A biomonitoring tool to identify and quantify the impacts of fine sediment in river and stream ecosystems Matt D. Turley A thesis submitted in partial fulfilment of the requirements of the University of Brighton for the degree of Doctor of Philosophy October 2017 Abstract In rivers and streams, fine sediment pollution is one of the most commonly attributed causes of ecological degradation. As fine sediment is also an important natural component of these ecosystems, and is variable both temporally and spatially, setting environmental targets and using conventional monitoring to determine where fine sediment is causing ecological degradation, is a complex challenge. An alternative approach is the use of biomonitoring tools, which utilise biota to gauge and track changes in the environment. This thesis examines the current state of sediment- biomonitoring, considers the numerous theoretical and methodological decisions made during tool development, and applies a best practice approach to the development and testing of a sediment-specific tool. An existing biological index, which utilises knowledge of biological and ecological traits, is used as a basis for this development, following an evaluation of its performance over 835 minimally impacted temperate river and stream sites. The index is further developed using empirical data to assign indicator weights to individual taxa. The resulting index, the Empirically-weighted Proportion of Sediment-sensitive Invertebrates (E-PSI) index had moderate to strong correlations with fine sediment in independent test datasets of minimally (n = 84) (family-level: rs = -0.72; mixed-level: rs = -0.70; p < 0.01) and agriculturally impacted sites (n = 754) (family-level: rs = -0.68, p < 0.01). The E-PSI index has retained a biological basis, is easily integrated into regulatory agency protocols, and can be applied retrospectively to historic datasets. Despite the improved performance, a high amount of variation was observed between E-PSI and fine sediment cover. This is likely the result of the presence of multiple pressures, uncertainties concerning sediment-biota interactions, and the relatively low precision of sediment quantification techniques. Due to the prevalence of freshwater non-native invasive species, the effects of North American signal crayfish (Pacifastacus leniusculus) invasions on sediment- iii biomonitoring and fine sediment are also investigated. Additionally, given the subjective nature and lack of representativeness of many existing sediment quantification techniques, a novel, more objective, verifiable, and non-destructive method is developed and presented as “proof of concept”. This thesis contributes significantly to the literature concerning biomonitoring tool development and testing, and has resulted in a sediment-specific index that has a stronger correlation with its specific pressure, than the average biomonitoring tool used throughout Europe. The E-PSI index can be used alongside a suite of other biomonitoring tools, to identify the most likely causes of ecological degradation, and inform more targeted monitoring. iv Table of contents Abstract………………….……………………………………………………………….……..iii Table of Contents….. .................................................................................................... v List of Figures…………………………………………………………………………….…...xiii List of Tables…………….……………………………………………………………...…….xvi List of Equations ....................................................................................................... xviii List of Supplementary Material ................................................................................. xviii Acknowledgements ..................................................................................................... xix Abbreviations and acronyms ....................................................................................... xx Author’s Declaration ................................................................................................... xxi Chapter 1 Introduction ........................................................................................... 1 1.1 Background .................................................................................................. 1 1.1.1 Sources of fine sediment ......................................................................... 2 1.1.2 Impacts of elevated fine sediment loads .................................................. 5 1.1.3 Ecosystem monitoring and management ................................................. 6 1.1.3.1 Conventional monitoring of fine sediment ............................................. 8 1.1.3.2 Biomonitoring ....................................................................................... 9 1.2 Thesis aim and objectives ......................................................................... 10 1.2.1 Aim ........................................................................................................ 10 1.2.2 Objectives .............................................................................................. 11 Chapter 2 Biomonitoring of rivers and streams ................................................. 13 2.1 Introduction ................................................................................................ 14 2.2 The biomonitoring approach ..................................................................... 15 2.2.1 Developing a biomonitoring tool ............................................................. 19 2.2.2 Biomonitoring and ecological theory ...................................................... 21 2.2.3 Biotic elements used for biomonitoring tools .......................................... 21 2.2.3.1 Biomonitoring approaches using macroinvertebrates ......................... 23 v 2.2.3.2 Biomonitoring approaches using fish .................................................. 24 2.2.3.3 Biomonitoring using diatoms .............................................................. 25 2.2.4 Reference-based approach in the UK – RIVPACS/RICT ....................... 26 2.2.5 Sampling procedures ............................................................................. 29 2.2.6 Taxonomy-based indices ....................................................................... 30 2.2.6.1 Taxonomic resolution of biomonitoring tools ...................................... 30 2.2.7 Trait-based indices ................................................................................ 32 2.2.8 Pressure-specific biomonitoring tools .................................................... 35 2.2.9 Confounding pressures .......................................................................... 36 2.2.10 Sediment-specific biomonitoring ............................................................ 41 2.2.10.1 Sediment-specific indices developed globally..................................... 42 2.2.11 Uncertainties ......................................................................................... 47 2.3 Conclusion .................................................................................................. 48 Chapter 3 Evaluating the performance of sediment-specific biomonitoring tools across a wide range of temperate river and stream ecosystems ................ 51 3.1 Abstract ....................................................................................................... 51 3.2 Introduction ................................................................................................ 52 3.2.1 Aims and objectives ............................................................................... 54 3.2.2 Ephemeroptera, Plecoptera and Trichoptera metrics ............................. 55 3.2.3 The Proportion of Sediment-sensitive Invertebrates (PSI) index ............ 55 3.2.3.1 Evaluating the theoretical basis and development of the PSI index .... 56 3.2.3.2 Uncertainties associated with the PSI index ....................................... 58 3.3 Methods ....................................................................................................... 59 3.3.1 Data ....................................................................................................... 59 3.3.1.1 Macroinvertebrate data ...................................................................... 60 3.3.1.2 Fine sediment data ............................................................................ 61 3.3.2 Statistical analyses ................................................................................ 62 vi 3.4 Results ........................................................................................................ 63 3.4.1 Biological indices and fine sediment metrics .......................................... 63 3.4.2 Taxonomic resolution............................................................................. 66 3.4.3 Discrimination ability of the best performing index ................................. 66 3.4.4 Comparisons between the biological indices ......................................... 67 3.5 Discussion .................................................................................................. 69 3.5.1 The ability of the best-performing index to indicate fine sediment conditions ............................................................................................................ 69 3.5.2 Effect of taxonomic resolution on the performance of the index ............. 71 3.5.3 Effect of substratum particle size on the performance of the index ........ 72 3.5.4 Independence