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Characterization of Stormwater Runoff in Lisbon Based on Microbial Source Tracking Methods

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Characterization of Stormwater Runoff in Lisbon Based on Microbial Source Tracking Methods Characterization of Stormwater Runoff in Lisbon Based on Microbial Source Tracking Methods Gaspar Maria de Castelo Branco Teixeira de Queiroz (Bachelor) Dissertation to obtain the Master’s Degree in Civil Engineering Juri President: Professor Doutor Antonio´ Jorge Silva Guerreiro Monteiro Supervisor: Professora Doutora Filipa Maria Santos Ferreira Supervisor: Doutor Ricardo Jaime Pereira Rosario´ dos Santos Members: Professora Doutora Ana Fonseca Galvao˜ Doutora Sara Luisa Proenc¸a Garcia Cordeiro Dias Teles October 2012 Cover Image: c WEB2DNA Art Project R Baekdal This document was produced using LATEX “Why is my District death-rate low?” Said Binks of Hezabad. “Well, drains, and sewage-outfalls are My own peculiar fad. learnt a lesson once, It ran Thus,” quoth that most veracious man: — “It was an August evening and, in snowy garments clad, I paid a round of visits in the lines of Hezabad; When, presently, my Waler saw, and did not like at all, A Commissariat elephant careering down the Mall. I couldn’t see the driver, and across my mind it rushed That that Commissariat elephant had suddenly gone musth. I didn’t care to meet him, and I couldn’t well get down, So I let the Waler have it, and we headed for the town. The buggy was a new one and, praise Dykes, it stood the strain, Till the Waler jumped a bullock just above the City Drain; And the next that I remember was a hurricane of squeals, And the creature making toothpicks of my five-foot patent wheels. He seemed to want the owner, so I fled, distraught with fear, To the Main Drain sewage-outfall while he snorted in my ear— Reached the four-foot drain-head safely and, in darkness and despair, Felt the brute’s proboscis fingering my terror-stiffened hair. Heard it trumpet on my shoulder — tried to crawl a little higher — Found the Main Drain sewage outfall blocked, some eight feet up, with mire; And, for twenty reeking minutes, Sir, my very marrow froze, While the trunk was feeling blindly for a purchase on my toes! It missed me by a fraction, but my hair was turning grey Before they called the drivers up and dragged the brute away. Then I sought the City Elders, and my words were very plain. They flushed that four-foot drain-head and — it never choked again! You may hold with surface-drainage, and the sun-for-garbage cure, Till you’ve been a periwinkle shrinking coyly up a sewer. I believe in well-flushed culverts.... This is why the death-rate’s small; And, if you don’t believe me, get shikarred yourself. That’s all.” KIPLING, “Municipal” in Departmental Ditties. Acknowledgments I should not wish to say another word before crediting those who, magna cum laude, have directly contributed to the successful completion of this work. In the midst of a worldwide economical crisis, I find myself thankfully indebted to: The unyielding enthusiasm of my Supervisors — Filipa and Ricardo — who have with great success always kept me under the weather. The invaluable work of the Lab Team — Silvia, Teresa and Mario — in particular Silvia, for her tireless patience to explain the ‘abc’ of Microbiology, which turned out to have no ‘a’ in it. The unstoppable runs of the Strike Team — Cecilia and Teresa — for all the rainwater they collected... in their hair. The endless support of the Operations and Logistics Team — Kika and my Parents — for lending their time, car and fridge, for stormwater keeping. And, of course, the irreplaceable contribution of our Sponsors and Data Suppliers — the IGIDL and the LNEC — for giving us the rain we danced for. iii Abstract Recent studies acknowledge the great impact that stormwater can have in receiving waters, some- times as great as wastewater, especially in urban contexts. Despite being widely studied, pollution modelling of urban stormwater runoff has proven an extremely difficult challenge due to a significant spacial and temporal variability, and a short understanding of the accumulation processes of diffuse source pollutants during dry weather. Current water quality evaluation is based, among others, in the level of faecal contamination, which is measured through faecal indicator bacteria, such as E. coli and enterococci. As pollution mitigation measures are currently converging towards treat-at-source solutions, it seems urgent to pinpoint the source of the detected faecal pollution, in urban environments. Microbial source tracking methods are promising tools in finding the source of any contamination, but despite their fast development and numerous applications, they haven’t yet been used to track faecal pollution in urban stormwater runoff. This study tested water samples from three different catchments in the city of Lisbon for E. coli and enterococci, as well as the COD parameter. It further developed the characterization of stormwater runoff by testing the presence of faecal contamination from Humans, Dogs and Cats — three species considered relevant in the urban context — through the PCR technique targeting species-specific mitochondrial DNA from the selected species. This study demonstrates a high degree of faecal pollution in stormwater runoff, in the vast majority of cases being well above the legal limit for discharges, and thus highlighting the need for stormwater treatment at WWTPs prior to discharge. Also, faecal pollution of any human, canine or feline nature was found in most of the tested samples. Keywords Stormwater runoff; microbial source tracking; faecal contamination; polymerase chain reaction; mitochondrial DNA. v Resumo Estudos recentes reconhecem o grande impacto que as aguas´ pluviais podem ter nos meios re- ceptores, por vezes equiparavel´ ao das aguas´ residuais, especialmente em contexto urbano. Apesar de amplamente estudadas, modelar escorrenciasˆ pluviais em termos de carga poluente e´ bastante dif´ıcil, dada a grande variabilidade espacial e temporal dos poluentes, e uma fraca compreensao˜ dos fenomenos´ de acumulac¸ao˜ de poluentes de origem difusa em tempo seco. A actual avaliac¸ao˜ da qualidade da agua´ e´ baseada, entre outros, no n´ıvel de contaminac¸ao˜ fecal, que e´ medido atraves´ de indicatores fecais bacterianos, como a E. coli e os enterococos intestinais. As medidas de mitigac¸ao˜ da poluic¸ao˜ temˆ recentemente convergido para soluc¸oes˜ de tratamento na origem, pelo que se torna urgente avaliar a origem da poluic¸ao˜ detectada em ambiente urbano. Os metodos´ de microbial source tracking permitem identificar as origens de uma dada contamina- c¸ao,˜ mas apesar do seu rapido´ desenvolvimento e numerosas aplicac¸oes,˜ ainda nao˜ foram utilizadas para localizar a origem da poluic¸ao˜ fecal em escorrenciasˆ pluviais urbanas. Este estudo testou varias´ amostras de escorrenciasˆ pluviais, recolhidas em tresˆ bacias difer- entes na cidade de Lisboa, quanto a` presenc¸a de E. coli, enterococos intestinais e quantificac¸ao˜ do parametroˆ CQO. Aprofundou ainda mais a caracterizac¸ao˜ da poluic¸ao˜ em escorrenciasˆ pluviais testando a contaminac¸ao˜ fecal quanto a esta ter sido originada por Humanos, Caes˜ e Gatos — tresˆ especies´ consideradas relevantes ao contexto urbano — atraves´ da tecnica´ de PCR aplicada a sequenciasˆ espec´ıficas de DNA mitocondrial para as especies´ indicadas. Este estudo demonstra os elevados n´ıveis de poluic¸ao˜ em escorrenciasˆ pluviais para os tresˆ parametrosˆ analisados (CQO, E. coli e enterococos), na grande maioria dos casos bastante acima do limite legal para a descarga de efluentes, salientando a necessidade de tratamento das aguas´ pluviais em ETAR, antes da descarga. Na maioria das amostras foi detectada poluic¸ao˜ fecal de origem quer humana, felina ou canina quer uma combinac¸ao˜ das tres.ˆ Palavras Chave Escorrenciasˆ pluviais; microbial source tracking; contaminac¸ao˜ fecal; polymerase chain reaction; DNA mitocondrial. vii Contents 1 Introduction 1 1.1 Whys, Whats and Hows . .2 1.2 Thesis Outline — The plot ...................................4 2 Framing the Work 5 2.1 Phenomena and Parameters . .6 2.1.1 Basic Concepts . .6 2.1.2 Monitoring Parameters . .7 2.1.3 Advanced Concepts . .9 2.2 Urban Water Pollution . 12 2.2.1 BMPs and current approaches . 12 2.2.2 (in)Sanitary Engineering? . 18 3 State of the Art 19 3.1 Urban Stormwater Runoff . 20 3.1.1 Characterization . 20 3.1.2 Urban Response . 24 3.1.3 Modelling Runoff . 26 3.2 Dealing with rainwater in Portugal . 30 4 Microbiology 33 4.1 Escheri. what? . 34 4.1.1 A Microscopic Overview of Pathogenic Organisms . 34 4.1.2 Bacteria . 35 4.1.3 Protozoa, Helminths and Viruses . 36 4.2 Microbial Source Tracking Methods . 37 4.2.1 The Point of Indicators . 37 4.2.2 Tracking the Source . 38 4.2.3 The Methods . 38 4.2.4 Current Issues and Future Research . 40 4.3 Case-Study Techniques . 41 4.3.1 Polymerase Chain Reaction (PCR) . 41 ix 4.3.2 Mitochondrial Markers . 43 5 Case-Study 45 5.1 Objectives . 46 5.2 The Basins . 46 5.2.1 Alcantara Basin . 47 5.2.2 Bairro das Ilhas . 49 5.2.3 Madalena . 50 5.2.4 WWTP in Alcantara . 50 5.3 The Laboratory . 51 5.3.1 Collected samples . 51 5.3.2 COD analysis . 52 5.3.3 E. coli and enterococci analysis . 53 5.3.4 DNA extraction procedures . 53 5.3.5 Single and nested PCR procedures — Primer design . 54 5.4 Processing Results . 55 5.4.1 Rain Data . 55 5.4.2 Crossing Data . 57 6 Conclusions and Future Work 65 6.1 Epilogue . 66 6.2 Prospective Sequels . 68 Bibliography 69 Appendix A Article submitted to ENASB A-1 x List of Figures 2.1 Effects of Imperviousness in Runoff . .6 2.2 Urban Diffuse Pollution Sources . .7 2.3 Coliform Hierarchy . .8 2.4 First Flush phenomenon. 10 2.5 Detection of First Flush using dynamic EMC .
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