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Study of the Genetic Basis of Denitrification in Pure Culture Denitrifiers Isolated from Activated Sludge and Soil

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Study of the Genetic Basis of Denitrification in Pure Culture Denitrifiers Isolated from Activated Sludge and Soil Study of the genetic basis of denitrification in pure culture denitrifiers isolated from activated sludge and soil Kim Heylen Dissertation submitted in fulfillment of the requirements for the degree of Doctor ( Ph.D.) in Sciences, Biotechnology December 2007 Promotor: Prof. Dr. Paul De Vos Co-promotor: Prof. Dr. Ir. Willy Verstraete EXAMINATION COMMITTEE Prof. Dr. Savvas Savvides (chairman) Faculty of Sciences, UGent, Ghent Prof. Dr. Paul De Vos (promotor) Faculty of Sciences, UGent, Ghent Prof. Dr. Ir. W. Verstraete (co-promotor) Faculty of Bioscience Engineering, UGent, Ghent Prof. Dr. Ir. N. Boon Faculty of Bioscience Engineering, UGent, Ghent Prof. Dr. Ir. Mike S.M. Jetten Faculty of Science, Radboud Universiteit Nijmegen, The Netherlands Dr. C. Etchebehere Faculty of Science, Universidad de la República, Uruguay Prof. Dr. Anne Willems Faculty of Sciences, UGent, Ghent "Eindelijk ist gedaan. Oef!" Dat is zowat het eerste gevoel dat in me opkomt. Niet dat de jaren hier steeds kommer en kwel waren - ik heb zo genoten van de vele reizen, de leuke (en minder leuke) collega's, de verhuis van het achtste naart vierde, de (zatte) recepties, de nieuwjaarsetentjes, de vrijdagavonden bij Christiane, de feestweken... Achterafgezien is alles zeer vlot gegaan, maar als je er middenin zit, ervaar je dat wel anders. Iemand heeft me ooit gezegd dat naarmate je meer twijfelt, je beter bezig bent. Voor mij is dat een beetje de samenvatting van vier jaar doctoreren. Eigenlijk ben ik voor het oog van mijn collega's volwassen geworden... En is het nu tijd voor het serieuzere werk. Natuurlijk had ik dit doctoraat nooit alleen kunnen volbrengen. Vele mensen hebben hun steentje bijgedragen, via wetenschappelijk input, of gewoon door er te zijn in moeilijke en/of zotte momenten. Ik ben niet echt prozaïsch aangelegd, maar ik doe een poging om iedereen te bedanken. Eigenlijk is het allemaal begonnen met mijn master thesis bij Geert en Margo. Margo heeft me al de kneepjes van het microbiologische vak geleerd, en is eigenlijk 'verantwoordelijk' voor al mijn latere werk. Ik heb me tijdens die thesis super geamuseerd, niet in het minste door Liesbeth Masco, Robin en Evie. En ik heb er een goei vriendin aan overgehouden, en mijn ventje... Na die thesis begon een doctoraat op het labo voor Microbiologie me wel aan te spreken. Allé, na een beetje rondvragen, kon ik toch bij Paul een doctoraat starten rond denitrificatie. Dus, een verhuis naar het achtste. Iedereen is dit natuurlijk al vergeten, maar ik heb me daar toen een half jaar zeer rustig en stil gehouden (ja, dat kan ik ook). Mijn partner in crime werd Bram. Gelukkig bezat hij alle kwaliteiten die ik nodig had in een buurman: dezelfde voorliefde voor harde, ietwat cynische humor, bestand tegen mijn gezaag en geklaag en in staat om me telkens weer vertrouwen te geven in mijn werk. Natuurlijk was er ook Liesbeth Lebbe, onze ancien. Altijd goed gezind, zo zot als een achterdeur, een echte spring- in-'t-veld, maar ook steeds bezorgd en een luisterend oor ter beschikking. En dan nog een verdomd goei laborante. Zo maken ze er geen twee. Als eerste wapenfeit moest ik van Paul helemaal alleen naar een congres in Marburg. Tof! Maar eigenlijk was dit een fantastisch begin voor mijn doctoraat. Bij mijn terugkeer ben ik met veel goesting en volle overgave begonnen aan mijn werk. Dit is het perfecte voorbeeld van Pauls input voor mijn doctoraat: veel impulsen, veel vertrouwen en veel vrijheid. Waarvoor veel dank. Natuurlijk waren Prof Verstraete en Nico er ook om mijn wetenschappelijke wandel te begeleiden. Het was een unieke kans om te mogen samenwerken met een 'instituut' als Prof. Verstraete. Uw eigenzinnige perceptie en uw immense creativiteit waren een zeer goede leerschool. Bedankt voor uw vertrouwen in mij. En wat zou ik de laatste vier jaar gedaan hebben zonder Nico. Steeds maar een telefoontje of emailtje weg, steeds bereid om te helpen of om een zoveelste draft van een paper na te lezen. Nen hele dikke merci. Alsof soort soort zoekt, werd ons labootje uitgebreid met nog enkele prettig gestoorde figuren, zoals Caroline en Joachim, en later ook nog An en Emly. Zij zorgden samen met Liesbeth voor een enorm plezante werksfeer. Soms was effectief 'werken' een beetje moeilijk (tijdens het zingen van Strangers in the Night bijvoorbeeld), maar dat werd ruimschoots gecompenseerd door leuke dynamiek en het sympathieke groepsgevoel. Jeroen Adam bracht dan weer wat zen opt labo. An heeft gaandeweg een beetje de rol van Bram overgenomen en fungeerde de laatste maanden als mijn klankbord. Blijkbaar kon ik toch niet zonder. Natuurlijk zijn er nog andere collega's die een verschil hebben gemaakt. Bij de start van mijn doctoraat had ik twee voorbeelden, en eigenlijk is dat niet meer veranderd. Door het niveau van hun werk en hun aanpak heb ik altijd opgekeken naar Peetse en Tom Coenye. En door onze babbels, was het nu op een vrijdagavond in een bruin café, na een nieuwjaarsetentje of in een trendy bar in Toronto, hebben ze me een figuurlijke schop onder mijn kont gegeven en aangezet tot nadenken. De andere doctoraatstudenten waren ook een steun en toeverlaat. Vooral dan Ilse. Het was enorm leuk samen de toerist uit te hangen. En dan nog Jeanine en Paul Segers, twee gemotiveerde mensen zonder wie ons labo nooit zo vlot zou draaien. Uiteraard zijn er naast het werk nog enkele mensen die een groot verschil hebben gemaakt en mijn leven de laatste vier jaar. Ira en Ariane zijn er altijd geweest. We hebben elkaar misschien niet veel gezien, vooral het laatste jaar niet, maar gewoon weten dat jullie steeds voor me klaarstonden als ik het weer eens niet zag zitten of om die eerste publicatie te vieren, dat was voor mij enorm belangrijk. Sven, wat had ik zonder jou het laatste jaar gedaan. Een huis verbouwen en doctoreren in hetzelfde jaar, weeral typisch voor mij. Godzijdank dat je positieve ingesteldheid ons door alles doorsleurt. En last but not least, mijn ouders. Ik weet eigenlijk niet hoe ik moet omschrijven wat zij voor mij betekenen en betekend hebben tijdens mijn 'academische loopbaan'. Al de kansen die jullie mij gegeven hebben en jullie voortdurende onvoorwaardelijke steun heeft mij gemaakt tot wie ik ben. Ik zie jullie graag… Enorm bedankt, Kim. CONTENTS Background and aim..........................................................................................................9 1. Introduction.........................................................................................................................11 1.1. Denitrification......................................................................................................14 1.1.1. Definition..............................................................................................14 1.1.2. Importance...........................................................................................15 1.2. Distribution of the denitrifying ability...............................................................18 1.3. Key enzymes of the denitrification process....................................................19 1.3.1. Nitrite reduction..................................................................................19 1.3.2. Nitric oxide reduction..........................................................................21 1.4. Current denitrification research........................................................................24 1.5. Conceptual framework of the thesis.................................................................26 1.5.1. Cultivation-dependent research and alternatives..........................26 1.5.2. Strategy followed and overview of chapters...................................27 1.6. References............................................................................................................28 2. Isolation, characterization and identification of denitrifying bacteria from the en- vironment.................................................................................................................................35 2.1. Cultivation of heterotrophic denitrifying bacteria: optimization of isolation conditions and diversity study................................................................37 2.2. Diversity of heterotrophic denitrifiers isolated from soil using a multiple-media set......................................................................................................53 2.3. Back & forth.........................................................................................................65 3. Functional phylogenetic analysis of pure culture denitrifiers......................................69 3.1. The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers...............................................................................................71 3.2. Nitric oxide reductase (norB) gene sequence analysis reveals discrepancies with nitrite reductase (nir)gene phylogeny in cultivated denitrifiers.............................................................................................................89 3.3.Functional gene study on heterotrophic denitrifiers isolated from soil ..............................................................................................................................103 3.4. Back & forth.......................................................................................................119 4. Screening for denitrification genes undectable with PCR..........................................123 4.1. Simple screening method for norB
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