Changes in bacterial abundance and community structure associated with flooding in paddy soil

doi:10.3724/SP.J.1003.2014.14053

Abstract

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

Jingbo Kan, Lina Li, Dong Qu, Baoli Wang. Changes in bacterial abundance and community structure associated with flooding in paddy soil[J]. Biodiv Sci, 2014, 22(4): 508-515.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2014.14053

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

Figures/Tables 6

Fig. 1 The abundance of bacteria at different flooding time

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.

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

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

Fig. 3 Scatter plot of PCA analysis by UniFrac

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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