15N-isotopic labelling will be used to track processes and active microorganisms involved in methylamine degradation using DNA-stable isotope probing, molecular techniques and isotope ratio mass spectrometry.

Further reading

Journal:  

Oudova-Rivera, B., Wright, C.L., Crombie, A.T., Murrell, J.C., and Lehtovirta-Morley, L.E. (2023) ‘The effect of methane and methanol on the terrestrial ammonia-oxidizing archaeon ‘Candidatus Nitrosocosmicus franklandus C13’’, Environmental Microbiology, 25(5), pp. 948-961. https://doi.org/10.1111/1462-2920.16316 

Wright, C.L., Schatteman, A., Crombie, A.T., Murrell, J.C., and Lehtovirta-Morley, L.E. (2020) ‘Inhibition of Ammonia Monooxygenase from Ammonia-Oxidizing Archaea by Linear and Aromatic Alkynes’, Applied and Environmental Microbiology, 86(9), pp. e02388-19. doi: https://doi.org/10.1128/AEM.02388-19 

Fitzsimons, M.F., Airs, R., and Chen, Y. (2024) ‘The occurrence and biogeochemical cycling of quaternary, ternary and volatile amines in marine systems’, Frontiers in Marine Sciences, in press. 

Purchase, M.L., Bending, G.D., and Mushinski, R.M. (2023) ‘Spatiotemporal variations of soil reactive nitrogen oxide fluxes across the anthropogenic landscape’, Environmental Science & Technology, 57 (43), pp. 16348-16360. doi: https://doi.org/10.1021/acs.est.3c05849 

Glover, H.E. (1982) ‘Methylamine, an inhibitor of ammonium oxidation and chemoautotrophic growth in the marine nitrifying bacterium Nitrosococcus oceanus’, Archives of Microbiology, 132, pp. 37–40. doi: https://doi.org/10.1007/BF00690814