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Impacts of intensive agriculture on soil fauna and ecosystem function Trading function for dependence? Tiffany Jade Aslam Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds School of Biology April 2015 - ii - The candidate confirms that the work submitted is her own, except where work which has formed part of jointly-authored publications has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. Chapter 3 is based on the following jointly-authored publication: Aslam, T.J., Benton, T.G., Nielsen, U.N., Johnson, S.N., 2015. Impacts of eucalypt plantation management on soil faunal communities and nutrient bioavailability: trading function for dependence? Biology and Fertility of Soils 51(5): 637-64. DOI: 10.1007/s00374-015-1003-6. Scott Johnson (SNJ) designed the experiment based on knowledge of the existing experimental setup at the Hawkesbury Institute for the Environment (HIE), University of Western Sydney, with input from the candidate (Tiffany Aslam; TJA) and Uffe Nielsen. TJA collected the data with assistance from two research technicians at the HIE. TJA analysed the data, with input from Tim Benton (TGB). TJA wrote and revised the manuscript. SNJ produced Figure 3.1. All co-authors made suggestions to the manuscript and subsequent revisions. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. The right of Tiffany Jade Aslam to be identified as Author of this work has been asserted by her in accordance with the Copyright, Designs and Patents Act 1988. Copyright © 2015 Tiffany Jade Aslam and The University of Leeds - iii - Funding This project was funded by a Natural Environment Research Council (NERC) Doctoral Training Grant (DTG), with the exception of Chapter 3, which was funded by a research exchange grant from the Hawkesbury Institute for the Environment, University of Western Sydney. Collaborative work described in Chapter 4 was supported by a White Rose Consortium grant, although the candidate’s own work was funded by the NERC DTG. Contribution to chapters Chapters 1 and 6 were written by TJA with input from TGB. The study described in Chapter 2 was designed by TJA with input from TGB. All data was collected by TJA with the exception of the climate data which was generated by an automated weather station located at the University of Leeds farm. TJA analysed the data and wrote the chapter, and TGB gave feedback throughout. The study described in Chapter 4 was designed by Les Firbank (University of Leeds) and Jonathan Leake (University of Sheffield). TJA designed the soil invertebrate surveys and collected soil invertebrate data with assistance from Louise White1. Laura Petteway2 assisted with springtail identification. TJA analysed the data and wrote the chapter, and TGB gave feedback throughout. The study described in Chapter 5 was designed by TJA, with input from TGB. TJA collected and analysed the data, and wrote the chapter. TGB gave feedback throughout. Lizzie Fry1 and Rebecca Owens1 assisted with soil pH measurements. Megan Herbert1 assisted with barley harvesting. Micky Langdale3 provided the information provided in Table 5.1. 1 University of Leeds undergraduate volunteers 2 University of Leeds MRes volunteer 3 Operations Director, Stockbridge Technology Centre Ltd. - iv - Acknowledgements First and foremost, I am grateful to my supervisor, Tim Benton, for his guidance, support and patience throughout the PhD process. Also at the University of Leeds, sincere thanks to Steve Sait, Bill Kunin, Les Firbank and the extended Kunin group, particularly Richard German, Mark Goddard, Richard Gunton and Charlie Marsh, for interesting and stimulating discussions, help and support. Special thanks to Marianne Mugabo and Andrea Barden for being a tonic to challenging days. Finally, thanks go to the following undergraduate students and visitors for volunteering time and energy: Zoë Deal, Elizabeth Fry, Megan Herbert, Rebecca Owens, Louise White and, in particular, Laura Petteway. At Spen Farm, thanks to Kevin White, Jo Carter and Fiona Reynolds for assistance with moving equipment and sourcing materials. At the University of Western Sydney, I am grateful to Goran Lopaticki, Gillian Powell and James Ryalls for assistance with fieldwork during a hot Australian summer. Thanks to Burhan Amiji for useful information on the HFE plots and to Uffe Nielsen for spending time teaching soil mite and nematode identification. Lastly, wholehearted thanks to Scott Johnson for being a helpful and supportive mentor and friend, and for encouraging me to pursue a PhD. At Stockbridge Technology Centre, thanks to Pat Croft, Dave George and Micky Langdale for accommodating me during the fieldwork forming the basis of Chapter 5. I am also grateful to my examiners, Karl Ritz and Chris Hassall, whose considered suggestions greatly benefited this thesis. On a personal note, I am grateful to my family and friends for continuous support throughout the PhD process. In particular, thanks to Paul Hicks for offering a sounding board for various setups and for taking the time to build my Tullgren funnels, and to his wonderful son Joe for providing endless encouragement, R advice and assistance in the construction of emergency rabbit defences. Finally, Gil, thank you for inspiring my love of the natural world and for my earliest memories of searching for, and being fascinated with, soil fauna. - v - Abstract Soils form the basis of agroecosystems, generating the fuel, food and fodder needed to sustain human life. Soil biological communities contribute to almost all ecosystem processes, yet our understanding of how intensive agriculture impacts on these communities, and on fauna-function relationships, lags far behind that of above-ground systems. This thesis investigates the impacts of intensive agriculture, and in particular fertiliser use, on relationships between soil invertebrate abundance, community structure and ecosystem function both above-ground and below-ground. The impacts of fertilisation, including organic and inorganic fertiliser regimes applied at different rates, and irrigation were quantified using realistic experimental field plots in temperate arable and plantation systems. Furthermore, the effects of a gradient of arable management intensity and the value of non-crop habitats in providing refugia for soil fauna were investigated using woodland-to-field transects. Impacts on soil invertebrates, including soil mites, springtails and nematodes, were quantified in terms of changes in abundance and shifts in community structure. Measures of ecosystem function included above-ground productivity, plant nutrient bioavailability and organic matter decomposition. Impacts of fertilisers were complex and varied between systems and faunal groups. Notably, we observed that inorganic fertiliser application reduced soil mite and nematode abundance when applied with irrigation in water-limited, sandy soils. In general, astigmatid mites responded less negatively, or even positively, to intensive management. We observed strong evidence of non-crop habitats providing refugia for soil fauna, and in particular poor dispersers, in intensive arable landscapes. This thesis advances our understanding of soil invertebrate ecology in intensively- managed agricultural systems. We discuss our findings in the context of the sustainable management of soils under a growing population, and suggest directions for future research. - vi - Table of Contents Acknowledgements .................................................................................................... iv Abstract ....................................................................................................................... v Table of Contents ....................................................................................................... vi List of Tables ............................................................................................................... x List of Figures ............................................................................................................ xi 1. General introduction ....................................................................................... 1 Abstract ...................................................................................................... 1 1.1 Soil-derived ecosystem services and soil natural capital ........................... 2 1.2 Soil fauna and their contribution to ecosystem services ............................ 3 1.3 Soil fauna and ecosystem disservices ....................................................... 11 1.4 Threats to soil fauna ................................................................................. 12 1.4.1 Agricultural intensification .......................................................... 13 1.4.1.1 Tillage .............................................................................. 14 1.4.1.2 Agrochemical use ............................................................. 16 1.4.2 Invasive species ............................................................................ 17 1.4.3 Climate change ............................................................................. 17 1.5 Research gaps ..........................................................................................
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    DIRECTEUR DE LA PUBLICATION / PUBLICATION DIRECTOR : Bruno David Président du Muséum national d’Histoire naturelle RÉDACTRICE EN CHEF / EDITOR-IN-CHIEF : Laure Desutter-Grandcolas ASSISTANTE DE RÉDACTION / ASSISTANT EDITOR : Anne Mabille ([email protected]) MISE EN PAGE / PAGE LAYOUT : Anne Mabille COMITÉ SCIENTIFIQUE / SCIENTIFIC BOARD : James Carpenter (AMNH, New York, États-Unis) Maria Marta Cigliano (Museo de La Plata, La Plata, Argentine) Henrik Enghoff (NHMD, Copenhague, Danemark) Rafael Marquez (CSIC, Madrid, Espagne) Peter Ng (University of Singapore) Jean-Yves Rasplus (INRA, Montferrier-sur-Lez, France) Jean-François Silvain (IRD, Gif-sur-Yvette, France) Wanda M. Weiner (Polish Academy of Sciences, Cracovie, Pologne) John Wenzel (The Ohio State University, Columbus, États-Unis) COUVERTURE / COVER : Habitus and color patterns of some species described in the article. Zoosystema est indexé dans / Zoosystema is indexed in: – Science Citation Index Expanded (SciSearch®) – ISI Alerting Services® – Current Contents® / Agriculture, Biology, and Environmental Sciences® – Scopus® Zoosystema est distribué en version électronique par / Zoosystema is distributed electronically by: – BioOne® (http://www.bioone.org) Les articles ainsi que les nouveautés nomenclaturales publiés dans Zoosystema sont référencés par / Articles and nomenclatural novelties published in Zoosystema are referenced by: – ZooBank® (http://zoobank.org) Zoosystema est une revue en flux continu publiée par les Publications scientifiques du Muséum, Paris / Zoosystema is a fast track journal published by the Museum Science Press, Paris Les Publications scientifiques du Muséum publient aussi / The Museum Science Press also publish: Adansonia, Geodiversitas, Anthropozoologica, European Journal of Taxonomy, Naturae, Cryptogamie sous-sections Algologie, Bryologie, Mycologie. Diffusion – Publications scientifiques Muséum national d’Histoire naturelle CP 41 – 57 rue Cuvier F-75231 Paris cedex 05 (France) Tél.