A D ia t o m -Ba se d M o d el t o M o n it o r T r o ph ic S t a t u s in L o w l a n d R iv e r s U sin g A r t ific ia l Su b st r a t a Thesis submitted for the degree of Doctor of Philosophy in the University of London by Benjamin John Goldsmith University College London 2002 (Submitted April 2000) ProQuest Number: U643959 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest U643959 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 A b st r a c t The aim of this thesis was to develop the methodologies required to sample diatoms from lowland rivers in southern England, and to use these techniques to establish a diatom-based model to assess trophic status. A number of different artificial and natural substrata were compared from four lowland river sites of contrasting nutrient chemistry to assess the most suitable means of obtaining representative, repeatable and diverse diatom assemblages. Natural substrata supported more variable diatom assemblages than the artificial substrata and could not be kept constant between all lowland river sites. Thus two artificial substrata were chosen for diatom sampling: rough ceramic tiles and frayed polyethylene rope. From a chemical survey of 115 lowland river sites, 61 were chosen which covered a wide phosphorus gradient (3-7530 pgL'^ FRP). From these sites the two artificial substrata were used to collect diatom samples, in order to develop two independent diatom training sets. Multivariate statistical techniques (PCA, DCA and CCA) were used to investigate the chemical relationships, species relationships and environmental-species interactions. From these analyses a strong, independent, relationship was identified between the diatom assemblages and the phosphorus concentration of the river sites. These data were demonstrated to be suitable for weighted average (WA) modelling. Weighted average regression and calibration techniques were used to generate diatom-based transfer functions, from which river phosphorus levels could be estimated with an acceptable level of error (r^ > 0.80, RMSEP < 0.30). When tested on independently derived diatom samples, the models performed well if the diatoms had been collected at the same time of year as the training set samples (autumn). Considerable seasonal variation was demonstrated within the diatom assemblages however, and the predictive power of the autumn-based models was greatly reduced when applied to samples collected at other times of the year. This thesis demonstrates that with carefully chosen sampling techniques, diatoms can be used as a reliable bio-monitoring tool for the assessment of phosphorus levels in lowland rivers. It is suggested that with the temporal and spatial extension of the training sets developed in this thesis, diatoms could provide a fast and effective means of assessing and monitoring the trophic status of lowland rivers. A cknowledgements This work was funded jointly by the University College London Graduate School and ENSIS Limited. Fieldwork support and equipment was funded by UCL Graduate School and the Department of Geography, UCL. I am indebted to many friends and colleagues who have contributed both personally and professionally to the completion of this research. In particular, I would like to thank Dr. Tim Allott, Prof. Rick Battarbee and Dr. Eileen Cox for their supervision, enthusiasm and encouragement, throughout this study. Their input and support has been invaluable. I am grateful to Dr. Roger Flower for inspiration and help in the field in the formative stages of this study. The idea of using rope as an artificial substratum is acknowledged to Roger. I would also like to thank Anna McQueen, Eileen Cox, Tim Allott, Ewan Shilland and Janet Hope for their assistance with fieldwork. The encouragement and help of Dr. Martyn Kelly was also greatly appreciated. Particular thanks go to Janet Hope. The laboratory analyses would not have been possible without Janet’s vast knowledge and experience. I am also grateful to Sarah James for assisting with cation analysis at Royal Holloway and Bedford New College, and to Tony Osborn for helping with anion analysis in the Department of Geological Sciences, UCL. Finally, I would like to thank all those members of the ECRC and Department of Geography at UCL , who have provided me with help, encouragement and numerous distractions from the path of true science: you know who you are. And to Felicity for companionship in the field, and constant support and patience during the writing of this thesis. Co n t e n t s T it l e P a g e 1 A b s t r a c t 2 A cknowledgements 3 Co n t e n t s 4 L is t o f F ig u r e s 9 L is t o f T a b l e s 14 L ist o f P l a t e s 18 R One Introduction 20 1.1 Background 20 1.2 Eutrophication - Sources and Effects 21 1.2.1 River Eutrophication - The Legal Position 23 1.3 River Monitoring 26 1.3.1 The Biological Component 27 1.3.2 Diatoms as Indicators of Water Quality 28 1.3.3 The use of Diatoms to Monitor Rivers 30 1.3.3.1 Diversity Measurements 31 1.3.3.2 Diatom Ecology and Water Quality Assessment 32 1.3.3.3 Diatom Indices 32 1.4 Sampling River Diatoms 34 1.4.1 The Diatom Assemblages 35 1.4.1.1 The Epipelon 35 1.4.1.2 The Epiphyton 36 1.4.1.3 The Epilithon 37 1.4.2 Artificial Substrata 38 1.4.3 Sample Representivity 40 1.4.3.1 The Accumulation of Dead Cells 41 1.4.3.2 The Effects of Grazing 42 1.4.3.3 Seasonality 43 1.4.3.4 The Physical Environment 44 1.5 Thesis Aims 44 1.6 Definition of Trophic Status 45 1.7 Thesis Outline 45 RTWO M e t h o d s 47 2.1 Study Region 47 2.2 Water Chemistry 50 2.2.1 Sample Collection 50 2.2.2 Field Analysis 51 pH 51 Total Alkalinity 52 Conductivity 52 Current Velocity 52 Temperature 53 2.2.3 Laboratory Analysis 53 Ortho-Phosphate (FRP) 54 Nitrate 54 Total Phosphorus and Total Nitrogen 55 Silica 55 Cation Analysis - ICP 56 Anion Analysis - IC 57 Contamination 57 2.3 Diatom Sampling 57 2.3.1 Natural Substratum Sampling 58 Cobbles 58 Sediment Samples 58 Submerged Macrophytes 59 2.3.2 Artificial Substratum Sampling 59 Clay Tiles 60 Rope 60 Glass and Perspex 61 2.4 Diatom Slide Preparation and Counting 61 2.4.1 Preparatory Methods 61 Epilithon and Tile Samples 62 Epiphyton and Rope Samples 62 Epipelic Samples 62 2.4.2 Quantitative Assessment 63 2.43 Slide Preparation 63 2.4.4 Archiving 63 2.4.5 Diatom Counting 64 2.4.6 Counting LiveiDead Cell Ratios 64 2.4.7 Diatom Identification 65 2.5 Data Storage, Manipulation and Analyses 66 :r T h r e e T h e S e l e c t io n o f a S u it a b l e Su b s t r a t u m f r o m w h ic h TO S a m p l e D ia t o m s 68 3.1 Introduction 68 3.2 Aims 68 3.3 Methods 69 3.3.1 Site Selection 69 3.3.2 Water Sampling 72 3.3.3 Diatom Sampling 73 3.4 Results 75 3.4.1 Water Chemistry 75 3.4.2 Diatom Samples 75 3.4.3 Between-Site Species Variation 83 3.4.3.1 Variance Partitioning 86 3.4.4 Within-Site Variation 88 3.4.4.1 Alton 88 3.4.4.2 Hawbridge 90 3.4.4.3 The Elstead Sites 92 3.4.5 Within Substratum Variation 93 3.4.6 Diatom Diversity 95 3.4.7 Dead Cells as a Potential Source of Error 97 3.5 Discussion 98 3.5.1 The Epipelon 99 3.5.2 The Epiphyton 99 3.5.3 The Epilithon 100 3.5.4 Rope 101 3.5.5 Smooth Tile 101 3.5.6 Rough Tile 102 3.5.7 Dead Cells 102 3.6 Conclusions 103 :r F o u r T r a in in g S e t s - S it e s , S p e c ie s a n d E n v ir o n m e n t 104 4.1 Introduction 104 4.2 Aims 105 4.3 Methods 105 4.3.1 Site Selection 105 4.3.2 Diatom Sampling 107 4.3.3 Water Sampling 109 4.3.4 Data Analysis 109 4.4 Results 111 4.4.1 Site Selection 111 4.4.2 Sample Collection 114 Presence of Natural Epilithon 115 4.4.3 Chemistry 115 4.4.3.1 Rope Training Set Chemistry 118 Principal Components Analysis (PCA) 119 4.4.3.2 Tile Training Set Chemistry 123 Principal Components Analysis (PCA) 124 4.4.4 Diatom Assemblages 127 4.4.4.1 Rope Training Set 127 Diatom Species Occurrence and Abundance 127 Detrended Correspondence Analysis of the Rope Species Data 129 4.4.4.2 Tile Training Set 133 Diatom Species Occurrence and Abundance (Tile) 135 Detrended Correspondence Analysis of the Tile Species Data 136 4.4.5 Direct Species - Environment Relationships 139 4.4.5.1 Species Relationships with TP and Alkalinity 139 Rope Training Set 139 Tile Training set 142 4.4.5.2 Canonical Correspondence Analysis (CCA) 144 Rope Training Set 145 Forward selection of environmental variables 149 Tile Training Set 150 Forward selection of environmental variables 153 4.5 Discussion 155 4.5.1 Site Selection 155 4.5.2 Sample Collection 156 4.5.3 Environmental Relationships 156 Phosphorus 157 Alkalinity 158 pH 158 Nitrate 159 Silica 159 Conductivity and Ionic Composition 159 Flow 160 Overview 160 4.5.4 Diatom Assemblages 161 Species Diversity 161 Rope Training Set 162 Tile Training Set 164 4.5.5 Direct Species - Environment Relationships 165 Rope Training Set 166 Tile Training Set 168 4.5.6 The Suitability of River Diatoms for Modelling Phosphorus 169 4.6 Conclusions and Summary 172 Ch a p t e r F iv e The Development of Diatom-Based M odels for the Assessment of Trophic Status in Lowland Rivers 174 5.1 Introduction 174 5.2 Aims 174 5.3 The Theory of Weighted Averaging Methods 175 5.3.1 Weighted Averaging (WA) 175 5.3.2 Weighted Averaging - Partial Least Squares (WA-PLS) 177 5.4 Methods 178 5.5 Results 180 5.5.1 Rope Training Set Data 180 TP 181 FRP 185 5.5.2 Tile Training Set Data 192 TP 193 FRP 196 5.5.3 Comparison of the Models 201 5.5.4 Indicator Species: WA Optima and Species Distributions 205 Rope 206 Tile 220 5.6 Discussion 235 5.6.1 Model Selection 235 5.6.2 Outlier Samples 238 5.6.3 Indicator Species 241 5.6.4.