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Microbial Communities Driving Emerging Contaminant Removal. Impact of Treated Wastewater on the Ecosystem Eloi Parladé Molist

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Microbial Communities Driving Emerging Contaminant Removal. Impact of Treated Wastewater on the Ecosystem Eloi Parladé Molist ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Departament de Gen`eticai Microbiologia Universitat Aut`onomade Barcelona Microbial communities driving emerging contaminant removal. Impact of treated wastewater on the ecosystem by Eloi Parlad´eMolist Directed by: Maira Mart´ınez-AlonsoPh.D & N´uriaGaju Ricart Ph.D January, 2018 Microbial communities driving emerging contaminant removal. Impact of treated wastewater on the ecosystem A thesis submitted in partial fulfillment of the requirements for the degree of PhD program in Microbiology by Eloi Parlad´eMolist With the approval of the supervisors, Dra. Maira Mart´ınez-Alonso Dra. N´uriaGaju Ricart Bellaterra, January 2018 "I wish there was a way to know you're in the good old days before you've actually left them." -Andy Bernard This work has been funded by the Spanish Ministry of Economy and Competitive- ness (project CTM2013-48545-C2-1-R), State Research Agency (project CTM2016- 75587-C2-1-R), co-financed by the European Union through the European Regional Development Fund (ERDF) and supported by the Generalitat de Catalunya (Con- solidated Research Groups 2014-SGR-559/2017-SGR-1762 and 2014-SGR-476/2017- SGR-14). Eloi Parlad´eMolist thanks Universitat Aut`onoma de Barcelona for the PIF pre-doctoral grant. Abstract Rising awareness of pollutants not previously detected or monitored (emerging contaminants) has brought new challenges to the scientific community focused in environmental remediation. This thesis aimed to assess the microbial communities responsible of emerging contaminant removal in a variety of human-engineered systems as well as to evaluate the impact of the resulting effluents when they are used as reclaimed water. Molecular microbiology methods were used along with bioinformatic tools to assess the development of enrichment cultures and bioreactors driven by bacteria, algae and fungi, capable of pollutant removal. The bacterial genera Dehalogenimonas and Dehalobacterium were identified as the responsible of organohalide degradation in two enrich- ment cultures and their concomitant microbiota was assessed to denote putative synergies. The specialized community developed in a pilot-scale photobioreactor was also elucidated during urban wastewater treatment, with efficient removal of pollutants and pharmaceuticals. Efficiency of en- richment cultures, obtained from natural environments, over algal pure cultures was demonstrated in the removal of estrogenic compounds. Moreover, filamentous cyanobacteria were linked to a fast and efficient recovery of photosynthetic biomass. The dynamics of indigenous bacteria, fungi, and the inoculated strain of Trametes versicolor were assessed in continuous bioreactors and fungal biopiles treating hospital wastewater and sewage sludge, respectively. Both the inoculated fungus and some bacterial communities were correlated to the removal of pharmaceutical families. Fi- nally, the effect of effluents obtained from fungal treatment over soil ecosystems were compared to conventionally-treated wastewater in laboratory model systems (microcosms), showing up a similar behavior to the negative controls that did not contain pharmaceuticals. 6 Resum Actualment, un dels nous reptes de la comunitat cient´ıfica´esfer front a l'increment de contaminants emergents als ambients naturals. La bioremediaci´os'ha perfilat com una bona alternativa per donar resposta a aquesta necessitat. El prop`ositd'aquesta tesi ha estat estudiar les comunitats micro- bianes responsables de l’eliminaci´ode contaminants emergents en diversos sistemes artificials, aix´ı com determinar l'impacte dels efluents resultants quan s'utilitzen com a aigua regenerada. Diferents t`ecniquesmoleculars i eines bioinform`atiqueshan perm`escaracteritzar els cultius d'enriquiment establerts, aix´ıcom els bioreactors amb bacteris, algues i fongs, capa¸cosd'eliminar contaminants. Els generes bacterians Dehalogenimonas i Dehalobacterium s'han identificat com a responsables de la degradaci´od'organohalonenats en dos cultius d'enriquiment i la seva microbiota acompanyant ha estat avaluada per posar de manifest possibles sinergies. Paral·lelament, s'ha caracteritzat la comunitat desenvolupada en un fotobioreactor a escala pilot durant l’eliminaci´ode contaminants i productes farmac`euticsa partir d'aig¨uesresiduals urbanes. Pel que fa a compostos estrog`enics, s'ha demostrat una millor capacitat d’eliminaci´oper part dels cultius d'enriquiment de microor- ganismes fototr`oficsen comparaci´oamb cultius purs. A m´es a m´es, s'ha relacionat la pres`enciade cianobacteris filamentosos amb una recuperaci´or`apidai efica¸cde la biomassa fotosint`etica. D'altra banda, s'ha analitzat la din`amicade bacteris i fongs, aix´ıcom de Trametes versicolor inoculat en bioreactors continus i biopiles f´ungiquesutilitzats per tractar aig¨uesresiduals hospital`ariesi llots de depuradora. Tant el fong inoculat com algunes de les comunitats bacterianes ind´ıgenes s'han correlacionat amb l’eliminaci´od'alguns grups de f`armacs.Finalment, s'ha avaluat l'impacte dels efluents obtinguts a partir de diferents tractaments d'aig¨uesresiduals hospital`ariesirrigant micro- cosmos que mimetitzaven el s`ol. Els resultats obtinguts han posat de manifest que els efluents f´ungicses comporten de manera similar als controls negatius sense productes farmac`eutics. 7 Acknowledgements Gaireb´equatre anys de tesi s´ondif´ıcilsde resumir en uns par`agrafsd'agra¨ıments. Sense intenci´o que s'allargui gaire, dedico primer de tot el meu treball a la meva fam´ılia.Sobretot als meus pares, la meva germana i els meus avis, que em van donar el suport i recursos necessaris per fer possible que als 18 anys un jove Eloi s'independitz´esa Cerdanyola i emprengu´esel viatge que l'ha dut fins aqu´ı. El bloc llarg d'agra¨ıments va pels amics, la fam´ıliaque escull cadasc´u. Primer els de casa, que diuen, agraeixo en grup a tots els Moixernons. Gr`aciesen especial als que us heu preocupat sempre per si acabava ja o no la tesi, ja sabeu qui sou. A en Cristian, en Vila, en Marc, l'Uri i en Mardu per les reunions peri`odiqueson recordem els v/bells temps del RO. Als PV's tamb´eper tenir els bra¸cos oberts quan em presento despr´esde mesos desaparegut. Un cop fora de casa, agrair el suport incondicional dels companys de pis que m'han aguantat a Torrent 57 i Sant Antoni 52. En especial, en Marc, el Sebas, el Juanca, l'Arnau, el Toni i l'Alfredo (revisors express de la tesi). Tamb´eals companys i amics de la carrera de microbiologia, per quatre anys fant`asticsde cr´eixercom a persona. En especial, una forta abra¸cadaper l'Edu, la Jenni i la Marta. Entre tot aix`o,em toca agrair a la Merc`eque ens obr´ısles portes del seu laboratori a mi i l'Edu i que ens inspir´esamb la seva passi´oper la ci`encia. Parlant d’inspiraci´o,la necess`ariaper escriure la tesi (i fer jocs de taula) no sempre v´etreballant; les millors pauses per dinar i desconectar no haurien estat possibles sense el Marc, l'Olivia, el Ferran, el Pablo, la Mara, el Jofre, el Samir, en Mart´ıi la D´ebora. Repetint agra¨ıment, gr`acies a en Marc per fer que el laboratori sigui un lloc on sempre tinc ganes d'anar. A l'Oihane i la Jenni, per les mil ajudes en gestions i laboratori, a m´esde tota la gent del grup de microbiologia ambiental i molecular, no tindria prou espai per agrair-vos tots els favors! 8 Pel que fa al contingut de la tesi, les col·laboracions han sigut essencials perqu`eels cap´ıtolstinguin cara i ulls. Moltes gr`aciesa tota la gent de l'ICRA i el departament d'enginyeria qu´ımica,biol`ogica i ambiental per donar-ho tot i fer que puguem tenir uns articles fant`astics. Despr´esde la meva etapa de docent, no puc deixar d'agrair a tots els petits micros que han fet que em senti part de moltes promocions. En especial, Marina, Tamara i Cl`audia per recordar-vos de mi quan era lluny. Tamb´eper compartir cerveses, berenars i festes. Alex, menci´oespecial per la teva infalibilitat quan hi ha un pla d'´ultimahora. A m´es, no m'estic oblidant de vosaltres, amb qui he compartit de la m`apart d'aquest cam´ı d'aventures, sense qui no seria el que s´ocara. Nat`aliai Roc´ıo,sobren les paraules. Thanks to Jorge and Albert for opening Davis doors to me and making possible my stay. To Jordan for always keeping it chill and fun, Jon for the necessary common sense and advise, Rachel and Mike for the great trip to Tahoe, Seiji for his determination and making fencing possible for me, and Alec for fencing, chilling and partying with me when I had no one around. I also wanted to thank the Davis boardgamers, I felt always at home and enjoyed every single afternoon. Jason, thanks for inviting me to your place and review Gem Mayhem. Little things meant a lot to me. Special mention to my friend Rob, for being yourself and accompanying me in the adventures at the other side of the globe. Last but not least, res de tot aix`ono hauria estat possible sense l'empenta, motivaci´oi oportunitat que la N´uriai la Maira m'han donat a la universitat. Van confiar en mi al laboratori i m'han donat suport per seguir a l'investigaci´o,fent possible la realitat d'aquesta tesi.
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