Modelling of Intertidal Floodplains for Enhanced Estuarine Transport and Decay of Faecal Indicator Organisms from a Diffuse Source

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Modelling of Intertidal Floodplains for Enhanced Estuarine Transport and Decay of Faecal Indicator Organisms from a Diffuse Source Modelling of intertidal floodplains for enhanced estuarine transport and decay of faecal indicator organisms from a diffuse source A thesis submitted to Cardiff University in candidature for the degree of Doctor of Philosophy 1st October 2019 Amyrhul A bu Baka r Hydro -environmental Research Centre School of Engineering, Cardiff University, Cardiff CF24 3AA, U .K. Abstract The noncompliance of microbiological quality to the standards of the EU Water Framework Directive at shellfish harvesting waters in the UK has become a serious threat to human health. The infected filter -feeding shellfish by enteric bacteria or viruses from these waters is major to the spreading of foodborne diseases as humans consumed them raw or undercooked. Although the quality of effluents fr om the wastewater treatment works has been improved significantly, diffuse source of pathogens from urban and agricultural settings remained as the reason to the microbiological noncompliance. The exploitation of natural wetlands along with poor management practices at catchments delivered the overloading of faecal contaminants from sources into the receiving water. In this study, a developed hydro -environmental model is novel in contribut ing to the understanding of the microbial behaviour on the implicit response to the complex estuarine environment from the perspective of their morphological characteristics . Besides, the extended modelling domain at intertidal floodplains is novel in contribut ing to the representation of the tidal creek connectivity with the sub -mesh scale design based on the hydrological characteristic of the complex floodplain topography . Furthermore, t he modelled of FIO transport and decay from intertidal marshlands is novel in contributing to the inclusion of the diffuse source with th e integration to the release -kinetic model and based on an active source at the wetting and drying boundary . The hydrodynamic calibration at several sites resulted in an optimum Manning’s n of 0.025. The successful integration between the bathymetric and topographic data at intertidal floodplains resulted in a significant improvement for the tidal circulation within the study area. The sensitivity analysis on the diffusive transport has suggested the decrease in the tracer diffusivity with the increase in the mesh resolution, with the concentration gradient has increased with the decrease of the former parameter. The sensitivity analysis on the bottom roughness has suggested the increase in the tracer retention at floodplains with the increase in the roughn ess during low tides, with the concentration in subtidal channels was less sensitive to the roughness changes during high tides. The sensitivity analysis on the microbial kinetic has suggested that MS2 coliphage experienced the biphasic decay in the estuar ine environment, with the T 90 value ranged at 1 hour and from 50 to 125 hours for the first and second components decay respectively. The sensitivity analysis on the FIOs transport from the diffuse i source has suggested the increase in the spreading area an d the flush -out mass with the decrease in , with the earlier release resulted in the higher FIOs concentration at shellfish harvesting waters for the case of the conservative mass and vice versa for the case of the decay. The FIOs distribut ion has indicated that shellfishes near tidal creeks of the adjacent marshland were highly exposed to the faecal contamination as compared at the far -field sites. Keywords: Hydrodynamic modelling, intertidal floodplains, pollutant transport, microbial tracer, biphasic decay, faecal indicator organisms, diffuse source, release kinetic, shellfish contamination ii Acknowledg ement There are a great number of individual s and organization s that have contributed to the completion of this PhD thesis. In particular, I would like to thank my research supervisors, Dr Reza Ahmadian and Professor Roger A . Falconer for their initial ideas, continued support and constructive criticism throughout my research activit y at Cardiff University . I would also like to thank the official sponsor, Majlis Amanah Rakyat (Malaysia) for the financial support through the scheme of postgraduate sponsorship besides the Food Standard Agency (UK) for the research studentship. I would like to thank the Environment Agency and Natural Resources Wales and the team from the Centre for Research into Environment and Health (CREH) of Aberystwyth Universit y and the City and County of Swansea for the data provided under the Interreg 4A Smart Coasts and Sustainable Communities Project. I would also like to thank the user community of the TELEMAC Modelling System and its managing consortium for the modelling guidance through the model application and development. In addition, I would like to thank the Advanced Research Computing at Cardiff (ARCCA) for the supercomputing facilit y and technical support offered throughout the research period. I would like to thank the staff at the office of Postgraduate Research for the ir continued assistance in the manag ement of this research. I would also like to thank research fellow s at the Hydro -environmental Research Centre in particular, those who have shared their insight towards the improvement of knowledge . My parents, wife, son, sibling and in -laws are those who deserve the most appreciation upon this achievement . I thank them for their unconditional support throughout my PhD journey . iii Table of contents Abstract ................................ ................................ ................................ ................................ ....... i Acknowledgement ................................ ................................ ................................ ................... iii Table of content s................................ ................................ ................................ ....................... iv List of figures ................................ ................................ ................................ ............................ ix List of tables ................................ ................................ ................................ ........................... xvii List of acronyms ................................ ................................ ................................ .................. xviii List of public ations ................................ ................................ ................................ ................ xxii Chapter 1: Introduction ................................ ................................ ................................ .............. 1 1.1 Motivation ................................ ................................ ................................ ........................ 1 1.2 Water quality standard ................................ ................................ ................................ ..... 2 1.3 Loughor Estuary ................................ ................................ ................................ ............... 3 1.4 Water quality monitoring and modelling ................................ ................................ ......... 5 1.5 Research objectives ................................ ................................ ................................ .......... 7 1.6 Thesis organisation ................................ ................................ ................................ .......... 8 Chapter 2: Literature review ................................ ................................ ................................ .... 10 2.1 Introduction ................................ ................................ ................................ .................... 10 2.2 Review of SEBC modelling studies ................................ ................................ ............... 10 2.2.1 Hydrodynamic modelling ................................ ................................ ....................... 10 2.2.2 Water quality modelling ................................ ................................ ......................... 12 2.3 Overview of mesh sizing criteria ................................ ................................ ................... 13 2.3.1 A -priori criteria ................................ ................................ ................................ ....... 13 2.3.2 A -posteriori criteria ................................ ................................ ................................ .17 2.3.3 Mesh discretisation at floodplains ................................ ................................ .......... 20 2.3.3.1 Si gnificance horizontal length scales ................................ ................................ ... 20 2.3.3.2 Topographically significant points ................................ ................................ ...... 21 2.3.3.3 Features incorporation into mesh discretization ................................ .................. 26 iv 2.3.3.4 Sub -grid -scale parameterization ................................ ................................ .......... 26 2.4 Overview of floodplain roughness parameterisation ................................ ..................... 28 2.4.1 USDA Soil Conservation Service and related methods ................................ .......... 29 2.4.2 Vegetation drag model ................................ ................................ ............................ 30 2.4.3 Floodplain roughness parametrisation ................................ ................................ .... 30 2.5 Review on bacteriophage as a microbial tracer ...............................
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