Characterisation and exploitation of bacterial endophytes in C4 energy crops

Lead Research Organisation: Aberystwyth University
Department Name: IBERS

Abstract

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Description Sustainable production of high yielding energy crops is essential in order to meet targets for fossil fuel substitution and atmospheric carbon reduction. Bacterial endophytes with the potential to fix nitrogen have been identified in two of the world's leading bioenergy crops: sugarcane and Miscanthus. The aim of this partnership was to initiate a new collaboration between laboratories in the UK (IBERS) and Brazil (University of São Paulo, USP) working on different aspects of bacterial endophytes, in order to exchange expertise, enhance the fundamental understanding of the bacteria-C4 grass symbiosis and exploit this knowledge to develop biofertilisers for sustainable bioenergy cultivation on land sub-optimal for the production of primary food crops.
This award was unusual in that only the original Brazilian partner was not funded, and so new partners in EMBRAPA Agrobiologia and more recently Universidade Federal do Rio de Janeiro (UFRJ) were identified as part of the project. PI Farrar travelled annually to Brazil to visit with partners and held a workshop in Aberystwyth. Summary of activities:
October/November 2012: Iain Donnison and Kerrie Farrar met with researchers Heloiza Ramos Barbosa, Felipe Ibanez de Santi Ferrara & Simone Ichiwake at the USP where we were given a tour of research facilities in the departments of microbiology and botany, USP. We attended the first 2 day BIOEN BBEST conference at FAPESP, Sao Paulo. The BIOEN programme spans crop genomes to ethanol and other products and has many parallels with the bioenergy and biorefining work being carried out at IBERS. Farrar and Donnison met with Rui Lopes at the British Consulate (FCO) Science and Innovation team in Sao Paulo, where sustainable energy and innovation were highlighted as key areas of scientific exchange between the two countries. Finally we travelled to EMBRAPA Agrobiologia, Seropedica, where we met with researchers (Bob Boddey, Segundo Urquiaga, Claudia Pozzi Jantalia, Luc Rouws and Jean-Luis Simoes-Araujo); toured the facilities, including labs (molecular biology, microbiology, proteomics, microbial ecology), glasshouses and field site (Pennisetum and sugarcane; and exchanged methodology and results (culturing, semi solid growth media assays, tissue culture, clone libraries, functional assays, molecular characterisation). Outcomes included plans for collaborative research, potential for exchange of personnel and students, and advertisement of the new IBERS MSc in Green Biotechnology & Innovation Management.
October 2013: Iain Donnsion was part of a British Scientific delegation to Belem/Caxiuana as part of an event held to celebrate 20 years of the Scientific Station Ferreira Penna.
October 2013: Kerrie Farrar visited the Center for Nuclear Energy in Agriculture (CENA), Piracicaba, as part of a delegation with Naill McNamara (CEH, Lancaster) and Christian Davies (Shell, Houston, USA). We met with Carlos and Eduardo Cerri (USP) to discuss sustainable agriculture of energy crops (sugarcane and Miscanthus) and related projects. We were given a tour of the USP, Piracicaba campus and attended a workshop on sustainable agriculture at CENA. NMcN stayed for a further two days for further discussion including arranging for Arlete Simoes Barneze (MSc student at CENA) to come to the UK to undertake her PhD as a jointly supervised project between CENA, CEH Lancaster and Aberystwyth via a FAPESP funded scholarship. Unfortunately it was not possible for AB to be registered at Aber for a PhD at CEH due to Tier 4 visa restrictions.
Farrar then travelled to Sao Paulo to meet with Glaucia Mendes de Sauza (USP/FAPESP) and Rubens Maciel Fillo (UNICAMP) at FAPESP and discussed options for links to BIOEN (BBEST conference 2014) and identifying BIOEN researchers with complementary research areas and obtaining contact emails for them. Farrar contacted Adriana Hemerly (UFRJ) who is interested in collaboration re endophytes. Farrar attended British Council briefing at the British Consulate with Maraian Gray (Aberystwyth University International Officer). Met Liane Hentschke (CNPq) following her keynote talk, who indicated there would be research calls between BBSRC and CNPq including the areas of biodiversity, bioenergy and food security. Met with Rui Lopes and Caroline Cowan (Science and Innovation team) to discuss opportunities for UK-Brazil collaboration. Attended BC networking event for UK and Brazilian universities at the consulate. Farrar had breakfast with Liane Hentschke (CNPq) where we discussed the Welsh Government funded BEACON project as a model for academic-industrial research. Later attended British Consulate recruitment fair with Marian Gray and visited the botanical gardens.
Farrar met with Luc Rouws, Segundo Urquiaga, Veronica Reiss, Ivo Baldani, Luc Rouws and Marcia Coelho at EMBRAPA, Seropedica. We discussed exchange of methodology, joint publication based on comparing our existing research results (endophytes and BNF in Sugarcane, Miscanthus and Pennisetum), options for exchanging students/personnel and development of outline proposals for future funding under BBSRC-CNPq calls.
October 14. Kerrie Farrar and David Bryant visited Adriana Hemerly and Paulo Ferreira at UFRJ where they gave a departmental talk and finalised a joint Newton Fund proposal. They then visited and toured the Brazilian Bioethanol Science and Technology Laboratory (CTBE), Campinas and finally attended the BBEST conference in Campos do Jordão.
June 1015. The award also part-funded a workshop in Aberystwyth which was attended by Brazilian researchers from these institutions plus additional partners from James Hutton Institute and Lancaster University in the UK and Universidade Estadual do Norte Fluminese (UENF) in Brazil. Partners have exchanged expertise, specifically methodology and knowledge of the two crop systems, and molecular, culturing and physiological methodology applicable to bacterial endophyte research. It seems there is not much similarity in the diversity of bacterial endophytes in tropical sugarcane and temperate Miscanthus in terms of species present, however there may be more functional similarities, e.g. plant growth promotion and/or biological nitrogen fixation, and this is under further investigation in subsequent projects.
This IPA has been instrumental in establishing a strong collaboration and building a wider network. Partners in this project were initially successful in securing a Newton Fund award '14CONFAP Comparative genomic and physiological analysis of C4 plant-microbe symbiosis' and more recently the BBSRC-CONFAP Virtual Joint Centre 'UK-Brazil Nitrogen Fixation Centre'.
Exploitation Route Findings from the Newton Fund awards will be of use to sustainable agriculture, in particular sugarcane and Miscanthus production in Brazil and Europe respectively.
Sectors Agriculture, Food and Drink,Energy,Environment

 
Description BBSRC iCASE Endophytic bacteria: co-existence and chemical warfare
Amount £95,042 (GBP)
Funding ID BB/M01505X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 09/2019
 
Description BBSRC-Newton Fund Call for Virtual Joint Centres with Brazil, China and India in Agricultural Nitrogen 'Understanding and exploiting biological nitrogen fixation for improvement of Brazilian agriculture'
Amount £209,428 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2016 
End 12/2018
 
Description Characterisation and exploitation of bacterial endophytes in C4 energy crops UK-Brazil partnering award
Amount £36 (GBP)
Funding ID BB/J020486/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2012 
End 10/2016
 
Description IBERS studentship 'Targeting extremophilic bacterial endosymbionts for plant growth promotion and phytoremediation applications'
Amount £54,000 (GBP)
Organisation Aberystwyth University 
Sector Academic/University
Country United Kingdom
Start 01/2016 
End 12/2018
 
Description KESS2
Amount £52,885 (GBP)
Organisation European Social Fund (Welsh Government/ EU) 
Sector Public
Country United Kingdom
Start 12/2018 
End 12/2021
 
Description NRN-LCEE Returning Fellowships
Amount £9,990 (GBP)
Funding ID R39GO1/CC8004/RFS008 
Organisation Welsh Assembly 
Sector Public
Country United Kingdom
Start 05/2018 
 
Description UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP VJC Nitrogen) 
Organisation Brazilian Agricultural Research Corporation
Department Embrapa Agrobiologia
Country Brazil 
Sector Private 
PI Contribution WP2.2 Isolate and characterize epiphytic and endophytic bacteria from C4 plants and select the most efficient strains in terms of plant growth promotion WP2.3 Molecular tagging to visualise colonisation and localisation in planta WP2.4 Phenomics analysis of plant growth in response to inoculation under limited nitrogen and/or water WP3 Identify genetic components required for efficient crop-microbe interactions
Collaborator Contribution WP1 Strategies for engineering ammonium excretion in diazotrophic endophytes WP2.1 Devise selection strategies to isolate efficient endophytes using serial inoculation WP2.5 Quantitate nitrogen fixation using 15N WP4. Evaluate the effectiveness of inoculants in field trials
Impact UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP). We are a virtual joint centre working to develop innovative technologies to increase crop productivity in Brazil using nitrogen-fixing bacteria as a sustainable source of fixed nitrogen. In turn this will reduce the input of chemical fertilisers in agriculture and mitigate the environmental and economic impacts of reactive nitrogen pollution.
Start Year 2016
 
Description UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP VJC Nitrogen) 
Organisation Federal Institute of Rio Grande do Sul
Country Brazil 
Sector Academic/University 
PI Contribution WP2.2 Isolate and characterize epiphytic and endophytic bacteria from C4 plants and select the most efficient strains in terms of plant growth promotion WP2.3 Molecular tagging to visualise colonisation and localisation in planta WP2.4 Phenomics analysis of plant growth in response to inoculation under limited nitrogen and/or water WP3 Identify genetic components required for efficient crop-microbe interactions
Collaborator Contribution WP1 Strategies for engineering ammonium excretion in diazotrophic endophytes WP2.1 Devise selection strategies to isolate efficient endophytes using serial inoculation WP2.5 Quantitate nitrogen fixation using 15N WP4. Evaluate the effectiveness of inoculants in field trials
Impact UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP). We are a virtual joint centre working to develop innovative technologies to increase crop productivity in Brazil using nitrogen-fixing bacteria as a sustainable source of fixed nitrogen. In turn this will reduce the input of chemical fertilisers in agriculture and mitigate the environmental and economic impacts of reactive nitrogen pollution.
Start Year 2016
 
Description UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP VJC Nitrogen) 
Organisation Federal University of Paraná
Country Brazil 
Sector Academic/University 
PI Contribution WP2.2 Isolate and characterize epiphytic and endophytic bacteria from C4 plants and select the most efficient strains in terms of plant growth promotion WP2.3 Molecular tagging to visualise colonisation and localisation in planta WP2.4 Phenomics analysis of plant growth in response to inoculation under limited nitrogen and/or water WP3 Identify genetic components required for efficient crop-microbe interactions
Collaborator Contribution WP1 Strategies for engineering ammonium excretion in diazotrophic endophytes WP2.1 Devise selection strategies to isolate efficient endophytes using serial inoculation WP2.5 Quantitate nitrogen fixation using 15N WP4. Evaluate the effectiveness of inoculants in field trials
Impact UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP). We are a virtual joint centre working to develop innovative technologies to increase crop productivity in Brazil using nitrogen-fixing bacteria as a sustainable source of fixed nitrogen. In turn this will reduce the input of chemical fertilisers in agriculture and mitigate the environmental and economic impacts of reactive nitrogen pollution.
Start Year 2016
 
Description UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP VJC Nitrogen) 
Organisation Federal University of Rio de Janeiro
Country Brazil 
Sector Academic/University 
PI Contribution WP2.2 Isolate and characterize epiphytic and endophytic bacteria from C4 plants and select the most efficient strains in terms of plant growth promotion WP2.3 Molecular tagging to visualise colonisation and localisation in planta WP2.4 Phenomics analysis of plant growth in response to inoculation under limited nitrogen and/or water WP3 Identify genetic components required for efficient crop-microbe interactions
Collaborator Contribution WP1 Strategies for engineering ammonium excretion in diazotrophic endophytes WP2.1 Devise selection strategies to isolate efficient endophytes using serial inoculation WP2.5 Quantitate nitrogen fixation using 15N WP4. Evaluate the effectiveness of inoculants in field trials
Impact UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP). We are a virtual joint centre working to develop innovative technologies to increase crop productivity in Brazil using nitrogen-fixing bacteria as a sustainable source of fixed nitrogen. In turn this will reduce the input of chemical fertilisers in agriculture and mitigate the environmental and economic impacts of reactive nitrogen pollution.
Start Year 2016
 
Description UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP VJC Nitrogen) 
Organisation James Hutton Institute
Department Ecological Sciences
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution WP2.2 Isolate and characterize epiphytic and endophytic bacteria from C4 plants and select the most efficient strains in terms of plant growth promotion WP2.3 Molecular tagging to visualise colonisation and localisation in planta WP2.4 Phenomics analysis of plant growth in response to inoculation under limited nitrogen and/or water WP3 Identify genetic components required for efficient crop-microbe interactions
Collaborator Contribution WP1 Strategies for engineering ammonium excretion in diazotrophic endophytes WP2.1 Devise selection strategies to isolate efficient endophytes using serial inoculation WP2.5 Quantitate nitrogen fixation using 15N WP4. Evaluate the effectiveness of inoculants in field trials
Impact UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP). We are a virtual joint centre working to develop innovative technologies to increase crop productivity in Brazil using nitrogen-fixing bacteria as a sustainable source of fixed nitrogen. In turn this will reduce the input of chemical fertilisers in agriculture and mitigate the environmental and economic impacts of reactive nitrogen pollution.
Start Year 2016
 
Description UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP VJC Nitrogen) 
Organisation John Innes Centre
Department Molecular Microbiology
Country United Kingdom 
Sector Private 
PI Contribution WP2.2 Isolate and characterize epiphytic and endophytic bacteria from C4 plants and select the most efficient strains in terms of plant growth promotion WP2.3 Molecular tagging to visualise colonisation and localisation in planta WP2.4 Phenomics analysis of plant growth in response to inoculation under limited nitrogen and/or water WP3 Identify genetic components required for efficient crop-microbe interactions
Collaborator Contribution WP1 Strategies for engineering ammonium excretion in diazotrophic endophytes WP2.1 Devise selection strategies to isolate efficient endophytes using serial inoculation WP2.5 Quantitate nitrogen fixation using 15N WP4. Evaluate the effectiveness of inoculants in field trials
Impact UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP). We are a virtual joint centre working to develop innovative technologies to increase crop productivity in Brazil using nitrogen-fixing bacteria as a sustainable source of fixed nitrogen. In turn this will reduce the input of chemical fertilisers in agriculture and mitigate the environmental and economic impacts of reactive nitrogen pollution.
Start Year 2016
 
Description UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP VJC Nitrogen) 
Organisation State University of the North of Parana
Country Brazil 
Sector Academic/University 
PI Contribution WP2.2 Isolate and characterize epiphytic and endophytic bacteria from C4 plants and select the most efficient strains in terms of plant growth promotion WP2.3 Molecular tagging to visualise colonisation and localisation in planta WP2.4 Phenomics analysis of plant growth in response to inoculation under limited nitrogen and/or water WP3 Identify genetic components required for efficient crop-microbe interactions
Collaborator Contribution WP1 Strategies for engineering ammonium excretion in diazotrophic endophytes WP2.1 Devise selection strategies to isolate efficient endophytes using serial inoculation WP2.5 Quantitate nitrogen fixation using 15N WP4. Evaluate the effectiveness of inoculants in field trials
Impact UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP). We are a virtual joint centre working to develop innovative technologies to increase crop productivity in Brazil using nitrogen-fixing bacteria as a sustainable source of fixed nitrogen. In turn this will reduce the input of chemical fertilisers in agriculture and mitigate the environmental and economic impacts of reactive nitrogen pollution.
Start Year 2016
 
Description UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP VJC Nitrogen) 
Organisation University of Oxford
Department Department of Plant Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution WP2.2 Isolate and characterize epiphytic and endophytic bacteria from C4 plants and select the most efficient strains in terms of plant growth promotion WP2.3 Molecular tagging to visualise colonisation and localisation in planta WP2.4 Phenomics analysis of plant growth in response to inoculation under limited nitrogen and/or water WP3 Identify genetic components required for efficient crop-microbe interactions
Collaborator Contribution WP1 Strategies for engineering ammonium excretion in diazotrophic endophytes WP2.1 Devise selection strategies to isolate efficient endophytes using serial inoculation WP2.5 Quantitate nitrogen fixation using 15N WP4. Evaluate the effectiveness of inoculants in field trials
Impact UK-Brazil Nitrogen Fixation Centre (BBSRC-CONFAP). We are a virtual joint centre working to develop innovative technologies to increase crop productivity in Brazil using nitrogen-fixing bacteria as a sustainable source of fixed nitrogen. In turn this will reduce the input of chemical fertilisers in agriculture and mitigate the environmental and economic impacts of reactive nitrogen pollution.
Start Year 2016
 
Description UNDERSTANDING AND EXPLOITING BIOLOGICAL NITROGEN FIXATION FOR IMPROVEMENT OF BRAZILIAN AGRICULTURE 
Organisation John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Co-I on Virtual Joint Centre award
Collaborator Contribution PI and Co-Is on Virtual Joint Centre award
Impact Due to start 2016
Start Year 2016