This electronic thesis or dissertation has been downloaded from Explore Bristol Research, http://research-information.bristol.ac.uk Author: Welsby, Holly J Title: Feeding the Ocean? A biological mediation of estuarine silicon General rights Access to the thesis is subject to the Creative Commons Attribution - NonCommercial-No Derivatives 4.0 International Public License. A copy of this may be found at https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode This license sets out your rights and the restrictions that apply to your access to the thesis so it is important you read this before proceeding. Take down policy Some pages of this thesis may have been removed for copyright restrictions prior to having it been deposited in Explore Bristol Research. 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Author: Supervisors: Holly Jo Welsby Doctor Katharine Hendry Doctor Rupert Perkins Professor Marian Yallop Professor Sandra Arndt A dissertation submitted to the University of Bristol in accordance with the requirements for award of the degree of Degree of Doctor of Philosophy in the Faculty of Science. School of Earth Sciences May 2019 Word count: 56,763 Abstract Riverine dissolved silicon (DSi) and biogenic silica (BSi) are altered along the estuarine gradient by several biological and abiological processes governed by physical forcings. An important area controlling silicon (Si) transport in estuaries, which is often over- looked, is the benthic diatom-dominated biofilm system on intertidal mudflats. Here, the hypertidal Severn Estuary, southwest UK has been used as a case study to improve our understanding of DSi and BSi transport in these benthic-dominated systems. Be- tween 2016 and 2018, ecological surveys were carried out along the River Severn, and its estuary and tributaries (Wye, Usk, Avon, and Cardiff Bay), alongside surveys of the benthic biofilms on the intertidal mudflats. A combination of high turbidity, lack of stratification, low nutrient concentrations and low residence times restricted phytoplankton development in the Severn and its tributaries. Low phytoplankton DSi uptake, land-use changes and groundwater supply, 30 contributed to the isotopically light river water (denoted by δ SiDSi: +0.61-1.05‰). River and tidal hydrodynamics drove spatio-temporal changes in dissolved constituents; the longitudinal profiles followed the classical view of dilution with downstream trans- port, resulting in low concentrations in the Bristol Channel. Despite other estuarine systems retaining DSi (global average of 20%), the hypertidal regime of the Severn Es- tuary coupled to the low pelagic uptake of DSi, prevented any significant DSi retention. Several sources of BSi into the estuary water column were identified. Siliceous phy- toplankton contributed to a small amount of the estuarine BSi budget, whilst riverine inputs of BSi (e.g. phytoliths), and most importantly, benthic-sourced BSi, influenced the spatio-temporal changes in estuarine BSi. Relatively high BSi concentrations were measured in the upper Severn Estuary (maximum of 14.9 mg/L), and accounted for over 66% of the total bioavailable Si present in the estuary, and were characterised by 30 isotopically heavy waters (δ SiDSi). It was hypothesised that the BSi originated from the diatom-dominated biofilms on the intertidal mudflats. The biofilms were found to be biomass-rich (173.6±24.7 µg/g dw. sed. chl a content) with high productivity (rel- ative electron transport rates of 155±13 rel. units), driven by their photoprotective adaptions (behavioural and photophysiological down-regulation) to these harsh inter- tidal environments. The biofilm organisms had a high potential to consume DSi and biomineralize BSi, despite the short emersion periods, and contributed to isotopically heavy mudflat water (+1.19-2.03 ‰), alongside abiological processes when biological activity was suppressed. The shear stress of the fast-flowing tidal currents would have exceeded the erosion thresholds of the biofilms, despite the biofilms exhibiting sediment biostabilization properties (total and colloidal-S carbohydrates). These tidal currents likely eroded and transported the sediment-polymer-diatom matrix, and thus BSi into the water column (maximum of 91.4 mg BSi/L), with SPM and BSi remaining tightly coupled in the near-bed suspension (fluid-mud layer) and the surf zone (biofloccula- tion). The combination of physical forcings (erosion, deposition, burial, dispersion and advection) reduced the BSi concentration in the surf zone (maximum 15.4 mg BSi/L). Here, a modified version of the one-dimensional reactive transport Carbon-Generic Estuarine Model has been applied as an alternative tool to disentangle the complex hydro-biogeochemical estuarine processes. Maximum erosion rates of sediment and eroded benthic BSi occurred in the river-estuarine transition zone as a function of es- tuarine convergence and tidal/fluvial dynamics. The simulations produced the upper ii Estuarine Turbidity Maximum (ETM) zone, with the location and turbidity concentra- tions in-line with previous published ETM values. These model outputs can be used to inform future sampling strategies especially in this zone. The first time-series datasets of DSi and BSi, as well as Si isotopes in the Severn are presented. These have improved our understanding of the complex processes governing Si transport in hypertidal, benthic-dominated estuaries, and improves our understanding of the importance of estuaries in the terrestrial Si export, which is key to decipher the global Si budget. Regarding the Severn, with the pressures of climate change and the need to find predictable, renewable energy on the rise, the development of tidal power in the Severn Estuary is almost inevitable. The vital role these biofilms play as a food source, in stabilizing sediment and as an essential component of the Severn's Si cycle, must be considered prior to these developments. iii Declaration I declare that the work in this dissertation was carried out in accordance with the re- quirements of the University's Regulations and Code of Practice for Research Degree Programmes and that it has not been submitted for any other academic award. Except where indicated by specific reference in the text, the work is the candidate's own work. Work done in collaboration with, or with the assistance of, others, is indicated as such. Any views expressed in the dissertation are those of the author. Signed ...................................................................... Date ........................................................................ iv To Dad. v Acknowledgements First, I would like to express my sincere gratitude to my supervisor Dr Kate Hendry. Since meeting Kate during my first year of my undergraduate at Cardiff University back in 2011, she has supported me on several projects including my integrated Masters dissertation, which led to this PhD at the University of Bristol. None of this would have been possible if it weren't for Kate. She helped secure the Tratman Scholarship that has allowed me to carry out this research, and over the last three years she has been very supporting through every aspect of my work. The past two years have been the most difficult of my life so far, and Kate has done her utmost to support me through these times; she has never given up on me and she is always enthusiastic and positive! Kate has given me many opportunities throughout my PhD, from which I have learnt new skills, and has helped me become a better researcher. She also encouraged networking and attending conferences; some of which have led to some of the best experiences of my life. Kate is without a doubt, one of the best supervisor a PhD student could wish for, and it has been a great privilege working with her. Secondly, I would like to sincerely thank Dr Rupert Perkins. I have also known Roo since my first year at Cardiff University. Not only has he given me valuable support throughout my undergraduate degree, his advice, guidance and patience throughout my PhD has been most helpful. Without Roo, I would never have been introduced to this field of work! Roo was also very kind to lend a lot of his equipment for this study. Thirdly, I would like to thank Prof. Sandra Arndt, my third supervisor, who introduced us to the reactive transport model applied in this thesis. I would like to thank her for her patience and continued help over the years, and for accommodating me at the University of Brussels. Fourthly, I would like to thank Prof. Marian Yallop for her kind and continued support over the course of the PhD. I have learnt new skills from Marian, and I am extremely grateful for her time measuring the mudflat samples for chlorophyll a content and carbohydrate concentrations. Accompanying these acknowledgements, I would like to thank everyone who assisted me during fieldwork. For those who helped on the research vessels, I'd like to thank Ian Fryett (skipper), Jen Pinnion, Scott Armstrong, Lucy Taylor and Dr Elaine Mawbery. I would also like to express my thanks to all who assisted me sampling the intertidal mudflats and the rivers; Leanne Staddon, Timothy Gregory, Frances Boreham, Edward Bunker, James Chen. A special thanks goes to Jolene Cook for her help sampling the mudflats and for her work in the laboratory. I would also like to thank two Biology undergraduate students, Kate Spence and Aidan Byrne, for their extensive help in the summer of 2017 sampling the intertidal mudflats and measuring samples in the labora- tory.