东乡野生稻可培养内生细菌群落组成及多样性

doi:10.17520/biods.2019219

生物多样性 ›› 2019, Vol. 27 ›› Issue (12): 1320-1329. DOI: 10.17520/biods.2019219

• 研究报告: 微生物多样性 • 上一篇下一篇

东乡野生稻可培养内生细菌群落组成及多样性

陈志远¹,刘珺¹,杨星鹏¹,刘梦¹,汪涯²,张志斌^1,^*(),朱笃^1,^2,^*

1 江西师范大学生命科学学院, 江西省亚热带植物资源保护与利用重点实验室, 南昌 330022
2 江西科技师范大学生命科学学院, 江西省生物加工过程重点实验室, 南昌 330013

收稿日期:2019-07-07 接受日期:2019-10-20 出版日期:2019-12-20 发布日期:2020-02-22
通讯作者: 张志斌,朱笃
基金资助:
国家自然科学基金(31760160);江西省自然科学基金(20171BAB204009);江西省自然科学基金(20181BAB215044);江西师范大学研究生创新项目(YJS2018080);江西师范大学研究生创新项目(YC2019-S121)

Community composition and diversity of cultivable endophytic bacteria isolated from Dongxiang wild rice

Zhiyuan Chen¹,Jun Liu¹,Xingpeng Yang¹,Meng Liu¹,Ya Wang²,Zhibin Zhang^1,^*(),Du Zhu^1,^2,^*

1 Key Laboratory of Protection and Utilization of Subtropical Plant Resources of Jiangxi Province, College of Life Sciences, Jiangxi Normal University, Nanchang 330022
2 Key Laboratory of Bioprocess Engineering of Jiangxi Province, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013

Received:2019-07-07 Accepted:2019-10-20 Online:2019-12-20 Published:2020-02-22
Contact: Zhang Zhibin,Zhu Du

摘要/Abstract

摘要：

内生细菌对宿主植物生长发育和生理代谢具有重要影响, 揭示其群落组成和多样性具有重要的生物学和生态学意义。本研究采用可培养法从东乡野生稻(Oryza rufipogon)不同组织中分离获得94株内生细菌, 基于16S rRNA基因序列比对和系统发育分析将其归属于变形菌门、放线菌门和厚壁菌门3门14科17属, 其中芽孢杆菌属(Bacillus)和微小菌属(Microbacterium)为优势属, 分别占总株数的27.7%和20.2%。不同组织中内生细菌的分布和多样性存在差异, 根中内生细菌数量最多(34株, 36.2%), 叶次之(32株, 34.0%), 茎最少(28株, 29.8%); 根中内生细菌Shannon-Wiener多样性指数(H′ = 2.52)、Simpson优势度指数(D = 0.88)和Pielou均匀度指数(E = 0.72)均高于茎与叶, 根和茎的Jaccard相似性系数(C = 0.29)低于根和叶(C = 0.47)以及茎和叶(C = 0.45)。研究结果表明, 东乡野生稻内生细菌具有丰富的物种多样性, 并且不同组织部位的内生细菌组成存在差异, 根中内生细菌多样性最丰富。

关键词: 野生稻, 植物内生菌, 分类, 系统发育, 组成分析

Abstract

Endophytic bacteria are essential to the growth and metabolism of their host plants. To better understand the community structure and diversity of endophytic bacteria on plants, we isolated 94 strains of endophytic bacteria from the roots, stems and leaves of Dongxiang wild rice (Oryza rufipogon). Subsequent 16S rRNA sequence alignments and phylogenetic analyses revealed that the 94 strains could be categorized into 17 genera of 14 families in 3 phyla (Proteobacteria, Actinobacteria, and Firmicutes).Bacillus and Microbacterium, accounting for 27.7% and 20.2% of the diversity, respectively, were the two most dominant genera. The distribution and diversity of endophytic bacteria differed across different tissues of Dongxiang wild rice: the roots contained the most endophytic bacteria strains (n = 34, 36.2%), followed by leaves (n = 32, 34.0%), and stems (n = 28, 29.8%). Shannon-Wiener diversity index (H′ = 2.52), Simpson dominance index (D = 0.88) and Pielou evenness index (E = 0.72) were higher in the roots than in the stems or leaves. Meanwhile, the Jaccard similarity index between roots and stems (C = 0.29) was lower than that between roots and leaves (C = 0.47), or that between stems and leaves (C = 0.45). Our efforts to uncover the diversity of endophytic bacteria in Dongxiang wild rice confirms that roots contain the most diverse strains but that the composition of endophytes varies across tissues.

Key words: Oryza rufipogon, endophytes, classification, phylogeny, composition analysis

陈志远, 刘珺, 杨星鹏, 刘梦, 汪涯, 张志斌, 朱笃 (2019) 东乡野生稻可培养内生细菌群落组成及多样性. 生物多样性, 27, 1320-1329. DOI: 10.17520/biods.2019219.

Zhiyuan Chen, Jun Liu, Xingpeng Yang, Meng Liu, Ya Wang, Zhibin Zhang, Du Zhu (2019) Community composition and diversity of cultivable endophytic bacteria isolated from Dongxiang wild rice. Biodiversity Science, 27, 1320-1329. DOI: 10.17520/biods.2019219.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2019219

https://www.biodiversity-science.net/CN/Y2019/V27/I12/1320

图/表 5

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代表菌株			NCBI库中相似度最高菌种	基因登录号	序列相		分离菌株数				培养基分离菌株数
Representative strains			(登录号)	GenBank accession	似度		No. of strains				No. of strains from medium
			Closest relatives in NCBI	no.	Identity
			(GenBank accession no.)		(%)		根		茎	叶	NA	BPA	R2A	TSA	NA×10
							Root		Stem	Leaf	NA	BPA	R2A	TSA	NA×10
变形菌门 Proteobacteria
	泛菌属 Pantoea						5		1	6	3	2	3	2	2
		JXR10	Pantoea sp. (JX994157.1)	KP980595	100
		JXS8	Pantoea sp. (KJ733870.1)	KP980579	100
		JXL1	Pantoea sp. (KJ733870.1)	KP980566	100
	鞘氨醇单胞菌属 Sphingomonas						1		-	1	-	1	-	1	-
		JXR34	Sphingomonas yanoikuyae (KJ009425.1)	KP980605	100
		JXL6	Sphingomonas sanguinis (NR113637.1)	KP980568	100
	土壤杆菌属 Agrobacterium						-		3	1	1	-	1	-	2
		JXS10	Agrobacterium sp. (GQ169803.1)	KP980581	100
		JXL9	Agrobacterium sp. (KJ184856.1)	KP980570	100
	甲烷细菌属 Methylobacterium						1		1	1	-	1	-	1	1
		JXR16	Methylobacterium sp. (KM083547.1)	KP980599	100
		JXS9	Methylobacterium sp. (AB604650.1)	KP980580	100
		JXL16	Methylobacterium sp. (KM083546.1)	KP980572	100
	假单胞菌属 Pseudomonas						1		-	1	-	-	-	-	2
		JXR26	Pseudomonas sp. (HE978359.1)	KP980602	100
		JXL21	Pseudomonas fulva (AY741159.1)	KP980573	100
	寡养单胞菌属Stenotrophomonas						-		3	-	-	1	-	1	1
		JXS14	Stenotrophomonas maltophilia (JN571747.1)	KP980583	100
	根瘤菌属 Rhizobium						-		1	-	1	-	-	-	-
		JXS18	Rhizobium sp. (JN082742.1)	KP980584	100
	不动杆菌属 Acinetobacter						1		-	-	1	-	-	-	-
		JXR29	Acinetobacter oleivorans (KJ806471.1)	KP980603	100
放线菌门 Actinobacteria
	微小菌属 Microbacterium						1		8	10	5	3	6	2	3
		JXR14	Microbacterium trichothecenolyticum (KF953537.1)	KP980598	100
		JXS2	Microbacterium sp. (AB773218.1)	KP980577	100
		JXL7	Microbacterium sp. (EU741023.1)	KP980569	100
		JXL12	Microbacterium laevaniformans	KP980571	100
		JXL12	(KC252695.1)	KP980571	100
	短杆菌属 Curtobacterium						1		2	1	-	1	2	-	1
		JXR24	Curtobacterium citreum (KC329830.1)	KP980601	100
		JXS1	Curtobacterium luteum (JQ660182.1)	KP980576	97
		JXL30	Curtobacterium sp. (KC841444.1)	KP980575	100
	分支杆菌属 Mycobacterium						2		-	-	1	-	-	-	1
		JXR17	Mycobacterium sp. (AB605021.1)	KP980600	100
	节杆菌属 Arthrobacter						3		-	-	1	-	-	-	2
		JXR12	Arthrobacter phenanthrenivorans (KC934897.1)	KP980596	100
代表菌株				NCBI库中相似度最高菌种	基因登录号	序列相		分离株数			培养基分离株数
Representative strains				(登录号)	GenBank accession	似度		No. of strains			No. of strains from medium
				Closest relatives in NCBI	no.	Identity
				(GenBank accession no.)		(%)		根	茎	叶	NA	BPA	R2A	TSA		NA×10
								Root	Stem	Leaf	NA	BPA	R2A	TSA		NA×10
	雷弗森菌属 Leifsonia							3	-	-	-	-	1	-		2
		JXR6		Leifsonia sp. (KJ944083.1)	KP980592	100
	红球菌属 Rhodococcus							1	-	-	-	-	-	1		-
		JXR8		Rhodococcus equi (NR041910.1)	KP980594	100
厚壁菌门 Firmicutes
	类芽孢杆菌属 Paenibacillus							3	-		1	1	-	1		-
		JXR1		Paenibacillus agarexedens (KC355292.1)	KP980588	100
		JXR5		Paenibacillus sp. (KJ000069.1)	KP980591	99
		JXR30		Paenibacillus vulneris (KM272755.1)	KP980604	100
	芽孢杆菌属 Bacillus							7	9	10	8	8	1	2		7
		JXR2		Bacillus cereus (KF831402.1)	KP980589	100
		JXR3		Bacillus sp. (JX566646.1)	KP980590	100
		JXS6		Bacillus subtilis (KP229430.1)	KP980578	100
		JXS20		Bacillus sp. (KM555037.1)	KP980585	100
		JXS25		Bacillus mojavensis (HQ123468.1)	KP980587	97
		JXL24		Bacillus sp. (KP119613.1)	KP980574	100
	赖氨酸芽孢杆菌属 Lysinibacillus							4	-	1	1	-	2	1		1
		JXR13		Lysinibacillus sphaericus (KM070813.1)	KP980597	100
		JXL2		Lysinibacillus fusiformis (JN867122.1)	KP980567	100
总计 Total								34	28	32	23	18	16	12		25

代表菌株			NCBI库中相似度最高菌种	基因登录号	序列相		分离菌株数				培养基分离菌株数
Representative strains			(登录号)	GenBank accession	似度		No. of strains				No. of strains from medium
			Closest relatives in NCBI	no.	Identity
			(GenBank accession no.)		(%)		根		茎	叶	NA	BPA	R2A	TSA	NA×10
							Root		Stem	Leaf	NA	BPA	R2A	TSA	NA×10
变形菌门 Proteobacteria
	泛菌属 Pantoea						5		1	6	3	2	3	2	2
		JXR10	Pantoea sp. (JX994157.1)	KP980595	100
		JXS8	Pantoea sp. (KJ733870.1)	KP980579	100
		JXL1	Pantoea sp. (KJ733870.1)	KP980566	100
	鞘氨醇单胞菌属 Sphingomonas						1		-	1	-	1	-	1	-
		JXR34	Sphingomonas yanoikuyae (KJ009425.1)	KP980605	100
		JXL6	Sphingomonas sanguinis (NR113637.1)	KP980568	100
	土壤杆菌属 Agrobacterium						-		3	1	1	-	1	-	2
		JXS10	Agrobacterium sp. (GQ169803.1)	KP980581	100
		JXL9	Agrobacterium sp. (KJ184856.1)	KP980570	100
	甲烷细菌属 Methylobacterium						1		1	1	-	1	-	1	1
		JXR16	Methylobacterium sp. (KM083547.1)	KP980599	100
		JXS9	Methylobacterium sp. (AB604650.1)	KP980580	100
		JXL16	Methylobacterium sp. (KM083546.1)	KP980572	100
	假单胞菌属 Pseudomonas						1		-	1	-	-	-	-	2
		JXR26	Pseudomonas sp. (HE978359.1)	KP980602	100
		JXL21	Pseudomonas fulva (AY741159.1)	KP980573	100
	寡养单胞菌属Stenotrophomonas						-		3	-	-	1	-	1	1
		JXS14	Stenotrophomonas maltophilia (JN571747.1)	KP980583	100
	根瘤菌属 Rhizobium						-		1	-	1	-	-	-	-
		JXS18	Rhizobium sp. (JN082742.1)	KP980584	100
	不动杆菌属 Acinetobacter						1		-	-	1	-	-	-	-
		JXR29	Acinetobacter oleivorans (KJ806471.1)	KP980603	100
放线菌门 Actinobacteria
	微小菌属 Microbacterium						1		8	10	5	3	6	2	3
		JXR14	Microbacterium trichothecenolyticum (KF953537.1)	KP980598	100
		JXS2	Microbacterium sp. (AB773218.1)	KP980577	100
		JXL7	Microbacterium sp. (EU741023.1)	KP980569	100
		JXL12	Microbacterium laevaniformans	KP980571	100
		JXL12	(KC252695.1)	KP980571	100
	短杆菌属 Curtobacterium						1		2	1	-	1	2	-	1
		JXR24	Curtobacterium citreum (KC329830.1)	KP980601	100
		JXS1	Curtobacterium luteum (JQ660182.1)	KP980576	97
		JXL30	Curtobacterium sp. (KC841444.1)	KP980575	100
	分支杆菌属 Mycobacterium						2		-	-	1	-	-	-	1
		JXR17	Mycobacterium sp. (AB605021.1)	KP980600	100
	节杆菌属 Arthrobacter						3		-	-	1	-	-	-	2
		JXR12	Arthrobacter phenanthrenivorans (KC934897.1)	KP980596	100
代表菌株				NCBI库中相似度最高菌种	基因登录号	序列相		分离株数			培养基分离株数
Representative strains				(登录号)	GenBank accession	似度		No. of strains			No. of strains from medium
				Closest relatives in NCBI	no.	Identity
				(GenBank accession no.)		(%)		根	茎	叶	NA	BPA	R2A	TSA		NA×10
								Root	Stem	Leaf	NA	BPA	R2A	TSA		NA×10
	雷弗森菌属 Leifsonia							3	-	-	-	-	1	-		2
		JXR6		Leifsonia sp. (KJ944083.1)	KP980592	100
	红球菌属 Rhodococcus							1	-	-	-	-	-	1		-
		JXR8		Rhodococcus equi (NR041910.1)	KP980594	100
厚壁菌门 Firmicutes
	类芽孢杆菌属 Paenibacillus							3	-		1	1	-	1		-
		JXR1		Paenibacillus agarexedens (KC355292.1)	KP980588	100
		JXR5		Paenibacillus sp. (KJ000069.1)	KP980591	99
		JXR30		Paenibacillus vulneris (KM272755.1)	KP980604	100
	芽孢杆菌属 Bacillus							7	9	10	8	8	1	2		7
		JXR2		Bacillus cereus (KF831402.1)	KP980589	100
		JXR3		Bacillus sp. (JX566646.1)	KP980590	100
		JXS6		Bacillus subtilis (KP229430.1)	KP980578	100
		JXS20		Bacillus sp. (KM555037.1)	KP980585	100
		JXS25		Bacillus mojavensis (HQ123468.1)	KP980587	97
		JXL24		Bacillus sp. (KP119613.1)	KP980574	100
	赖氨酸芽孢杆菌属 Lysinibacillus							4	-	1	1	-	2	1		1
		JXR13		Lysinibacillus sphaericus (KM070813.1)	KP980597	100
		JXL2		Lysinibacillus fusiformis (JN867122.1)	KP980567	100
总计 Total								34	28	32	23	18	16	12		25

组织名称 Tissue	细菌属数 Genus	多样性指数 Shannon- Wiener index	优势度指数 Simpson index	均匀度指数 Pielou index
根 Root	14	2.52	0.88	0.72
茎 Stem	8	1.81	0.80	0.54
叶 Leaf	9	2.09	0.74	0.60

组织名称 Tissue	细菌属数 Genus	多样性指数 Shannon- Wiener index	优势度指数 Simpson index	均匀度指数 Pielou index
根 Root	14	2.52	0.88	0.72
茎 Stem	8	1.81	0.80	0.54
叶 Leaf	9	2.09	0.74	0.60

东乡野生稻可培养内生细菌群落组成及多样性

Community composition and diversity of cultivable endophytic bacteria isolated from Dongxiang wild rice

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