Microbial degradation of isoprene in the terrestrial environment
Lead Research Organisation:
University of East Anglia
Department Name: Environmental 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.
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.
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.
People |
ORCID iD |
John Murrell (Principal Investigator) | |
Andrew Crombie (Researcher) |
Publications
Carrión O
(2018)
Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment.
in Microbiome
Carrión O
(2020)
Molecular Ecology of Isoprene-Degrading Bacteria.
in Microorganisms
Crombie AT
(2017)
Draft Genome Sequences of Three Terrestrial Isoprene-Degrading Rhodococcus Strains.
in Genome announcements
Crombie AT
(2018)
Poplar phyllosphere harbors disparate isoprene-degrading bacteria.
in Proceedings of the National Academy of Sciences of the United States of America
Crombie AT
(2015)
Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle.
in Environmental microbiology
Dawson RA
(2023)
Peering down the sink: A review of isoprene metabolism by bacteria.
in Environmental microbiology
Dawson RA
(2022)
'Omics-guided prediction of the pathway for metabolism of isoprene by Variovorax sp. WS11.
in Environmental microbiology
Dawson RA
(2020)
Isoprene Oxidation by the Gram-Negative Model bacterium Variovorax sp. WS11.
in Microorganisms
El Khawand M
(2016)
Isolation of isoprene degrading bacteria from soils, development of isoA gene probes and identification of the active isoprene-degrading soil community using DNA-stable isotope probing.
in Environmental microbiology
Gibson L
(2021)
Isoprene-degrading bacteria associated with the phyllosphere of Salix fragilis, a high isoprene-emitting willow of the Northern Hemisphere.
in Environmental microbiome
Description | We have isolated a large number of isoprene degrading bacteria (approximately 50) from the terrestrial environment including several Rhodococcus species. We have genome sequences for several of these key isolates and have metabolic blueprints for each which have been analysed in terms of their growth potential on a number of ecologically-important substrates in addition to isoprene. Interestingly several have an inducible propane monooxygenase system which allows them to also grow on propane. We have also shown that isoprene monooxygenase is the key enzyme responsible for isoprene degradation in these key strains of Rhodococcus thus indicating a unifying mechanism for the bacterial metabolism of isoprene which is initiated by a soluble diiron centre monooxygenase. The importance of glutathione in isoprene metabolism has also been established as have molecular genetics methods for the analysis of the physiology of key Rhodococcus strains. An inducible enzyme system consisting of at least 12 different genes/proteins is required for growth of our model Rhodococcus strain on isoprene and we have shown that epoxyisoprene, rather than isoprene, is an inducer of isoprene metabolism. We have identified all the genes predicted to be essential for isoprene degradation and shown that they are carried on a large plasmid in Rhodococcus strain AD45. This has profound implications for the horizontal gene transfer of isoprene degrading ability in microbes. We have sequenced the genomes of several isolates. This has given us valuable information on the genomic context of the isoprene monooxygenase gene clusters in these isoprene degraders. The gene isoA, encoding the large subunit of the hydroxylase component of isoprene monooxygenase is highly conserved in all isolates and thus is an ideal functional gene marker for the presence of these microbes in the environment. We have developed PCR primer sets specific for isoA, which has allowed us to retrieve isoA genes from enrichment cultures and from environmental samples in order to develop cultivation-independent techniques for these important trace gas degrading bacteria. We have shown that isoprene degrading potential is present in all soils tested and also on the leaves of plants, close to the principle source of isoprene to the atmosphere. This again has profound implications for the metabolism of isoprene at source i.e. when produced by trees. We have showed that many different soils can metabolise isoprene at both low (near ambient) and high concentrations, and that different microbes may be responsible for degradation and low and high concentrations. In-situ measurements of isoprene consumption in soil reveal that early estimates of soil consumption were too high. These findings have major implications for the role of isoprene degraders in reducing isoprene levels in the atmosphere and the biological consumption terms in any future modelling of the isoprene cycle will need to reflect this new information. We have developed the methods and carried out experiments with 13C labelled isoprene, using DNA stable isotope probing, and identified the active isoprene degrading bacteria in many different soils, including those close to isoprene-emitting trees, marine sediments and isoprene degraders on the leaves of Poplar and Willow trees. We have also characterised key isolates from these samples. We are completing the analysis of metagenome and metatranscriptome data from enrichments from Poplar leaves which will enable us to identify any novel genes or pathways involved in isoprene metabolism. We now have a detailed mechanistic understanding of the genetics of isoprene metabolism, have developed the tools to identify isoprene degraders in environmental samples, and have investigated the diversity and ecology of isoprene degraders in several contrasting environments. These data show that isoprene degraders are abundant in the environment and may be important in moderating emissions to the atmosphere of this climate-active trace gas. |
Exploitation Route | Detailed knowledge about the mechanisms of microbial degradation of isoprene will be useful to other environmental microbiologists and industrialists interested in use of soluble diiron centre monooxygenases for bioremediation and biotransformations. Synthesis of high value chemicals and chiral synthons. The structure and function of isoprene monooxygenase will be of great interest to biochemists and chemists. Information distribution, diversity and activity of isoprene degrading bacteria in the environment will be essential for researchers modelling climate change and the influence of atmospheric trace gases which have a global warming or global cooling effect. Information on the presence of isoprene degrading bacteria on the leaves of plants will be of importance for mitigating the effects of isoprene emissions by biofuel crops such as poplar and willow. Potential interest with policy makers, Defra, Met Office the Environment Agency and industry. |
Sectors | Agriculture, Food and Drink,Chemicals,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology |
URL | http://www.isopreneresearch.com |
Description | Findings have informed the general public and policy makers about the importance of the microbiology of atmospheric trace gases and microbes in biogeochemical cycling and their potential in the production of bulk and fine chemicals. |
Sector | Environment |
Impact Types | Cultural,Societal,Policy & public services |
Description | BBSRC DTP Studentship |
Amount | £120,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 10/2016 |
End | 09/2020 |
Description | Collaborative research |
Amount | $120,000 (USD) |
Organisation | DuPont |
Sector | Private |
Country | United States |
Start | 05/2013 |
End | 05/2016 |
Description | Summer vacation studentship |
Amount | £2,500 (GBP) |
Organisation | Society for Applied Microbiology |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 06/2015 |
End | 09/2015 |
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 | Chinese Academy of Science Award Lecture to general public |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Fighting climate change with microbiology. Chinese Academy of Sciences Distinguished Professorship Award Lecture, Nanjing, China, September, 2015 |
Year(s) Of Engagement Activity | 2015 |
Description | EMBO Conference presentation |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Biogeochemical cycling of atmospheric trace gases. EMBO, Heidelberg, Germany, October 2015 |
Year(s) Of Engagement Activity | 2015 |
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 | Industrial engagement National Biotechnology Institute Montreal Canada |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Research presentation Methanotrophs and methane monooxygenases. NRC-BRI Montreal, April 2015 |
Year(s) Of Engagement Activity | 2015 |
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 | Planet Earth Summer School UEA |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Stimulated interest in microbiology Increased interest in UEA and Environmental Sciences |
Year(s) Of Engagement Activity | 2014 |
Description | Podcast |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Increased public awareness of our science More enquiries about research |
Year(s) Of Engagement Activity | 2013 |
URL | http://www.jcmurrell.co.uk |
Description | Poster presentations GRC |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Poster presentations at Gordon Research Conference, Applied and Environmental Microbiology |
Year(s) Of Engagement Activity | 2013,2015 |
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 | Research presentations at national and international conferences |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | At least 10 research presentations at National and International scientific meetings, workshop and end-user engagement activities, including China, USA, Australia, Germany. Audiences included researchers, postgraduate students, industrialists, policy makers, government organizations |
Year(s) Of Engagement Activity | 2015,2016 |
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 | School visit |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Stimulated interest in environmental microbiology Increased applications to UEA |
Year(s) Of Engagement Activity | 2014 |
Description | School visit Ipswich |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | Over 100 sixth form students attended my lecture on Fighting climate change with microbiology |
Year(s) Of Engagement Activity | 2016 |
Description | University Open Days and Summer Schools |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Presentations on research at Open Days, School Visits, Summer Schools (approximately three per year) |
Year(s) Of Engagement Activity | 2015,2016 |
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 |