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研究生：	陳玄莊 Huyen-Trang, Tran,
論文名稱：	總體基因體與全基因體分析顯現來自越戰的戴奧辛汙染對越南中部的土壤微生物相造成長期衝擊性影響 Metagenomic and whole-genome analyses revealed a long-term impact of dioxin contamination from the US-Vietnam War on the soil microbiomes in Central Vietnam
指導教授：	蔣鎮宇 Chiang, Tzen-Yuh
學位類別：	博士 Doctor
系所名稱：	生物科學與科技學院 - 生命科學系 Department of Life Sciences
論文出版年：	2019
畢業學年度：	107
語文別：	英文
論文頁數：	111
外文關鍵詞：	16S Metagenomics, Whole genome sequence, Agent Orange, the US-Vietnam War, dioxin hotspots, bacterial succession, Bacillus, Dioxin degradation pathway
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Understanding the assembly and evolution of soil microbiome after long-term chemical disturbances isa fundamental question in microbial ecology. However, this knowledge is poorly understood because of lacking material in nature and limited methods. Studying the contaminated land after the US-Vietnam War is an option for filling this gap. Accordingly, I used 16S metagenomics to investigate the diversity, structure, and evolution of bacterial community of the lands in Central Vietnam, the most serious areasuffered a long-term impact of dioxin contamination from the US-Vietnam War,withtwo different datasets (dioxin hotspot vs. non-polluted sites and four states mimicking secondary succession after contamination).Besides, whole-genome approaches were used to study the evolution of dioxin-degrading genes for three Bacillusspp. isolated from the contaminated soil. Here, although bacterial diversity did not significantly differ in dioxin hotspot and non-polluted sites, high levelof dioxin largely altered the bacterial structure. During the secondary succession, soil bacterial community gradually changedover time and became similar to pre-disturbance. However, a reduction of diversity occurred at the end of restoration, the discriminant taxa in each state changing greatly, and weak network organization all suggesteda delayed recoveryunder dioxin disturbance. Besides, niches model better explained the community dynamics in both dioxin hotspot and non-polluted sites, indicating that ecological selection maybeinvolved in the community assembly. The microbial community in the dioxin area has completed the resistance state (fluctuating environment) and entered the resilience state (constant environment). On the other hand, genome alignments suggestedthat the three Bacillus isolated from dioxin hotspots are closer with twenty-four Bacillus that involved in the dioxin degradation pathway (DDP). They possessedthree genes out of the15keys genes in DDP, includingdxnB and carC, the key enzymes for degrading complex structure of dioxins. Phylogenetic analysis showed the threeisolates tend to be clusteredcomparing with the other species belonging toBacillus. In addition, the trees ofthree DDP genes did not match with the 16S tree, suggesting natural selection may trigger DDP gene diversification in responseto environmental changes. Taken together, these findings revealed permanent changes in soil microbial communities and diversifying selection in Bacillusspp. after the long-term dioxin contamination in Central Vietnam.

ABSTRACT 	I
ACKNOWLEDGEMENTS 	II
TABLE OF CONTENTS 	III
LIST OF TABLES 	VI
LIST OF FIGURES 	VII
ABBREVIATIONS  	IX
CHAPTER ONE. GENERAL INTRODUCTION 	1
A. Research background 	1
1.1. The use of dioxin-containing herbicides in Vietnam by US forces during the US-Vietnam War 	1
1.2. Overall consequence of used dioxin-containing herbicides in Vietnam to environment and human health 	2
1.3. Estimation of residual dioxin in southern Vietnam environment 	6
1.4. Different rates of vegetation restoration on dioxin-contaminated lands	7
1.5. Dioxin-degrading bacteria 	7
1.6. 16S Metagenomics approach for identification of bacteria 	8
1.7. Chronosequence approach for microbiome dynamic during long time series	9
1.8. Layer of soil profile	9
1.9. Microbial succession after disturbance	10
1.10. Niches and Neutral model	10
B. Aim of thesis and overal pipeline of the studies	10
CHAPTER TWO. COMPARISON OF DIVERSITY, STRUCTURE, AND EVOLUTION OF BACTERIAL COMMUNITES BETWEEN DIOXIN HOTSPOTS AND NEIGHBORHOODS BY 16S METAGENOMICS 	12
2.1. Introduction 	12
2.2. Materials and methods 	14
2.2.1. Site descriptions and sampling..	14
2.2.2. DNA extraction and PCR 	14
2.2.3. Metagenomics sequencing and analysis………………………………….………15
2.3. Results 	17
2.3.1. General descriptions of microbial community by reads, OTUs number and assignation levels.	17
2.3.2. Alpha diversity 	17
  2.3.3. Bacterial taxa and composition	18
2.3.4. Bacteria community phenotype 	18
2.3.5. Evolution dynamics of microbial communities 	19
2.4. Discussions 	19
2.4.1. The difference in depth is not enough to make a difference .	19
2.4.2. Changes in structure of bacterial community as affected by dioxin contamination 	19
  2.4.3. High concentration of dioxin did not reduce the diversity of bacterial communities 	20
2.4.4. Selection is the most powerful factor driven by the evolution of bacterial community 	21
2.5. Conclusion	22
CHAPTER THREE. DELAY RECOVERY OF SOIL BACTERIAL COMMUNITY FOLLOWING DIOXIN DISTURBANCE FROM THE US-VIETNAM WAR	23
3.1. Introduction 	23
3.2. Materials and methods 	25
3.2.1. Site descriptions and sampling..	25
3.2.2. DNA extraction andPCR …………………………………………………..…… 27
3.2.3. Metagenomics sequencing and analysis..	27
3.3. Results 	29
3.3.1. Chemical-physical characteristic of soil samples 	29
3.3.2. Integration of multiple primers in bacterial identification by 16S Metagenomics 29
  3.3.3. Bacterial diversity during chronosequence ………….…………………………..30
3.3.4. Bacterial communities over time	30
3.3.5. Environmental condition related bacterial communities across chronosequence .31
3.3.6. OTU bacterial networks in each state of chronosequence 	32
3.4. Discussions 	33
3.4.1. Dramatically shift of bacterial community from S0 to S1	33
3.4.2. Bacterial community gradually changes over time 	36
3.4.3. Changed back toward the original state or delay or permanent changes 	37
3.5. Conclusion	38
CHAPTER FOUR. ASSEMBLY, ANNOTATION GENOME, AND EVOLUTION OF THREE Bacillus spp. ISOLATED FROM DIOXIN-CONTAMINATED SOIL AT DANANG AIRBASE VIETNAM	39
4.1. Purpose	39
4.2. Materials and methods 	39
4.2.1. Pick up three Bacillus species to further study..	39
4.2.2. Whole sequencing, assembly and annotation for three Bacillus genomes ……….40
4.2.3. Evolution analysis ..	41
4.3. Results and discussions	42
4.3.1. Isolation and bacterial identification 	42
4.3.2. Whole sequencing, assembly and annotation for three Bacillus genomes 	42
  4.3.3. Evolution	43
4.4. Conclusion	46
CHAPTER FIVE.GENERAL CONCLUSION AND SUGGESTIONS	47
5.1. Research synthesis 	47
5.2. Recommendation of my future work 	48
REFERENCES 	49
LIST OF TABLES

Table 2.1. Samples information	58
Table 2.2. Summary of sequencing reads and Operational taxonomic unit (OTUs) number	59
Table 2.3. Summary taxonomic assignation at different levels 	60
Table 3.1. Characteristic of the soil samples from 6 sites in four states of chronosequence in Central Vietnam	61
Table 3.2. List of analytical methods for soil parameters in this study	63
Table 3.3.Summary number of reads according to multiple primer pairs	65
Table 3.4. Summary of haplotypes and operational taxonomical unit (OTU) numbers detected using multiple markers ………………………………………………………..66
Table 3.5. Comparisons of diversity indices among soil states and soil sites …………..67
Table 3.6. OTUs lists that showed negative or positive correlation with 2,3,7,8-TCDD …………………………………………………………………………..68
Table 3.7. Summary network attributes in each state based on OTUs table (>0.5%)…..69
Table 4.1. A list of microbiota in dioxin-contaminated soil were detected by cultures ………………………………………………………………………………….70
Table 4.2. Raw data of DNA sequencing ……………………………………………..73
Table 4.3. Basic genome features of 3 Bacillus species ….…………………………….74
Table 4.4. Species, accession numbers, and general feature of Bacillus sp. used in this study ………………………………………………………………………………….....75
Figure 2.1. Sampling map ………………………………………………………………76
Figure 2.2. Proportion of total bacterial reads assigned to taxonomical ranks………………………………………………………………………... …………..77
Figure 2.3. The comparisons of Shannon diversity between two groups and four sub-groups ………………………………………………………………………………78
Figure 2.4. Read distribution of sequences assigned to phylum (A) and class (B) level across two groups and four sub-group ……...……………………………... …………..79
Figure 2.5. Volcano plot for OTUs distribution indioxin hotspot (H) and neighborhood (N)……………………….………………………………………………………………80
Figure 2.6. Principal components analysis (PCA) plots of 16 bacterial communities across two groups sub-groups.…………………………………………………….…….81
Figure 2.7. Metabolism comparison between dioxin hotspot (H) and neighborhood (N)82
Figure 2.8. Energy comparison between dioxin hotspot (H) and neighborhood (N).…..83
Figure 2.9. Evolution in each sample based on 16S database ….…………………...…84
Figure 2.10. Possible scenarios of bacterial communities changed by dioxin ……........86
Figure 3.1. Definition of the soil microbial communities mimic four states of soil microbial chronosequence in central Vietnam …………………………………………87
Figure 3.2. Map of sampling locations, soils properties, temperature and precipitation across mimickingstates …………………………………………...…………………...88
across mimicking states …………………………………………...……………………89
Figure 3.3. DNA gel electrophoresis of 31 samples before sending forNGS sequencing………………………………………………………………………………90
Figure 3.4. 16S Metagenomics work flow in study of Chapter 3………………..…...…91
Figure 3.5. Dioxin concentration distribution across mimicking states ………………..92
Figure 3.6. Bacterial community structure in the central Vietnam across mimicking chronosequence …………………………………………………………………………93Figure 3.7. Distribution of bacterial phyla across samples and their correlation with total TEQ …………………………………….…………………………………………….…94
Figure 3.8. Discriminant taxa significantly generated by LEfSe analysis for four states ……………………………………………………………………………………95
Figure 3.9. NMDS fitting with soils-properties and top 15 phyla ……………………...96
Figure 3.10. Co-occurrence network analysis of bacteria in each mimicking state ……97
Figure 3.11. Venn diagram between S0 and S3…………………………………………98
Figure 4.1. Assembly workflow …………………………………………………….….99
Figure 4.2. The phylogeny of these fifty-six microorganism that isolated from dioxin contamination …………………………………………………………………………100
Figure 4.3. Dioxin degradation pathway on KEGG …………………………………..101
Figure 4.4. Aligning entire genomes (Ba) with reference genome by MUMmer ……..102
Figure 4.5. Phylogenetic reconstruction based on 16S and u-COGs ………………….103
Figure 4.6. Violin plots (A box plot-density trace synergism) for COGs number in different groups ………………………………………………………………………..104
Figure 4.7. Variation Orthologous Groups (COG) functional groups at class level induced by different treatments ……………………………………………….………105
Figure 4.8. Comparative analyses of COGs shared inside group and between groups .107
Figure 4.9. Phylogeny trees of genes involved in DDP based on COGs database ……108
Figure 4.10. Orthologous genes of three Bacillus in dioxin hotspot (H) involve in Dioxin degradation pathway …………………………………………………………………..109

                                    

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