Metagenomics Study of the Taxonomic and Functional Compositions of Microbial Communities in Fine Dust Particulate Matter

Abstract

Asian dust events or known as the Yellow dust events in South Korea is a seasonal phenomenon that usually occurs during spring time which also affecting the other East Asian countries (China and Japan) due to the global dust transportation. The dust particles are usually dispersed from the semi-arid or arid region such as the Gobi Desert and the Taklamakan Desert in Mongolia across the vast ocean to a more humid mainland. During these phenomenal events, the level of the dust particles increases significantly, increasing the levels of associated chemical components and microorganisms. In the great concerns of the elevated particulate matter (PM) level especially the fine fraction (PM with an aerodynamic diameter < 2.5 µm, PM2.5) known as the event days had raised the effort of understanding the microbial community abundance and composition shift in between the non-event days and event days. Depending on the sizes of the dust particles, it is usually the smaller particles that have higher risk and greater impact on human health. The inhalation of this PMs could lead to the increase of risk in respiratory disease problems, asthmatic patients, allergies, and reduced in lung functions. By far, most studies have conducted the impact of the chemical components of the PM towards human health and yet there is still limited study in the biological components of the PM. Indeed, the various chemical and biological components in airborne PM can pose a threat to human health. Nevertheless, it is known that the microorganisms including bacteria and fungi are successful life forms because of their ability to reproduce rapidly, adaptability to new environments, and capacity to disperse globally, especially through wind or as bioaerosols. These bioaerosols may contains critical human or plant pathogenic species which can cause diseases and bring harms to the human health as well as agriculture economic growth. Furthermore, the bioaerosols can also contain the airborne components of microorganisms including secondary metabolites such as endotoxins and mycotoxins which some are carcinogenic and the toxins can have serious human health impacts. Despite of these airborne microorganisms to be widely dispersed in the atmosphere, there are still lacking of knowledge about the airborne microorganisms. This is because most of the studied conducted on airborne microbes were based on the cultivation technique and slowly changes to the culture-independent method such as 16S rRNA targeted-gene sequencing analysis. 16S rRNA gene analysis or also known as polymerase chain reaction (PCR)-based analysis is one of the most commonly use molecular technique to characterize the microbial community because it can provide rapid information and able to use on a minute amount of genomic DNA. In addition to the culture-independent analysis, there is a more recent and advanced method which can study both microbial community as well as its metabolic potential that is the whole metagenomics shotgun sequencing (WMS). Therefore, the importance of knowing the key microbial genes of the sampled community can give better understanding of the microbes behavior in the atmosphere. More knowledge can be obtained on how these airborne microbes can survives in the harsh conditions (high levels of UV radiation, low water activity, and extreme temperatures). Therefore, in order to study the airborne microorganisms of the collected samples, this dissertation is divided into 4 main objectives as follows: 1. Selecting the appropriate aerosol samplers for maximum efficiency of bioaerosols collection 2. Characterization of the airborne bacterial and fungal community in the collected samples by culture-independent analysis 3. Increased the understanding of the characterized airborne bacterial and fungal community and composition shifts in between the non-event and event day samples by using whole metagenomics shotgun sequencing 4. To develop more optimize sampling and processing method for direct application of whole metagenomics shotgun sequencing The presented thesis contributes to emphasize the importance of understanding the airborne microbial community especially during the elevated level of PMs during the event days. Among the significance findings from this dissertation were the bacterial community differed between the non-event and event days sample. In certain cases, the Proteobacteria was more prevalent during non-event day, while Bacteroidetes dominated during event day. Even though the bacteria were more dominant in the aerosol samples compared to the fungal community, based on the findings in this study, there is still a notable abundance of fungal community in the samples. Ascomycota group were highly abundant especially during the event day. This could lead to the assumptions that Ascomycota which mainly consists of spore-forming fungi, can attached to the dust particles and be carried away through wind dispersal. Furthermore, several pathogenic genera were identified and the proportion was higher during the event days. In related to the functional composition, it seems that the abundance of nitrogen-fixing bacteria is also associated with the abundance of functional genes related to nitrogen metabolism. Nevertheless, the techniques used in this dissertation can also be applied for other environmental samples such as bioreactor or other microbiomes. Depending on the research objectives, one can choose their own approach that is suitable to the study. The application of metagenomics studies can give more insight in related to the microbial community and its metabolic potential. Also, increasing the datasets of the studies for research feasibility as well as finding of novel genes or organisms especially for the uncultured organisms. In conclusion, the decrease in sequencing costs and improvements in sequencing technology has resulted in a dramatic increase in the availability of sequencing data over the past decade. Whole metagenomics shotgun sequencing is becoming a popular strategy for various analyses, and in one of these days, it might replace the PCR-based analysis.