Integrating carbon systems

Lead Research Organisation: Rothamsted Research
Department Name: Unlisted

Abstract

This project is part of the Cropping Carbon Institute Strategic Programme that aims to build a whole systems understanding of carbon allocation both above- and below-ground to provide the knowledge for achieving an optimal balance between harvestable and sequestered carbon in perennial cropping systems. This project provides underpinning through pursuit of a gene-led approach to identify key QTL for variety improvement and through use of statistics, bioinformatics and process-based modelling to integrate, interpret and instruct the experimental programme. There are 6 Work Packages (WP).

We will integrate ‘omics and primary trait data into a discovery pipeline to deliver new functional candidate genes, gene interaction networks and pathways based on methods developed within Ondex (WP3.1). We will incorporate analysis of the metabolome, transcriptome and genetic data in willow using our emerging technologies for systems-based analysis of QTL intervals and by comparing mQTL positions with QTL positions currently available or newly mapped (WP3.2). Both transgenic and genetic approaches will be used to validate candidate genes (WP3.3).

We aim to tackle challenges of integrating process-based and statistical models to capture the interaction of plant and environmental processes and to incorporate new system components and advanced statistics. Using willow we will:
-Synthesise the data of primary and secondary metabolites in different compartments of woody plants and develop new conceptual models (WP 3.4).
- Dissect the carbon allocation process by including physiological control mechanisms in the dynamics of morphological development (primary traits) and quantitatively model the environmental control mechanisms for shifts in carbon forms and allocation between plant organs (sink-source) and the soil (WP3.5).
-Use a Bayesian approach to calibrate model components, using “omics” and plant and soil data from a wide variety of sources (WP3.6).

Publications

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Gritsch C (2015) G-fibre cell wall development in willow stems during tension wood induction. in Journal of experimental botany

 
Description We are developing mathematical models of bioenergy crop performance to assist with identification of key steps which limit biomass yield and which would be suitable targets for breeding. Also to better understand the impact of bioenergy crops as a carbon sink and source for new products. Recent development include:

A sink-source interaction model has been further developed using new data to test light interception and dynamics of carbon assimilation and partitioning in willow. A Bayesian form of the model was implemented to evaluate uncertainty in model parameters and to integrate new experimental evidence.

New parameters of the bud flush model for willow were derived, calibrated using RRes data and validated using IBERS data from BSBEC-BioMASS. The Bayesian form of the crop growth model was expanded to parameters of the bud flush model, which was compared to estimates generated from leaf area index dynamics.
Exploitation Route Development of policy around landuse needs better models of energy crop production and how performance varies under different management strategies and how production will be affected climate change
Sectors Agriculture, Food and Drink,Energy

 
Description SCOPE Bioenergy: Sustainability
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact Recommendations were made about the adoption of bioenergy by governments worldwide using sustainability criteria.
 
Description Bioenergy Value Chains: Whole systems analysis and optimization
Amount £219,000 (GBP)
Funding ID EP/K036734/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 09/2013 
End 08/2017
 
Description Climate-KIC ADMIT
Amount £43,300 (GBP)
Organisation European Institute of Innovation and Technology (EIT) 
Sector Public
Country Hungary
Start 01/2014 
End 12/2017
 
Title LUCASS - Model for Light Use and Carbon Allocation in Salix Species 
Description LUCASS is a mathematical, process-based plant growth model, embedded in a energy-water-balance simulation framework, provided with external parameter data base and Global Sensitivity Analysis and Bayesian calibration. 
Type Of Material Model of mechanisms or symptoms - non-mammalian in vivo 
Year Produced 2016 
Provided To Others? Yes  
Impact This tool can rank the parameters according to their impact on growth and yield formation which is extremely useful for the characterisation of geno- and phenotypes. The simulation tool is connected to a spatial pedoclimatic data base which allows exploring Gene x Environment interaction and optimizing ideotypes for different environments. Documentation and parameter data base are published as Open Access in connection with the paper by Cerasuolo. See doi for downloads 
 
Description Sub-contractor to Imperial College of Science, Technology and Medicine, London in the EIT-funded project ADMIT-Bio-Succinnovate under the Climate-KIC programme 
Organisation Imperial College London
Country United Kingdom 
Sector Academic/University 
PI Contribution We supported the spatially specific estimates of biomass in different UK regions available for the bio-economy, here the resource for bio-renewable succinic acid. We trained and co-supervised the PhD student Yuanzhi Ni at Centre for Environmental Policy, Imperial College London, to calibrate, validate and upscale an existing process-based crop growth model. We agreed to carry out the following services for Imperial: 2.1. (a) those as set out in Schedule 1 annexed hereto which includes the provision of an interim report including yield, spatial carbon stocks maps and Land based GHG emission factors for feedstock supply locations (England, Wales, Hungary and France) to be delivered by end of November 2016. A conference paper and a peer-reviewed paper are published/under review, respectively.
Collaborator Contribution Partner at Imperial College (Dr Jeremy Woods, Centre for Environmental Policy) were leader of Work Package 8 in the Bio-Succinnovate project. We were initially a partner in our own right but changed to being a subcontractor (16122 -Consultancy agreement Rothamsted Biosuccinnovate). Imperial College administered and paid a reasonable fee (€15k).
Impact Conference paper at the International Bioenergy Conference and Exhibition, Shanghai: Assessing Availability and Environmental Impacts of Lignocellulosic BIOMASS Feedstock Supply - Case Study for a Catchment in England (9 pages) Ni, YZ, Mwabonje, O., Richter, G., Qi, A., Yeung, K, Patel, M. Woods, J. (2018) ASSESSING AVAILABILITY AND ENVIRONMENTAL IMPACTS OF LIGNOCELLULOSIC BIOMASS FEEDSTOCK SUPPLY - CASE STUDY FOR A CATCHMENT IN ENGLAND Biofpr (Accepted for publication; revisions to be submitted by 8 April 2018)
Start Year 2015
 
Description 25th International Poplar Commission 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Oral presentation to research community, growers companies and policy makers. Its aims were to bring together researchers on poplar and other fast growing trees to present their current works/projects and interact. It allowed me to present my current work with the LUCASS model (and publicize LUCASS) and meet new researchers.
Year(s) Of Engagement Activity 2016
 
Description 2nd Annual Plant Genomics Congress - London -Progressing Gene Discovery in Salix: Genetic and Genomic Approaches 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation to largely research audience but media and policy makers attended.
Year(s) Of Engagement Activity 2014
 
Description 6th World Congress on Biofuel and Bioenergy, 5-6 Sept 2017; Keynote 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact About 60 people from all over the world and all kinds of professions, policy makers, industrial and scientific background attend a 2-day conference with about 30 talks. It was very interesting and has led to a number of follow-up contacts, e.g. with Turkey and the US/Canada. I was invited to give a keynote on the theme of "Biomass resource optimization tools in the food-fuel-environment context" which was very well received and discussed. Abstract: Multiple and increasing demands for renewable resources affect the bio-economy as a whole but escalate in particular around bioenergy and biofuel. For many reasons, perennial crops, like short-rotation coppice (SRC), Miscanthus [1, 2] and grassland are attractive choices. The purpose of this talk is to illustrate in three examples the use of advanced mathematical optimization tools to increase the production and performance of whole systems exploiting synergies and calculating trade-offs. Methodology: (1) A process-based model (PBM) for simulating trait and environmental effects on plant growth is to optimize G x E solutions for low-input SRC [3]. (2) Up-scaled PBMs using scenario simulations for different crop systems were used [4] to estimate available biomass resources and the yield gap resulting from fertilizer and livestock reduction. (3) A whole systems optimization framework, the Bioenergy Value Chain Model (BVCM) [5] is presented that allows evaluating the biomass flow through the value chain under market and ecosystem constraints. Findings: The PBM for SRC-willow identified a limited number of robust trait-related parameters that can be used to accelerate the selection and breeding process. An environmental (pedo-climatic) scenario analysis enabled us to ascertain the best variety for droughty environments with the highest water use efficiency and least impact on water resources. For UK grassland system we estimated a yield gap of 6 to 20 million tons of exploitable biomass when recommended N-fertilizer would be applied. Extending these results to the BVCM additional biogas from grassland biomass trade-offs from increased nitrous oxide emissions are calculated. Conclusion: PBM for plant growth will be extended to optimize SRC traits for the industrial scale land reclamation of heavy metal contamination. Recommendations for best combinations of genotype x environment x management can be derived from these simulations and scaled up to optimize land use between bioenergy, food and other ecosystem services.
Year(s) Of Engagement Activity 2017
URL https://biofuels-bioenergy.conferenceseries.com/europe/
 
Description Biomass and Energy Crops V Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact There were talks and discussion over two days and an open panel discussion and interviews on the second day, see link below
Year(s) Of Engagement Activity 2015
URL https://www.youtube.com/channel/UCZCMCCAkmtgV5TsNaBCpdIQ/videos
 
Description Developing Sustainable Bioenergy Crops for Future Climates - Oxford 24-27 September 2017 - Invited talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact IN SILICO EXPLORATION OF GENOTYPE X ENVIRONMENT X MANAGEMENT EFFECTS FOR SHORT ROTATION WILLOW
Richter, Goetz Michael1, Richard, Benjamin1, Qi, Aiming1, Cerasuolo, Marianna2
1) Dept. of Sustainable Agriculture Science, Rothamsted Research, Harpenden, AL5 2JQ, UK
2) Dept. of Mathematics, University of Portsmouth, Lion Gate Bldg., Portsmouth, PO1 3HF, UK.

ABSTRACT:

Future climate scenarios are especially uncertain in terms of water availability related to rainfall distribution. The conflict with food crops regarding land use exacerbates the need for bioenergy crops with low water demand and high water use efficiency (WUE). Here, we illustrate: (1) how canopy structure and size of willow genotypes (Salix ssp.) affect the resource use efficiency (light, water) and (2) how phenotypic differences compensate negative environment effects (soil, climate).
Our model optimizes explicitly traits of light interception with parameters of vertical and horizontal leaf distribution [1] and simulates the evapotranspiration as a function of leaf area, root distribution and water stress sensitivity [2]. The model and its parameter sensitivity was evaluated against long time series of biomass and water dynamics in two contrasting UK sites. In a large scenario analysis across a wide range of climate-soil combinations we identified the respective best performers and calculated the probability of exceeding an economic threshold yield (9 t ha-1).
The sensitivity analysis revealed that parameters of canopy structure ranked highly (11th, 15th) under conditions of ample water supply. Their rank dropped under water stress (24th, 30th), when parameters of root growth and water stress became dominant (9th), which showed differences between phenotypes.
The scenario analysis showed that apart from the UK's Southwest the production on marginal soils (water availability <100 mm) was unlikely to be economically sustainable. Under high evaporation demand (south UK) the effects of phenotypic differences (canopy size) on biomass production were smaller than in the north. Under highest water stress (south-east) small canopy had a significantly higher WUE through exploiting soil water.
In conclusion, modelling identified consistently traits of smaller canopies paired with strong root development for selection of drought resistant phenotypes. Trade-offs with water savings are being analysed.

References
[1] Cerasuolo M, Richter GM, Cunniff J, et al. (2013). Agr. Forest Meteorol. 173:127-38.
[2] Cerasuolo M, Richter GM, Richard B, Cunniff J, et al., (2016). J Exp. Bot. 67(3):961-77.
Year(s) Of Engagement Activity 2009,2017
URL http://www.watbio.eu/bioenergy-genomics-17-oxford-conference/bioenergy-genomics-17-programme/
 
Description INTERNATIONAL UNION OF FOREST RESEARCH ORGANIZATIONS 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact IUFRO officeholder - Deputy Coordinator 2.04.10 - Genomics
Year(s) Of Engagement Activity 2010,2011,2012,2013,2014
 
Description International Bioenergy (Shanghai) Conference and Exhibition (IBSCE 2017) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Presentation by PhD student co-supervised with Imperial College London
Year(s) Of Engagement Activity 2017
URL http://programme.ibsce.com/abstract.php?idabs=14586&idses=658&idtopic=1
 
Description International Bioenergy Conference 2017, Manchester 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented a poster: "Estimating spatially explicit biomass productivity for grassland types in the UK
Abstract: BACKGROUND: Grasslands represent more than two thirds of UK agricultural land. Reduced demand for home-grown and grassland-based dairy and meat products have caused a productivity gap, which could be used for bioenergy. Within a whole systems analysis of bioenergy the objectives were to model attainable productivities on temporary, permanent and rough-grazing grasslands. We present results for (1) scaling up process-based model (PBM) into biophysical meta-models (MM), and (2) estimating feedstock availability for food and fuel/fibre, now and in the future (2050s).
Results
The calibrated PBM simulates observed biomass yields well (Figure 2A) and up-scaling into MMs (Figure 2B) caused only small rise in uncertainty in yield prediction (R2 from 82.1 to 73.5%). The distribution of survey-based modelled feedstock availability (Figure 3) shows regional hotspots for temporary and permanent grassland potentially available for energy.
Future projections (Figure 4) show highest potential gains in temporary grassland due to technological progress, which can be extrapolated using the national areas (Table 1). Conclusions and Future Work
Productivity on temporary grassland bears the highest gains due to management & inputs.
First question is how innovations will increase productivity of temporary and permanent grassland (e.g. use of high sugar grass) and second, how can incentives close the yield gap?
Yield distributions will be used in the whole systems analyses to identify desirable options for bioenergy production in balance with other competing ecosystem services.
Year(s) Of Engagement Activity 2017
 
Description International Bioenergy Conference from 22 to 24 March 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr. Richard presented a poster on "Optimizing regional phenotypes of SRC-willow to improve resource use efficiency and reduce environmental impact" (Richard, Qi and Richter). The poster session was started with a flash talk in front of the poster. It was followed the next day by a SHARE (Early-career researchers group on biomass and bioenergy) event with a visit of Manchester University and networking opportunity with Mendeley.
Year(s) Of Engagement Activity 2017
 
Description Living Planet Symposium 2016 - Satellite-derived NDVI to assess productivity of renewable energy and improve plantings of novel biomass crops. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Richter, G.M., Barker, A., Agostini, F., Qi, A., 2016. Satellite-derived NDVI to assess productivity of renewable energy and improve plantings of novel biomass crops. Living Planet Symposium 2016. ESA Communications, Noordwijk, NL, Prague, Czech Republic.
Year(s) Of Engagement Activity 2016
URL http://lps16.esa.int/
 
Description Pathways to delivering a nexus approach 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Participants in your research and patient groups
Results and Impact Discussion on priorities to focus research in this area

Report published for use by Research Councils
Year(s) Of Engagement Activity 2014
 
Description Plant & Animal Genome XXIV Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This was a poster presentation at the major international conference where willow genomics is presented and discussed. P0266
Year(s) Of Engagement Activity 2016
URL https://pag.confex.com/pag/xxiv/webprogram/start.html
 
Description Plant and Animal Genome 2013 - A Mutated Myb Transcription Factor Underlies YLD1 - a Major Yield QTL In Salix 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at international conference
Year(s) Of Engagement Activity 2013
 
Description SCOPE Bioenergy Sustainability workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Activity is on-going as we are preparing chapter for publications but results have already been disseminated at one international conference

too early to say
Year(s) Of Engagement Activity 2013
 
Description SUPERGEN Bioenergy Hub SHARE network 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact An event for PhD students and early career researchers.
Year(s) Of Engagement Activity 2016
 
Description UK-Norway symposium. Harpenden, June 2013 - Gene Discovery and genetic improvement of willow biomass. Valorising woody biomass 
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 Presentation to bilateral research and strategy meeting - Norway and UK on Valorising Woody Biomass
Year(s) Of Engagement Activity 2013