The Abundance and Diversity of Small Mammals and Birds in Mature Crops
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The Abundance and diversity of small mammals and birds in mature crops of the perennial grasses Miscanthus x giganteus and Phalaris arundinacea grown for biomass energy Susan Jennifer Clapham October 2011 Thesis submitted for the degree of Doctor of Philosophy, Cardiff School of Biosciences, Cardiff University Declarations & Statements DECLARATION This work has not previously been accepted in substance for any degree and is not concurrently submitted in candidature for any degree. Signed ………………………………………… (candidate) Date: 31 October 2011 STATEMENT 1 This thesis is being submitted in partial fulfilment of the requirements for the degree of PhD. Signed ……………………………………..……(candidate) Date: 31 October 2011 STATEMENT 2 This thesis is the result of my own independent work/investigation, except where otherwise stated. Other sources are acknowledged by explicit references. Signed ………………………………………… (candidate) Date: 31 October 2011 STATEMENT 3 I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loan, and for the title and summary to be made available to outside organisations. Signed ………………………………………… (candidate) Date: 31 October 2011 STATEMENT 4: PREVIOUSLY APPROVED BAR ON ACCESS I hereby give consent for my thesis, if accepted, to be available for photocopying and for inter-library loans after expiry of a bar on access previously approved by the Graduate Development Committee. Signed ………………………………………… (candidate) Date: 31 October 2011 Acknowledgements Many thanks to the following people who made this thesis possible: Paul Ratcliffe and Pembrokeshire Bioenergy for use of the biomass and maize crops at site ‘N’. Richard Lewis, Clerkenhill Farm, Slebech for access to the barley comparison field at site ‘N’. Peter Davenport, John Amos, Richard Collins and the Lugg Valley Growers for use of the crops at site ‘HM’. Aldwyn Clarke, ADAS for managing site ‘PP’. Cardiff University and the Llysdinam Estate for the use of site ‘LL’. Geoffrey Phillips and the keepers at the Slebech Estate for information on species seen in the crops and permission to collect barn owl pellets from their buildings. Dr Roger Trout and Dr Amanda Lloyd for advice on handling and marking harvest mice. Bob and Annie Haycock for information on Pembrokeshire small mammal records. Derek Crawley for information on and photos of harvest mouse nests in Miscanthus in Staffordshire. Dr Rachel Smith, Dr Kerry Murton and Dr Danni Fry for proving that it was possible to complete and survive a PhD studentship. Emily Howe, Kate McCrum, Helen Pitt, Alexandria Hale and Lauren Preston-Mafham for spending many unsocial, wet, cold, midge-ridden hours assisting with fieldwork. Matthew Postles for his many weeks of mind-numbing invertebrate identification and counts. My parents and family for quietly supporting my endeavours. The late Bernard and Lilian Heald for sharing their love of the natural world with their granddaughter, and Geoff Liles for his contagious enthusiasm for wildlife. Dr Clare Benskin, Annabel Rice and Parveen Bruce for being the most wonderful and supportive friends. Llysdinam Charitable Trust and Cardiff University School of Biosciences for funding. Dr Fred Slater and Dr Rob Thomas for guiding the work and the writing in the right direction. And finally to Mr BG Jenkins for telling an 11 year old child that she would be a failure in life. I hope I’ve finally proved you wrong. S.J. Clapham ii Thesis Summary Low-carbon energy production is potentially a major method of reducing greenhouse gas emissions and anthropogenic climate change. In the UK, tall perennial grass crops show potential as “biomass crops”, providing renewable energy sources with a low net carbon cost. However, conversion of large areas of farmland to biomass production would constitute a major land-use change with possible negative effects on native biodiversity, particularly as some biomass crop types are not native to the UK. The aim of this thesis was to assess biological diversity within mature (>3 years old) crops of non-native Miscanthus x giganteus and native Phalaris arundinacea. Biomass crop structural characteristics and management regimes were recorded, and their biodiversity was surveyed with particular reference to birds and small mammals in comparison with adjacent land uses. Food resources in terms of non- crop vegetation and invertebrates were also recorded. Live-trapping revealed eight species of small mammal in the study crops, including a conservation priority species, the harvest mouse Micromys minutus, which was most abundant in Phalaris crops. Phalaris also contained the highest small mammal diversity, but the field headlands held the greatest small mammal abundance. Trapping and direct observations revealed a higher abundance and diversity of birds in the Miscanthus crops in comparison with Phalaris. Most of the bird species found in biomass crops were associated with woodland or reedbed rather than farmland habitat. Phalaris crops had a higher percentage of ground cover of the crop itself and non- crop vegetation, whereas Miscanthus fields had greater cover of crop litter. Miscanthus crops contained fewer invertebrates than Phalaris or the field headlands. Management specific to biomass grass crops involves harvest in spring, thus providing winter habitat of importance to birds and small mammals. The crop fields also provide a refuge for invertebrates and non-crop vegetation and overall, supported high levels of biodiversity. S.J. Clapham iii Table of Contents Page Declarations i Acknowledgements ii Thesis summary iii Contents iv List of figures xiii List of tables xvi Species lists xxi Chapter 1 General introduction 1 Abstract 2 1.1 Biomass crops as mitigation for anthropogenic climate 3 change 1.1.1 Atmospheric greenhouse gases 3 1.1.2 Temperature increases 4 1.1.3 Mitigation 4 1.1.4 Biomass fuel 5 1.1.5 Biomass energy production as a carbon emission reduction 5 strategy 1.1.6 Microalgae and cyanobacteria as biofuels 7 1.1.7 Second generation processes for producing energy from 7 biomass 1.1.8 Perennial grass types 8 1.1.9 Markets for biomass 8 1.1.10 Properties of good biomass for combustion 9 1.2 Miscanthus 9 1.2.1 Miscanthus - description and agronomy 9 1.2.2 Fertilizers, productivity and longevity 12 1.2.3 Timing of Miscanthus harvest 14 1.3 Phalaris 16 1.3.1 Phalaris description and agronomy 16 1.3.2 Fertilizers, productivity and longevity 19 1.3.3 Timing of harvest 19 1.4 Considerations for both grasses 20 1.4.1 Stem content 20 1.4.2 Lodging 20 S.J. Clapham iv 1.4.3 Carbon balance and future climate scenarios 22 1.4.4 Invasiveness 24 1.4.5 Economics and farmer attitudes 25 1.4.6 Pests and diseases 26 1.5 Other uses for perennial grass crops 27 1.5.1 Animal bedding 27 1.5.2 Animal fodder 27 1.5.3 Phytoremediation 27 1.5.4 Phytochemicals 28 1.6 Biodiversity and biomass crops: an introduction 28 1.6.1 Biodiversity and land use change 28 1.6.2 Impact on wildlife of biomass grass crops 29 1.7 Aims of this thesis 30 1.8 Introduction to the field sites 31 1.8.1 Llysdinam 31 1.8.2 Narberth 33 1.8.3 Pwllpeiran 35 1.8.4 Hinton Manor 37 1.9 References 39 Chapter 2 Non-crop vegetation and invertebrates 46 as food resources in biomass Grass crops Abstract 47 2.1 Introduction 48 2.1.1 Weeds and invertebrates 48 2.1.2 Weeds and vertebrates 50 2.1.3 Invertebrates as a food resource 52 2.1.4 Management effects and agricultural intensification 54 2.1.5 Agri-environment schemes 55 2.1.6 Weed and arthropod diversity in biomass crops 56 2.1.7 Assessing abundance 58 Pitfall trapping 58 Vacuum sampling 60 Swish-net / sweep net 60 Pan traps 61 Sticky traps 61 2.1.8 Aims 62 S.J. Clapham v 2.2 Materials and methods 63 2.2.1 Invertebrates 63 Pitfall traps 63 Vortis suction sampling 64 Yellow pan traps 65 Sweep netting 65 Sticky traps 66 Butterflies 66 2.2.2 Identification and counts 67 2.2.3 Data analysis 67 Presence and counts 67 2.2.4 Vegetation 68 2.2.5 Data analysis 69 2.3 Results 70 2.3.1 Invertebrates 70 2.3.2 Habitat differences 72 2.3.3 Invertebrate families 74 2.3.4 Size classes 77 2.3.5 Distance into the crop 78 2.3.6 Seasonal changes 78 2.3.7 Sticky traps and height in Miscanthus 79 2.3.8 Diversity indices 80 2.3.9 Lepidoptera 81 2.3.10 Vegetation 82 2.3.11 Crop height 84 2.3.12 Non-crop vegetation diversity 86 2.3.13 Distance into crops 86 2.4 Discussion 87 2.4.1 Invertebrate composition 87 2.4.2 Invertebrates unique to crop habitat 89 2.4.3 Beneficial invertebrates in the crops 90 2.4.4 Invertebrates as food resources 94 2.4.5 Weed abundance 96 2.4.6 Invertebrate diversity and weed diversity 97 2.4.7 Weed and invertebrate associations 98 2.4.8 Weeds as food resources for vertebrates 102 2.4.9 Limitations of survey methodology 103 2.4.10 General conclusions 105 2.5 References 107 2.5.1 Resources used for the identification of invertebrates 115 S.J. Clapham vi Chapter 3 Biomass grass crops as new agricultural 117 habitat for small mammals Abstract 118 3.1 Introduction 119 3.1.1 Small mammal species 119 3.1.2 Distribution, abundance and diet 119 Muridae 119 Cricetidae 122 Soricidae 123 3.1.3 Population dynamics 126 3.1.4 Predators 127 Birds 127 Reptiles and amphibians 128 Mammals 128 3.1.5 Feeding ecology on agricultural land 128 3.1.6 Agri-environment schemes, set-aside land and new 129 woodland subsidies 3.1.7 Arable land 132 3.1.8 Hedges and woodlands 133 3.1.9 Grazing and agricultural practices 134 3.1.10 Energy crops 135 3.1.11 Aims 137 3.2 Materials and methods 138 3.2.1 (a) Year 1 surveys and sites 138 3.2.1 (b) Live trapping 138 3.2.2 (a) Year 2 surveys and site 140 3.2.2 (b) Live trapping 141 3.2.3 Vegetation and crop characteristics 143 3.2.4 Data analysis 144 3.2.5 Abbreviations 145 3.3 Results 146 3.3.1 Small mammal captures 146 3.3.2 Crop preference 149 Year 1 149 Year 2 151 3.3.3 Edge effect 155 3.3.4 Seasonal changes in small mammal assemblage 156 3.3.5 (a) Diversity indices 159 3.3.5 (b) Seasonal diversity changes 160 S.J.