Aquatic Parasite Information – a Database on Parasites of Freshwater and Brackish Fish in the ...

272 Pages·2017·6.09 MB·English

by  Bernice Brewster

Aquatic Parasite Information – a Database on Parasites of
Freshwater and Brackish Fish in the United Kingdom

A thesis submitted to Kingston University London
for the Degree of Doctor of Philosophy

by

Bernice BREWSTER
BSc (Hons.) London
June 2016
Declaration
This thesis is being submitted in partial fulfilment of the requirements of Kingston
University, London for the award of Doctor of Philosophy.
I confirm that all work included in this thesis was undertaken by myself and is the result
of my own research and all sources of information have been acknowledged.

Bernice Brewster
2nd June 2016

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Abstract

A checklist of parasites of freshwater fish in the UK is an important source of
information concerning hosts and their distribution for all aspects of scientific research.
An interactive, electronic, web-based database, Aquatic Parasite Information has
been designed, incorporating all freshwater and brackish species of fish, parasites,
taxonomy, synonyms, authors and associated hosts, together with records for their
distribution. One of the key features of Aquatic Parasite Information is this checklist
can be updated.
Interrogation of Aquatic Parasite Information has revealed that some parasites of
freshwater and brackish species of fish, such as the unicellular groups or those
metazoans that are difficult to identify using morphological characters, are under
reported. Aquatic Parasite Information identified the monogenean family
Dactylogyridae and the cestodes infecting UK freshwater fish as under-represented
groups, owing to the difficulties identifying them morphologically. Both the
Dactylogyridae and cestodes have implications for pathology, outbreaks of disease
and morbidity in freshwater fish in the UK, therefore accurate identification is critical.
Studies were undertaken using both standard morphological techniques of histology
and molecular techniques to identify dactylogyrid species and tapeworms commonly
found parasitizing fish in the UK. Morphological studies demonstrated that histological
processes could lead to distortion of the specimens and permanent mounting may
affect the orientation which may obscure vital characters. Molecular techniques were
successfully employed using ITS1 for the Dactylogyridae and cox1 and r28s for the
cestodes, to demonstrate genetic variability for the interspecific identification of
species. Histology, scanning electron microscopy and molecular techniques have also
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identified an Atractolytocestus sp. tapeworm, parasitizing carp in the UK, as a
potentially new species.
Analysis of parasite records extracted from Aquatic Parasite Information has
implicated freshwater fishery management policies as impacting on the dissemination
and distribution of parasites, resulting in the spread of some species and decline of
others.

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Acknowledgments
I gratefully acknowledge the support, guidance and dedication of my Supervisors Dr
Ruth Kirk, Dr Scott Lawton, Dr James Denholm-Price, the late Professor Angela
Russell-Davies and Dr Chris Williams. I am indebted to Mr Sivasankara Desikan for
designing the front-ends for Aquatic Parasite Information, enabling the content of the
database to be accessible on the internet and for his patience throughout the process.
I am also indebted to Amy Reading and Nigel Hewlett, Environment Agency, National
Fisheries Laboratory for providing me with cestode specimens for molecular work and
data relating to fish movements.

This project could never have taken place without all the fish traders and fish farmers
who have unknowingly contributed by delivering samples of fish for examination for
movement consent.

Finally, a special thanks to my family and friends for putting up with the fish stuff, my
constant mess and chaos and also to Finzi who has had to wait ‘forever’, every day
for a walk.

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Table of Contents

Declaration i
Abstract ii
Acknowledgements iv
Table of contents v
List of figures x
List of tables xv

Chapter 1. General Introduction and rationale for the project
1.1 Current legislation and regulations 1
1.2 Importation of freshwater fish 4
1.2.1 Aquaculture 4
1.2.2 Ornamental market 5
1.2.3 Recreational angling 8
1.3 Introduction of novel parasites 10
1.4 Aquaculture in the UK 12
1.5 Changing populations of fish predators 16
1.6 Aquatic Parasite Information 19
1.6.1 Database design 20
1.6.2 Interrogating the database 21
1.7 Morphological and molecular study of species of Dactylogyrus
(Monogenea; Dactylogyroidea) associated with coarse fish 21
1.8 Cestodes of freshwater fish in the UK 22
1.9 Identification of Atractolytocestus species (Cestoda: 23
Caryophyllidea; Lytocestidae) infecting common carp
(Cyprinus carpio) in the UK

1.10 Concluding remarks 24
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1.11 Aims and Objectives 26
Chapter 2. Aquatic Parasite Information database
2.1 Introduction 27
2.2 Database software design 29
2.3 Data sources 31
2.4 Data overview 32
2.5 Concluding remarks 49

Chapter 3. Aquatic Parasite Information Database, Category 2 parasite distribution
3.1 Introduction 51
3.2 Methods 57
3.3 Results and discussion 58
3.4 Concluding remarks 93

Chapter 4. Morphological and molecular study of species of Dactylogyrus
(Monogenea: Dactylogyroidea) associated with coarse fish
4.1 Introduction 94
4.2 Materials and methods 98
4.2.1 Collection of dactylogyrids from UK freshwater fish 98
4.2.2 Preparation of Dactylogyrus specimens for 98
morphological study

4.2.3 DNA extraction and PCR amplification 101

4.2.4 Sequence assembly, initial identification and 102
phylogenetics

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4.2.5 Markers for species identification and inter- and 104
intraspecies molecular diversity

4.3 Results
4.3.1 Morphometric analysis of Dactylogyrus species from 105
carp, bream, roach and tench

4.3.2 Morphological description of Dactylogyrus species 105
4.3.3 Initial identification of sequences using BLASTn 114
4.3.4 Phylogenetic reconstruction 115
4.3.5 Diversity and phylogenetic power of ITS1 in resolving 120
Dactylogyrus taxonomy

4.4 Discussion of results 124
4.5 Concluding remarks 130

Chapter 5. Cestodes of freshwater fish in the UK
5.1 Introduction 132
5.2 Materials and methods 133
5.2.1 Collection of cestodes from UK freshwater fish 133
5.2.2 Preparation of cestodes for morphological study 134
5.2.3 DNA extraction and PCR amplification 135
5.2.4 Assembly of Caryophyllidea and Bothriocephalidea 136
cox1 and r28s rDNA fragments, molecular identification of
species and phylogenetic analysis
5.2.5 Markers for species identification, inter- and 141
intra-species molecular diversity

5.3 Results 141

5.3.1 Morphology of cestodes identified from UK species 141
of freshwater fish
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5.3.2 Caryophyllidea morphology 142

5.3.3 Bothriocephalidea morphology 148

5.3.4 Sequence assembly and initial comparison of 149
species and phylogenetics based on Caryophyllidea
cox1, r28s and Bothriocephalidea r28s

5.3.5 Caryophyllidea phylogeny 152

5.3.6 Bothriocephalidea phylogeny 153

5.3.7 Diversity and phylogenetic power of cox1 and 164
r28s in resolving Caryophyllidea and
Bothriocephalidea taxonomy

5.4 Discussion 171

5.4.1 Caryophyllidea 171

5.4.2 Freshwater Bothriocephalidea 175

5.5. Concluding Remarks 177

Chapter 6. Identification of Atractolytocestus (Cestoda: Caryophyllidea: Lytocestidae)
species parasitizing common carp (Cyprinus carpio) in the United Kingdom

6.1 Introduction 179

6.2 Materials and methods 182

6.2.1 Histological preparation of Atractolytocestus species 183

6.2.2 Preparation of Atractolytocestus for scanning electron 183
microscopy

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6.2.3 DNA extraction and amplification 184

6.2.4 Assembly of Atractolytocestus cox1, molecular 185
identification of species and phylogenetic analysis

6.2.5 Intra-species molecular diversity 186

6.3 Results 186

6.3.1 Morphology of Atractolytocestus huronensis and 186
Atractolytocestus sp. from Pease Pottage,
West Sussex

6.3.2 Initial comparison of Atractolytocestus sequences 190
and phylogenetics based on cox1

6.3.3 Intraspecific molecular variance of Atractolytocestus 191
cox1 sequences

6.4 Discussion 195

6.5 Concluding remarks 199

Chapter 7. Summary 200

Appendix 1. Database software design 207

Appendix 2. Fish hosts and associated parasites 212

Appendix 3. Freshwater fish parasite distribution in the UK 221

References 240

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