Microbial Diversity in Rhizosphere and Non-rhizosphere Soils of Paris polyphylla var. chinensis Plants
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摘要:
目的 研究七叶一枝花野生环境和人工栽培中根际与非根际土壤细菌群落结构的差异，为揭示野生七叶一枝花和移栽七叶一枝花土壤的细菌群落结构，明确不同栽培模式下土壤细菌群落的变化，探究野生七叶一枝花土壤细菌的多样性的优势。 方法 本研究提取七叶一枝花土壤宏基因组DNA，采用illumina miseq 2×300 bp进行高通量测序；对两种栽培模式土壤的细菌多样性进行分析；在不同水平上分析两种栽培模式下的显著性差异，并通过LDA EffectSize组间群落差异分析两种栽培模式中起关键作用的门和属。 结果 研究结果表明七叶一枝花土壤中细菌多样性丰富，包括21个门、33个纲、52个目、89个科和160个属。七叶一枝花非根际土壤细菌多样性指数Chao、Ace、Shannon和Simpson指数显示非根际土壤细菌群落具有更高的丰富性和多样性。在门水平和科水平没有显著差异。在纲水平，具有显著差异的是绿菌纲Chlorobia，其在七叶一枝花根际土壤中的含量低于非根际土壤；在目水平，具有显著差异的是绿菌目Chlorobiales和粘球菌目Myxococcales，其在七叶一枝花根际土壤中的含量低于非根际土壤；在属水平，具有显著差异的是不动杆菌属Acinetobacter和Rudaea，其在七叶一枝花根际土壤中的含量低于非根际土壤；在种水平，具有显著差异的是Mucilaginibacter ximonensis、uncultured Nannocystineae bacterium、unculturedSingulisphaera sp.、uncultured Solibacteraceae bacterium和uncultured Xanthomonadaceae bacterium，其在七叶一枝花根际土壤中的含量均低于非根际。 结论 本研究表明七叶一枝花非根际土壤细菌群落具有更高的丰富性和多样性，为进一步探索七叶一枝花的土壤微生物环境奠定基础。 Abstract:Objective The microbial communities in rhizosphere and non-rhizosphere soils growing Paris polyphylla var. chinensis plants were analyzed and compared in the field as well as in laboratory. Method The high throughput sequencing Illumina Miseq 2×300 bp was applied to sequence total DNA of the microbes in the soils. The LDA Effect Size analysis was used to examine the differences on selected microbial groups between the communities in the field and laboratory. Result The microbial diversity in the soils of P. polyphylla was rich with 21 phyla, 33 classes, 52 orders, 89 families, and 160 genera identified. The Chao, Ace, Shannon, and Simpson indices on the soil samples indicated that the non-rhizosphere soil was more abundant and diverse than the rhizosphere soil. However, there were no significant differences between them on the phylum or family level. Among the differentially abundant groups, Chlorobia on the class level, Chlorobiales and Myxococcales on the order level, and Acinetobacter and Rudaea on the genus level were significantly lower in the rhizosphere. Conclusion This study not only shows that Paris polyphylla var. chinensis non-rhizosphere soil bacterial communities have higher abundance and diversity, but also lays the foundation for further exploration of the soil microbial environment of Paris polyphylla var. chinensis. -
Key words:
- Paris polyphylla var. chinensis /
- rhizosphere /
- soil /
- diversity
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图 1 七叶一枝花土壤细菌16S rRNA相似水平为97%的稀释性曲线
Figure 1. Rarefaction curves of soil bacteria with 97% similarity on 16S rRNA
图 2 七叶一枝花土壤细菌物种（OTU）组成的韦恩图分析
注：左绿色表示根际土壤细菌物种，右粉色为非根际土壤细菌物种，中间为二者重叠部分
Figure 2. Venn analysis on OTUs of soils
Note: Green colored area on the left represents bacteria in rhizosphere soil; pink colored area on the right represents bacteria in non-rhizosphere soil; and, middle is overlap between two groups.
图 3 七叶一枝花根际与非根际土壤细菌物种（OTU）组成的差异
Figure 3. Venn analysis on OTUs of rhizosphere and non-rhizosphere soils
图 4 门（A）和属（B）水平的微生物组成、相对丰度
Figure 4. Relative abundance of predominant bacteria on phylum level (A) and genus level (B)
图 6 纲（A）、目（B）、属（C）和种（D）水平的微生物组间群落显著性差异
Figure 6. Differentially abundant groups on class level (A), order level (B), genus level (C), and species level (D)
图 8 基于OTU水平的PCoA
Figure 8. Principal co-ordinates analysis (PCoA) based on OTU of 8 samples
图 9 七叶一枝花根际和非根际土壤的unweighted.unifrac差异性矩阵热图（相似水平97%）
Figure 9. Heatmap of unweighted.unifrac dissimilarity matrix of soils
表 1 七叶一枝花土壤样本信息
Table 1. Sources of soil samples
编号 Number 采集地 Collection location 移栽时间/年 Transplanting time/year 采集地样品名称 The name of the sample YR1 福建省南平市建瓯吉阳镇郭岩山双龙庙 wild 8-3br YNR1 福建省南平市建瓯吉阳镇郭岩山双龙庙 wild 8-4br YR2 福建省南平市建瓯吉阳镇郭岩山双龙庙 wild 8-3bl YNR2 福建省南平市建瓯吉阳镇郭岩山双龙庙 wild 8-4bl ZR1 福建省南平市建瓯吉阳镇郭岩山双龙庙 5 8-1 ZNR1 福建省南平市建瓯吉阳镇郭岩山双龙庙 5 8-2 ZR2 福建省南平市政和县官湖村王坑陇 2 8-5 ZNR2 福建省南平市政和县官湖村王坑陇 2 8-6 
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表 2 七叶一枝花土壤的细菌分离数量
Table 2. Plate counts of soil samples
样品名称
Sample name细菌含量
Bacteria content/
（106 cfu·g−1）样品名称
Sample name细菌含量
Bacteria content/
（106 cfu·g−1）YR1 5.05±0.43 b YNR1 4.70±0.54 c YR2 8.10±0.35 a YNR2 8.55±0.32 a ZR1 3.50±0.61 c ZNR1 6.85±0.47 b ZR2 5.50±0.38 b ZNR2 1.75±0.26 d 注：数据后不同小写字母表示在0.05水平上差异显著。
Note: Data with different lowercase letters indicate significant differences at 0.05 level.
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表 3 七叶一枝花土壤样本不同分类阶元细菌物种（OTU）数量
Table 3. OTUs of soil samples on different biological classification levels
样本名称 Sample name OTU 门水平 Phylum 纲水平 Class 目水平 Order 科水平 Family 属水平 Genus 种水平 Species YR1 1173 19 31 44 73 114 125 YR2 1122 20 28 42 73 114 130 ZR1 1198 21 31 47 78 142 140 ZR2 630 20 27 34 62 88 85 YNR1 1049 21 30 46 77 123 131 YNR2 1173 19 29 40 70 117 128 ZNR1 1417 21 31 48 81 138 149 ZNR2 904 20 27 36 64 108 104
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表 4 七叶一枝花土壤的Alpha多样性指数
Table 4. Alpha diversity of soils
样本名称 Sample name Chao Ace Shannon Simpson coverage YR1 1383.4930 1353.6621 5.2116 0.0200 0.9929 YR2 1266.0820 1239.7667 5.4007 0.0143 0.9943 ZR1 1318.3147 1313.4214 5.5856 0.0112 0.9944 ZR2 758.2692 708.8108 4.1124 0.0588 0.9967 YNR1 1252.7638 1229.8781 5.1894 0.0166 0.9933 YNR2 1347.2803 1314.3759 5.1740 0.0303 0.9937 ZNR1 1544.8750 1515.2990 5.9857 0.0070 0.9944 ZNR2 1013.1720 995.5008 5.0457 0.0211 0.9956
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