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Deciphering the mycobiome of indoor environments by high-throughput sequencing

Periodic Reporting for period 1 - MycoIndoor (Deciphering the mycobiome of indoor environments by high-throughput sequencing)

Okres sprawozdawczy: 2018-03-01 do 2020-02-29

The overall assembly of fungi in buildings is often known as the ‘indoor mycobiome’. Dampness- and mould-related indoor air quality problems are relevant health concerns due to their association with allergies, asthma and other respiratory symptoms. Previous studies have stated that geography and climate are the most important determinants of indoor mycobiomes, with the outdoor air as the key source of spores. Other studies indicated that various building and occupancy characteristics were key determinants of the indoor mycobiome. High-throughput sequencing (HTS), and in particular its use in DNA metabarcoding analyses, has lately become a key tool for surveying environmental microbial communities. The majority of existing DNA-based mycobiome studies have focussed on specific building units, at a local scale. However, indoor mycobiomes may show significant differences depending on the regional climatic and environmental conditions, and must therefore be characterised at various scales in different parts of the world. Northern Europe possess a marked climatic gradient that enables to study the effect of regional climatic variability on the indoor mycobiomes.
The overarching aim of the MycoIndoor project was to improve the knowledge about the indoor mycobiome in Northern Europe by implementing state-of-the-art molecular approaches, and identify the main determinants of compositional variation in the indoor mycobiome. More specifically, the following three objectives were addressed: (i) to construct a reference DNA sequence database for widespread cultivable indoor fungi in Norway, (ii) to analyse the small-scale spatiotemporal variation in the indoor mycobiome within single buildings, and (iii) to characterise the geographical variation of the indoor mycobiome on a larger scale (Norway) and reveal broad scale environmental drivers for variation in the indoor mycobiome.
MycoIndoor project has been a joint effort of the Oslo Mycology Group at the University of Oslo in collaboration with Mycoteam AS. The scientific activities of this project were mainly conducted by the Principal Investigator (PI) Pedro M. Martin Sanchez, from 1st March 2018 to 29th February 2020, under the supervision of Prof. Håvard Kauserud.
The three mentioned objectives were coupled to three scientific work packages (WPs):
WP1: Sequence database for cultivable Scandinavian indoor fungi. A collection of fungal isolates were molecularly characterized by DNA (Sanger) sequencing of their ribosomal inter transcribed spacers (ITS). This database included 200 airborne fungi from kindergartens and 22 material-colonising fungi from private houses. This library was very useful to improve the taxonomic assignment of the HTS data from the environmental samples studied in the WPs 2 and 3.
WP2: Local in-depth survey of the indoor mycobiome. Two different studies were conducted: (Study 2.1) spatiotemporal monitoring of two kindergartens, investigating the mycobiome variation in different parts of buildings during a one-year period; and (Study 2.2) the characterization of the indoor mycobiome associated with mould-damaged buildings (22 houses in Oslo), comparing the fungi growing on different damaged materials and their influence on other parts of buildings.
WP3: Large-scale survey of the Norwegian indoor mycobiome. We organized a large citizen science dust sampling campaign in 290 houses throughout Norway coupled to the subsequent DNA metabarcoding analyses of the mycobiomes (Study 3).
Overview of main MycoIndoor results achieved so far:
Although we are still working on the final data analyses of the local surveys (WP2), the preliminary results of study 2.1 showed that sampling location and sampling time were the main contributors to the variation in the fungal community composition in the monitored kindergartens. The sampling location factor was a relevant determinant showing different community composition depending on the kindergarten compartment sampled (outdoor vs. indoor). We also found clear seasonal patterns in the variation of fungal communities, especially evident for outdoor samples. Some occupant characteristics (number of children/adults and their activities) were also relevant determinants of indoor mycobiomes in kindergartens, acting as fungal indoor sources. The expected knowledge from the study 2.2 includes: a more complete picture of fungi associated with material deterioration in houses, comparison between classical (microscopy) and DNA-based approaches, and the influence of mould problems on the indoor air quality and the human exposure in different house compartments.
The large-scale survey (WP3) was able to unravel the main factors shaping the indoor mycobiomes throughout Norway. A relatively low overall variation (15%) in the fungal community composition was explained by the studied variables (outdoor environment, building and occupants). However, all variables had a significant influence. Overall, after excluding the key influence of the house compartment factor (7.66% of the variation), results clearly demonstrated that regional-scale climate is the most important driver of indoor mycobiomes (4.18%). Occupant and building factors also showed significant influences but with much lesser extents (1.44% and 1.11%, respectively). In agreement with some previous studies, we observed a consistent pattern of higher fungal richness and alpha diversity in indoor than outdoor samples, and slightly higher alpha diversity in the north region. The fungal composition in the outdoor samples was clearly different from that of the indoor samples. As reported in previous studies, fungi from outdoor air were relevant contributors to the indoor mycobiomes. However, a comparison on a house-by-house basis revealed that only 15% of detected species were shared between outdoor and indoor samples, while 75% appeared uniquely in one of the house compartments (outside, living room and bathroom). Therefore, our study confirmed the importance of fungal indoor sources such as occupants, organic matter and potential mould growth on surfaces.
The MycoIndoor project, including the large-scale citizen science study, has effectively been communicated to a broad audience through several outreach activities, acting as an excellent tool to promote the research and its benefits to the society. In addition, with the communications in conferences and the expected open access publications in international journals (5 manuscripts in preparation), this project will have a relevant impact on the related scientific areas (microbiology of the built environment, fungal ecology and human exposure), as well as the commercial activities related to the building microbiology.
During the MycoIndoor project, the PI has acquired new skills in HTS data analysis, bioinformatics and statistics, which are essential for his research independence as environmental microbiologist. He has improved his abilities managing and coordinating projects, supervising students and writing scientific publications and grant proposals. He has stablished a relevant network for his future career including partners from academic and non-academic sectors. In conclusion, this fellowship has considerably enriched the PI’s expertise and research background, which should have a relevant positive impact on his career allowing future possibilities for reaching a permanent position in any European research institution.
Mould damages in houses
Moulds under the microscope