淹水培养过程中水稻土细菌丰度与群落结构变化

doi:10.3724/SP.J.1003.2014.14053

摘要/Abstract

摘要：

水稻土是非常复杂又典型的生态系统, 分析淹水培养过程中水稻土细菌的丰度和群落结构变化规律, 可以客观反映水稻土中细菌群落结构信息, 为深入探讨水稻土细菌微生物对稻田的影响和在生态系统中的作用(营养元素转换、重金属还原与抑制甲烷生成过程等)提供实验基础与理论依据。作者采用淹水非种植水稻土微环境模式系统, 提取水稻土淹水培养1 h和1、5、10、20、30、40、60 d后的微生物总DNA, 利用Real-time PCR和PCR-DGGE (denaturing gradient gel electrophoresis)技术检测了淹水培养过程中细菌丰度与群落结构的变化。结果表明: 淹水水稻土中细菌的丰度在1 d时最大, 并在40 d到达第二个峰值, 说明淹水过程改变了细菌的丰度。基于16S rRNA基因V3区的DGGE图谱分析显示, 淹水过程中细菌的群落结构发生了演替性变化: r-策略生存的细菌仅存在于淹水初期; k-策略生存的细菌存在于淹水后期; r-和k-策略共生存的细菌存在于整个淹水过程中, 淹水后期k-策略的细菌占据优势。淹水培养过程中优势种群多样性指数大体呈现先上升后减小的趋势。主成分分析(PCA)将淹水处理过程分成几类不同的生境, 反映出中、后期细菌群落结构较为稳定; 测序结果表明, 32个优势条带所代表的细菌分别属于厚壁菌门、绿弯菌门、拟杆菌门、变形菌门和酸杆菌门, 且与来自不同地域的水稻土、其他类型土壤、活性污泥以及湖泊沉积物等生态系统的细菌关系密切。

关键词: 淹水水稻土, 细菌, 16S rRNA, 丰度, 群落结构, r-/k-策略, 演替

Abstract

Paddy soil is a complex and typical ecosystem. Investigating changes to paddy soil bacterial communities during flooding can provide a theoretical basis for further exploring bacterial effects on and functions in ecosystems, e.g. nutrient transformations, the suppression of methanogenesis and bioremediation of heavy metal pollution. In this study, bacterial genomic DNA was analyzed from 8 paddy soil samples with flooding periods of 1 h, 1 d, 5 d, 10 d, 20 d, 30 d, 40 d and 60 d, respectively. 16S rRNA gene-based real-time PCR and PCR-DGGE (denaturing gradient gel electrophoresis) were used to study abundance and community structure during different flooding periods. The highest bacterial abundance was observed at 1 d with the second highest value at 40 d, indicating that bacterial abundance fluctuated over the flooding period. Succession of bacterial community structure was observed along the entire flooding period: r-strategists were only present in the early flooding stage; k-strategists emerged and were dominant in the late flooding stage; r-k-strategists symbiotic organisms were present in the entire flooding period. The diversity of the bacterial community during the flooding period rose initially and then tended to drop as succession took place. Principal Components Analysis based on digitized DGGE patterns indicated that the changes to bacterial community structure slowed during the mid- to late flooding stages. Sequencing results showed that Firmicutes, Chloroflexi, Bacteroidetes, Proteobacteria and Acidobacteria, which have close phylogenetic relationships with the groups from paddy soils and other soils of different regions, activated sludge systems and lake sediments, were the dominant habitants of the study site.

Key words: flooding paddy soil, bacteria, 16S rRNA, abundance, community structure, r-/k- strategy, succession

阚靖博, 李丽娜, 曲东, 王保莉 (2014) 淹水培养过程中水稻土细菌丰度与群落结构变化. 生物多样性, 22, 508-515. DOI: 10.3724/SP.J.1003.2014.14053.

Jingbo Kan, Lina Li, Dong Qu, Baoli Wang (2014) Changes in bacterial abundance and community structure associated with flooding in paddy soil. Biodiversity Science, 22, 508-515. DOI: 10.3724/SP.J.1003.2014.14053.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2014.14053

https://www.biodiversity-science.net/CN/Y2014/V22/I4/508

图/表 6

图1 淹水培养过程中水稻土细菌丰度

Fig. 1 The abundance of bacteria at different flooding time

图2 水稻土淹水培养不同时期细菌群落DGGE图谱。泳道1-8分别代表淹水处理的1 h、1 d、5 d、10 d、20 d、30 d、40 d和60 d。

Fig. 2 DGGE profiles of bacterial community in different flooding time of paddy soil. Lane 1-8 showed the samples of flooding time of 1 h, 1 d, 5 d, 10 d, 20 d, 30 d, 40 d and 60 d, respectively.

表1 水稻土淹水培养不同时期细菌群落的多样性指数

Table 1 Diversity indices of bacterial community in different flooding periods of a paddy soil

淹水时间 Flooding time	丰富度指数 Margalef index (d_Ma)	Shannon指数 Shannon-Wiener index (H')	均匀度指数 Evenness index (E)	Simpson指数 Simpson index (D_s)
1 h	3.954	2.991	0.941	0.948
1 d	3.655	2.962	0.932	0.945
5 d	5.102	3.304	0.945	0.965
10 d	5.371	3.368	0.955	0.965
20 d	5.316	3.379	0.950	0.966
30 d	5.657	3.382	0.959	0.965
40 d	5.328	3.261	0.917	0.963
60 d	4.914	3.228	0.931	0.963

表2 水稻土淹水培养不同时期细菌群落的相似性指数(%)

Table 2 Similarity index (%) of bacterial community in different flooding periods of a paddy soil

淹水时间 Flooding time	1 h	1 d	5 d	10 d	20 d	30 d	40 d	60 d
1 h	100
1 d	79.167	100
5 d	70.175	70.175	100
10 d	67.857	62.069	92.537	100
20 d	61.017	57.627	85.294	89.855	100
30 d	62.069	58.621	86.567	91.177	95.652	100
40 d	61.017	57.627	85.294	86.957	91.429	95.652	100
60 d	57.143	57.143	83.087	84.849	86.567	90.909	95.522	100

图3 用UniFrac构建的不同淹水阶段的主成分关联分析散点图

Fig. 3 Scatter plot of PCA analysis by UniFrac

图4 基于16S rRNA基因V3区的序列构建的细菌系统发育树。黑体字表示本文获得的优势条带编号, 刻度尺表示10%序列估计偏差; U. 代表uncultured。

Fig. 4 Phylogenetic tree constructed with neighbor-joining methods based on 16S rRNA V3 gene sequences. Boldface type indicates bands number obtained in this study. The scale bar represents 10% estimated sequence divergence. U. stands for uncultured.

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