Diversity and distribution of cultivable Bacillus-like species in soils collected from Wuyishan Nature Reserve

doi:10.17520/biods.2016085

Abstract

Abstract:

The present paper reported the distribution and diversity of cultivable Bacillus-like species in soils from Wuyishan National Nature Reserve. In June 2012, 75 soil samples were collected from the peak, middle and base of the Huanggang Mountain, Tongmuguan, Guadun, and Dazhulan in the reserve. The Bacillus-like species were isolated by plating the series dilution after 80℃water bath heating the soil samples and then identified using 16S rRNA gene sequence analysis. Results showed that 418 strains isolated from the soil samples belonged to 42 Bacillus-like species, which were grouped into eight genera containing Bacillus, Brevibacillus, Fictibacillus, Lysinibacillus, Paenibacillus, Psychrobacillu, Rummeliibacillus and Viridibacillus. Furthermore, Bacillus was the dominant genus, followed by the genera Paenibacillus and Lysinibacillus. The greatest number of Bacillus-like species was isolated from the soils in Dazhulan, while the fewest were found at the middle and base of Huanggang Mountain. The quantities of Bacillus-like species in soils collected from Guadun and Dazhulan were more than 3.6×10⁶ cfu/g soil, but less than 4.9×10⁵ cfu/g soil at the top and middle of Huanggang Mountain. Bacillus cereus, B. mycoides, B. thuringiensis, and Lysinibacillus xylanilyticus were isolated from all six sites, which were dominated by B. thuringiensis and L. xylanilyticus. The Shannon-Wiener diversity index and Pielou’s evenness index for Bacillus-like species isolated from Tongmuguan were higher than those at the other five sites, while the lowest Shannon-Wiener diversity index, Pielou’s evenness index and Simpson index values were found in the soils from Guadun. There was a significant correlation between the altitude and the quantity of B. mycoides and B. thuringiensis, with correlations of 0.852 and -0.834, respectively. Additionally, highly significant correlations were found between the altitude and the isolating frequency of B. cereus, B. mycoides and B. thuringiensis, with correlations of 0.960, 0.952 and -0.931, respectively. These results indicated the abundance and diversity of the Bacillus-like species community and bacteria species were extremely rich in Wuyishan Nature Reserve.

Key words: Wuyishan Nature Reserve, Bacillus-like species, 16S rRNA, diversity, isolating frequency

Cibin Ge, Rong Zheng, Bo Liu, Guohong Liu, Jianmei Che, Jianyang Tang. Diversity and distribution of cultivable Bacillus-like species in soils collected from Wuyishan Nature Reserve[J]. Biodiv Sci, 2016, 24(10): 1164-1176.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2016085

https://www.biodiversity-science.net/EN/Y2016/V24/I10/1164

Figures/Tables 7

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采集地点 Location	海拔 Altitude (m)	土壤样品数 No. of samples	生境类型 Habitat	土壤类型 Agrotype
黄岗山顶部 Peak of the Huanggang Mountain (PHM)	2,158	15	草甸、岩石 Meadow, rock	山地草甸土 Mountain meadow soil
黄岗山中部 Middle of the Huanggang Mountain (MHM)	1,700	13	树林、草丛、路边等 Forest, grass, roadside	黄壤 Yellow soil
黄岗山底部 Base of the Huanggang Mountain (BHM)	1,100	7	树林、草丛、路边等 Forest, grass, roadside	红黄壤、黄壤 Red and yellow soil, yellow soil
桐木关 Tongmuguan (TMG)	890	12	树林、草丛、路边等 Forest, grass, roadside	红黄壤 Red and yellow soil
挂墩 Guadun (GD)	1,200	14	树林、草丛、路边等 Forest, grass, roadside	红黄壤、黄壤 Red and yellow soil, yellow soil
大竹岚 Dazhulan (DZL)	1,000	14	树林、草丛 Forest, grass	红黄壤、黄壤 Red and yellow soil, yellow soil

采集地点 Location	海拔 Altitude (m)	土壤样品数 No. of samples	生境类型 Habitat	土壤类型 Agrotype
黄岗山顶部 Peak of the Huanggang Mountain (PHM)	2,158	15	草甸、岩石 Meadow, rock	山地草甸土 Mountain meadow soil
黄岗山中部 Middle of the Huanggang Mountain (MHM)	1,700	13	树林、草丛、路边等 Forest, grass, roadside	黄壤 Yellow soil
黄岗山底部 Base of the Huanggang Mountain (BHM)	1,100	7	树林、草丛、路边等 Forest, grass, roadside	红黄壤、黄壤 Red and yellow soil, yellow soil
桐木关 Tongmuguan (TMG)	890	12	树林、草丛、路边等 Forest, grass, roadside	红黄壤 Red and yellow soil
挂墩 Guadun (GD)	1,200	14	树林、草丛、路边等 Forest, grass, roadside	红黄壤、黄壤 Red and yellow soil, yellow soil
大竹岚 Dazhulan (DZL)	1,000	14	树林、草丛 Forest, grass	红黄壤、黄壤 Red and yellow soil, yellow soil

类群 Group	代表菌株 Strains	登录号 GenBank accession no.	最相近菌种 Closest match	相似性 Sequence identity (%)
芽胞杆菌属 Bacillus	FJAT-16209	KF278157	阿氏芽胞杆菌 Bacillus aryabhattai	100.0
	FJAT-16883	KF278197	巴达维亚芽胞杆菌 B. bataviensis	100.0
	FJAT-16354	KF278179	科研中心芽胞杆菌 B. cecembensis	95.95
	FJAT-16889	KF278199	蜡样芽胞杆菌 B. cereus	100.0
	FJAT-16469	KF278181	根内芽胞杆菌 B. endoradicis	99.12
	FJAT-16705	KF278193	盐敏芽胞杆菌 B. halmapalus	98.52
	FJAT-16532	KF278187	印空研芽胞杆菌 B. isronensis	100.0
	FJAT-16048	KF278123	万里浦芽胞杆菌 B. manliponensis	98.46
	FJAT-16291	KF278168	地衣芽胞杆菌 B. licheniformis	99.85
	FJAT-16872	KF278195	黄海芽胞杆菌 B. marisflavi	100.0
	FJAT-16134	KF278130	甲基营养型芽胞杆菌 B. methylotrophicus	99.86
	FJAT-16162	KF278147	壁芽胞杆菌 B. muralis	99.85
	FJAT-16884	KF278198	蕈状芽胞杆菌 B. mycoides	100.0
	FJAT-16339	KF278175	休闲地芽胞杆菌 B. novalis	99.83
	FJAT-16201	KF278155	假蕈状芽胞杆菌 B. pseudomycoides	99.85
	FJAT-16578	KF278189	沙福芽胞杆菌 B. safensis	100.0
	FJAT-17017	KF278204	简单芽胞杆菌 B. simplex	100.0
	FJAT-17042	KF278206	特基拉芽胞杆菌 B. tequilensis	99.89
	FJAT-16178	KF278153	苏云金芽胞杆菌 B. thuringiensis	100.0
	FJAT-16301	KF278171	韦氏芽胞杆菌 B. weihenstephanensis	100.0
短芽胞杆菌属 Brevibacillus	FJAT-16350	KF278177	土壤短芽胞杆菌 Brevibacillus agri	99.38
虚构芽胞杆菌属 Fictibacillus	FJAT-17014	KF278203	南海虚构芽胞杆菌 Fictibacillus nanhaiensis	100.0
赖氨酸芽胞杆菌属 Lysinibacillus	FJAT-16156	KF278145	纺锤形赖氨酸芽胞杆菌 Lysinibacillus fusiformis	100.0
	FJAT-16167	KF278149	延长赖氨酸芽胞杆菌 L. macroides	99.57
	FJAT-16506	KF278185	芒果土赖氨酸芽胞杆菌 L. mangiferahumi	99.98
	FJAT-16266	KF278163	马赛赖氨酸芽胞杆菌 L. massiliensis	97.51
	FJAT-16248	KF278158	低硼赖氨酸芽胞杆菌 L. parviboronicapiens	99.22
	FJAT-16141	KF278135	球形赖氨酸芽胞杆菌 L. sphaericus	99.14
	FJAT-16140	KF278134	解木糖赖氨酸芽胞杆菌 L. xylanilyticus	100.0
类芽胞杆菌属 Paenibacillus	FJAT-16151	KF278140	蜂房类芽胞杆菌 Paenibacillus alvei	98.82
	FJAT-16703	KF278192	蜜蜂类芽胞杆菌 P. apiarius	98.88
	FJAT-16893	KF278200	栗树类芽胞杆菌 P. castaneae	98.05
	FJAT-16129	KF278128	埃及类芽胞杆菌 P. elgii	99.40
	FJAT-16135	KF278131	灿烂类芽胞杆菌 P. lautus	99.13
	FJAT-16879	KF278196	松树类芽胞杆菌 P. pini	99.98
	FJAT-16903	KF278201	台中类芽胞杆菌 P. taichungensis	100.0
	FJAT-16927	KF278202	土地类芽胞杆菌 P. terrigena	97.61
嗜冷芽胞杆菌属 Psychrobacillus	FJAT-16132	KF278129	奇特嗜冷芽胞杆菌 Psychrobacillus insolitus	98.70
嗜冷芽胞杆菌属 Psychrobacillus	FJAT-16497	KF278183	忍冷嗜冷芽胞杆菌 P. psychrodurans	99.82
鲁氏芽胞杆菌属 Rummeliibacillus	FJAT-16098	KF278125	厚细胞鲁氏芽胞杆菌 Rummeliibacillus pycnus	98.39
绿芽胞杆菌属 Viridibacillus	FJAT-17036	KF278205	沙地绿芽胞杆菌 Viridibacillus arenosi	100.0
绿芽胞杆菌属 Viridibacillus	FJAT-16340	KF278176	田地绿芽胞杆菌 V. arvi	100.0

类群 Group	代表菌株 Strains	登录号 GenBank accession no.	最相近菌种 Closest match	相似性 Sequence identity (%)
芽胞杆菌属 Bacillus	FJAT-16209	KF278157	阿氏芽胞杆菌 Bacillus aryabhattai	100.0
	FJAT-16883	KF278197	巴达维亚芽胞杆菌 B. bataviensis	100.0
	FJAT-16354	KF278179	科研中心芽胞杆菌 B. cecembensis	95.95
	FJAT-16889	KF278199	蜡样芽胞杆菌 B. cereus	100.0
	FJAT-16469	KF278181	根内芽胞杆菌 B. endoradicis	99.12
	FJAT-16705	KF278193	盐敏芽胞杆菌 B. halmapalus	98.52
	FJAT-16532	KF278187	印空研芽胞杆菌 B. isronensis	100.0
	FJAT-16048	KF278123	万里浦芽胞杆菌 B. manliponensis	98.46
	FJAT-16291	KF278168	地衣芽胞杆菌 B. licheniformis	99.85
	FJAT-16872	KF278195	黄海芽胞杆菌 B. marisflavi	100.0
	FJAT-16134	KF278130	甲基营养型芽胞杆菌 B. methylotrophicus	99.86
	FJAT-16162	KF278147	壁芽胞杆菌 B. muralis	99.85
	FJAT-16884	KF278198	蕈状芽胞杆菌 B. mycoides	100.0
	FJAT-16339	KF278175	休闲地芽胞杆菌 B. novalis	99.83
	FJAT-16201	KF278155	假蕈状芽胞杆菌 B. pseudomycoides	99.85
	FJAT-16578	KF278189	沙福芽胞杆菌 B. safensis	100.0
	FJAT-17017	KF278204	简单芽胞杆菌 B. simplex	100.0
	FJAT-17042	KF278206	特基拉芽胞杆菌 B. tequilensis	99.89
	FJAT-16178	KF278153	苏云金芽胞杆菌 B. thuringiensis	100.0
	FJAT-16301	KF278171	韦氏芽胞杆菌 B. weihenstephanensis	100.0
短芽胞杆菌属 Brevibacillus	FJAT-16350	KF278177	土壤短芽胞杆菌 Brevibacillus agri	99.38
虚构芽胞杆菌属 Fictibacillus	FJAT-17014	KF278203	南海虚构芽胞杆菌 Fictibacillus nanhaiensis	100.0
赖氨酸芽胞杆菌属 Lysinibacillus	FJAT-16156	KF278145	纺锤形赖氨酸芽胞杆菌 Lysinibacillus fusiformis	100.0
	FJAT-16167	KF278149	延长赖氨酸芽胞杆菌 L. macroides	99.57
	FJAT-16506	KF278185	芒果土赖氨酸芽胞杆菌 L. mangiferahumi	99.98
	FJAT-16266	KF278163	马赛赖氨酸芽胞杆菌 L. massiliensis	97.51
	FJAT-16248	KF278158	低硼赖氨酸芽胞杆菌 L. parviboronicapiens	99.22
	FJAT-16141	KF278135	球形赖氨酸芽胞杆菌 L. sphaericus	99.14
	FJAT-16140	KF278134	解木糖赖氨酸芽胞杆菌 L. xylanilyticus	100.0
类芽胞杆菌属 Paenibacillus	FJAT-16151	KF278140	蜂房类芽胞杆菌 Paenibacillus alvei	98.82
	FJAT-16703	KF278192	蜜蜂类芽胞杆菌 P. apiarius	98.88
	FJAT-16893	KF278200	栗树类芽胞杆菌 P. castaneae	98.05
	FJAT-16129	KF278128	埃及类芽胞杆菌 P. elgii	99.40
	FJAT-16135	KF278131	灿烂类芽胞杆菌 P. lautus	99.13
	FJAT-16879	KF278196	松树类芽胞杆菌 P. pini	99.98
	FJAT-16903	KF278201	台中类芽胞杆菌 P. taichungensis	100.0
	FJAT-16927	KF278202	土地类芽胞杆菌 P. terrigena	97.61
嗜冷芽胞杆菌属 Psychrobacillus	FJAT-16132	KF278129	奇特嗜冷芽胞杆菌 Psychrobacillus insolitus	98.70
嗜冷芽胞杆菌属 Psychrobacillus	FJAT-16497	KF278183	忍冷嗜冷芽胞杆菌 P. psychrodurans	99.82
鲁氏芽胞杆菌属 Rummeliibacillus	FJAT-16098	KF278125	厚细胞鲁氏芽胞杆菌 Rummeliibacillus pycnus	98.39
绿芽胞杆菌属 Viridibacillus	FJAT-17036	KF278205	沙地绿芽胞杆菌 Viridibacillus arenosi	100.0
绿芽胞杆菌属 Viridibacillus	FJAT-16340	KF278176	田地绿芽胞杆菌 V. arvi	100.0

芽胞杆菌种类 Bacillus-like species	黄岗山顶部 Peak of the Huanggang Mountain		黄岗山中部 Middle of the Huanggang Mountain		黄岗山底部 Base of the Huanggang Mountain		桐木关 Tongmuguan		挂墩 Guadun		大竹岚 Dazhulan		总体 Total
芽胞杆菌种类 Bacillus-like species	频度 Frequency	数量 Quantification	频度 Frequency	数量 Quantification	频度 Frequency	数量 Quantification	频度 Frequ-ency	数量 Quantification	频度 Frequency	数量 Quantification	频度 Frequency	数量 Quantification	频度 Frequency	数量 Quantification
Bacillus aryabhattai	0	0	7.69	0.02	14.29	0.10	8.33	2.42	14.29	0.05	14.29	0.62	9.33	3.20
B. bataviensis	0	0	0	0	0	0	0	0	0	0	7.14	0.43	1.33	0.43
B. cecembensis	6.67	0.01	0	0	0	0	0	0	0	0	0	0	1.33	0.01
B. cereus	66.67	0.26	53.85	1.27	28.57	0.72	16.67	0.29	42.86	0.64	21.43	0.40	40	3.58
B. endoradicis	13.33	0.02	7.69	0.02	0	0	0	0	0	0	0	0	4.00	0.03
B. halmapalus	0	0	0	0	0	0	0	0	7.14	0.01	0	0	1.33	0.01
B. isronensis	6.67	0.01	0	0	0	0	0	0	0	0	0	0	1.33	0.01
B. manliponensis	0	0	0	0	0	0	0	0	14.29	0.07	0	0	2.67	0.07
B. licheniformis	6.67	0.03	0	0	0	0	0	0	0	0	0	0	1.33	0.03
B. marisflavi	0	0	0	0	0	0	0	0	0	0	7.14	0.11	1.33	0.11
B. methylotrophicus	6.67	0.01	0	0	0	0	8.33	0.01	0	0	0	0	2.67	0.02
B. muralis	0	0	0	0	0	0	25.00	0.67	0	0	14.29	0.77	6.67	1.43
B. mycoides	100.0	3.26	69.20	1.42	28.57	0.95	16.67	0.47	7.14	0.04	14.29	1.24	41.33	7.37
B. novalis	6.67	0.07	0	0	0	0	0	0	0	0	0	0	1.33	0.07
B. pseudomycoides	0	0	0	0	28.57	0.21	8.33	0.42	42.86	2.44	14.29	0.09	14.67	3.16
B. safensis	0	0	7.69	0.01	0	0	0	0	14.29	0.36	0	0	4.00	0.36
B. simplex	26.67	0.18	0	0	0	0	0	0	0	0	7.14	0.05	6.67	0.23
B. tequilensis	0	0	0	0	0	0	0	0	0	0	7.14	16.19	1.33	16.19
B. thuringiensis	20	0.18	30.77	0.63	100.0	6.73	83.33	11.00	71.43	3.24	85.71	13.47	61.33	35.25
B. weihenstephanensis	0	0	7.69	0.02	0	0	0	0	0	0	0	0	1.33	0.02
Brevibacillus agri	6.67	0.19	0	0	0	0	0	0	0	0	0	0	1.33	0.19
Fictibacillus nanhaiensis	0	0	0	0	0	0	0	0	0	0	7.14	0.10	1.33	0.10
Lysinibacillus fusiformis	0	0	0	0	28.57	0.31	8.33	0.58	0	0	0	0	4.00	0.89
L. macroides	6.67	0.02	0	0	0	0	8.33	0.08	0	0	0	0	2.67	0.10
L. mangiferahumi	13.33	0.15	0	0	0	0	0	0	7.14	0.04	0	0	4.00	0.19
L. massiliensis	0	0	0	0	14.29	0.14	0	0	0	0	0	0	1.33	0.14
L. parviboronicapiens	0	0	0	0	28.57	1.29	16.67	0.65	0	0	0	0	5.33	1.93
L. sphaericus	0	0	0	0	0	0	8.33	0.13	7.14	0.04	21.43	0.87	6.67	1.03
L. xylanilyticus	60	0.27	30.77	0.11	57.14	0.74	58.33	3.68	78.57	3.22	21.43	1.08	50.67	9.10
Paenibacillus alvei	0	0	0	0	14.29	0.03	0	0	7.14	28.57	0	0	2.67	28.60
P. apiarius	0	0	0	0	0	0	0	0	7.14	0.31	0	0	1.33	0.31
P. castaneae	0	0	0	0	0	0	0	0	0	0	7.14	0.04	1.33	0.04
P. elgii	0	0	0	0	0	0	0	0	7.14	0.01	0	0	1.33	0.01
P. lautus	0	0	0	0	0	0	8.33	0.05	0	0	0	0	1.33	0.05
P. pini	0	0	0	0	0	0	0	0	0	0	7.14	0.57	1.33	0.57
P. taichungensis	0	0	0	0	0	0	8.33	0.07	0	0	7.14	0.48	2.67	0.54
P. terrigena	0	0	0	0	0	0	0	0	0	0	7.14	0.01	1.33	0.01
Psychrobacillus insolitus	0	0	0	0	0	0	8.33	0.31	0	0	0	0	1.33	0.31
Psychrobacillus psychrodurans	13.33	0.11	7.69	0.01	0	0	0	0	0	0	0	0	4.00	0.12
Rummeliibacillus pycnus	0	0	0	0	0	0	0	0	64.29	0.64	0	0	12.00	0.64
Viridibacillus arenosi	26.67	0.11	0	0	0	0	8.33	1.33	14.29	0.11	14.29	0.31	12.00	1.86
V. arvi	20	0.01	7.69	0.01	0	0	0	0	0	0	0	0	5.33	0.02
总计 Total	-	4.866	-	3.485	-	11.222	-	22.137	-	39.761	-	36.795	-	-