Title Page
Contents
Ⅰ. INTRODUCTION 16
1.1. Isolation bacteria from the soil 16
1.2. Polyphasic taxonomy 17
1.2.1. Genotypic methods 17
1.2.2. Phenotypic methods 18
1.2.3. Chemotaxonomy 19
1.3. Report of the genera of bacteria in this research 20
1.3.1. The genus Microvirga 20
1.3.2. The genus Hymenobacter 21
1.4. NGS (Next Genome Sequencing) 22
1.4.1. Illumina Sequencing 22
1.4.2. Analysis 26
Ⅱ. METHODS 27
2.1. Isolation and cultural conditions 27
2.2. Genotypic taxonomy 28
2.2.1. DNA extraction of novel bacteria 28
2.2.2. 16S rRNA gene sequencing 28
2.2.3. Genome sequencing 29
2.3. Phenotypic taxonomy 32
2.3.1. Gram staining test 32
2.3.2. Transmission electron microscopy 32
2.3.3. Catalase & Oxidase activities test 32
2.3.4. Growth & API test 32
2.4. Molecular taxonomy 33
2.4.1. Phylogenetic analysis 33
2.4.2. An Up–to–date Bacterial Core Gene set (UBCG) 34
2.4.3. Average Nucleotide Identity (ANI) 35
2.4.4. DNA-DNA Hybridization (DDH) 35
2.4.5. GC content 35
2.5. Chemotaxonomy 36
2.5.1. Fatty acid analysis 36
2.5.2. Polar lipid analysis 38
2.5.3. Isoprenoid quinine analysis 38
Ⅲ. RESULTS 39
3.1. Novel species of the genus Microvirga 39
3.1.1. Microvirga pudoricolor sp. nov. (strain BT291T)[이미지참조] 39
3.1.2. Microvirga alba sp. nov. (strain BT350T)[이미지참조] 53
3.2. Novel species of the genus Hymenobacter 67
3.2.1. Hymenobacter lucidus sp. nov. (strain BT178T)[이미지참조] 67
3.2.2. Hymenobacter nitidus sp. nov. (strain BT635T)[이미지참조] 83
Ⅳ. DISCUSSION 98
4.1. Description of Microvirga pudoricolor sp. nov. 98
4.2. Description of Microvirga alba sp. nov. 100
4.3. Description of Hymenobacter lucidus sp. nov. 102
4.4. Description of Hymenobacter nitidus sp. nov. 104
REFERENCE 105
ABSTRACT 117
국문요약 121
Table 1. Information of isolated strains. 27
Table 2. Quality control thresholds for each step in the NGS workflow. 31
Table 3. Rapid Annotation using Subsystem Technology (RAST) classification of strain BT291T.[이미지참조] 45
Table 4. Average nucleotide identity (ANI) analysis and digital DNA-DNA hybridization analysis between new species Microvirga pudoricolor BT291T and type strains of Microvirga species for which all genomes have been published.[이미지참조] 46
Table 5. Different characteristics of Microvirga pudoricolor and closely related species of genus Microvirga. 48
Table 6. The negative results of strain BT291T in API 20NE test and API ZYM test.[이미지참조] 50
Table 7. Cellular fatty acid profiles of Microvirga pudoricolor sp. nov., and closely related species of genus Microvirga. 51
Table 8. Rapid Annotation using Subsystem Technology (RAST) classification of strain BT350T.[이미지참조] 59
Table 9. Average nucleotide identity (ANI) analysis and digital DNA-DNA hybridization analysis between new species Microvirga alba BT350T and type strains of Microvirga species for which all genomes have been published.[이미지참조] 60
Table 10. Different characteristics of Microvirga alba and closely related species of genus Microvirga. 62
Table 11. The negative results of strain BT350T in API 20NE test and API ZYM test.[이미지참조] 64
Table 12. Cellular fatty acid profiles of Microvirga alba sp. nov., and closely related species of genus Microvirga. 65
Table 13. Genome assembly statistics of strain BT178T and the type strains of Hymenobacter species for which genomes have been published.[이미지참조] 74
Table 14. Rapid Annotation using Subsystem Technology (RAST) classification of strain BT178T.[이미지참조] 75
Table 15. Average nucleotide identity (ANI) values and in silico DNA-DNA hybridization values between strain BT178T and type strains of...[이미지참조] 76
Table 16. Different characteristics of Hymenobacter lucidus and closely related species of genus Hymenobacter. 78
Table 17. The negative results of strain BT178T in API 20NE test and API ZYM test.[이미지참조] 80
Table 18. Cellular fatty acid profiles of Hymenobacter lucidus sp. nov., and closely related species of genus Hymenobacter. 81
Table 19. Genome assembly statistics of strain BT635T and the type strains of Hymenobacter species for which genomes have been published.[이미지참조] 89
Table 20. Rapid Annotation using Subsystem Technology (RAST) classification of strain BT635T.[이미지참조] 90
Table 21. Average nucleotide identity (ANI) values and in silico DNA-DNA hybridization values between strain BT635T and type strains of...[이미지참조] 91
Table 22. Different characteristics of Hymenobacter nitidus and closely related species of genus Hymenobacter. 93
Table 23. The negative results of strain BT635T in API 20NE test and API ZYM test.[이미지참조] 95
Table 24. Cellular fatty acid profiles of Hymenobacter nitidus sp. nov., and closely related species of genus Hymenobacter. 96
Figure 1. DNA - BLT complex construction. 24
Figure 2. iSeq 100 using SBS Chemistry with one-channel detection. 25
Figure 3. Sample preparation. 37
Figure 4. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 16S rRNA gene sequences showing the relationships... 42
Figure 5. Maximum-Parsimony phylogenetic tree based on 16S rRNA gene sequences, showing the relationships strain BT291T with closely related...[이미지참조] 43
Figure 6. Maximum-Likelihood phylogenetic tree based on 16S rRNA gene sequences showing the relationships of strain BT291T with closely related...[이미지참조] 44
Figure 7. Transmission electron micrograph of strains BT291T from cultures grown on R2A agar for three days at 25 ℃.[이미지참조] 47
Figure 8. Polar lipid profiles of strain BT291T after two-dimensional chromatography.[이미지참조] 52
Figure 9. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 16S rRNA gene sequences showing the relationships... 56
Figure 10. Maximum-Parsimony phylogenetic tree based on 16S rRNA gene sequences, showing the relationships strain BT350T with closely related...[이미지참조] 57
Figure 11. Maximum-Likelihood phylogenetic tree based on 16S rRNA gene sequences showing the relationships of strain BT350T with closely related...[이미지참조] 58
Figure 12. Transmission electron micrograph of strains BT350T from cultures grown on R2A agar for three days at 25 ℃.[이미지참조] 61
Figure 13. Polar lipid profiles of strain BT350T after two-dimensional chromatography.[이미지참조] 66
Figure 14. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 16S rRNA gene sequences showing the relationships... 70
Figure 15. Maximum-Parsimony phylogenetic tree based on 16S rRNA gene sequences, showing the relationships strain BT178T with closely related...[이미지참조] 71
Figure 16. Maximum-Likelihood phylogenetic tree based on 16S rRNA gene sequences showing the relationships of strain BT178T with closely related...[이미지참조] 72
Figure 17. Genome-based phylogenetic tree reconstructed using an up-to-date bacterial core gene (UBCG) set showing the phylogenetic relationships... 73
Figure 18. Transmission electron micrograph of strains BT178T from cultures grown on R2A agar for three days at 25 ℃.[이미지참조] 77
Figure 19. Polar lipid profiles of strain BT178T after two-dimensional chromatography.[이미지참조] 82
Figure 20. Neighbor-joining phylogenetic tree reconstructed from a comparative analysis of 16S rRNA gene sequences showing the relationships... 86
Figure 21. Maximum-Parsimony phylogenetic tree based on 16S rRNA gene sequences, showing the relationships strain BT635T with closely related...[이미지참조] 87
Figure 22. Maximum-Likelihood phylogenetic tree based on 16S rRNA gene sequences showing the relationships of strain BT635T with closely related...[이미지참조] 88
Figure 23. Transmission electron micrograph of strains BT635T from cultures grown on R2A agar for three days at 25 ℃.[이미지참조] 92
Figure 24. Polar lipid profiles of strain BT635T after two-dimensional chromatography.[이미지참조] 97