生物多样性 ›› 2019, Vol. 27 ›› Issue (12): 1320-1329. DOI: 10.17520/biods.2019219
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,*
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:
Zhiyuan Chen1,Jun Liu1,Xingpeng Yang1,Meng Liu1,Ya Wang2,Zhibin Zhang1,*(),Du Zhu1,2,*
Received:
2019-07-07
Accepted:
2019-10-20
Online:
2019-12-20
Published:
2020-02-22
Contact:
Zhang Zhibin,Zhu Du
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。
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.
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 | ||||||||||||||||
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 | |||||||||||||||
(KC252695.1) | ||||||||||||||||||
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 | ||||||||||||||||
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 |
表1 东乡野生稻不同组织中内生细菌的分布情况
Table 1 The distribution of endophytic bacteria isolated from different tissues of Dongxiang wild rice
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 | ||||||||||||||||
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 | |||||||||||||||
(KC252695.1) | ||||||||||||||||||
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 | ||||||||||||||||
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 |
图1 东乡野生稻不同组织内生细菌在牛肉膏蛋白胨培养基(NA)、Baird-Parker agar (BPA)、任氏培养基(R2A)、胰酶大豆琼脂培养基(TSA)和10倍稀释牛肉膏蛋白胨培养基(NA × 10)上的分离情况。(A)东乡野生稻不同组织在不同培养基中的分离菌株数; (B)不同培养基分离菌株百分比。
Fig. 1 The endophytic bacteria isolated by nutrient agar, Baird-Parker agar, Reasoner’s 2A agar Tryptone soy agar and 10-fold nutrient agar from each tissues of Dongxiang wild rice. (A) The amount of endophytic bacterial, derived from any tissues of Dongxiang wild rice, isolated from different mediums; (B) The percentage of the isolated strains from each medium.
图2 东乡野生稻内生细菌16S rRNA基因序列系统进化树(分支中加粗菌株为东乡野生稻内生细菌, 非加粗菌株为近缘菌株)
Fig. 2 Neighbor-joining tree based on 16S rRNA gene sequences showing the phylogenetic relationships among the strains and their closely related taxa. The thicker branches represent endophytic bacteria of Dongxiang wild rice and the others represent related strains.
图3 东乡野生稻不同组织内生细菌属水平上的分布。(A)根; (B)茎; (C)叶。
Fig. 3 Distribution of endophytic bacteria from different tissues of Dongxiang wild rice at the genus level. (A) Root; (B) Stem; (C) Leaf.
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 |
表2 东乡野生稻不同组织内生细菌的多样性指数(按属进行计算)
Table 2 Diversity analysis of endophytic bacteria in different tissues of Dongxiang wild rice (according to genera)
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 |
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