Computational Analysis of Bioaerosol
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Computational analysis of Bioaerosol: The analysis of molecular genetic datasets in context of environmental factors Dissertation zur Erlangung des Grades: „Doktor der Naturwissenschaft“ am Fachbereich Biologie Johannes-Gutenberg-Universität Mainz Vorgelegt von Daniel Andrew Pickersgill Geb. am 12.04.1980 in Rom, Italien. Mainz, 2018 Table of Contents Abstract .................................................................................................................................................... I Zusammenfassung .................................................................................................................................. II 1 Introduction ..................................................................................................................................... 1 2 Motivation and Research Objectives ............................................................................................. 4 2.1 Methodological Objectives: .......................................................................................................... 4 2.2 Research Objectives: .................................................................................................................... 4 3 Major Results and Conclusions ...................................................................................................... 5 4 References ....................................................................................................................................... 9 Appendix A: Abbreviations .................................................................................................................. 12 Appendix B: List of Publications and Contributions .......................................................................... 13 Appendix C: Selected Publications ...................................................................................................... 16 Abstract From an ecological perspective, primary biological aerosol particles (PBAP) play a central role in the spread and reproduction of many organisms. Many pathogens of plants and humans, as well as allergens, spread through the atmosphere. They can be highly efficient ice nuclei, potentially influencing the hydrological cycle and global energy budget. Despite the far- reaching influences in ecology, agriculture, human health and climate, the spatial and temporal dynamics in composition and abundancy of PBAP are not well characterised. In this thesis, the atmospheric diversity and abundancies of heterogeneous types of PBAP are investigated. For this, data science methods are utilised to programmatically process and analyse complex data structures within a database system. The focus is on Sanger, NGS and quantitative PCR datasets of the highly allergenic plants, ragweed and mugwort, plant pathogenic oomycetes, fungi and prokaryotic archaea. A novel insight into the fine fraction (<3 µm) concentrations of mugwort and ragweed revealed higher concentrations of ragweed despite it being far less abundant in the local flora. Wind back trajectory analysis point to pollen-rupture during long-range transport from the Mediterranean, which also may explain the higher allergenic potential of ragweed compared to mugwort. Both fungi and oomycetes diversity displayed high seasonal dynamics. Average temperature, more than close temporal vicinity, led to similar compositions. Similar tendencies in the abundancies of different oomycetes taxa indicate the same factors influencing atmospheric occurrence. For fungi independent communities were identified on coarse and fine filter samples. Patterns in the temporal and size fraction occurrences of the most abundant taxa allowed the identification of sporulation strategies amongst fungi with similar lifestyles. Comparison of Archaea datasets from continental and marine air samples revealed higher proportions of the soil-associated Thaumarchaeota in continental samples (86% vs 60%) and increase of Euryarchaeota in marine samples (40% vs 14%). Thaumarchaeota and methanogenic Euryarchaeota peaked late in the year, presumably due to increased emissions from bare soil and fertilisation on agricultural land. These results provide new information and insights into the dynamics of PBAP which can be beneficial for diverse fields such as atmospheric, agricultural and medical sciences. I Zusammenfassung Aus ökologischer Sicht spielen Primäre Biologische Aerosolpartikel (PBAP) eine zentrale Rolle bei der Verbreitung und Vermehrung vieler Organismen. Viele Pflanzen- und Humanpathogene, wie auch Allergene, sind in der Atmosphäre präsent. Als effiziente Eiskeime könnten PBAP einen Einfluss auf den Wasserzyklus und globalen Energiehaushalt haben. Trotz der weitreichenden potenziellen Einflüsse, sind die räumlichen und zeitlichen Dynamiken in Zusammensetzung und Vielfalt nur unzureichend charakterisiert. In dieser Arbeit werden atmosphärische Diversität und Abundanzen heterogener Typen von PBAP untersucht. Hierbei werden Methoden der data science eingesetzt um programmatisch komplexe Datenstrukturen innerhalb eines Datenbanksystems zu prozessieren und analysieren. Der Fokus liegt auf Sanger- NGS- und quantitativen PCR Datensätzen von Oomyceten, Fungi, Archaea und den Allergenen Pflanzen Ambrosia und Artemisia. Neue Einblicke in die Feinstaubkonzentrationen (<3 µm) von A. vulgaris und A. artemisiifolia zeigen höhere Konzentration von A. artemisiifolia, obwohl es in der regionalen Pflanzenwelt weit weniger häufig ist. Wind Rückwärtstrajektorien lassen einen Langstreckentransport und dadurch bedingtes Platzen der Pollen vermuten, welches das hohe Allergiepotenzial erklären könnte. Die Diversität von Fungi und Oomyceten zeigt hohe saisonale Dynamik. Die mittlere Temperatur, mehr als die zeitliche Nähe, führte zu ähnlichen Zusammensetzungen. Ähnliche Tendenzen in der Konzentration verschiedener Oomycetentaxa deuten auf die gleichen Faktoren die das atmosphärische auftreten beeinflussen. In Grob- und Feinstaub wurden voneinander unabhängige Gemeinschaften der Fungi identifiziert. Muster im zeitlichen Auftreten, innerhalb der zwei Größenfraktionen, erlaubten die Identifikation von Sporulationsstrategien der Taxa mit ähnlichen Lebensweisen. Der Vergleich von Archaea aus kontinentalen und marinen Luftproben, zeigte einen höheren Anteil erdassoziierter Thaumarchaeota in kontinentalen Proben (86 % zu 60 %) und einen höheren Anteil Euryarchaeota in den marinen Proben (40 % zu 14 %). Die Thaumarchaeota und die methanogenen Euryarchaeota erreichten ihre höchste Vielfalt spät im Jahr, vermutlich aufgrund nackter Erde und Düngemitteleinsatz auf Agrarflächen. Die Ergebnisse liefern neue Informationen und Einblicke in die Dynamiken von PBAP welche Nutzen für diverse Disziplinen wie z.B. atmosphärische, Agrar-, und medizinische Wissenschaften haben können. II 1 Introduction In recent decades the recognition of the fragility of planet earth’s climate and the influence of anthropogenic emissions thereupon, has led to the atmospheric sciences becoming one of the most prominent fields in modern day science. Within atmospheric research, the effects of aerosols, which are generally defined as liquid or solid particles suspended in a gas, are one of the central topics (Boucher et al., 2013; Pöschl, 2005). They play roles in a multitude of atmospheric chemical and physical processes, such as the global hydrological cycle, where they act as cloud condensation or ice nuclei and directly and indirectly influence the earth’s energy budget through absorption and reflection of solar radiation (Seinfeld & Pandis, 2016). The expanding field of aerosol research also led to renewed interest into the influence of natural emissions from the biosphere in the atmosphere and earth system as a whole. Primary biological aerosol particles (PBAP) are defined as aerosols of biological origin released in the particle phase from the biosphere into the atmosphere (Deepak, 1991; Després et al., 2012; Fröhlich-Nowoisky et al., 2016; Matthias-Maser, Bogs, & Jaenicke, 2000). They are a highly diverse and complex group of aerosols and include anything from prokaryotes such as bacteria and archaea, eukaryotes such as fungal spores or plant pollen, viruses and even cellular components, fragments or excretions of organisms, all with differing physico-chemical properties. Different types of PBAP can span the entire aerosol size range, which per definition is from roughly 1 nm, limited by rapid particle aggregation, to 100 µm, limited by rapid sedimentation (Seinfeld & Pandis, 2016), with viruses and cellular components such as proteins in the nanometre size range up to the upper boundary seen for many species of plant pollen and fungal spores. However, typical viable and abundant PBAP, such as bacteria, fungal spores and pollen are, almost exclusively, found in the super-micron size range at the upper end of the aerosol size spectrum (Fröhlich-Nowoisky et al., 2016). The atmospheric composition of PBAP in both diversity and abundancy are temporally and spatially highly variable (Fröhlich-Nowoisky et al., 2012). As major groups of viable PBAP, such as fungal spores, bacteria or pollen, are quite large from an aerosol perspective, they are removed relatively quickly and efficiently through dry and wet deposition, i.e. removal by sedimentation or precipitation (Iribarne & Cho, 1980). This leads to the near-surface boundary layer composition being strongly influenced by emissions from the surrounding local to regional biosphere (Aylor, 1999; Bowers et al., 2013; Gregory,