A multidisciplinary study of DMSP production and lysis - from enzymes to organisms to process modelling.

Lead Research Organisation: University of East Anglia
Department Name: Biological Sciences

Abstract

A billion tonnes of the compatible solute dimethylsulfoniopropionate (DMSP) is made each year by marine phytoplankton, seaweeds, corals, coastal plants and, as shown by us, marine bacteria. DMSP has key roles in marine ecosystems when released into the environment, serving as an osmoprotectant and key nutrient for marine microbial communities. DMSP is also the main precursor of the climate-cooling gas dimethylsulfide (DMS). Many organisms cleave DMSP, producing ~300 million tonnes of DMS annually, ~10 % of which is released into the air. DMS oxidises in the atmosphere, producing aerosols that can lead to increased cloud cover and potential effects on climate, or be returned to land in rain, a key step in the global sulfur cycle. DMSP and DMS are also chemoattractants for many organisms which associate them with food.

Despite the importance of DMSP, knowledge of how and why it is produced is quite superficial. We know that DMSP and DMS production is highly variable between and within the different groups of producers, but the reasons for this variability are not understood, mainly because genes encoding DMSP synthesis enzymes have yet to be identified and DMSP lyases have only just been identified in a DMSP-producing organism.

Our preliminary work has identified dsy genes which encode key DMSP synthesis enzymes in bacteria, diatoms, dinoflagellates, corals and haptophytes - the major groups of marine DMSP-producers. Variability in DMSP/DMS production may stem from their different Dsy enzymes.

Our aim is to establish "why some organisms make more DMSP than others and the contribution of different organisms to global DMSP and DMS production".

It is possible that variability in DMSP production in different organisms stems from the differing efficiencies or expression of their Dsy enzymes. To test this, we will use biochemical techniques to characterise the different Dsy enzymes of the major classes of DMSP-producers.

We will study how diverse, model DMSP-producers express their DMSP and DMS synthesis enzymes in response to varying conditions, since the expression level may govern the amount of DMSP produced. This may shed light on the effects of climate change, e.g., if Dsy and DMSP lyase expression is increased by higher temperatures. For the important DMSP/DMS-producing algae Emiliania huxleyi and Symbiodinium, we will precisely locate the Dsy enzymes within the cell as this will help in understanding the role(s) of DMSP in these organisms. By relating cellular location and Dsy enzymology data to DMSP (and synthesis intermediates) and DMS concentrations, production rates in key DMSP producers and the conditions that enhance accumulation, we will more fully understand why high variability in DMSP and DMS production exists.

As future changes in environmental conditions will likely affect DMSP/DMS production, and potentially climate, and vice versa, it is important to understand and predict these effects. Current estimates of DMSP/DMS production are likely inaccurate due to a lack of integrated studies combining molecular, biogeochemical, process and modelling data. Here, we will carry out a detailed, year-long study at the coastal site L4 in the English Channel (chosen for its location and range of contextual data). We will study the diversity and expression of key genes in DMSP/DMS synthesis, DMSP synthesis rates, group-specific phytoplankton DMSP production, bulk standing stocks of DMSP (and synthesis intermediates) and DMS and microbial diversity over a seasonal succession. Our studies will tell us which organisms produce DMSP/DMS, production rates and concentrations, the genes used and under what conditions. Using these data, we will input critical state and rate parameters into a new model for DMSP/DMS dynamics, allowing the contribution of different taxa to global production of DMSP/DMS to be more accurately predicted, along with any possible effects of climate change.

Planned Impact

We show for the first time that marine bacteria can produce dimethylsulfoniopropionate (DMSP), and identify the key gene in DMSP synthesis in these bacteria and all the major classes of DMSP-producing algae. Many of these microbes also lyse DMSP, making the climate-active gas dimethylsulfide (DMS). Our work is important because DMSP/DMS are made in large amounts globally and have key roles in sulfur and nutrient cycling, signalling pathways and climate. The proposed project is driven by the need for a mechanistic understanding of these pathways, the biodiversity of microbes carrying out these processes and environmental stimuli that regulate DMSP/DMS production. Our work will provide essential data for future modelling of DMSP/DMS production in marine environments.

Our work will be of interest to scientists including microbiologists, molecular ecologists, computational biologists, biological modellers and biochemists due to the range of data generated. The resources generated from the English Channel will be invaluable and complement existing biological knowledge of important ecosystems.

DMSP/DMS research is well-represented in recent high impact journals and has been a well-funded and publicised area of NERC research, e.g. a special report on microbial DMS production in Planet Earth (2009). Here the editor highlighted the phrase "It is astonishing that we still do not know of a single gene for DMSP synthesis", emphasising the potential impact of our work. Thus, we are confident our project will be of interest to a wide scientific audience. We will disseminate our findings in the best international peer-reviewed journals and strive to include other publications in journals that have wider audiences, e.g. Microbiology Today.

There is evidence that the media/general public found our previous NERC-funded work into DMSP/DMS to be interesting e.g. the Todd et al (2007) Science paper led to appearances on TV, radio interviews and press reports throughout the world. We will continue to disseminate our findings to the public and media through e.g. UEA, PML, our websites, Twitter and NERC.

Our outreach component of Pathways to Impact focuses on delivering its outcomes mainly to our younger generation. This will be done through SAW (Science Art Writing) and Research Network events (ResNet), and will involve local schools. We will host students in our labs and continue our outreach work to students around Devon and East Anglia via visits, talks and student projects. The posting of material outlining our work on our websites and Twitter will allow us to reach a wider audience.

There are potential commercial and policy outputs from our work. DMSP/DMS research has applications of interest to industry. The co-products of DMSP lyase enzymes, hydroxypropionate or acrylate are high-value chemicals, e.g. in the plastics industry. Also, DMSP is an antistress compound and osmolyte in environments with high salt/sulfur levels, and DMS is a desirable flavour in e.g. beer, wine or other foodstuffs. The ability of the organisms to produce both DMSP/DMS without expensive feedstock addition clearly offers potential benefits to industry. Knowing factors controlling DMSP/DMS production in different producers may allow for optimisation of the processes. The use of genetics and metabolic engineering could be used to improve yield and efficiency and/or introduce pathways into other organisms, e.g. one could potentially engineer methanogenic bacteria or crops to produce these products. As part of our impact plan, we will explore the potential of these ideas through interactions with chemists and industry.

This research will benefit wider society through improvements in policy facilitated by our new model for DMSP/DMS dynamics and its feeding into the European Regional Seas Ecosystem Model (ERSEM). These models can inform policymakers on the potential environmental consequences of changes in DMSP/DMS production under future climate scenarios.

Publications

10 25 50

 
Description - We have shown the DSYD (formally DsyD), DsyB and DSYB (formally DsyH) purify as active S-methyltransferases working on MTHB with SAM as the methyl donor.
- We have quantified kinetic parameters of a model DSYD, DsyB and DSYB and determined several key catalytic residues through site-directed mutagenesis.
- In collaboration with Yu-Zhong Zhang, crystal structures have been solved for a model DsyB and DSYB which identified homodimeric states and SAM-binding sites.
- We have shown that the production of DMSP in model diatoms, haptophytes and dinoflagelletes is in many cases regulated by environmental factors such as salinity and nitrogen availability.
- We have shown that DSYD, dsyB/DSYB transcription and protein levels in an organism report on the levels of DMSP produced.
- We have localised both DSYD, DSYB and DMSP, using Immunolabeling and Raman spectroscopy respectively, in model haptophytes and diatoms.
Exploitation Route Our findings will:
- provide tools for the scientific community to assess the production of DMSP in natural environments.
- will allow scientists to predict major and minor DMSP producers from environmental sequence and conditions data.
- allow the study of variance in the key enzymes in the processes of DMSP production by phytoplankton in important natural environments.
- allow modellers to adjust DMS and DMSP production models based on our findings of conditions that affect DMSP production in key phytoplankton.
- allow scientists to assay the key enzymes involved in DMSP production from biological samples using methods developed here.
Sectors Environment

 
Description Work completed during this grant has been published in the recent Curson et al. Nature Microbiology paper, from which 5 news stories have been produced (links below). These news articles highlight the identification of a gene involved in producing a marine molecule with environmental impacts for the general public. https://www.sciencedaily.com/releases/2018/02/180226122612.htm https://www.eurekalert.org/pub_releases/2018-02/uoea-sdk022218.php http://www.sciencenewsline.com/news/2018022622270077.html https://phys.org/news/2018-02-scientists-key-gene-marine-molecule.html https://www.longroom.com/discussion/908862/scientists-discover-key-gene-for-producing-marine-molecule-with-huge-environmental-impacts
First Year Of Impact 2018
Impact Types Cultural

 
Title Develped sensitive methods for the detection of betaine, DMSP and their synthesis intermediates from biological samples. 
Description We have developed biological sample preparation and liquid chromatography mass spectrometry methods that allow us to detect and quantify betaine, DMSP and their synthesis intermediates from biological samples. 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact The development of these methods has allowed us to quantify the activity of betaine and DMSP synthesis enzymes from biological samples something that was essential for our protects (e.g. NERC NE/J01138X/1). 
 
Description Collaboration with JB Raina at the University of Technology Sydney, Australia 
Organisation University of Technology Sydney
Country Australia 
Sector Academic/University 
PI Contribution Myself and my research team (including Dr Carrion, Dr Curson and Dr Pinchbeck; and PhD students Ana Bermejo Martinez and Beth Williams) collaborate with Dr Raina to carry out the localisation of isotopes within microbes using NANOSIMS technology.
Collaborator Contribution We identified novel genes involved in the cycling of DMSP/DMS and of betaine in multiple different prokaryotic and eukaryotic microbes. We shared our data with Dr Raina who used his expertise to link our localisation work of key enzymes to the localisation of key labelled compounds within our model organisms.
Impact Our most recent Nature Microbiology paper Curson et al., (2018) DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton, was an out put from this collaboration. The work is multidisciplinary involving: Molecular biology, Molecular Ecology, bioinformatics, algal physiology, NANOSIMS and ImmunoGold localisation for example.
Start Year 2017
 
Description Crystallisation of enzymes involved in DMSP synthesis 
Organisation Shandong University
Country China 
Sector Academic/University 
PI Contribution Collaborating with Dr. Yu-Zhong Zhang (Shandong University, China) we have provided clones of the key enzymes involved in DMSP synthesis for further purification and crystallisation.
Collaborator Contribution Dr. Yu-Zhong Zhang (Shandong University, China) has purified and crystallised key enzymes involved in DMSP synthesis.
Impact As a result of this collaboration the structure of key enzymes involved in DMSP synthesis has been crystallised. This will be included in the forthcoming publications.
Start Year 2015
 
Description DMSP catabolism by important pelagic bacteria 
Organisation Oregon State University
Country United States 
Sector Academic/University 
PI Contribution We have identified novel DMSP catabolic genes in marine SAR11 bacteria. We have cloned, overexpressed and purified these enzymes and characterised their biochemical properties.
Collaborator Contribution Stephen Giovannoni at Oregon State University has grown SAR11 bacteria, characterised their DMSP catabolic phenotypes and has carried out detailed proteomics and bioinformatics studies
Impact This work is currently in review in Nature Journal. The study is multi-disciplinary involving microbiology, bioinformatics, biochemistry and molecular biology.
Start Year 2012
 
Description Microbial generation of dimethylsulphide that is independent of dimethylsulphoniopropionate 
Organisation University of Barcelona
Country Spain 
Sector Academic/University 
PI Contribution The visiting PhD student Ornella Carrion Fonseca identified a bacterium that produced dimethylsulphide (DMS) independent of dimethylsulphoniopropionate (DMSP). Within my lab we characterised the novel pathway of DMS production and isolated the first gene involved in this process. We mutated the gene and studied its biochemistry and occurrence in other microbes. Elena Mercadé Gil (University of Barcelona) on DMSP-independent DMS production pathways
Collaborator Contribution Elena Mercadé Gil and Ornella Carrion Fonseca at The University of Barcelona isolated the bacterium from Antarctic sediment and carried out some localisation experiments, and gas chromatography mass spectrometry work.
Impact I obtained a full NERC grant based around these findings (NE/M004449/1) with Prof. Colin Murrell (CoI) and Dr Carrion Fonseca (Researcher/CoI). we currently working on reviews to a publication reporting this work in nature Communications. The work is multi-disciplinary involving microbiology, biogeochemistry, biochemistry, bioinformatics and physiology.
Start Year 2013
 
Description Microbial synthesis of dimethylsulphoniopropionate and dimethylsuphide (Prof. Xiao-Hua Zhang Ocean University, China) 
Organisation Ocean University of China
Country China 
Sector Academic/University 
PI Contribution Collaborating with Prof. Xiao-Hua Zhang (Ocean University, China) we are characterising the molecular genetic systems utilised by marine organisms in their catabolism and synthesis of dimethylsulphoniopropionate (DMSP).
Collaborator Contribution Prof. Xiao-Hua Zhang (Ocean University, China) has isolated thousands of marine microbes and is screening them for their ability to produce and catabolise dimethylsulphoniopropionate (DMSP). Any positive strains are shipped to UEA for molecular characterisation.
Impact There are no output as yet but a full NERC grant will be submitted on this subject in January 2015.
Start Year 2013
 
Description Relating denitrification to DMSP cycling 
Organisation University of East Anglia
Department Biomedical Research Centre
Country Unknown 
Sector Academic/University 
PI Contribution Through work on our current NERC grants, we collaborate with Prof. David Richardson, Dr Gary Rowley and Dr Andrew Gates on work relating the process of denitrification to DMSP cycling in important marine prokaryotes and eukaryotes. We provide expertise, bacterial and plankton model organisms and methods to characterise these processes in the marine environment. We cosupervise PhD students with these collaborators on this topic.
Collaborator Contribution Prof. David Richardson, Dr Gary Rowley and Dr Andrew Gates provide expertise in the denitrification process.
Impact 1 NERC EnvEast PhD studentiship and 1 UEA-funded PhD studentship.
Start Year 2016
 
Description Subcellular localisation of DMSP and DMS-producing enzymes in eukaryotes and prokaryotes 
Organisation University of Barcelona
Country Spain 
Sector Academic/University 
PI Contribution Collaborating with Dr. Elena Mercade (University of Barcelona, Spain) we are growing eukaryotes and prokaryotes that produce DMSP and/or DMS and providing specific antibodies against the enzymes involved to localise them at a subcellular level.
Collaborator Contribution Dr. Elena Mercade (University of Bacelona, Spain) has prepared samples for immunogold labelling with the specific antibodies provided by us and used Transmission Electronic Microcoscopy to localise the enzymes involved in DMSP and/or DMS synthesis in the cells.
Impact The collaboration has successfully allowed the localisation of key enzymes involved in DMSP and/or DMS production in diatoms and bacteria. These results will be included in the forthcoming publications.
Start Year 2014
 
Description The importance of bacterial DMSP production in Chinese Mangroves. 
Organisation Huazhong Agricultural University
Department College of Veterinary Medicine
Country China 
Sector Academic/University 
PI Contribution We provide knowledge and expertise on bacterial DMSP production to enable an environmental microbiological study of the importance of bacteria in DMSP production in Chinese mangrove swamps. This involved us designing enrichment experiments for the isolation of DMSP-producing bacteria. We provided ratified gene probes and techniques to study the expression and abundance of key genes involved in DMSP production in environmental samples. Furthermore, we provided expertise in the analysis of metagenomic data generated from mangrove swamp environmental samples.
Collaborator Contribution Prof. Youguo Li obtained samples from local mangrove swamps and conducted experiments to study the importance of bacteria in DMSP production under the guidance of our group. This involved the isolation of high quality DNA and RNA which is being analysed for the abundance and diversity of bacterial DMSP synthesis genes.
Impact Nothing yet.
Start Year 2016
 
Description The importance of bacterial DMSP production in coral reef environments. 
Organisation Australian Government
Department Australian Institute of Marine Science
Country Australia 
Sector Public 
PI Contribution We provide knowledge and expertise on bacterial DMSP production to enable an environmental microbiological study of the importance of bacteria in DMSP production in coral reefs. This involved us designing enrichment experiments for the isolation of DMSP-producing bacteria. We provided ratified gene probes and techniques to study the expression and abundance of key genes involved in DMSP production in environmental samples. Furthermore, we provided expertise in the analysis of metagenomic data generated from coral reef environmental samples.
Collaborator Contribution Dr David Bourne and Dr Jean-Baptiste Raina obtained samples from coral reefs and conducted experiments to study the importance of bacteria in DMSP production under the guidance of our group. This involved the isolation of high quality DNA and RNA which is being analysed for the abundance and diversity of bacterial DMSP synthesis genes. Dr Raina is localising DMSP in model phytoplankton for our project using nanoSIMS.
Impact None yet.
Start Year 2015
 
Description The importance of bacterial DMSP production in coral reef environments. 
Organisation University of Technology Sydney
Country Australia 
Sector Academic/University 
PI Contribution We provide knowledge and expertise on bacterial DMSP production to enable an environmental microbiological study of the importance of bacteria in DMSP production in coral reefs. This involved us designing enrichment experiments for the isolation of DMSP-producing bacteria. We provided ratified gene probes and techniques to study the expression and abundance of key genes involved in DMSP production in environmental samples. Furthermore, we provided expertise in the analysis of metagenomic data generated from coral reef environmental samples.
Collaborator Contribution Dr David Bourne and Dr Jean-Baptiste Raina obtained samples from coral reefs and conducted experiments to study the importance of bacteria in DMSP production under the guidance of our group. This involved the isolation of high quality DNA and RNA which is being analysed for the abundance and diversity of bacterial DMSP synthesis genes. Dr Raina is localising DMSP in model phytoplankton for our project using nanoSIMS.
Impact None yet.
Start Year 2015
 
Description The production of betaine by marine phytoplankton (Dr Ruth Airs PML) 
Organisation Plymouth Marine Laboratory
Country United Kingdom 
Sector Academic/University 
PI Contribution During our NERC grant (NE/J01138X/1) we identified candidate genes involved in the synthesis of betaine. We have shown that model diatoms make betaine and that our candidate genes when cloned and expressed confer the ability to produce betaine and confer salt tolerance to Escherichia coli. In collaboration with Dr Ruth Airs we have established liquid chromatography mass spectrometry methods to detect betaine and dimethylsulphoniopropionate (DMSP) from biological samples.
Collaborator Contribution Dr Ruth Airs at PML helped us to develop and establish liquid chromatography mass spectrometry methods to detect betaine and dimethylsulphoniopropionate (DMSP) from biological samples.
Impact My postdoctoral researcher Research technicians on the NERC Grant (NE/J01138X/1) have presented our findings at the research conferences detailed below: -The Molecular Life of Diatoms, Paris, Dr Andrew Curson (Tues 25th June) -MMEG Molecular Microbial Ecology Group 2013, University of Essex, Ana Bermejo Martinez (Tues 17th Dec 2013) -6th International symposium on biological and environmental chemistry of DMS(P) and related compounds, ICM-CSIC, Barcelona, Ana Bermejo Martinez (26th - Fri 30th May 2014) As a result of this work we put together a NERC ENVEAST PhD proposal with Dr Todd as PI, and Dr Ruth Airs and Prof, Mock as CoIs. The work is multi-disciplinary as it involves phytoplankton physiology, biogeochemistry, microbiology, biochemistry, molecular genetics, molecular ecology and analytical biology.
Start Year 2013
 
Description Work into oxidation of methanethiol by marine organisms (Hendrik ?Schaefer, Warwick) 
Organisation University of Warwick
Department School of Life Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution My research team carried out microarray analysis on marine organisms that oxidise methanethiol (MeSH) looking at the catabolism of dimethylsulfoniopropionate (DMSP). These arrays showed that a gene encoding the MeSH oxidase was enhanced at the level of transcription by DMSP. We made transcriptional fusions to the mto gene and confirmed its induction by DMSP. We also isolated its divergently transcribed transcriptional regulator and showed that it controls the DMSP induction of the mto gene. We made a mutation in the mto gene in model marine organisms.
Collaborator Contribution Hendrik ?Schaefer isolated the MeSH oxidase and characterised its biochemical properties at the University of Warwick. He also has used molecular ecological techniques to study the variance of this gene in many environments.
Impact A pre-submission abstract was submitted to nature, but rejected. The project is multi-disciplinary involving, microbial ecology, molecular genetics and biochemistry.
Start Year 2012
 
Description 'DMSP production in marine bacteria and algae: idenitification of novel synthesis genes' research talk at Microbiology Society Annual Conference in Belfast April 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Research talk at Microbiology Society annual conference, presenting a summary of research work in Todd's lab.
Year(s) Of Engagement Activity 2019
 
Description 'Marine Microbial DMSP Synthesis - from genes to microbes to pathways' at GEOMAR in Kiel, Germany in October 2018. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited research presentation at GEOMAR in Kiel Germany, presenting a summary of research work in Todd's lab.
Year(s) Of Engagement Activity 2018
 
Description 'Marine Microbial DMSP Synthesis - from genes to microbes to pathways' at the Marine Microbes GRC 2018, Lucca, Italy, 1-6th July 2018. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited research talk at the Gordon Research Conference Marine Microbes conference, covering all research work from the Todd group.
Year(s) Of Engagement Activity 2018
 
Description 'Surface marine sediments are factories for DMSP and the climate active gas DMS' at the ASM Microbe meeting, June 2019, San Francisco. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited reesearch presnetation at ASM conference in San Francisco, summarising the reseacrh from Todd's lab.
Year(s) Of Engagement Activity 2019
 
Description Convenor of the biogeochemical cycling and climate session and talking at ISME 2018, Leipzig 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited convenor of the biogeochemical cycling and climate session and presenter of research encompassing all my DMS/P related grants.
Year(s) Of Engagement Activity 2018
 
Description Invited Oral presentation at Microbiology Society Annual meeting, April 2017, Edinburgh. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited speaker at the Microbiology Society Annual meeting, April 2017, Edinburgh. Here I presented findings from all my grants related to DMS/P research.
Year(s) Of Engagement Activity 2017
 
Description Invited oral presentation at the 5th International Symposium on Microbial Sulfur Metabolism, April 2018, Vienna 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited speaker at the 5th International Symposium on Microbial Sulfur Metabolism, April 2018, Vienna. Here I will overview all major outcomes from my grants concerning DMS/P research.
Year(s) Of Engagement Activity 2018
 
Description Invited presentation at the ASM Microbe meeting, June 2017, New Orleans. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited presentation at the ASM Microbe meeting, June 2017, New Orleans. Here I presented the major outcomes from all my research grants related to DMS/P
Year(s) Of Engagement Activity 2017
 
Description Marine Microbes GRC 2018, Lucca, Italy, 1-6th July 2018. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited presenter at the prodigious Gordon Research Conference on Marine Microbiology.
Year(s) Of Engagement Activity 2018