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Fungal Communities in Archives: Assessment Strategies and Impact on Paper Con- Servation and Human Health Fungal

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Ana Catarina Martiniano da Silva Pinheiro Licenciada em Conservação e Restauro pela Universidade Nova de Lisboa Licenciada em Ciências Farmacêuticas pela Universidade de Lisboa [Nome completo do autor] [Nome completo do autor] [Habilitações Académicas] Fungal Communities in Archives: Assessment Strategies and Impact on Paper [Nome completo do autor] [Habilitações Académicas] Conservation and Human Health Dissertação para obtenção do Grau de Doutor em [Habilitações Académicas] Ciências[Nome da completoConservação do autor] pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia [NomeDissertação complet parao obtençãodo autor] do[Habilitações Grau de Mestre Académicas] em [Engenharia Informática] Orient ador: Doutora Filomena Macedo Dinis, Professor Auxiliar com Nomeação De- finitiva, DCR, FCT-UNL Co-orientadores:[Nome completo Doutora doLaura autor] Rosado, [Habilitações Instituto Nacional Académicas] de Saúde Doutor Ricardo Jorge I.P. Doutora Valme Jurado, Instituto de Recursos Naturales y Agrobiología, CSIC [Nome completo do autor] [Habilitações Académicas] Júri Presidente Prof. Doutor Fernando Pina Arguentes Doutor António Manuel Santos Carriço Portugal, Professor Auxiliar Doutor Alan Phillips, Investigador Vogais Doutora Maria Inês Durão de Carvalho Cordeiro, Directora da Biblioteca Nacional Doutora Susana Marta Lopes Almeida, Investigadora Auxiliar iii October, 2014 Fungal Communities in Archives: Assessment Strategies and Impact on Paper Con- servation and Human Health Fungal Copyright © Ana Catarina Martiniano da Silva Pinheiro, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa. A Faculdade de Ciências e Tecnologia e a Universidade Nova de Lisboa têm o direito, perpétuo e sem limites geográficos, de arquivar e publicar esta dissertação através de exemplares impressos reproduzidos em papel ou de forma digital, ou por qualquer outro meio conhecido ou que venha a ser inventado, e de a divulgar através de reposi- tórios científicos e de admitir a sua cópia e distribuição com objectivos educacionais ou de investigação, não comerciais, desde que seja dado crédito ao autor e editor. iii Dedicated to my family v Acknowledgments An endeavour such as a Philosophical Degree is never accomplished without the help and encouragement of a world of people. Because memory may fail me I would like to express my deep gratitude also to everyone I do not mention in the next lines. This PhD was developed at the Department of Conservation and Restoration (FCT-UNL), the Mycology Laboratory at the National Institute of Health (URSZ, DDI, INSA IP) and the Instituto de Recursos Naturales y Agrobiologia de Sevilla – Consejo Superior de Investigaciones Cientificas (IRNAS-CSIC). It would not have been possible to gather together these three institutions without the support of the Fundação para a Ciência e Technology (SFRH/BD/36005/2007). I would like to thank the Faculty of Science and Technology and the Conserva- tion and Restoration Department for stimulating the pursuit of higher knowledge and creating the conditions for the journey. Included are all the teachers and professionals in this institution. I would also like to thank Dr. Rui Silva (CENIMAT, FCT-UNL) for his time and help. Everyone at the archives where this study was performed: Arquivo Histórico Ul- tramarino, Arquivo Distrital de Évora, Instituto de Habitação e Reabilitação Urbana and Torre do Tombo. Thank you for opening your doors and helping on the execution of this study. A particular note of gratitude to Doutora Maria Filomena Macedo Dinis, Assis- tant Professor at DCR-FCT/UNL, who supervised this work improving it with her in- puts, valuable advices and guidance. My gratitude goes also to Dr. Valme Jurado, PhD and Prof. Dr. Cesareo Saiz- Jimenez, PhD, for letting me in their team in Sevilla and for all the efforts in guiding me. A very warmth thank you to everyone at the INSA’s Mycology Laboratory, espe- cially Doutora Laura Rosado, João Brandão, Cristina Verissimo, Raquel Sabino, Helena Parada and D. Nazaré. They made it possible to perform this study and, in the end, be- came so much more than just lab partners. vii To Catarina Silva, Sonia Pedro, Ana Cardoso and Luis Vieira for their help in the molecular biology field. A special thank you to Carla Viegas and Susana Viegas (ESTESL) for all the ener- gy and expertise. You are truly inspirational. Mathilda Larsson and Silvia Sequeira, for their inputs and shared concerns. You were a precious help! Maria João Pereira and Ana Zélia Miller for carving the way and being an inspiration and helpful hand. To Phil Harrison from Transgenomic for the support while handling the DHPLC. To all my friends for their support. Even from a distance. Finally a very grateful thank you to my family for their encouragement and pres- ence. A special note of gratitude for my husband for his patience and reassurance dur- ing the stressful moments and also a special note for my daughter…Hope this makes them proud. viii The faculty of art is to change events; the faculty of science is to foresee them. — Henry Thomas Buckle 'The Influence of Women on the Progress of Knowledge,’ a discourse delivered at the Royal In- stitution (19 Mar 1858) reprinted from Fraser's Magazine (Apr 1858) in The Miscellaneous and Posthumous Works of Henry Thomas Buckle (1872), Vol. 1, 4. ix The main results presented in this PhD Dissertation have been published in interna- tional journals included in the Science Citation Index (SCI): Pinheiro, A.C., Viegas, C., Viegas, S., Veríssimo, C., Brandão, J. & Macedo, M.F. (2014). Particulate Matter Distribution in Selected Portuguese archives: A Preliminary Study. International Journal of Conservation Science, 5 (2), 139-150. Pinheiro, A.C., Viegas, C., Viegas, S., Veríssimo, C., Brandão, J. & Macedo, M.F. (2012). Indoor Air Quality in Portuguese archives: a Snapshot on Exposure Levels, Journal of Toxicology and Environmental Health, Part A: Current Issues, 75(22-23), 1359-70. Pinheiro, A. C., Macedo, M. F., Jurado, V., Sáiz-Jiménez, C., Viegas, C., Brandão, J., & Rosado, L. (2011). Mould and yeast identification in archival settings: Preliminary re- sults on the use of traditional methods and molecular biology options in Portuguese archives. International Biodeterioration and Biodegradation, 65(4), 619-627 Pinheiro, A.C, Oliveira B.P, Veríssimo, C., Brandão, J., Rosado, L., Jurado, V., Macedo, M.F. (2012). Identification of a fungal community on gilded wood carved heritage. Journal of Cultural Heritage, 14 (1), 76-81. xi xii Abstract Fungi are ubiquitous and, as such, are current contaminants in archives and librairies. Provided the adequate relative humidity, temperature and water activity, however, they can stop being innocent inhabitants and become dangerous threats to the organic materials that hold our written heritage. Their impact, however, is not re- stricted to the assets of an archive or library. New concerns arise from their incredible ability to thrive as human health can also be affected. In a contaminated environment, staff and attendees share the same space with fungal communities and the human body can suffer from this interaction in the most diverse ways. So, indoor air quality studies in archives and libraries should always comprehend not only the study of fun- gal communities but also their analysis under two perspectives: documents safekeep- ing and human health protection. In this study it was important to determine the conditions provided by some of our heritage holder’s institutions and develop the best strategy to identify their fungal flora. This strategy encompassed both air and surfaces and both traditional culturing methods and molecular biology protocols. Knowing the environment in Portuguese institutions is essential for the development of guidelines and establishment of recom- mendations. Only by using this knowledge can a safer environment be created and the purpose of keeping our heritage while maintaining our health is fully attained. Keywords: Fungi, archives, indoor air quality, health, conservation xiii Resumo Os fungos existem em todos os ambientes e, como tal, não surpreende a sua presença em arquivos e bibliotecas. No entanto, quando existem as condições certas de humidade relativa, temperatura e actividade da água, os fungos deixam de ser simples ocupantes e transformam-se numa perigosa ameaça ao nosso património. O seu impac- to, no entanto, não se limita ao acervo de um arquivo ou biblioteca. Da sua incrível te- nacidade nascem novas preocupações, desta vez relacionadas com a saúde humana. Num ambiente contaminado, tanto funcionários como visitantes podem sofrer com es- ta interacção. É por este motivo que os estudos de qualidade do ar interior nestas insti- tuições deverão sempre incluir não só o estudo das comunidades fúngicas como a sua análise sob ambas as perspectivas: a salvaguarda da nossa herança escrita e protecção da saúde humana. Neste estudo foi importante conhecer as condições fornecidas por alguns dos nossos Arquivos e desenvolver a melhor estratégia para a identificação da microflora fúngica. Enquadradas nesta estratégia estiveram amostras de ar e de superficies tendo sido usados tanto os métodos tradicionais de cultura como protocolos de biologia mo- lecular. Conhecer o ambiente é essencial para o desenvolvimento de directrizes e recomendações. Só utilizando este conhecimento é que será possível criar ambientes mais seguros onde a salvaguarda do património pode caminhar lado a lado com a ma- nutenção da nossa saúde enquanto cuidadores. Palavras-chave:
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  • Microscopic Fungi on Cadavers and Skeletons from Cave and Mine Environments

    Microscopic Fungi on Cadavers and Skeletons from Cave and Mine Environments

    CZECH MYCOLOGY 70(2): 101–121, AUGUST 19, 2018 (ONLINE VERSION, ISSN 1805-1421) Microscopic fungi on cadavers and skeletons from cave and mine environments 1 2 1,2 1,2 ALENA NOVÁKOVÁ *, ALENA KUBÁTOVÁ ,FRANTIŠEK SKLENÁŘ ,VÍT HUBKA 1 Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, CZ-142 20 Praha 4, Czech Republic 2 Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-128 01 Praha 2, Czech Republic *corresponding author: [email protected] Nováková A., Kubátová A., Sklenář F., Hubka V. (2018): Microscopic fungi on ca- davers and skeletons from cave and mine environments. – Czech Mycol. 70(2): 101–121. During long-term studies of microscopic fungi in 80 European caves and mine environments many cadavers and skeletons of animals inhabiting these environments and various animal visitors were found, some of them with visible microfungal growth. Direct isolation, the dilution plate method and various types of isolation media were used. The resulting spectrum of isolated fungi is presented and compared with records about their previous isolation. Compared to former studies focused mainly on bat mycobiota, this paper contributes to a wider knowledge of fungal assemblages colonising various animal bodies in underground environments. The most interesting findings include ascocarps of Acaulium caviariforme found abundant on mam- mals cadavers, while Botryosporium longibrachiatum isolated from frogs, Chaetocladium jonesiae from bats and Penicillium vulpinum from spiders represent the first records of these species from cadavers or skeletons. Key words: European caves, abandoned mines, dead bodies, bones, mammals, frogs, spiders, isopods, micromycetes.