中国农业科技导报 ›› 2023, Vol. 25 ›› Issue (3): 66-77.DOI: 10.13304/j.nykjdb.2021.0647
收稿日期:
2021-08-03
接受日期:
2022-01-13
出版日期:
2023-03-15
发布日期:
2023-05-22
作者简介:
赵柏霞 E-mail: zhaobaixia1979@126.com
基金资助:
Received:
2021-08-03
Accepted:
2022-01-13
Online:
2023-03-15
Published:
2023-05-22
摘要:
为探明甜樱桃内生细菌种群结构及多样性,以‘砂蜜豆’甜樱桃根、主干树皮和枝条3个组织的内生细菌为研究对象,对其16S rRNA V3~V4区进行高通量测序。结果表明,‘砂蜜豆’甜樱桃不同组织内生细菌群落多样性及功能存在较大差异。不同组织中共获得有效序列9 665 813条,聚类为1 386个OTU(operational taxonomic units),隶属于20个门、43个纲、79个目、162个科和346个属。在门水平,变形菌门(Proteobacteria)在各组织中的丰度均最高,是最优势菌门。在属水平,根部内生细菌的优势菌属为链霉菌属(Streptomyces)、类固醇杆菌属(Steroidobacter)和乳酸杆菌属(Lactobacillus);枝条内生细菌中鞘氨醇单胞菌(Sphingomonas)的相对丰度较高;主干树皮内生细菌的优势菌属为拟杆菌属(Bacteroides)。PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states)基因预测表明,内生细菌功能主要涉及多糖、萜类和酮类、酶及维生素等次生代谢产物的生物合成。综上所述,甜樱桃内生细菌具有丰富的种群多样性,为今后开发利用甜樱桃内生细菌资源奠定了基础。
中图分类号:
赵柏霞, 闫建芳. 高通量技术分析‘砂蜜豆’甜樱桃不同组织内生细菌多样性[J]. 中国农业科技导报, 2023, 25(3): 66-77.
Baixia ZHAO, Jianfang YAN. Diversity Analysis of Endophytic Bacterial Community in Different Tissues of ‘Summit’ Sweet Cherry Using High-throughput Sequencing[J]. Journal of Agricultural Science and Technology, 2023, 25(3): 66-77.
组织 Tissue | 多样性指数 Alpha diversity | |||
---|---|---|---|---|
Chao1指数 Chao1 index | ACE指数 ACE index | Shannon指数Shannon index | Simpson指数 Simpson index | |
SG | 1 003.00±4.78 a | 1 095.69±6.89 a | 6.96±0.13 a | 0.975 8±0.04 a |
SZ | 917.77±2.39 b | 1 044.61±7.55 b | 6.36±0.07 b | 0.907 2±0.02 b |
SP | 919.73±6.02 b | 1 033.86±3.66 b | 6.07±0.12 b | 0.871 8±0.09 b |
表1 供试样品内生细菌多样性指数
Table 1 Alpha diversity index of endophytic bacteria within the test samples
组织 Tissue | 多样性指数 Alpha diversity | |||
---|---|---|---|---|
Chao1指数 Chao1 index | ACE指数 ACE index | Shannon指数Shannon index | Simpson指数 Simpson index | |
SG | 1 003.00±4.78 a | 1 095.69±6.89 a | 6.96±0.13 a | 0.975 8±0.04 a |
SZ | 917.77±2.39 b | 1 044.61±7.55 b | 6.36±0.07 b | 0.907 2±0.02 b |
SP | 919.73±6.02 b | 1 033.86±3.66 b | 6.07±0.12 b | 0.871 8±0.09 b |
样品 Sample | 门 Phylum | 纲 Class | 目 Order | 科 Family | 属 Genus |
---|---|---|---|---|---|
SG | 19 | 42 | 78 | 162 | 346 |
SZ | 20 | 43 | 79 | 157 | 324 |
SP | 20 | 40 | 74 | 146 | 306 |
表2 ‘砂蜜豆’甜樱桃不同组织内生细菌群落细菌学分类阶层总数
Table 2 Total numbers of bacterial taxa detected in different tissues of ‘Summit’
样品 Sample | 门 Phylum | 纲 Class | 目 Order | 科 Family | 属 Genus |
---|---|---|---|---|---|
SG | 19 | 42 | 78 | 162 | 346 |
SZ | 20 | 43 | 79 | 157 | 324 |
SP | 20 | 40 | 74 | 146 | 306 |
样本 Sample | 组间差异显著的分类单元 Classification units with significant differences between groups | LDA 值LDA value | P值 P value |
---|---|---|---|
SZ | 细菌界,厚壁菌门,杆菌纲 Bacteria, Firmicutes, Bacilli | 4.60 | 0.007 3 |
SP | 细菌界,变形菌门,α-变形菌纲,根瘤菌目 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales | 5.18 | 0.048 8 |
SP | 细菌界,变形菌门,α-变形菌纲,根瘤菌目,布鲁氏菌科 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales, Brucellaceae | 5.27 | 0.021 8 |
SG | 细菌界,放线菌门,放线菌纲,链孢囊菌目 Bacteria, Actinobacteria, Actinobacteria, Streptosporangiales | 4.30 | 0.024 4 |
SG | 细菌界,变形菌门,α-变形菌纲,根瘤菌目,黄色杆菌科 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales, Xanthobacteraceae | 4.06 | 0.021 0 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,黄色类固醇杆菌属 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Incertae _Sedis, Steroidobacter | 4.56 | 0.024 9 |
SG | 细菌界,变形菌门,α-变形菌纲,根瘤菌目,慢生根瘤菌科,慢生根瘤菌属 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales, Bradyrhizobiaceae, Bradyrhizobium | 4.0 | 0.018 3 |
SG | 细菌界,变形菌门,α-变形菌纲,鞘脂单胞菌目,鞘脂单胞菌科,新鞘氨醇杆菌属 Bacteria, Proteobacteria, Alphaproteobacteria, Sphingomonadales, Sphingomonadaceae, Novosphingobium | 4.11 | 0.024 4 |
SG | 细菌界,放线菌门,放线菌纲, 链孢囊菌目,高温单孢菌科 Bacteria, Actinobacteria, Actinobacteria, Streptosporangiales, Thermomonosporaceae | 4.28 | 0.024 4 |
SG | 细菌界,变形菌门,α-变形菌纲,红螺菌目,红螺菌科 Bacteria, Proteobacteria, Alphaproteobacteria, Rhodospirillales, Rhodospirillaceae | 4.17 | 0.024 4 |
SG | 细菌界,放线菌门,放线菌纲,链霉菌目 Bacteria, Actinobacteria, Actinobacteria, Streptomycetales | 4.56 | 0.009 7 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,黄单胞菌科,未定属 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Incertae_Sedis, uncultured_bacterium_f_Xanthomonadales_Incertae_Sedis | 4.09 | 0.023 1 |
SG | 细菌界,放线菌门 Bacteria, Actinobacteria | 5.06 | 0.007 3 |
SG | 细菌界,变形菌门,α-变形菌纲,鞘脂单胞菌目,鞘脂单胞菌科,鞘氨醇盒菌属 Bacteria, Proteobacteria, Alphaproteobacteria, Sphingomonadales, Sphingomonadaceae, Sphingopyxis | 4.28 | 0.023 1 |
SG | 细菌界,放线菌门,放线菌纲 Bacteria, Actinobacteria, Actinobacteria | 5.06 | 0.007 3 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,Acidibacter,未定种Bacteria,Proteobacteria,Gammaproteobacteria,Xanthomonadales,Xanthomonadales_Incertae _Sedis, Acidibacter, uncultured_bacterium_g_Acidibacter | 4.09 | 0.024 9 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,未定属,未定种 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Ince rtae_Sedis, uncultured_bacterium_f_Xanthomonadales_Incertae_Sedis, uncultured_bacterium_f_Xanthomonadales_Incertae_Sedis | 4.09 | 0.023 1 |
SG | 细菌界,变形菌门,α-变形菌纲,红螺菌目 Bacteria, Proteobacteria, Alphaproteobacteria, Rhodospirillales | 4.21 | 0.021 0 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,黄色类固醇杆菌,未定种 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_ Incertae_Sedis, Steroidobacter, uncultured_bacterium_g_Steroidobacter | 4.46 | 0.024 9 |
SG | 细菌界,变形菌门,α-变形菌纲,根瘤菌目,慢生根瘤菌科 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales, Bradyrhizobiaceae | 4.00 | 0.018 3 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Incer tae_Sedis | 4.80 | 0.024 4 |
SG | 细菌界,放线菌门,放线菌纲,链霉菌目,链霉菌科,链霉菌属 Bacteria, Actinobacteria, Actinobacteria, Streptomycetales, Streptomycetaceae, Streptomyces | 4.54 | 0.009 7 |
表3 LEfSe统计检验结果 (续表 Continued)
Table 3 Results of LEfSe statistical test
样本 Sample | 组间差异显著的分类单元 Classification units with significant differences between groups | LDA 值LDA value | P值 P value |
---|---|---|---|
SZ | 细菌界,厚壁菌门,杆菌纲 Bacteria, Firmicutes, Bacilli | 4.60 | 0.007 3 |
SP | 细菌界,变形菌门,α-变形菌纲,根瘤菌目 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales | 5.18 | 0.048 8 |
SP | 细菌界,变形菌门,α-变形菌纲,根瘤菌目,布鲁氏菌科 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales, Brucellaceae | 5.27 | 0.021 8 |
SG | 细菌界,放线菌门,放线菌纲,链孢囊菌目 Bacteria, Actinobacteria, Actinobacteria, Streptosporangiales | 4.30 | 0.024 4 |
SG | 细菌界,变形菌门,α-变形菌纲,根瘤菌目,黄色杆菌科 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales, Xanthobacteraceae | 4.06 | 0.021 0 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,黄色类固醇杆菌属 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Incertae _Sedis, Steroidobacter | 4.56 | 0.024 9 |
SG | 细菌界,变形菌门,α-变形菌纲,根瘤菌目,慢生根瘤菌科,慢生根瘤菌属 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales, Bradyrhizobiaceae, Bradyrhizobium | 4.0 | 0.018 3 |
SG | 细菌界,变形菌门,α-变形菌纲,鞘脂单胞菌目,鞘脂单胞菌科,新鞘氨醇杆菌属 Bacteria, Proteobacteria, Alphaproteobacteria, Sphingomonadales, Sphingomonadaceae, Novosphingobium | 4.11 | 0.024 4 |
SG | 细菌界,放线菌门,放线菌纲, 链孢囊菌目,高温单孢菌科 Bacteria, Actinobacteria, Actinobacteria, Streptosporangiales, Thermomonosporaceae | 4.28 | 0.024 4 |
SG | 细菌界,变形菌门,α-变形菌纲,红螺菌目,红螺菌科 Bacteria, Proteobacteria, Alphaproteobacteria, Rhodospirillales, Rhodospirillaceae | 4.17 | 0.024 4 |
SG | 细菌界,放线菌门,放线菌纲,链霉菌目 Bacteria, Actinobacteria, Actinobacteria, Streptomycetales | 4.56 | 0.009 7 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,黄单胞菌科,未定属 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Incertae_Sedis, uncultured_bacterium_f_Xanthomonadales_Incertae_Sedis | 4.09 | 0.023 1 |
SG | 细菌界,放线菌门 Bacteria, Actinobacteria | 5.06 | 0.007 3 |
SG | 细菌界,变形菌门,α-变形菌纲,鞘脂单胞菌目,鞘脂单胞菌科,鞘氨醇盒菌属 Bacteria, Proteobacteria, Alphaproteobacteria, Sphingomonadales, Sphingomonadaceae, Sphingopyxis | 4.28 | 0.023 1 |
SG | 细菌界,放线菌门,放线菌纲 Bacteria, Actinobacteria, Actinobacteria | 5.06 | 0.007 3 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,Acidibacter,未定种Bacteria,Proteobacteria,Gammaproteobacteria,Xanthomonadales,Xanthomonadales_Incertae _Sedis, Acidibacter, uncultured_bacterium_g_Acidibacter | 4.09 | 0.024 9 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,未定属,未定种 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Ince rtae_Sedis, uncultured_bacterium_f_Xanthomonadales_Incertae_Sedis, uncultured_bacterium_f_Xanthomonadales_Incertae_Sedis | 4.09 | 0.023 1 |
SG | 细菌界,变形菌门,α-变形菌纲,红螺菌目 Bacteria, Proteobacteria, Alphaproteobacteria, Rhodospirillales | 4.21 | 0.021 0 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,黄色类固醇杆菌,未定种 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_ Incertae_Sedis, Steroidobacter, uncultured_bacterium_g_Steroidobacter | 4.46 | 0.024 9 |
SG | 细菌界,变形菌门,α-变形菌纲,根瘤菌目,慢生根瘤菌科 Bacteria, Proteobacteria, Alphaproteobacteria, Rhizobiales, Bradyrhizobiaceae | 4.00 | 0.018 3 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Incer tae_Sedis | 4.80 | 0.024 4 |
SG | 细菌界,放线菌门,放线菌纲,链霉菌目,链霉菌科,链霉菌属 Bacteria, Actinobacteria, Actinobacteria, Streptomycetales, Streptomycetaceae, Streptomyces | 4.54 | 0.009 7 |
样本 Sample | 组间差异显著的分类单元 Classification units with significant differences between groups | LDA 值LDA value | P值 P value |
---|---|---|---|
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,Acidibacter Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Incer tae_Sedis, Acidibacter | 4.24 | 0.024 4 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales | 4.85 | 0.024 9 |
SG | 细菌界,放线菌门,放线菌纲,小单孢菌目,小单孢菌科,小单孢菌属 Bacteria, Actinobacteria, Actinobacteria, Micromonosporales, Micromonosporaceae, Micromonospora | 4.26 | 0.024 4 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,黄单胞菌科,罗河杆菌属 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadaceae, Rhodanobacter | 4.02 | 0.013 0 |
SG | 细菌界,变形菌门,δ-变形菌纲,粘球菌目 Bacteria, Proteobacteria, Deltaproteobacteria, Myxococcales | 4.15 | 0.020 9 |
SG | 细菌界,放线菌门,放线菌纲,小单孢菌目 Bacteria, Actinobacteria, Actinobacteria, Micromonosporales | 4.56 | 0.024 4 |
SG | 细菌界,放线菌门,放线菌纲,链霉菌目,链霉菌科 Bacteria, Actinobacteria, Actinobacteria, Streptomycetales, Streptomycetaceae | 4.56 | 0.009 7 |
SG | 细菌界,放线菌门,放线菌纲,链孢囊菌目,高温单孢菌科, 珊瑚状放线菌属 Bacteria, Actinobacteria, Actinobacteria, Streptosporangiales, Thermomonosporaceae, Actinocorallia | 4.31 | 0.002 4 |
SG | 细菌界,变形菌门,γ-变形菌纲 Bacteria, Proteobacteria, Gammaproteobacteria | 4.85 | 0.024 9 |
SG | 细菌界,放线菌门,放线菌纲,小单孢菌目,小单孢菌科 Bacteria, Actinobacteria, Actinobacteria, Micromonosporales, Micromonosporaceae | 4.55 | 0.024 4 |
SG | 细菌界,变形菌门,α-变形菌纲,鞘脂单胞菌目,鞘脂单胞菌科,鞘氨醇盒菌属,未定种Bacteria, Proteobacteria, Alphaproteobacteria, Sphingomonadales, Sphingomonadaceae, Sphingopyxis, uncultured_bacterium_Sphingopyxis | 4.31 | 0.023 1 |
表3 LEfSe统计检验结果 (续表 Continued)
Table 3 Results of LEfSe statistical test
样本 Sample | 组间差异显著的分类单元 Classification units with significant differences between groups | LDA 值LDA value | P值 P value |
---|---|---|---|
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,未定科,Acidibacter Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadales_Incer tae_Sedis, Acidibacter | 4.24 | 0.024 4 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales | 4.85 | 0.024 9 |
SG | 细菌界,放线菌门,放线菌纲,小单孢菌目,小单孢菌科,小单孢菌属 Bacteria, Actinobacteria, Actinobacteria, Micromonosporales, Micromonosporaceae, Micromonospora | 4.26 | 0.024 4 |
SG | 细菌界,变形菌门,γ-变形菌纲,黄单胞菌目,黄单胞菌科,罗河杆菌属 Bacteria, Proteobacteria, Gammaproteobacteria, Xanthomonadales, Xanthomonadaceae, Rhodanobacter | 4.02 | 0.013 0 |
SG | 细菌界,变形菌门,δ-变形菌纲,粘球菌目 Bacteria, Proteobacteria, Deltaproteobacteria, Myxococcales | 4.15 | 0.020 9 |
SG | 细菌界,放线菌门,放线菌纲,小单孢菌目 Bacteria, Actinobacteria, Actinobacteria, Micromonosporales | 4.56 | 0.024 4 |
SG | 细菌界,放线菌门,放线菌纲,链霉菌目,链霉菌科 Bacteria, Actinobacteria, Actinobacteria, Streptomycetales, Streptomycetaceae | 4.56 | 0.009 7 |
SG | 细菌界,放线菌门,放线菌纲,链孢囊菌目,高温单孢菌科, 珊瑚状放线菌属 Bacteria, Actinobacteria, Actinobacteria, Streptosporangiales, Thermomonosporaceae, Actinocorallia | 4.31 | 0.002 4 |
SG | 细菌界,变形菌门,γ-变形菌纲 Bacteria, Proteobacteria, Gammaproteobacteria | 4.85 | 0.024 9 |
SG | 细菌界,放线菌门,放线菌纲,小单孢菌目,小单孢菌科 Bacteria, Actinobacteria, Actinobacteria, Micromonosporales, Micromonosporaceae | 4.55 | 0.024 4 |
SG | 细菌界,变形菌门,α-变形菌纲,鞘脂单胞菌目,鞘脂单胞菌科,鞘氨醇盒菌属,未定种Bacteria, Proteobacteria, Alphaproteobacteria, Sphingomonadales, Sphingomonadaceae, Sphingopyxis, uncultured_bacterium_Sphingopyxis | 4.31 | 0.023 1 |
样本 Sample | 组间差异显著的分类单元 Classification units with significant differences between groups | LDA 值LDA value | P值 P value |
---|---|---|---|
SZ | 细菌界,厚壁菌门,杆菌纲,乳酸杆菌目,乳酸菌科,乳酸杆菌属 Bacteria, Firmicutes, Bacilli, Lactobacillales, Lactobacillaceae, Lactobacillus | 4.14 | 0.043 5 |
SZ | 细菌界,拟杆菌门 Bacteria, Bacteroidetes | 4.57 | 0.049 8 |
SZ | 细菌界,厚壁菌门 Bacteria, Firmicutes | 4.90 | 0.007 3 |
SZ | 细菌界,厚壁菌门,杆菌纲,乳酸杆菌目,肠球菌科 Bacteria, Firmicutes, Bacilli, Lactobacillales, Enterococcaceae | 4.07 | 0.034 6 |
SZ | 细菌界,厚壁菌门,杆菌纲,乳酸杆菌目 Bacteria, Firmicutes, Bacilli, Lactobacillales | 4.48 | 0.012 5 |
SZ | 细菌界,厚壁菌门,杆菌纲,乳酸杆菌目,肠球菌科,肠球菌属 Bacteria, Firmicutes, Bacilli, Lactobacillales, Enterococcaceae, Enterococcus | 4.01 | 0.030 8 |
表3 LEfSe统计检验结果
Table 3 Results of LEfSe statistical test
样本 Sample | 组间差异显著的分类单元 Classification units with significant differences between groups | LDA 值LDA value | P值 P value |
---|---|---|---|
SZ | 细菌界,厚壁菌门,杆菌纲,乳酸杆菌目,乳酸菌科,乳酸杆菌属 Bacteria, Firmicutes, Bacilli, Lactobacillales, Lactobacillaceae, Lactobacillus | 4.14 | 0.043 5 |
SZ | 细菌界,拟杆菌门 Bacteria, Bacteroidetes | 4.57 | 0.049 8 |
SZ | 细菌界,厚壁菌门 Bacteria, Firmicutes | 4.90 | 0.007 3 |
SZ | 细菌界,厚壁菌门,杆菌纲,乳酸杆菌目,肠球菌科 Bacteria, Firmicutes, Bacilli, Lactobacillales, Enterococcaceae | 4.07 | 0.034 6 |
SZ | 细菌界,厚壁菌门,杆菌纲,乳酸杆菌目 Bacteria, Firmicutes, Bacilli, Lactobacillales | 4.48 | 0.012 5 |
SZ | 细菌界,厚壁菌门,杆菌纲,乳酸杆菌目,肠球菌科,肠球菌属 Bacteria, Firmicutes, Bacilli, Lactobacillales, Enterococcaceae, Enterococcus | 4.01 | 0.030 8 |
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