Biodiv Sci ›› 2016, Vol. 24 ›› Issue (10): 1154-1163. DOI: 10.17520/biods.2016121
Special Issue: 土壤生物与土壤健康
• Original Papers: Microbial Diversity • Previous Articles Next Articles
Guohong Liu, Bo Liu*(), Yujing Zhu, Jianmei Che, Cibin Ge, Mingxing Su, Jianyang Tang
Received:
2016-05-04
Accepted:
2016-10-24
Online:
2016-10-20
Published:
2016-11-10
Contact:
Liu Bo
Guohong Liu, Bo Liu, Yujing Zhu, Jianmei Che, Cibin Ge, Mingxing Su, Jianyang Tang. Diversity of Bacillus-like species in Taiwan[J]. Biodiv Sci, 2016, 24(10): 1154-1163.
序号 No | 土样编号 Soil no. | 市/县 City/county | 采集地点 Location | 生境类型 Habitat type | 采集日期 Collecting date |
---|---|---|---|---|---|
1 | 4570 | 台北市 Taipei City | 阳明山花钟 Flower-clock, Yangmingshan | 草地 Grassland | 2011-08-28 |
2 | 4569 | 阳明山蒋介石雕像 Statue of Chaing Kai-shek, Yangmingshan | 草地 Grassland | 2011-08-28 | |
3 | 4568 | 士林官邸 Chaing Kai-shek Shilin Residence | 芭乐树下 Rhizosphere soils of a Guava tree | 2011-08-28 | |
4 | 4566 | 士林官邸 Chaing Kai-shek Shilin Residence | 白千层树下 Rhizosphere soils of Melaleuca alternifolia | 2011-08-28 | |
5 | 4567 | 士林官邸 Chaing Kai-shek Shilin Residence | 草地 Grassland | 2011-08-28 | |
6 | 4559 | 桃园县 Taoyuan County | 慈湖石像 Stone in Tzuhu | 裸土 Bare soil | 2011-08-27 |
7 | 4561 | 慈湖蒋寝 Chiang Kai-shek Bedroom in Tzuhu | 裸土 Bare soil | 2011-08-27 | |
8 | 4564 | 桃园大溪 Ta-Hsi town, Taoyuan | 九里香根际 Rhizosphere soils of Murraya paniculata | 2011-08-27 | |
9 | 4562 | 慈湖 Tzuhu | 黄花槐 Rhizosphere soils of Sophora xanthantha | 2011-08-27 | |
10 | 4575 | 中坜高速休息区 Highway resting area, Chungli, Taoyuan | 裸土 Bare soil | 2011-08-29 | |
11 | 4574 | 新竹县 Hsinchu County | 新竹食品研究所 Institute of Food Research, Hsinchu | 草地 Grassland | 2011-08-29 |
12 | 4576 | 苗栗县 Miaoli County | 西湖高速休息区 Highway resting area, Xizi Bay Spot, Kaohsiung | 裸土 Bare soil | 2011-08-30 |
13 | 4572 | 台中市 Taichung City | 台湾大学农学院 College of Agriculture, Taiwan University | 草地 Grassland | 2011-08-29 |
14 | 4582 | 南投县 Nantou County | 中台寺 Chung Tai Template | 林地 Forest land | 2011-08-27 |
15 | 4577 | 日月潭 Sun-Moon Lake | 草地 Grassland | 2011-08-30 | |
16 | 4579 | 日月潭宏观寺 Soils at Hongguan Temple, Sun-Moon Lake | 草地 Grassland | 2011-08-30 | |
17 | 4583 | 台一农场 Tai Yi Farm, Nantou | 草地 Grassland | 2011-08-31 | |
18 | 4580 | 嘉义市 Chiayi City | 嘉义大学 Chiayi University | 草地 Grassland | 2011-08-31 |
19 | 4587 | 高雄市 Kaohsiung City | 高雄农友种业 Kaohsiung Nongyou Seeding | 草地 Grassland | 2011-09-01 |
20 | 4585 | 高雄农友种业 Kaohsiung Nongyou Seeding | 草地 Grassland | 2011-09-01 |
Table 1 Information of soil samples from Taiwan
序号 No | 土样编号 Soil no. | 市/县 City/county | 采集地点 Location | 生境类型 Habitat type | 采集日期 Collecting date |
---|---|---|---|---|---|
1 | 4570 | 台北市 Taipei City | 阳明山花钟 Flower-clock, Yangmingshan | 草地 Grassland | 2011-08-28 |
2 | 4569 | 阳明山蒋介石雕像 Statue of Chaing Kai-shek, Yangmingshan | 草地 Grassland | 2011-08-28 | |
3 | 4568 | 士林官邸 Chaing Kai-shek Shilin Residence | 芭乐树下 Rhizosphere soils of a Guava tree | 2011-08-28 | |
4 | 4566 | 士林官邸 Chaing Kai-shek Shilin Residence | 白千层树下 Rhizosphere soils of Melaleuca alternifolia | 2011-08-28 | |
5 | 4567 | 士林官邸 Chaing Kai-shek Shilin Residence | 草地 Grassland | 2011-08-28 | |
6 | 4559 | 桃园县 Taoyuan County | 慈湖石像 Stone in Tzuhu | 裸土 Bare soil | 2011-08-27 |
7 | 4561 | 慈湖蒋寝 Chiang Kai-shek Bedroom in Tzuhu | 裸土 Bare soil | 2011-08-27 | |
8 | 4564 | 桃园大溪 Ta-Hsi town, Taoyuan | 九里香根际 Rhizosphere soils of Murraya paniculata | 2011-08-27 | |
9 | 4562 | 慈湖 Tzuhu | 黄花槐 Rhizosphere soils of Sophora xanthantha | 2011-08-27 | |
10 | 4575 | 中坜高速休息区 Highway resting area, Chungli, Taoyuan | 裸土 Bare soil | 2011-08-29 | |
11 | 4574 | 新竹县 Hsinchu County | 新竹食品研究所 Institute of Food Research, Hsinchu | 草地 Grassland | 2011-08-29 |
12 | 4576 | 苗栗县 Miaoli County | 西湖高速休息区 Highway resting area, Xizi Bay Spot, Kaohsiung | 裸土 Bare soil | 2011-08-30 |
13 | 4572 | 台中市 Taichung City | 台湾大学农学院 College of Agriculture, Taiwan University | 草地 Grassland | 2011-08-29 |
14 | 4582 | 南投县 Nantou County | 中台寺 Chung Tai Template | 林地 Forest land | 2011-08-27 |
15 | 4577 | 日月潭 Sun-Moon Lake | 草地 Grassland | 2011-08-30 | |
16 | 4579 | 日月潭宏观寺 Soils at Hongguan Temple, Sun-Moon Lake | 草地 Grassland | 2011-08-30 | |
17 | 4583 | 台一农场 Tai Yi Farm, Nantou | 草地 Grassland | 2011-08-31 | |
18 | 4580 | 嘉义市 Chiayi City | 嘉义大学 Chiayi University | 草地 Grassland | 2011-08-31 |
19 | 4587 | 高雄市 Kaohsiung City | 高雄农友种业 Kaohsiung Nongyou Seeding | 草地 Grassland | 2011-09-01 |
20 | 4585 | 高雄农友种业 Kaohsiung Nongyou Seeding | 草地 Grassland | 2011-09-01 |
代表菌株 Strain | 最相近菌种 Closed match | 16S rRNA登录号 16S rRNA accession no. | 相似性 Similarity (%) |
---|---|---|---|
FJAT-14427 | 假蕈状芽胞杆菌 Bacillus pseudomycoides | KC013911 | 100 |
FJAT-14428 | 黄海芽胞杆菌 Bacillus marisflavi | KC013912 | 99.71 |
FJAT-14429 | 朝日芽胞杆菌 Bacillus asahii | KC013913 | 99.87 |
FJAT-14435 | 简单芽胞杆菌 Bacillus simplex | KC013914 | 100 |
FJAT-14438 | 解木糖赖氨酸芽胞杆菌 Lysinibacillus xylanilyticus | KC013915 | 99.86 |
FJAT-14439 | 阿氏芽胞杆菌 Bacillus aryabhattai | KC013916 | 100 |
FJAT-14454 | 枯草芽胞杆菌 Bacillus subtilis | KC013931 | 99.89 |
FJAT-14481 | 蕈状芽胞杆菌 Bacillus mycoides | KC013917 | 97.98 |
FJAT-14485 | 长赖氨酸芽胞杆菌 Lysinibacillus macroides | KC013918 | 99.37 |
FJAT-14491 | 嗜气芽胞杆菌 Bacillus aerophilus | KC013919 | 100 |
FJAT-14498 | 壁芽胞杆菌 Bacillus muralis | KC013920 | 100 |
FJAT-14510 | 纺锤形赖氨酸芽胞杆菌 Lysinibacillus fusiformis | KC013921 | 100 |
FJAT-14535 | 土壤芽胞杆菌 Bacillus soli | KC013922 | 98.51 |
FJAT-14559 | 婴儿芽胞杆菌 Bacillus infantis | KC013923 | 99.81 |
FJAT-14564 | 球形赖氨酸芽胞杆菌 Lysinibacillus sphaericus | KC013925 | 98.81 |
FJAT-14586 | 苏云金芽胞杆菌 Bacillus thuringiensis | KC013926 | 100 |
FJAT-14602 | 坚强芽胞杆菌 Bacillus firmus | KC013927 | 98.86 |
FJAT-14603 | 海洋沉积芽胞杆菌 Bacillus oceanisediminis | KC013928 | 98.95 |
FJAT-14607 | 病研所芽胞杆菌 Bacillus idriensis | KC013929 | 100 |
FJAT-14613 | 蜡样芽胞杆菌 Bacillus cereus | KC013930 | 100 |
Table 2 Identification of Bacillus-like species by 16S rRNA sequencing
代表菌株 Strain | 最相近菌种 Closed match | 16S rRNA登录号 16S rRNA accession no. | 相似性 Similarity (%) |
---|---|---|---|
FJAT-14427 | 假蕈状芽胞杆菌 Bacillus pseudomycoides | KC013911 | 100 |
FJAT-14428 | 黄海芽胞杆菌 Bacillus marisflavi | KC013912 | 99.71 |
FJAT-14429 | 朝日芽胞杆菌 Bacillus asahii | KC013913 | 99.87 |
FJAT-14435 | 简单芽胞杆菌 Bacillus simplex | KC013914 | 100 |
FJAT-14438 | 解木糖赖氨酸芽胞杆菌 Lysinibacillus xylanilyticus | KC013915 | 99.86 |
FJAT-14439 | 阿氏芽胞杆菌 Bacillus aryabhattai | KC013916 | 100 |
FJAT-14454 | 枯草芽胞杆菌 Bacillus subtilis | KC013931 | 99.89 |
FJAT-14481 | 蕈状芽胞杆菌 Bacillus mycoides | KC013917 | 97.98 |
FJAT-14485 | 长赖氨酸芽胞杆菌 Lysinibacillus macroides | KC013918 | 99.37 |
FJAT-14491 | 嗜气芽胞杆菌 Bacillus aerophilus | KC013919 | 100 |
FJAT-14498 | 壁芽胞杆菌 Bacillus muralis | KC013920 | 100 |
FJAT-14510 | 纺锤形赖氨酸芽胞杆菌 Lysinibacillus fusiformis | KC013921 | 100 |
FJAT-14535 | 土壤芽胞杆菌 Bacillus soli | KC013922 | 98.51 |
FJAT-14559 | 婴儿芽胞杆菌 Bacillus infantis | KC013923 | 99.81 |
FJAT-14564 | 球形赖氨酸芽胞杆菌 Lysinibacillus sphaericus | KC013925 | 98.81 |
FJAT-14586 | 苏云金芽胞杆菌 Bacillus thuringiensis | KC013926 | 100 |
FJAT-14602 | 坚强芽胞杆菌 Bacillus firmus | KC013927 | 98.86 |
FJAT-14603 | 海洋沉积芽胞杆菌 Bacillus oceanisediminis | KC013928 | 98.95 |
FJAT-14607 | 病研所芽胞杆菌 Bacillus idriensis | KC013929 | 100 |
FJAT-14613 | 蜡样芽胞杆菌 Bacillus cereus | KC013930 | 100 |
Fig. 1 Neighbor-joining (NJ) phylogenetic tree of Bacillus-like species based on 16S rRNA gene sequences. Numbers indicate bootstrap values (> 50%) of NJ.
种名 Species | 台北市 Taipei City | 桃园县 Taoyuan County | 新竹县 Hsinchu County | 苗栗县 Miaoli County | 南投县 Nantou County | 台中市 Taichung City | 嘉义市 Chiayi City | 高雄市 Kaohsiung City | 总体 Total |
---|---|---|---|---|---|---|---|---|---|
阿氏芽胞杆菌 Bacillus aryabhattai | 100 | 100 | 0 | 0 | 75 | 100 | 0 | 100 | 85 |
苏云金芽胞杆菌 B. thuringiensis | 80 | 80 | 100 | 100 | 75 | 100 | 100 | 50 | 75 |
蜡样芽胞杆菌 B. cereus | 20 | 80 | 0 | 0 | 25 | 100 | 100 | 0 | 55 |
假蕈状芽胞杆菌 B. pseudomycoides | 60 | 20 | 0 | 0 | 0 | 0 | 100 | 100 | 35 |
解木糖赖氨酸芽胞杆菌 Lysinibacillus xylanilyticus | 20 | 40 | 0 | 0 | 25 | 0 | 0 | 0 | 25 |
纺锤形赖氨酸芽胞杆菌 L. fusiformis | 0 | 20 | 100 | 0 | 0 | 100 | 0 | 50 | 15 |
壁芽胞杆菌 B. muralis | 0 | 20 | 100 | 0 | 0 | 0 | 0 | 0 | 10 |
黄海芽胞杆菌 B. marisflavi | 20 | 0 | 100 | 0 | 0 | 0 | 0 | 0 | 10 |
坚强芽胞杆菌 B. firmus | 0 | 0 | 0 | 100 | 0 | 0 | 100 | 0 | 10 |
简单芽胞杆菌 B. simplex | 40 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 10 |
土壤芽胞杆菌 B. soli | 0 | 0 | 0 | 0 | 0 | 100 | 0 | 0 | 10 |
蕈状芽胞杆菌 B. mycoides | 0 | 0 | 0 | 0 | 25 | 0 | 0 | 0 | 5 |
朝日芽胞杆菌 B. asahii | 20 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 |
枯草芽胞杆菌 B. subtilis | 20 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 |
嗜气芽胞杆菌 B. aerophilus | 0 | 0 | 0 | 0 | 0 | 100 | 0 | 0 | 5 |
L. macroides | 0 | 0 | 0 | 100 | 0 | 0 | 0 | 0 | 5 |
婴儿芽胞杆菌 B. infantis | 0 | 0 | 0 | 100 | 0 | 0 | 0 | 0 | 5 |
球形赖氨酸芽胞杆菌 L. sphaericus | 0 | 0 | 0 | 0 | 25 | 0 | 0 | 0 | 5 |
病研所芽胞杆菌 B. idriensis | 0 | 0 | 0 | 0 | 0 | 0 | 100 | 0 | 5 |
海洋沉积芽胞杆菌 B. oceanisediminis | 0 | 0 | 0 | 0 | 0 | 0 | 100 | 0 | 5 |
Table 3 The frequency (%) of Bacillus-like species isolated from soils in Taiwan
种名 Species | 台北市 Taipei City | 桃园县 Taoyuan County | 新竹县 Hsinchu County | 苗栗县 Miaoli County | 南投县 Nantou County | 台中市 Taichung City | 嘉义市 Chiayi City | 高雄市 Kaohsiung City | 总体 Total |
---|---|---|---|---|---|---|---|---|---|
阿氏芽胞杆菌 Bacillus aryabhattai | 100 | 100 | 0 | 0 | 75 | 100 | 0 | 100 | 85 |
苏云金芽胞杆菌 B. thuringiensis | 80 | 80 | 100 | 100 | 75 | 100 | 100 | 50 | 75 |
蜡样芽胞杆菌 B. cereus | 20 | 80 | 0 | 0 | 25 | 100 | 100 | 0 | 55 |
假蕈状芽胞杆菌 B. pseudomycoides | 60 | 20 | 0 | 0 | 0 | 0 | 100 | 100 | 35 |
解木糖赖氨酸芽胞杆菌 Lysinibacillus xylanilyticus | 20 | 40 | 0 | 0 | 25 | 0 | 0 | 0 | 25 |
纺锤形赖氨酸芽胞杆菌 L. fusiformis | 0 | 20 | 100 | 0 | 0 | 100 | 0 | 50 | 15 |
壁芽胞杆菌 B. muralis | 0 | 20 | 100 | 0 | 0 | 0 | 0 | 0 | 10 |
黄海芽胞杆菌 B. marisflavi | 20 | 0 | 100 | 0 | 0 | 0 | 0 | 0 | 10 |
坚强芽胞杆菌 B. firmus | 0 | 0 | 0 | 100 | 0 | 0 | 100 | 0 | 10 |
简单芽胞杆菌 B. simplex | 40 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 10 |
土壤芽胞杆菌 B. soli | 0 | 0 | 0 | 0 | 0 | 100 | 0 | 0 | 10 |
蕈状芽胞杆菌 B. mycoides | 0 | 0 | 0 | 0 | 25 | 0 | 0 | 0 | 5 |
朝日芽胞杆菌 B. asahii | 20 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 |
枯草芽胞杆菌 B. subtilis | 20 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 5 |
嗜气芽胞杆菌 B. aerophilus | 0 | 0 | 0 | 0 | 0 | 100 | 0 | 0 | 5 |
L. macroides | 0 | 0 | 0 | 100 | 0 | 0 | 0 | 0 | 5 |
婴儿芽胞杆菌 B. infantis | 0 | 0 | 0 | 100 | 0 | 0 | 0 | 0 | 5 |
球形赖氨酸芽胞杆菌 L. sphaericus | 0 | 0 | 0 | 0 | 25 | 0 | 0 | 0 | 5 |
病研所芽胞杆菌 B. idriensis | 0 | 0 | 0 | 0 | 0 | 0 | 100 | 0 | 5 |
海洋沉积芽胞杆菌 B. oceanisediminis | 0 | 0 | 0 | 0 | 0 | 0 | 100 | 0 | 5 |
样本编号 Sample no. | 样本来源 Source | 菌种数 Strain number | Shannon指数 Shannon index (H') | Shannon指数平均值 Average of Shannon index |
---|---|---|---|---|
4570 | 台北市 Taipei City | 6 | 2.5850 | 2.0850 |
4569 | 5 | 2.3220 | ||
4568 | 4 | 2.0000 | ||
4566 | 5 | 2.3220 | ||
4567 | 3 | 1.5850 | ||
4559 | 桃园县 Taoyuan County | 2 | 1.0000 | 1.2925 |
4561 | 5 | 2.3220 | ||
4564 | 4 | 2.0000 | ||
4562 | 5 | 2.3220 | ||
4575 | 3 | 1.5850 | ||
4574 | 新竹县 Hsinchu County | 4 | 2.0000 | 2.0000 |
4576 | 苗栗县 Miaoli County | 5 | 2.3220 | 2.3220 |
4572 | 台中市 Taichung City | 6 | 2.5850 | 2.5850 |
4582 | 南投县 Nantou County | 3 | 1.5850 | 1.5850 |
4577 | 3 | 1.5850 | ||
4579 | 4 | 2.0000 | ||
4583 | 3 | 1.5850 | ||
4580 | 嘉义市 Chiayi City | 6 | 2.5850 | 2.5850 |
4585 | 高雄市 Kaohsiung City | 3 | 1.5850 | 1.7925 |
4587 | 4 | 2.0000 |
Table 4 The diversity of Bacillus-like species of the soil samples of counties and cities in Taiwan
样本编号 Sample no. | 样本来源 Source | 菌种数 Strain number | Shannon指数 Shannon index (H') | Shannon指数平均值 Average of Shannon index |
---|---|---|---|---|
4570 | 台北市 Taipei City | 6 | 2.5850 | 2.0850 |
4569 | 5 | 2.3220 | ||
4568 | 4 | 2.0000 | ||
4566 | 5 | 2.3220 | ||
4567 | 3 | 1.5850 | ||
4559 | 桃园县 Taoyuan County | 2 | 1.0000 | 1.2925 |
4561 | 5 | 2.3220 | ||
4564 | 4 | 2.0000 | ||
4562 | 5 | 2.3220 | ||
4575 | 3 | 1.5850 | ||
4574 | 新竹县 Hsinchu County | 4 | 2.0000 | 2.0000 |
4576 | 苗栗县 Miaoli County | 5 | 2.3220 | 2.3220 |
4572 | 台中市 Taichung City | 6 | 2.5850 | 2.5850 |
4582 | 南投县 Nantou County | 3 | 1.5850 | 1.5850 |
4577 | 3 | 1.5850 | ||
4579 | 4 | 2.0000 | ||
4583 | 3 | 1.5850 | ||
4580 | 嘉义市 Chiayi City | 6 | 2.5850 | 2.5850 |
4585 | 高雄市 Kaohsiung City | 3 | 1.5850 | 1.7925 |
4587 | 4 | 2.0000 |
Fig. 2 A dendrogram of Bacillus-like species isolated from Taiwan based on frequency of Bacillus-like species. The Ward’s method and Euclidean distance model were used to construct dendrogram.
Fig. 3 A dendrogram of collection sites in Taiwan based on frequency of Bacillus-like species. The Ward’s method and Euclidean distance model were used to construct dendrogramt.
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