Convergent adaption of bacterial community in a paddy field experiencing repeated drying-wetting cycles

Abstract:

[Objective] This study aims to explore the mechanism of bacterial taxa adapting to repeated drying-wetting cycles in a paddy field via culture-dependent DNA/RNA-based 16S rRNA gene analysis, and to assess whether air-dried paddy soil could be used for the study of microbial community structure.[Methods] The fresh soil representative of rice production in China was collected from Changshu city of Jiangsu province, and three consecutive cycles of air drying and wetting were conducted (drying or wetting state was maintained for seven days in each cycle). We then analyzed the changes of the abundance and community composition of soil bacteria by using 16S rRNA gene high-throughput sequencing and real-time fluorescence quantitative PCR respectively.[Results] The bacterial abundance decreased by 300-771 times at the DNA level while only by 1.95-5.60 times at the RNA level during the wetting-drying cycles. The bacterial diversity in the air-dried soil showed no significant difference from that in the wet soil at the DNA level, while was significantly higher than that in the wet soil at the RNA level. Non-metric multidimensional scaling (NMDS) and co-occurrence network analysis showed that the community structure of soil bacteria changed significantly during the drying-wetting cycles (P<0.05). The drying-wetting cycles caused significant changes in relative abundance of key taxa, and a total of 8 numerically dominant phyla was consistently observed at both the DNA and RNA levels (P<0.05). The drying-wetting cycles significantly increased the relative abundance of Chloroflexi and Actinobacteria, while significantly decreased that of Proteobacteria and Acidobacteria. A total of 7 246 microbial genera were detected during the three wetting-drying cycles. The relative abundance of 35 and 58 bacterial genera changed significantly at the DNA and RNA levels, respectively, in response to the drying-wetting cycles. Among all the bacterial genera with significant changes in relative abundance, only 4 genera showed significant changes at both DNA and RNA levels, accounting for only 1.09% of the detected genera in this study. Specifically, the relative abundance of KD4-96 significantly increased and that of bacteriap25 significantly decreased at DNA and RNA levels; the relative abundance of Nitrososphaeraceae and SC-I-84 decreased significantly at the DNA level while increased significantly at the RNA level.[Conclusion] The three wetting-drying cycles resulted in significant decrease in the absolute abundance of bacterial taxa. The 16S rRNA transcripts were two orders of magnitude lower than the 16S rRNA genes, which implied that 16S rRNA transcripts could be originated most likely from intact living cells, and soil extracellular DNA could have likely resulted in drastic variations of 16S rRNA genes. Intriguingly, the composition of bacterial taxa remained generally unchanged during the drying-wetting cycles at both DNA and RNA levels, suggesting strong capacity of bacterial taxa to recover from desiccation. Our results indicate that soil microorganisms have strong functional plasticity of being adaptive to drought, and air-dried soil can be used for microbiological research under certain circumstances.