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Molecular Identification of the Dominant Microbiota and Their Spoilage Potential of Crangon Crangon and Raja Sp

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Molecular Identification of the Dominant Microbiota and Their Spoilage Potential of Crangon Crangon and Raja Sp Promotors: Prof . dr. ir. Frank Devlieghere Department of Food Safety and Food Quality Faculty of Bioscience Engineering, Ghent University Dr. ir. Geertrui Vlaemynck Technology and Food Science Unit Institute for Agricultural and Fisheries Research, Melle Dean: Prof. dr. ir. Guido Van Huylenbroeck Rector: Prof. dr. Paul Van Cauwenberge Lic. Katrien Broekaert Molecular identification of the dominant microbiota and their spoilage potential of Crangon crangon and Raja sp. Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences Nederlandse titel: Moleculaire identificatie van de dominante microbiota en hun bederfpotentieel van Crangon crangon en Raja sp. To refer to this thesis: Broekaert, K. 2012. Molecular identification of the dominant microbiota and their spoilage potential of Crangon crangon and Raja sp. PhD dissertation, Faculty of Bioscience Engineering, Ghent University, Ghent. Cover: Photograph by Karl Van Ginderdeuren (www.karlvanginderdeuren.com) Printer: university Press ISBN-number: 978-90-5989-499-0 The author and the promotor give the authorisation to consult and to copy parts of this work for personal use only. Every other use is subject to the copyright laws. Permission to reproduce any material contained in this work should be obtained from the author. Dankwoord Dankwoord Met het schrijven van het dankwoord is er een einde gekomen aan een viertal jaar van veel praktisch werk, literatuurstudie en uiteraard ook plezier. Aangezien men een doctoraat nooit alleen maakt of schrijft is het nu tijd om verschillende mensen te bedanken voor hun steun, input, het creëren van een ontspannen werksfeer en dergelijke. Helaas ben ik niet zo’n proza schrijver, ook nu niet,… . Allereerst gaat een woord van dank uit naar Prof. Erik Van Bockstaele en Lieve Herman, zonder hun goedkeuring ging ik nooit kunnen starten zijn aan dit onderzoek en ging ik nooit op zo’n aangename werkplaats terecht gekomen zijn en uiteraard dus ook nooit zoveel te weten gekomen zijn over visserij, visserijproducten en het bederf ervan. Mijn promotoren Prof. Frank Devlieghere en Geertrui Vlaemynck verdienen eveneens een hartelijk dank om alles in goede banen te leiden en steeds mijn schrijfwerk, soms in extreme tijdsnood, te verbeteren. Geertrui V., vooral jij hebt me gedurende dit doctoraat bijgestaan met raad en daad. Het kwam zelfs zo ver dat we, zelfs in de gangen van het ILVO, mini-vergaderingen hielden, zodat het werk vlot vooruit ging. Vooral de laatste loodjes wogen zwaar, bedankt voor alles. Ook Marc, heel erg merci voor het helpen bij taxonomische raadsels, Pseudomonas problematiek, DGGE frustraties en dergelijke. Anders was ik er misschien nog niet uit. Bert, het was leuk om ons kennis rond garnaal en bederf van vis uit te wisselen: jij de biochemie, ik de microbiologie. Vooral de laatste tijd, dat we in dezelfde (schrijf)fase zaten, vlotte de samenwerking nog zo goed. Bedankt voor alle analyses die we samen deden en heel veel moed en succes met de laatste loodjes he! Dan, het labo moleculaire biologie, beter gekend als de “kelder”: alle doctoraatsstudenten bij elkaar onder het allesziend oog van Jessy (die helaas naar boven gemigreerd is intussen), Ann en Geertrui R. Jullie weten het misschien niet meer wegens de continue stroom van studenten en de miljoenen vragen die jullie al beantwoord hebben, maar ik ben niet vergeten hoe vaak jullie mij geholpen hebben met allerlei microbiologische en moleculaire problemen. Het is echt de ultieme droom van een student om zo’n bron van kennis achter de hand te hebben, want tenslotte beginnen we toch allemaal met een lichte vorm van angst aan dat onderzoek. Heel erg bedankt voor alles!! Ook de laboranten van het labo van Koen (Ann VDW, Elly, Vera) verdienen een pluim om me in gang te duwen op vlak van microbiologie. Geertrui R., Marijke, Ann en Pieter, door mijn zwangerschap ben ik naar jullie kant van het labo verhuisd en daar blijven hangen omdat het er zo gezellig was. Jullie hebben me dan ook het meest gesteund en op tijd en stond afgeleid, gedurende die lange periodes van schrijfwerk! Samen met alle Dankwoord passanten (Els, Hadewig, Valerie, Karen, Joris, Ambroos, Isabelle,… ,alle ex-collega’s en nieuwelingen (Nikki, Fien en Stefanie)) brainstormden we niet alleen over werkgerelateerde dilemma’s; jullie zorgden ook voor ontspannende babbels, een toffe sfeer, … Alleen, Ann, je hebt een ongelooflijk zangtalent, blijven oefenen, je komt er wel. Maar ik zou toch een andere muziekkeuze opteren! Ook het labo Levensmiddelenmicrobiologie van de Ugent wil ik graag bedanken, ik ben er niet zo vaak geweest, maar telkens kreeg ik een warme verwelkoming en hielpen jullie mij op weg. Tenslotte hebben we ook nog iedereen die me van visserijkennis en stalen voorzag: Willy Versluys, Peter Cooleman en de bemanning van de Jacob Kien, bedankt dat ik eens mee mocht met een echte garnalenkotter! Ik ben met een klein hartje vertrokken, maar met zoveel extra bagage aan kennis teruggekomen! Zoveel informatie en kennis kan je niet halen uit een boekske! Ook Stefan Hoffmann van ILVO-Visserij, hartelijk dank voor al de stalen die je me bezorgt hebt. En uiteraard mag ik Marijke B. niet vergeten! Merci om zo vaak naar het zee’tje te rijden achter vis! Ook alle anderen, die op de een of andere manier mijn weg kruisten, maar die ik hier, wegens zwangerschapsdementie (?), vergeten vermelden ben: bedankt! En last but not least… mijn familie, ook jullie hebben me enorm gesteund, niet enkel tijdens mijn doctoraat, maar ook in alle voorgaande jaren. Mijn ouders wil ik bij deze eens bedanken om me de kans te geven te studeren wat ik graag wou, er telkens voor mij te zijn en toch niet continue naar de vooruitgang van mijn doctoraat te vragen. En voor nog zovele ontelbare andere redenen, waaronder het voorzien van warme kost en ontspanning de laatste tijd! Bedankt dat Liseke de laatste maanden zo vaak bij jullie kon komen als ik weeral aan het werk was. Hiervoor ook een welgemeende merci aan mijn schoonouders. Filip, Femke en tante Leen, jullie hebben van op veilige afstand, mijn doctoraat beleefd, ook al omdat ik niet zo’n babbelgat ben, en al zeker niet over het werk. Maar toch hebben jullie gezorgd voor veel plezier en ontspanning. Meke, jij hebt spijtig genoeg de laatste maand niet meer meegemaakt. Maar toch zou ik je nog willen bedanken voor alles wat je ooit voor mij gedaan hebt en omdat ik tot recent elk weekend bij je kon “thuis”komen. En dan Thomas, lieve schat. Jou mag ik zeker niet vergeten. Je hebt me vaak moeten missen, maar je bleef me steunen in alles wat in deed. Exact 17 maand geleden hebben we ons eerste kleine meid mogen bewonderen en ook nu staan we samen voor een aantal nieuwe grote uitdagingen. Bedankt om me zoveel te helpen de laatste maanden met van alles en nog wat! Dankwoord Ook jij Lise, flinke lieve meid verdient hier een woordje van dank. Ooit zal je het misschien lezen als je in de boekenkast van mama zit. Wat vrij waarschijnlijk is, kleine kapoen en boekenworm. Ook al ben je nog zo klein, je hebt me vooral leren relativeren. En tijdens de lastige periodes van schrijven heb je me vaak getrakteerd op een zalig ontspannende pauze. Je hebt het de laatste tijd vooral met papa moeten doen, maar nu komt de mama-Lise tijd terug hoor. Al zijn we natuurlijk niet zo lang meer met drietjes, jouw baby-zusje zal er ook snel zijn. Vooral de kleinste telg van ons gezinnetje heeft alles meegemaakt van op de 1e rij. Acht en een halve maand lang hebben we samen geschreven aan dit boekje. Ik ben ervan overtuigd dat jij zorgde voor rust en kalmte. Tot gauw kleine zus! Bedankt allemaal!! Katrien Table of contents TABLE OF CONTENTS Table of contents Table of contents Table of contents……………………………………………………………………………. i List of non-standard abbreviations……………………………………………………….… ii General introduction of the thesis Chapter 1 Introduction, objectives and outline………………………………………… 1 Chapter 2 Seafood spoilage and quality analysis techniques: A literature overview 2.1. Microbiological and biochemical changes after catch………………………….. 4 2.2. Quality assessments of seafood in the industry…………………………………. 15 2.3. Target species and used detection and identification methods………………….. 19 Part I. Seafood quality assessments: optimisation of traditional detection techniques Chapter 3 Seafood quality analysis: Molecular identification of dominant microbiota after ice storage on several general growth media………………………………………. 30 Part II. Brown shrimp (Crangon crangon): The dominant microbiota and their spoilage potential Chapter 4 Molecular identification of the microbiota of peeled and unpeeled brown shrimp (Crangon crangon) during storage on ice and at 7.5°C………………………… 48 Chapter 5 Volatile compounds associated with Psychrobacter spp. and Pseudoalteromonas spp., the dominant microbiota of brown shrimp (Crangon crangon) during aerobic storage………………………………………………………… 77 Part III. Ray (Raja sp.): The dominant microbiota and their spoilage potential Chapter 6 The spoilage microbiota of ray (Raja sp.) during ice storage under different conditions: molecular identification and characterisation of the spoilage potential.......... 94 General conclusions, recommendations and perspectives..................................................... 118 References………………………………………………………………………………....... 129 Summary/samenvatting Summary……………………………………………………………………………….. 146 Samenvatting………………………………………………………………………….... 150 Curriculum vitae……………………………………………………………………………. 154 i List of non-standard abbreviations LIST OF NON-STANDARD
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