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Assessment and Mitigation of Airborne Contaminants from Swine Confinement Buildings

DC Field Value Language
dc.contributor.advisorProfessor Hong Lim Choi-
dc.contributor.author프리얀카-
dc.date.accessioned2017-07-13T08:23:54Z-
dc.date.available2017-07-13T08:23:54Z-
dc.date.issued2016-02-
dc.identifier.other000000131926-
dc.identifier.urihttps://hdl.handle.net/10371/119510-
dc.description학위논문 (박사)-- 서울대학교 대학원 : 농업생명과학대학 농생명공학부, 2016. 2. 최홍림.-
dc.description.abstractThe dominant factors influencing the abundance and community composition of bioaerosols in swine confinement buildings (SCBs) and their mitigation have been poorly studied. In this study, the indoor bioaerosols community structure and diversity were investigated in SCBs by using next generation sequencing platforms (454-pyrosequencing and Illumina). The effects of manure removal system and seasonal variations were investigated on bioaerosol communities obtained through NGS platforms. In this study, a biofiltration system was also used to explore how and to which extent it helped in mitigation of airborne contaminants emissions from SCBs.
The effect of manure removal systems (deep-pit manure removal with slats, scraper removal system, and deep-litter bed system) was studied on abundance and composition of airborne biotic contaminants in SCBs using cultivation-independent methods. The abundances of 16S rRNA genes and six tetracycline resistance genes (tetB, tetH, tetZ, tetO, tetQ, and tetW) were quantified using real-time PCR. The abundance of 16S rRNA gene and tetracycline resistance genes were significantly higher in SCBs equipped with a deep-pit manure removal system with slats, except for tetB gene. This observation contrasts with the trend found previously by culture-based studies. The aerial bacterial community composition, as measured by pairwise Bray–Curtis distances, varied significantly according to the manure removal system. 16S rRNA-based pyrosequencing revealed Firmicutes (72.4 %) as the dominant group with Lactobacillus as the major genus, while Actinobacteria constituted 10.7 % of the detectable bacteria. Firmicutes were more abundant in SCBs with deep-pit with slats, whereas Actinobacteria were highly abundant in SCBs with a deep-litter bed system. Overall, the results of this study suggested that the manure removal system played a key role in structuring the abundance and composition of airborne biotic contaminants in SCBs.
Little is known about the seasonal dynamics of biotic contaminants in SCBs. The biotic contaminants of seven SCBs were monitored during one visit in winter and one during summer. Paired-end Illumina sequencing of the 16S rRNA gene, V3 region, was used to examine seasonal shifts in bacterial community composition and diversity. The abundances of 16S rRNA genes and six tetracycline resistance genes (tetB, tetH, tetZ, tetO, tetQ, and tetW) were also quantified using real-time PCR. Bacterial abundances, community composition and diversity showed strong seasonal patterns defined by winter peaks in abundance and diversity. Microclimatic variables of SCBs, particularly air speed, PM2.5 and total suspended particles (TSP) were found significantly correlated to abundances, community composition, and diversity of bacterial bioaerosols. Seasonal fluctuations were also observed for four tetracycline resistance genes, tetH, tetO, tetQ, and tetW. The frequency of occurrences of these resistance genes were significantly higher in samples collected during winter and was also significantly correlated with air speed, PM2.5 and TSP. Overall, the results indicate that biotic contaminants in SCBs exhibit seasonal trends, and these could be associated with the microclimatic variables of SCBs.
Seasonal variations in community composition and diversity of airborne fungi were also studied in SCBs. Aerosol samples were collected from seven commercial swine farms in winter and summer. The internal transcribed spacer region 1 (ITS 1) of the ribosomal genes was sequenced using paired-end Illumina sequencing. Similarly to bacteria, indoor airborne fungal community composition and diversity were influenced by seasonal variations. However, the alpha and beta diversities showed very different patterns from one another, whereby alpha diversity peaked in winter and beta diversity peaked in summer. Several human allergen/pathogen related fungal genera were also identified in SCBs. Among these human allergen/pathogen related fungal genera, Candida, Aspergillus, Pichia, and Trichosporon varied significantly between seasons. In general, the relative abundance of human allergen/pathogen related fungal genera was higher in winter than in summer.
Biofiltration is known as one of cost-effective technology for treating the ventilation exhaust air from livestock buildings. However, little is known about the bacterial biofilm community immobilized in the packing material of biofilter which helps in breaking down of the contaminants present in air stream. A biological air filter system was used to reduce the emissions of airborne contaminants from SCBs, and also investigated the successional development of bacterial biofilm community in the packing material of biofilter by using the Illumina Miseq sequencing platform. It has been observed that the odorant reduction efficiency of biofilter was increased linearly with time. The results also indicated that bacterial biofilm community structure of biofilter exhibited a strong time successional pattern, and to a lesser extent, filtration stage and the interaction between time and filtration stage also led to a significant variation in community structure of bacterial biofilm. Certain bacterial phyla and genera with ability to degrade various odorants got enriched at later time point of the experiment which might result in reduction of a wide variety of odorants.
Overall, it has been found that the indoor bioaerosol community composition and diversity are to a large extent structured by manure removal system and seasonal variations. It has been also observed that biofilter system efficiently reduced the emissions of a large number of odorous gases from SCBs, and the correlations established between bacterial biofilm community succession and odorants removal could be helpful in establishing better management strategies to minimize the potential health impacts on both the farm workers and the public residing in close proximity to these buildings.
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dc.description.tableofcontentsCHAPTER 1. Airborne Contaminants Present in Swine Confinement Buildings and Their Control: An Introduction 1
1.1. Airborne contaminants present in swine confinement buildings 2
1.1.1. Particulate matter 2
1.1.2. Gaseous compounds 3
1.2. Bioaerosols and their characterization 4
1.2.1. Detection of bioaerosols by using cultivation- dependent approach 5
1.2.2. Detection of bioaerosols by using cultivation-independent metagenomic approach 7
1.3. Airborne contaminants mitigation strategies 9
1.3.1. Particulate matter mitigation 9
1.3.2. Gaseous compound mitigation 10
1.3.3. Bioaerosol mitigation 11
1.4. Objectives of this study 12

CHAPTER 2. Effect of Manure Removal System on Airborne Biotic Contaminants Present in Swine Confinement Buildings 14
2.1. Manure removal system influences the abundance and composition of airborne biotic contaminants in swine confinement buildings 15
2.1.1. Introduction 15
2.1.2. Materials and Methods 17
Characteristics of swine confinement buildings 17
Sample collection 18
DNA extraction and quantitative PCR 22
PCR amplification and pyrosequencing 23
Analysis of pyrosequencing data 25
Statistical processing and analysis of results 25
2.1.3. Results and discussion 26
Effect of manure removal system on bacterial 16S rRNA and tetracycline gene abundances 26
Effect of manure removal system on bacterial community composition and diversity 29
2.1.4. Conclusions 36

CHAPTER 3. Seasonal Variability in Airborne Biotic Contaminants in Swine Confinement Buildings 37
3.1. Seasonal variability in bacterial bioaerosols and antibiotic resistant genes in swine confinement buildings 38
3.1.1. Introduction 38
3.1.2. Materials and Methods 41
Characteristics of animal confinement buildings 41
Microclimate variables 41
Sample collection and DNA extraction 42
Illumina sequencing and data processing 43
Quantification of 16S rRNA and TcR genes 44
Statistical processing and analysis of results 45
3.1.3. Results and discussion 46
Season variations in microclimate variables and bacterial bioaerosols diversity 46
Effect of season and microclimatic parameters on community composition of bacterial bioaerosols 53
Comparison of aerial and fecal bacterial community 59
Seasonal variations in abundance of 16S rRNA and TcR genes 59
3.1.4. Conclusions 67
3.2. Seasonal variations in community composition and the diversity of airborne fungi in swine confinement buildings 68
3.2.1. Introduction 68
3.2.2. Materials and methods 70
Aerosol collection 70
DNA extraction and PCR amplification 70
Sequencing and data processing 70
Statistical analysis 71
3.2.3. Results and discussion 72
Effect of seasonal variations on fungal diversity 73
Effect of seasonal variations on fungal community composition 73
Potential human allergen/pathogen related fungal genera 80
3.2.4. Conclusions 84

CHAPTER 4. Mitigation of Airborne Contaminants Emission from Swine Confinement Buildings 85
4.1. Biofilter bacterial biofilm community succession reduces the emissions of airborne contaminants from swine confinement buildings 86
4.1.1. Introduction 86
4.1.2. Materials and Methods 87
Two-stage biofilter 87
Experimental setup and analysis of odorous gases 88
Sample collection and DNA extraction 91
Illumina sequencing and data processing 91
Statistical processing and analysis of results 92
4.1.3 Results and discussion 93
Odor reduction efficiency of biofilter 93
Successional development of bacterial biofilm community 93
4.1.4. Conclusions 103
GENERAL CONCLUSIONS 104
Significance of this study for swine farmers 106

REFERENCES 108

APPENDIX 133

ABSTRACT IN KOREAN 137
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dc.formatapplication/pdf-
dc.format.extent8241952 bytes-
dc.format.mediumapplication/pdf-
dc.language.isoen-
dc.publisher서울대학교 대학원-
dc.subjectbioaerosols-
dc.subjectbiofilter-
dc.subjectbacteria-
dc.subjectfungi-
dc.subjectIllumina-
dc.subjectinternal transcribed spacer-
dc.subjectmanure removal system-
dc.subjectpyrosequencing-
dc.subjectseasonal variations-
dc.subjectswine confinement buildings-
dc.subject16S rRNA gene-
dc.subject.ddc630-
dc.titleAssessment and Mitigation of Airborne Contaminants from Swine Confinement Buildings-
dc.typeThesis-
dc.contributor.AlternativeAuthorPriyanka Kumari-
dc.description.degreeDoctor-
dc.citation.pages156-
dc.contributor.affiliation농업생명과학대학 농생명공학부-
dc.date.awarded2016-02-
Appears in Collections:
College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Agricultural Biotechnology (농생명공학부)Theses (Ph.D. / Sc.D._농생명공학부)
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