The Abundance and diversity of small mammals and birds in mature crops of the perennial grasses

360 Pages·2012·5.3 MB·English

by  Jenny Clapham

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. Clapham vii
3.3.6 Crop management effects 163
3.3.7 Crop characteristics 165
3.3.8 Interspecific interactions 168
3.3.9 Feeding ecology 169
3.3.10 Mortalities 171
3.3.11 Multiple mammal captures, and non-mammal captures 171

3.4 Discussion 173
3.4.1 Trapping techniques 173
3.4.2 Abundance of individual small mammal species and crop 175
preference
3.4.3 Small mammal species diversity 177
3.4.4 Edge effect 177
3.4.5 Feeding ecology 178
3.4.6 Crop height and management 178
3.4.7 Seasonal effects 180
3.4.8 Relationship with other crop characteristics 182
3.4.9 Biomass crops in comparison with other agricultural land 183
uses
3.4.10 Arable crop comparison plots 184
3.4.11 Comparisons with woody biomass crops 185
3.4.12 Conclusions 185

3.5 References 187

Chapter 4

The harvest mouse Micromys minutus 194
in biomass grass crops

Abstract 195
4.1 Introduction 196
4.1.1 Post-glacial history and distribution of the harvest mouse 196
4.1.2 Morphology 197
4.1.3 Life-history and breeding biology 197
4.1.4 Feeding ecology 199
4.1.5 Habitat use 199
4.1.6 Nest-building habitat selection 200
4.1.7 Predation, competition and survival 202
4.1.8 Effects of land management 204
4.1.9 Population status 206
4.1.10 Benefits of harvest mouse presence in agricultural crops 211
4.1.11 Aims of the study 211

4.2 Materials and methods
213

S.J. Clapham viii
4.2.1 Traps 213
4.2.2 Transects 214
4.2.3 Biometric measurements and marking for individual 217
identification
4.2.4 Additional traps 219
4.2.5 Additional surveys 220
Trapping 220
Nest searches 220
Barn owl pellet analysis 221
Vegetation characteristics 222
4.2.6 Data analysis 222

4.3 Results 224
4.3.1 Number of small mammal captures 224
4.3.2 Crop preference and evidence of breeding 225
4.3.3 Distance into the crops 227
4.3.4 Times of day trapped 228
4.3.5 Recaptures 229
4.3.6 Body weight 231
4.3.7 Seasonal differences in captures 233
4.3.8 Captures at different heights 234
4.3.9 Crop characteristics and harvest mouse abundance 237
4.3.10 Barn owl pellets 237

4.4 Discussion 240
4.4.1 Presence of harvest mice and nests within the crops 240
4.4.2 Distance into crop 243
4.4.3 Activity throughout the day 244
4.4.4 Recaptures 244
4.4.5 Body weight variations 247
4.4.6 Seasonal differences in captures 249
4.4.7 Captures at different heights 252
4.4.8 Crop characteristics 253
4.4.9 Barn owl pellets 253
4.4.10 Context within Wales 255
4.4.11 Conclusions 256

4.5 References 257

S.J. Clapham ix