不同品种南瓜内生细菌多样性及PICRUSt基因功能预测分析

doi:10.3864/j.issn.0578-1752.2021.18.019

Abstract

Abstract:

【Objective】The aim of this study was to provide a theoretical basis for utilizing functional strains of endophytic bacteria in different varieties of pumpkins, as well as to explore new directions for pumpkin breeding. 【Method】The endophytic bacterial community composition and PICRUSt gene functions of 5 pumpkins varieties were analyzed based on MiSeq high-throughput sequencing results. The diversity and richness of endophytic bacterial community compositions in terms of 5 different pumpkin varieties were compared at phylum and genus levels.【Results】In total, 18 phyla, 30 classes, 101 orders, 199 families, 362 genera, 567 species and 863 OTUs could be obtained as the endophytic bacterial composition in 5 pumpkin varieties. There was no significant difference in endophytic bacteria diversity among pumpkin varieties. Significant differences in total numbers of endophytic bacteria were observed at different classification levels among pumpkin varieties. The proteobacteria was the dominant bacteria in terms of different 5 pumpkin varieties at the phylum level, but the abundance and proportion in every pumpkin variety were quite different. Moreover, Pseudomonas, Mycobacterium, Ensifer and Devosia were the dominant endophytic bacteria at genus level of different 5 pumpkin varieties, but their composition and abundance varied with pumpkin varieties. The composition and proportion of dominant endophytes at the phylum and genus level were similar between the hybrid and parent species. PICRUSt analysis also showed that endophytic bacteria inhabited in terms of different pumpkin varieties, mainly involved in 6 biological metabolic pathways and 46 sub-functions. However, there were no significant differences of endophytic bacterial genes in terms of different pumpkin varieties at the secondary functional layer. However, the numbers of gene functional copies varied with different varieties. The diversity and abundance of endophytic bacteria in terms of pumpkin were significantly affected by environmental factors. Moreover, the different endophytic bacterial community structures could be found in different pumpkin varieties. Meanwhile, a higher abundance of endophytic bacteria tended to enrich in terms of higher quality hybrids. Bacteria in 13 genera of bacteria, including Pseudomonas, Mycobacterium, Ensifer, and Devosia, etc, were the dominant endophytic bacterial genera in terms of 5 different pumpkin varieties. By contrast, Glycomyces, Candidatus_Rubidus, and Actinokineospora were the specific dominant endophytic bacterial genera in terms of Guifeng NO.7. In addition, 37 secondary functional layer functions were all the highest endophytic bacterial genes in terms of Guifeng NO.7 among the five pumpkin varieties, which involved the metabolisms of carbohydrate, amino acid, cofactors, and vitamins.【Conclusion】The higher dominant endophytic bacterial genus and the richer secondary functional genes were essential reasons for higher quality of Guifeng NO.7 than that of other four pumpkin varieties. Glycomyces, Candidatus_Rubidus, and Actinokineospora could be considered as the alternative benefit endophytic bacterial genera for improving pumpkin quality.

Key words: pumpkin (Cucurbita moschata Duch.), endophytic Bacteria, diversity, Miseq High-Throughput Sequencing, function rediction

HUANG ZiYue,LIU WenJun,QIN RenLiu,PANG ShiChan,XIAO Jian,YANG ShangDong. Endophytic Bacterial Community Composition and PICRUSt Gene Functions in Different Pumpkin Varieties[J].Scientia Agricultura Sinica, 2021, 54(18): 4018-4032.

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References 61

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样品 Sample	南瓜品种名称 Pumpkin variety	可溶性固形物 Soluble solid (%)	V_C含量 Vitamin C (mg/100 g)	可溶性蛋白 Soluble protein (g/100 g)	淀粉含量 Starch content (g/100 g)
1	桂丰7号香芋南瓜 Guifeng NO.7	7.97±0.9a	2.96±0.55a	3.09±0.22a	7.13±0.70a
2	桂丰8号南瓜Guifeng NO.8	6.87±0.15b	0.53±0.39d	2.79±0.33a	4.76±1.11b
3	杂交F₁代 Hybrid（G1519×G1511）	5.27±0.06c	1.7±0.04b	1.72±0.69b	3.52±0.05c
4	G1519	5.33±0.06c	0.95±0.27cd	1.59±0.16b	1.84±0.05d
5	G1511	4.97±0.12c	1.27±0.46bc	2.6±0.25a	1.58±0.10d

样品 Sample	香浓指数 Shannon index	辛普森指数 Simpson index	Ace指数 Ace index	Chao1指数 Chao1 index	覆盖率 Coverage rate
桂丰7号香芋南瓜 Guifeng NO.7	3.65±0.47a	0.11±0.06a	524.14±29.83a	508.14±43.73a	0.99
桂丰8号南瓜 Guifeng NO.8	3.45±0.73a	0.16±0.16a	535.75±94.62a	499.81±53.18a	0.99
杂交F₁代 Hybrid (G1519×G1511)	4.05±0.60a	0.08±0.06a	565.45±83.11a	554.50±78.32a	0.99
G1519	3.88±0.33a	0.07±0.05a	533.63±11.88a	531.93±16.20a	0.99
G1511	3.77±0.69a	0.11±0.08a	559.50±40.47a	571.41±34.24a	0.99

品种 Varity	门 Phylum	纲 Class	目 Order	科 Family	属 Genus	种 Species	OTU
桂丰7号香芋南瓜 Guifeng NO.7	19	28	88	158	294	434	604
桂丰8号南瓜 Guifeng NO.8	17	29	87	161	289	432	606
杂交F₁代 Hybrid (G1519×G1511)	17	27	87	166	312	473	686
G1519	18	29	89	171	306	449	628
G1511	17	29	89	165	299	444	646
总计 Total	18	30	101	199	362	567	863

门分类水平 Phylum level	桂丰7号 Guifeng NO.7	桂丰8号 Guifeng NO.8	杂交F₁代 Hybrid (G1519×G1511)	G1519	G1511
变形菌门 Proteobacteria	63.74%	76.26%	63.49%	76.55%	63.66%
放线菌门 Actinobacteria	30.55%	14.55%	28.55%	18.98%	32.28%
厚壁菌门 Firmicutes	3.31%	2.76%	4.51%	2.81%	2.10%
拟杆菌门 Bacteroidetes	1.46%	2.47%	1.64%	-	1.06%
衣原体门 Chlamydiae	-	2.27%	-	-	-
其他 Others	-	1.70%	1.77%	-	-

属分类水平 Genus level	桂丰7号 Guifeng NO.7	桂丰8号 Guifeng NO. 8	杂交F₁代 Hybrid (G1519×G1511)	G1519	G1511
假单胞菌属 Pseudomonas	26.86%	33.02%	19.45%	12.93%	25.88%
分支杆菌属 Mycobacterium	10.08%	1.75%	4.22%	3.06%	4.33%
Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium	2.41%	2.95%	5.98%	5.27%	1.28%
剑菌属 Ensifer	2.66%	1.56%	1.36%	8.28%	1.18%
unclassified_f__Rhizobiaceae	1.54%	3.79%	1.83%	6.77%	1.04%
德沃斯氏菌属 Devosia	1.64%	4.24%	3.14%	4.16%	1.74%
苯基杆菌属 Phenylobacterium	1.63%	1.03%	2.82%	3.26%	4.25%
鞘氨醇单胞菌属 Sphingomonas	3.07%	1.72%	3.31%	2.86%	1.93%
链霉菌属 Streptomyces	2.42%	1.50%	3.10%	1.32%	3.91%
细杆菌属 Microbacterium	1.29%	1.25%	1.46%	1.11%	4.93%
生根瘤菌属 Mesorhizobium	3.00%	1.49%	1.05%	1.91%	1.47%
假黄色单胞菌属 Pseudoxanthomonas	2.11%	1.41%	2.48%	1.03%	1.72%
芽孢杆菌属 Bacillus	1.77%	2.05%	1.96%	1.06%	1.09%
糖霉菌属 Glycomyces	3.48%	-	-	-	-
Candidatus_Rubidus	2.22%	-	-	-	-
Actinokineospora	1.55%	-	-	-	-
纤发菌属 Methylibium	-	-	-	1.84%	-

Endophytic Bacterial Community Composition and PICRUSt Gene Functions in Different Pumpkin Varieties

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一级功能层 Pathway level 1	桂丰7号 Guifeng NO.7	桂丰8号 Guifeng NO.8	杂交F₁代 Hybrid (G1519×G1511)	G1519	G1511
代谢 Metabolism	67.46%	65.45%	67.43%	66.44%	67.66%
环境信息处理 Environmental Information Processing	10.89%	11.77%	10.60%	11.25%	10.41%
细胞过程 Cellular Processes	7.51%	8.31%	7.31%	7.95%	7.19%
遗传信息处理 Genetic Information Processing	7.03%	7.12%	7.52%	7.01%	7.59%
人类疾病 Human Diseases	4.82%	5.16%	4.81%	5.14%	4.79%
有机系统 Organismal Systems	2.29%	2.19%	2.32%	2.21%	2.36%

二级功能层 Pathway level 2	桂丰7号 Guifeng NO.7	桂丰8号 Guifeng NO.8	杂交F₁代 Hybrid (G1519×G1511)	G1519	G1511
能量代谢 Energy metabolism	23.36%	19.44%	15.78%	19.90%	21.52%
类脂化合物代谢作用 Lipid metabolism	24.51%	19.17%	15.68%	19.32%	21.33%
碳水化合物代谢 Carbohydrate metabolism	23.53%	19.13%	15.92%	19.62%	21.80%
氨基酸代谢 Amino acid metabolism	23.79%	19.46%	15.60%	19.56%	21.60%
辅助因子和维生素的代谢 Metabolism of cofactors and vitamins	23.26%	19.80%	15.76%	19.63%	21.56%
其他氨基酸的代谢 Metabolism of other amino acids	23.85%	19.87%	15.55%	19.70%	21.03%
细胞运动 Cell motility	21.77%	22.53%	14.79%	20.98%	19.92%
循环系统 Circulatory system	21.45%	21.58%	15.20%	21.09%	20.68%
感染性疾病：病毒性 Infectious diseases: Viral	18.01%	27.21%	14.22%	20.36%	20.21%
信号分子和相互作用 Signaling molecules and interaction	21.17%	10.33%	43.16%	12.53%	12.81%
发育 Development	20.59%	21.21%	23.68%	19.04%	15.48%
细胞生长和死亡 Cell growth and death	21.58%	19.74%	15.44%	23.15%	20.08%
环境适应 Environmental adaptation	21.55%	20.17%	15.49%	22.56%	20.23%
消化系统 Digestive system	22.64%	19.28%	17.45%	17.83%	22.79%

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