棕榈科植物种子内生细菌群落多样性的高通量测序分析

Diversity of bacterial endophytes communities in the seeds of several Palmae plants via high throughput sequencing method

摘要:

[目的]探究棕榈科种子内生细菌群落组成及其随物种的差异。[方法]运用MiSeq高通量方法测定蒲葵、棕榈、加拿利海枣、山棕、软叶刺葵、短穗鱼尾葵及三药槟榔7种棕榈科种子内生细菌群落16S rRNA基因V3–V4区序列并进行生物信息学分析。[结果]7种测试种子中获得的V3–V4区有效序列数在2341–40671条之间，聚成97–590个操作分类单元（OTU），Shannon指数计算为1.35–2.94，以加拿利海枣种子最高，山棕种子最低；种群归类结果显示不同种子中测得的各级细菌分类阶层总数及组成不同，总丰度以厚壁菌门的肠球菌属最高，同为厚壁菌门的芽孢杆菌属次之；属级水平上，第一优势细菌属分别为：蒲葵种子（芽孢杆菌属，45.8%），棕榈种子（肠球菌属，51.2%），山棕种子（肠球菌属，12.1%），短穗鱼尾葵种子（肠球菌属，32.6%），三药槟榔种子（肠球菌属，42.9%），软叶刺葵种子（肠球菌属，28.3%），加拿利海枣种子（糖多孢菌属，31.2%）。各种子中次优势细菌属分别为：蒲葵种子（乳球菌属），棕榈、山棕及三药槟榔种子（类芽孢杆菌属），加拿利海枣种子（戈登氏菌属），软叶刺葵和短穗鱼尾葵种子（鞘脂单胞菌属）；PICRUST基因预测显示各种子均包含多个与人体器官及人类疾病相关的KEGG功能模块。此外，各种子中均产生了丰度较高的外源物质降解、萜和聚酮合成、多糖合成等有益功能信息。[结论]棕榈科植物种子内生细菌群落多样性较为丰富，群落组成随物种不同而异。各种子内生细菌群体中普遍含多个与人和动物体相关的种群和功能信息，也定殖多种具有益功能性状的细菌类群，值得进一步研究。

Abstract:

[Objective] To explore the diversity of bacterial endophyte communities in the seeds of Palmae plants species.[Methods] We investigated and characterized bacterial endophytes communities in the seeds of 7 different plant species within Palmae, including Livistona chinensis, Trachycarpus fortuneii, Phoenix canariensis, Arenga engleri, P. roebelenii, Caryota mitis and Areca triandra, by a MiSeq high throughput sequencing method followed by bioinformatics analysis targeted at V3-V4 regions of the 16S rRNA gene. [Results] We recovered a total of 2341-40671 V3-V4 valid sequences of 16S rRNA gene from the tested seeds, which clustered into 97-590 distinct operational taxonomic units (OTUs). And the Shannon index was calculated to be varying in the range from 1.35 to 2.94, with the highest detected from P. canariensis seed and the lowest form A. engleri seed. The results of taxonomic assignment showed that the total number of taxonomic taxa and population composition detected in different seeds was different. At the genus level, the genus Enterococcus belonging to Firmicutes was found to be the highest in total abundance across all seeds, followed by Bacillus belonging to the same bacterial phylum. The most dominant bacterial genera detected from the tested seeds were as follow:L. chinensis seed (Bacillus, 45.8%), T. fortuneii seed (Enterococcus, 51.2%), A. engleri seed (Enterococcus, 12.1%), C. mitis seed (Enterococcus, 32.6%) A. triandra seed (Enterococcus, 42.9%), P. roebelenii seed (Enterococcus, 28.3%), P. canariensis seed (Saccharopolyspora, 31.2%). And the sub-dominant bacterial genera were: Lactococcus (L. chinensis seed), Paenibacillus (T. fortunei seed, A. engleri seed, and A. triandra seed), Goodfellowiella (P. canariensis seed), Sphingomonas (P. roebelenii seed, and C. mitis seed). Furthermore, PICRUSt was used to determine potential functional profiles associated with the recovered sequences. Several KEGG orthology (KO) terms related to the human organs and human diseases were inferred from this analysis. In addition, the KO terms related to biosynthesis of terpenoids, polyketides, and glycan, as well as xenobiotics biodegradation showed relative high abundance in the predicted KO terms of the recovered sequences from each seed.[Conclusion] Seeds of Palmae plants colonize diverse bacterial endophytes, whose population compositions were different among the tested seeds. The bacterial endophyte communities of tested Palmae seeds consisted of many human-associated bacterial genera, and some potential functions related to human diseases were also included in the predicted KO terms of the seeds bacterial endophytes communities. Each tested seed also colonized some bacterial genera with beneficial function properties, being worth for further study.