Agroecology

a rigorous scientific basis for sustainable cropland...scales from individuals to landscapes...a hub for research and outreach in arable-grass systems

Aims and activities

The Agroecology Group aims to provide a rigorous scientific basis for sustainable croplands. We examine how plants, animals and microbes may interact to form a dynamic ecosystem supporting long-term economic offtake. Our home base is the maritime croplands of the north-east Atlantic, from where we collaborate in a range of climatic and ecological zones across Europe and beyond. Integral to our enterprise is a comprehensive and unique knowledge transfer chain that links research to applications in management, policy and the public understanding of science. We are active in global debates on food security, biodiversity and the sustainable use of resources. Contact: Geoff Squire [1]

• Research and applications
• Staff, capability, infrastructure
• Students, teaching,
• Outreach
• Funding
• Previous work
• Publications

Research and applications

Our research crosses scales from the individual to the landscape. Individuals are examined through the functional traits and properties that link them to each other and to their surrounds. Groups of individuals form populations that exchange genes and interact for sunlight, water and nutrients. Populations of different organisms - plants, insects, microbes - mediate the movement and transformation of energy and matter in fields and woodland. Fields, woods and other habitat form landscape mosaics through which individuals move and interact. Feedbacks occur between all scales: the landscape evolves because of the working of individuals, including people, while individuals are limited by the constraints of the landscape. Applications include:

• sustainable cropping systems - production within safe environmental limits
• environmental risk assessment - whole system approaches to hazard and exposure
• nitrogen cycling in croplands - N fixation, inputs and losses, N-efficient plants
• functional biodiversity - crops, wild plants, arthropods, microorganisms - their role in ecol
• weeds and aliens - pros and cons in crop-weed coexistence
• mathematuical modelling - systems, crops, communities, trophic interactions

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Staff, capability, infrastructure

We are mainly biologists, quantitative ecologists and mathematical modellers, whose scales of interest range from landscape to community and organism. Graham Begg [2] is a biologist/modeller working on population dynamics and landscape mosaics. Cathy Hawes [3], an ecologist, works on functional biodiversity and sustainable crop systems. Alison Karley [4] is a physiologist, looking at nutrient relations among plants, insects and endosymbionts. Pete Iannetta [5], ecologist, examines plant traits, notably in weeds and legumes. Geoff Squire [1] is a biologist, examining the links between individuals and fluxes in systems. Mark Young [6] provides bespoke GIS and IT solutions to aid databasing, remote recording and modeling. Euan James  [7]specialises in nitrogen fixation and legumes, locally an globally. Richard Dye, a software engineer and mathematical modeller, is currently working on landscape modelling in the PURE project.

Recent changes: Nick Birch has moved to the Chemical Ecology group at The James Hutton Institute but works closely with Agroecology on several EU projects; Scott Johnson has taken a position at the University of Western Sydney but retains working links through Technology Strategy Board projects and PhD students.

Technical staff include Gillian Banks and Linda Ford (Scottish Government funding), Anna Skiba (LINK / AMIGA), Carolyn Mitchell [8] (TSB), Paul Neave (Centre for Sustainable Cropping), Linda Nell (contract). Capabilities include the baseline data at the centre for Sustainable Cropping, major field surveys, controlled environment studies in glasshouse and growth chamber, molecular and biochemical laboratory analyses and plant-insect relations. Technical and scientific staff practise strict quality control procedures for collection, checking auditing and analysis of data. For information on students see below.

Capability and infrastructure

Over the last few years the team has built a strong and in many ways unique research infrastructure that is valued throughout the institute and by external collaborators.

• field platform, 40 hectares, at the Centre for Sustainable Cropping [9] at Balruddery Farm near Dundee – management and scientific direction provided by Agroecology to establish the Centre as the pre-eminent research platform for balancing provisioning and other services in the north European maritime region
• arable-grass farm network, eastern Scotland – currently >100 fields - in which biophysical indicators of soil and food webs are compared with management and offtake
• glasshouse, growth room, field plot facilities at The James Hutton Institute's farms

• nutrient extraction and analysis: EA, HPLC, ICP-MS, to quantify mineral nutrients, organic nutrients, secondary compounds, protein content
• molecular tools: markers and diagnostic methods to describe and quantify molecular diversity of weed, insect and microbial endosymbiont groups
• mathematical modelling: spatially-explicit, individual to landscape
• statistics: multivariate and univariate analyses, graphical data exploration, GLM, multiple linear regression, relational databases, etc. 

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Students and teaching 

The group hosts and supervises students at doctorate, masters and undergraduate levels. Typically 10-15 students are engaged in practical work in the group in any year. All students are registered at universities, including Aberdeen, Dundee, Durham, Edinburgh, York and St Andrews. We supervise students or link in other ways with universities overseas at Arkansas, Guelph, Idaho, Manitoba, Paris-Sud, Tromso, Trondheim, Wageningen and elsewhere.

Group members regularly lecture on university courses, notably at St Andrews and Dundee Universities, lecture to visiting students and interest groups, and are active in the Centre for Environmental Change and Human Resilience [10], a joint initiative between The James Hutton Institute and the University of Dundee. Professor Steve Hubbard provides close links and collaborations with universities of Dundee and St Andrews. Professor Janet Sprent, Emeritus, Dundee is closely associated with the group's work on legumes and nitrogen fixation.

Current and recent doctoral students

• Claire McFadden 2012-2015 Ecological engineering for conservation biocontrol of insect pests at field and landscape scales. James Hutton Institute (Graham Begg, Nick Birch), University of St. Andrews (Steve Hubbard)

• Ruth Wade 2011-2014 How will predicted changes in precipitation shape cVictor Martinez Herediaereal ecosystems? James Hutton Institute (Ali Karley, Scott Johnson) University of York (Sue Hartley, Biology) 

• Amanda Wilson 2011-2014 Determining the impact of agricultural systems on small mammals. James Hutton Institute (Brian Fenton, Graham Begg), University of St. Andrews (Steve Hubbard)

• Rebecca Cornwell 2011-2014 Dynamics of natural enemy resistance in aphid populations.  James Hutton Institute (Ali Karley, Misha Taliansky) University of Dundee (Mark Chaplain, Mathematics)
• Tim Lewis 2010-2013 Linking erosional processes with seedbank dynamics to inform sustainable cropping. CECHR studentship.  James Hutton Institute (Cathy Hawes, Blair McKenzie), University of Dundee (John Rowan, Environmental Sciences) 
• Abir Abusirwil 2010-2013 Pharmacological studies using myxospermous seed mucilage of the model plant Capsella bursa-pastoris L. Medik. (Shepherd's purse). James Hutton Institute (Pete Iannetta), University of Strathclyde (Val Ferro, Pharmacy and Biomedical Sciences). 
• Gillian Banks 2008-2012 Feral oilseed rape – role in environmental risk assessment and GM coexistence.  Staff member / SIGMEA project. James Hutton Institute (Geoff Squire, Cathy Hawes), University of Dundee (Steve Hubbard, Life Sciences )
• Hannah Clarke 2009-2012 Bacterial secondary symbionts of Macrosiphum euphorbiae and multi-trophic interactions.  James Hutton Institute (Ali Karley, Danny Cullen), University of Dundee (Steve Hubbard, Life Sciences)
• Ananthi Anadanadesan 2009-2012 Mathematical modelling of the spatio-temporal dynamics of aphid-plant-virus interactions.   EPSRC-CASE Studentship. James Hutton Institute (Ali Karley), University of Dundee (Mark Chaplain, Mathematics)
• Wenni Deng 2019-2012 (awarded) Understanding the dynamic properties of (Capsella bursa pastoris l. Medik) seed coat mucus. CECHR studentship. James Hutton Institute (Pete Iannetta), University of Dundee (Dong Sheng-Jeng, Civil Engineering). 
• Nicola Cook  2008-2011 (awarded) Population genetics of the farmland sawfly Dolerus aeneus (Hymenoptera, Symphyta).   BBSRC-CASE/Game and Wildlife Conservation Trust. James Hutton Institute (Ali Karley, Joanne Russell), University of Dundee (Steve Hubbard, Life Sciences), GWCT (Nick Sotherton)
• Emily Clark 2007-2010 (awarded) Molecular characterisation of the bacterial communities in cabbage aphid (Brevicoryne brassicae) and their associated fitness effects.  SCRI (Ali Karley, Tim Daniell), University of Dundee (Steve Hubbard, Life Sciences)  

Undergrad and masters students

• Sarah Doherty 2011-2012. One-year experience placement, Durham University, Biology. James Hutton Institute (Geoff Squire)
• Laura Lopez 2012. Funded by the ERASMUS training programme and Legume Futures for 4 months; from Sabadell (a city next to Barcelona), Spain; in the final year of her degree in biology, and wishes to specialise in plant-ecology, especially legumes, and has experience working with Trifolium (Pete Iannetta, Euan James)
• Victor Martinez Heredia 2013 Funded by the ERASMUS training programme for several months; from Valencia, Spain; in the final year of his degree in environmental science, wishes to specialise in molecular biology and is working with Pete Iannetta on transformation and cloning genes in shepherd's purse Capsella bursa-pastoris.

 Outreach

Research is closely tied to outreach and knowledge-exchange through the following channels:

• LEAF (Linking Environment and Farming) Innovation Centre [11] at The James Hutton Institute, coordinated by the Agroecology group
• Living Field [12]project on education, outreach and public understanding (managed by Agroecology and the Soil Ecology group)
• the Centre for Sustainable Cropping [9] – a long term research-to-application platform at The James Hutton Institute’s Balruddery Farm, coordinated by staff in Agroecology (Cathy Hawes)
• Environment, risk assessment and biodiversity – liaison with NGOs, UK government bodies, the EC and member states

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Funding

The Agroecology group is funded from three main sources - the Scottish Government, the EU and a range of industrial partnerships. The Scottish Government programme 2011-16 supports strategic research on ecosystem services, biodiversity and ecosystem function in the lowland arable-grass croplands of the north-east Atlantic. The group also contributes to work in the Scottish Government funded Centres of Expertise in Waters [13] and Climate Change.

EU grants and networks

The group is part of four EU networks linking more than 60 partners across Europe in major collaborative projects:

• PURE Integrated pest management in the EU FP7 PURE project, 2011-2014. Agroecology contact/workpackage leader/ecological engineering: Graham Begg [14]. JHI contact: Nick Birch [15]. Decision modelling: Geoff Squire [16]
• Legume Futures Legumes in European cropping systems: EU FP7, 2010-2013. Agroecology/JHI contact/ workpackage leader: Pete Iannetta [17]. Nitrogen Fixation: Euan James [18]. System design: Geoff Squire. 
• AMIGA Risk assessment of biotech crops in European agroclimatic regions: EU FP7 project, 2012-14. Agroeoclogy/JHI contact / WP leader: Geoff Squire [16]. IPM:  Nick Birch [19]. Ecological indicators: Cathy Hawes [20].
• SIGMEA Coexistence of GM cropping- EU FP6 SIGMEA [21] project (practical work completed, analysis continuing). Contact: Geoff Squire [22]

Industrial collaborations

UK industrial collaborations take scientific findings to applications on the land and in the processing plant. Current projects include definition and selection of wheat ideotypes for reduced input cropping (Sustainable Arable Link, 2011-2014); biopesticides as replacement for EU pesticide withdrawals (SCEPTRE, now managed through the Chemical Ecology group) and the following two Technology Strategy Board projects - Physical fruit and Beans4Feed.

• The Physical Fruit TSB project 2010-2014 Breeding for physical resistance traits – protecting soft fruit crops from pests and pathogens: field scale assessment of soft fruit physical traits against pests and pathogens; experimental trait testing and chemical analysis of accessions against target pests and pathogens; QTL mapping of traits and understanding of genetic control of resistances identified.Consortium: ADAS, GSK, Thomson & Thomson Ltd., LEAF, Adamston Farms Ltd., ReDeva Ltd., KG Growers Ltd., M & S Ltd. Agroecology contact: Ali Karley [23], Scott Johnson. Project leader: Julie Graham [24].  
• The Beans4Feeds TSB project 2012-2016 Development of protein-rich and starch-rich fractions from faba beans and salmon and terrestrial animal productivity: optimising the production of bean protein concentrate (BPC) using air classification; assess the impact of dietary inclusion of BPC vs. fishmeal vs. soya protein concentrate on the production and health of Atlantic salmon; establish the nutritional value of bean starch in diets of pigs and poultry; assess nutritional quality (protein and anti-nutritional factors) of existing and novel bean genetic resources for fish production; establish pilot plant for production of BPC by air classification. Consortium: University of Stirling, EWOS, Biomar, Scottish Agricultural College, University of Aberdeen, University of St Andrews, W.N. Lindsay, Limagrain UK Ltd., Marine Harvest Scotland Ltd., Harbro Ltd. Agroecology contact: Ali Karley, Pete Iannetta [17]. Institute contact: Gavin Ramsay [25].

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Previous work

Many of the skill sets current in agroecology developed at the Institute during the coordinated programmes funded by the Scottish Government in the late 1990s, and were refined through external projects 1998-2008 on the ecological and economic impacts of GM crops. Full details including publications can be found at the Ecological biosafety and geneflow [26] web pages on the previous SCRI website, or go directly via the following links to  the UK’s Farm Scale Evaluations of GMHT crops [27], the EU ECOGEN project on GM insect resistant crops; the GMO Guidelines [28] project in Brazil, Kenya and Vietnam (IOBC); the EU SIGMEA project on coexistence [21]; and a series of major projects on Gene movement and persistence [29] funded by Defra, RERAD and BBSRC.

The group and close colleagues, took lead roles in the 2006-11 RERAD programmes, notably in the Sustainable Crop Systems workpackage, and the BBSRC (trophic) LINK project (2005-2008).  

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Publications

A sample of recent peer reviewed publications. Please refer to staff pages for complete listings

Hawes C, Evans HF, Stewart AJA. 2013. Interference competition, not predation, explains the negative association between wood ants (Formica rufa) and abundance of ground beetles (Coleoptera: Carabidae). Ecological Entomology, DOI 10.1111/een.12021

Deng W, Iannetta PPM, Hallett PD, Toorop PE, Squire GR, Jeng D-S. 2013. The rheological properties of the seed coat mucilage of Capsella bursa-pastoris L.Medik. (shepherd’s purse) (2013) Biorheology 50, 57-67, DOI 10.3233/BIR-130627

Begg, G.S., Wishart, J., Young M.W., Squire, G.R., Iannetta, P.P.M. 2012. Genetic structure among arable populations of Capsella bursa-pastoris L. Medik is linked to functional traits and in-field conditions. Ecography 35, 446-457 doi:10.1111/j.1600-0587.2011.07030.x

Bingham, I.J., Karley, A.J., White, P.J., Thomas, W.T.B. & Russell, J.R. 2012.  Analysis of improvements in nitrogen use efficiency associated with 75 years of barley breeding.  European Journal of Agronomy 42, 49-58.

Valentine, T.A., Hallett, P.D., Binnie, K., Young, M.W., Squire, G.R., Hawes, C., Bengough, A.G. 2012.  Soil strength and macropore volume limit root elongation rates in many UK agricultural soils.  Annals of Botany 110, 259-270.  

Deng, W., Jeng, D.S., Toorop, P.E., Squire, G.R. and Iannetta, P.P.M. 2012. A mathematical model of mucilage expansion in myxospermous seeds of Capsella bursa-pastoris L. Medic (shepherd's purse). Annals of Botany 109, 419-427.

James, E.K., Baldani, J.I. 2012. The role of biological nitrogen fixation by non-legumes in the sustainable production of food and biofuels. Plant and Soil 356, 1–3.

Bagavathiannan M.V., Begg G.S., Gulden R.H., Van Acker R.C. 2012. Modelling the Dynamics of Feral Alfalfa Populations and Its Management Implications. PLoS ONE 7(6):e39440 

Suárez-Moreno, Z.R., Caballero-Mellado, J., Coutinho, B., Mendonça-Previato, L., James, E.K., Venturi V. 2012. Common features of environmental and potentially beneficial plant-associated Burkholderia. Microbial Ecology 63, 249-266.

Devos, Y., Hails, R.S., Messéan, A., Perry, J.N., Squire, G.R. 2012.  Feral genetically modified herbicide tolerant oilseed rape from seed import spills: are concerns scientifically justified?  Transgenic Research 21, 1-21.

Johnson, S.N., Young, M.W. & Karley, A.J. 2012.  Protected raspberry production alters aphid-plant interactions but not aphid population size.  Agricultural and Forest Entomology 14, 217-224.

Sausse, C., Colbach, N., Squire, G.R., Young, M.W. 2012.  How to manage the impact of gene flow on oilseed rape grain quality? Simulation case studies of three contrasted landscapes.  European Journal of Agronomy 38, 32-42.

Toorop, P.E., Cuerva R.C., Begg, G.S., Locardi, B., Squire, G.R., Iannetta, P.P.M. 2012.  Co-adaptation of seed dormancy and flowering time in the arable weed Capsella bursa-pastoris (shepherd's purse).  Annals of Botany 109, 481-489.

Clemente, M.R., Pilar Bustos-Sanmamed, P., Loscos, J., James, E.K., Pérez-Rontomé, C., Navascués, J., Gay, M., Becana, M. 2012. Thiol synthetases of legumes: immunogold localization and differential gene regulation by phytohormones.Journal of Experimental Botany 63, 3923–3934  

Birch, A.N.E., Begg, G.S., Squire, G.R. 2011. How agro-ecological research helps to address food security issues under new IPM and pesticide reduction policies for global crop production systems (Invited Review). Journal of Experimental Botany 62, 3251-3261.

Karley, A.J., Valentine, T.A., Squire, G.R. 2011. Dwarf alleles differentially affect barley root traits influencing nitrogen acquisition under low nutrient supply.  Journal of Experimental Botany 62, 3917-3927.

Squire, G.R., Breckling, B., Pfeilstetter, A., Jorgensen, R.B., Lecomte, J., Pivard, S., Reuter, H., Young, M.W. 2011. Status of feral oilseed rape in Europe: its minor role as a GM impurity and its potential as a reservoir of transgene persistence. Environmental Science and Pollution Research 18, 111-118.

Bohan, D.A., Powers, S.J., Champion, G., Haughton, A.J., Hawes, C., Squire, G.R., Cussans, J., Mertens, S.K. 2011.  Modelling rotations: can crop sequences explain arable weed seedbank abundance?  Weed Research 51, 422-432.

Cook, N., Aziz, N., Hedley, P.E., Morris, J., Milne, L., Karley, A.J., Hubbard, S.F. & Russell, J.R. 2011.  Transcriptome sequencing of an ecologically important graminivorous sawfly: a resource for marker development.  Conservation Genetics Resources 3, 789-795.

Debeljak, M., Squire, G.R., Kocev, D., Hawes, C., Young, M.W. & Džeroski, S. 2011.  Analysis of time series data on agroecosystem vegetation using predictive clustering trees.  Ecological Modelling 222, 2524-2529. 

Bontemps, C., Elliott, G.N., Simon, M.F., Dos Reis Júnior, F.B., Gross, E., Lawton, R.C., Neto, N.E., Loureiro, M.d., de Faria, S.M., Sprent, J.I., James, E.K. and Young, J.P.W. 2010. Burkholderia species are ancient symbionts of legumes. Molecular Ecology 19, 44-52.

Clark, E.L., Karley, A.J. & Hubbard, S.F. 2010.  Insect endosymbionts: manipulators of insect herbivore trophic interactions?  Protoplasma 244, 25-51.

Hawes, C., Squire, G.R., Hallett, P.D., Watson, C.A., Young, M.W. 2010. Arable plant communities as indicators of farming practice. Agriculture, Ecosystems and Environment 138, 17-26.

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