Microbial degradation of isoprene in the terrestrial environment

Lead Research Organisation: University of Essex
Department Name: Biological Sciences

Abstract

The Blue Mountains in Australia and Blue Ridge Mountains of Virginia, are so-named because of the blue haze that results from atmospheric reactions with isoprene, a gas produced in abundance by plants and especially many tree species. Trees that are starting to be grown widely as a source of bioenergy, namely willow and poplar, are among the highest isoprene emitters. Isoprene protects plants against heat and light-induced damage, and can also serve as a signaling molecule. Isoprene is so reactive with other chemicals in the lower atmosphere that it limits their capacity to react with methane and also generates ozone. Both ozone and methane are potent greenhouse gases, and ozone impairs plant growth. On the more positive side, isoprene can indirectly stimulate cloud formation which provides a cooling effect. Hundreds of studies have investigated isoprene production, primarily from trees, and examined the effect of a changing environment on its flux from tree to atmosphere.

In stark contrast, only a handful of studies have shown that microbes in the soil consume isoprene, and a few of those microbes have been grown in the laboratory. Microbes are abundant (several billion per teaspoon of soil and more than a million per square cm of leaf) and the most important catalysts for cycling chemicals in the environment. We know from studying the cycles of other climatically important gases, like methane, that microbial consumption is an extremely important process that is greatly influenced by climate change. From hundreds of methane-consuming bacteria in culture, we have extensive knowledge of their metabolic pathways, which allows the development of investigative tools to help inform land-use management decisions. For isoprene, which is produced in similar abundance to methane, we lack this knowledge and tools.

Therefore, in addition to those bacteria that we already have in culture, we propose to culture isoprene-degrading microbes, focusing on soil and leaf inhabitants. Using powerful genomic-based techniques, we will determine the DNA sequences of the genes involved in isoprene degradation. Additionally, we will use tools developed by the PI to identify and investigate those isoprene degraders that are not easy to grow. Most bacteria look alike and so we frequently use DNA sequences to study their roles in nature. Selected unique DNA sequences will be used to identify, view and count key species of isoprene-degrading bacteria in natural samples. This will enable us to determine precisely where they live, e.g. we envisage that they will be especially abundant around stomata (pores in the leaf) from where most isoprene escapes; and the use of state-of-the art imaging techniques (developed by our project partner) will allow us to identify which individual microbes are actively degrading isoprene in the soil or on the leaf surface.

Complementing this study, a PhD student will measure isoprene consumption in forest soils, and for the first time, on leaves from various tree species, comparing isoprene emitters with non-emitters as well as sun and shade leaves. We will test whether adding permutations of isoprene-degrading microbes to leaf surfaces enhances consumption, and by measuring the microbes' ability to survive or grow on the leaves, we will obtain insights into whether this is a potential strategy for reducing isoprene flux. All of the data emanating from this project will be valuable for management of natural woodlands and bioenergy crops, in relation to greenhouse gas emissions.

Planned Impact

The project will provide data on isoprene consumption in woodland environments, molecular tools to investigate isoprene degradation, an understanding of the abundance and distribution of isoprene-degrading microbes as well as their potential to mitigate isoprene emissions. All of this will impact on the management of natural woodland and plantations of bioenergy crops (that may supply 10% of the UK's energy), especially high isoprene emitters such as willow and poplar. Our research will have maximum impact because of the involvement of Dr J. Morison (Forest Research) as project partner, who has close collaborations with the Energy Technology Institute (ETI) and advises government departments. It complements Forest Research's core program on the carbon and greenhouse gas balances of UK forests, which underpins both policy and practice in support of major initiatives for enhanced woodland creation as part of UK emissions abatement policy and the new Natural Environment White Paper. A key outcome, with input from University of Essex Interdisciplinary Centre for Environment and Society (iCES) and FR, will be a briefing document aimed at stakeholders (e.g. Defra, DECC, World Meteorological Organisation, Met Office, UNEP, IPCC, and IOC), and we will participate in end-user led meetings during the course of the project. In addition to having FR as a key link, we will continue to engage with key individuals in the marine (e.g. SOLAS) and terrestrial VOC community (e.g. via ESF's VOCBAS initiative), who will be interested in applying our data to isoprene flux models.

As outlined in more detail in the Pathways to Impact there are many other potential applications of this work, e.g. oxygenases for production of chiral synthons as precursors to pharmaceuticals / agrichemicals. Our research should benefit the bioremediation industry, e.g. 1) by degradation of isoprene spills (800,000 tonnes pa of isoprene are produced by the petrochemical industry, and is set to increase with the advent of BioIsoprene synthesis); 2) because many isoprene degraders also degrade other volatile hydrocarbons like BTEX; and 3) isoprene degraders co-metabolise chlorinated solvents like TCE. In other words isoprene degraders may already play a major role in remediating some of the most abundant volatile pollutants, especially on the leaf surface. Again, this will impact on woodland management (our route to impact will be Forest Research), as well as planning green spaces in cities (our route to impact will be iCES who played a major role in the Government paper "UK National Ecosystems Assessment: Understanding Nature's Role in Society"). Interesting biotechnological leads will be followed up through regular meetings with our respective research and enterprise offices, which have experts in biotechnology patents. Depending on interest and stage of development, we may look to a NERC follow-on fund for further commercial development, or to collaborate with the bioremediation industry, with whom we are already well connected.

Our topical and novel research involving: plant-microbe interactions, discovery of novel microbial processes, mitigation of climate-active gases and biofuel crops, will capture the public's attention. Therefore we are proposing an attractive and informative web site, including video footage from fieldwork at Alice Holt, four school visits and regular press releases. All investigators have an excellent record of engaging with the public, e.g. via radio and the popular scientific press.

Publications

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Carrión O (2020) Molecular Ecology of Isoprene-Degrading Bacteria. in Microorganisms

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Crombie AT (2018) Poplar phyllosphere harbors disparate isoprene-degrading bacteria. in Proceedings of the National Academy of Sciences of the United States of America

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McGenity TJ (2014) Hydrocarbon biodegradation in intertidal wetland sediments. in Current opinion in biotechnology

 
Description Detailed understanding of the diversity of isoprene-degrading microbes in diverse habitats.
Mechanistic understanding of isoprene-degrading pathways via genome and functional analysis of isolates.
Exploitation Route Isoprene is on the agenda of diverse agencies, partly as a result of our research and associated briefing document
Sectors Environment

 
Description NERC Doctoral Training Programme (EnvEast)
Amount £75,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 10/2014 
End 04/2018
 
Description Society for General Microbiology, Summer vacation studentship
Amount £1,850 (GBP)
Funding ID VS12/26 
Organisation Society of General Microbiology 
Sector Charity/Non Profit
Country European Union (EU)
Start 07/2012 
End 08/2012
 
Description Society for General Microbiology, Vacation Scholarship
Amount £1,880 (GBP)
Funding ID VS14/27 
Organisation Society for Microbiology 
Sector Learned Society
Country United Kingdom
Start 07/2014 
End 09/2014
 
Description The Leverhulme Trust
Amount £200,000 (GBP)
Organisation The Leverhulme Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2017 
End 12/2020
 
Description The biogeochemical cycle of isoprene
Amount € 2,500,000 (EUR)
Organisation European Research Council (ERC) 
Sector Public
Country Belgium
Start 10/2016 
End 09/2022
 
Description Dupont - 13C-isoprene 
Organisation DuPont
Country United States 
Sector Private 
PI Contribution Sharing information about isoprene degradation
Collaborator Contribution Provision of 13C isoprene
Impact In progress
Start Year 2012
 
Description Salt-marsh BVOC flux 
Organisation University of York
Country United Kingdom 
Sector Academic/University 
PI Contribution Information about isoprene cycling. Sharing technologies.
Collaborator Contribution Measurements of isoprene on salt marshes. Sharing technologies.
Impact None yet - just some preliminary data
Start Year 2013
 
Description End-user workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact End user workshop with ~40 participants from research organisations, industry, Met office, Defra, Forestry Commission, Environment Agency.
Year(s) Of Engagement Activity 2016
URL http://www.isopreneresearch.com
 
Description Isoprene Briefing Document 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A briefing document outlining the microbial cycling of isoprene and its importance in the environment was prepared and circulated to approximately 200 researchers, industrialists, politicians, policy makers, NGOs, government organisations such as Met Office, Defra, Environment Agency, Forestry Commission, NERC.
Year(s) Of Engagement Activity 2016
URL http://www.isopreneresearch.com
 
Description Joint article with UEA for Laboratory News 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Not known.

Not known
Year(s) Of Engagement Activity 2014
 
Description Public lecture 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Lecture on isoprene degradation to Microbes in Norwich
Year(s) Of Engagement Activity 2017
 
Description School Visit Stalham Norfolk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Fighting climate change with microbiology Talk and discussion. approx. 100 pupils attended. Highly engaged in lecture and debate
Year(s) Of Engagement Activity 2016
 
Description Seminar at Chelsi 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Lots of questions and discussion.

not aware
Year(s) Of Engagement Activity 2012
 
Description Seminar at University of Warwick 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Led to discussions to co-write a grant proposal on a peripheral topic.

Grant proposal written.
Year(s) Of Engagement Activity 2013
 
Description Video on isoprene research 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact A video describing our isoprene research was made as part of a training programme for a PhD student Mr Gordon Murphy, associated with our research grant. This involved all personnel on the project and has been distributed via our purpose-built website on isoprene research.
Year(s) Of Engagement Activity 2015
URL http://www.isopreneresearch.com
 
Description Work placement by St Benedict's School 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Two-week visit, with a focus on isolation of isoprene-producing microbes

Good feedback from students
Year(s) Of Engagement Activity 2014