Ma B, Lyu X-F, Zha T, Gong J, He Y, Xu J-M
Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, Zhejiang University, Hangzhou, China; Laboratory of Microbial Ecology and Matter Cycles, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China.
J Appl Microbiol. 2015 Apr;118(4):890-900. doi: 10.1111/jam.12756. Epub 2015 Feb 4.
The response of microbial metagenome to polycyclic aromatic hydrocarbons (PAHs) degradation in the rice rhizosphere remains poorly understood. We investigated the spatial and temporal variations of microbial communities and reconstructed metagenomes along the rice rhizosphere gradient during PAHs degradation.
The experiment was performed in rhizoboxes, in which the rhizosphere region was divided into five 1-mm thick layers. Based on denaturant gradient gel electrophoresis profiling and sequencing of bacterial and archaeal 16S rRNA genes, predicted metagenomes were reconstructed. The microbial communities in the rice rhizosphere were influenced by the PAHs concentration and distance from the root surface during PAHs degradation. Correlation network analysis showed that archaea played an important role in PAHs degradation. Predicted metagenomes can be clustered into two groups with high and low PAHs degrading potential, respectively. The relative abundance of genes for defense mechanisms, replication, recombination and reparation was significantly higher in samples with high PAHs degrading potentials. The relative abundance of the dioxygenase gene was greater near the root surface of the rice. However, the abundance of aldolase and dehydrogenase was constant in rhizosphere soils at different distances from the root surface.
Distance from root surface and PAH concentrations affected the microbial communities and metagenomes in rice rhizosphere. The abundance of dioxygenase genes relating to PAH degradation in metagenomes mirrored the PAH degradation potential in rice rhizosphere.
Our findings suggested that the predicted metagenomes reconstructed from 16S rRNA marker gene sequences provide further insights into the spatial variation and dynamics of microbial functioning that occur during bioremediation.
微生物宏基因组对水稻根际多环芳烃（PAHs）降解的响应仍知之甚少。我们研究了PAHs降解过程中沿水稻根际梯度的微生物群落的时空变化，并重建了宏基因组。
实验在根箱中进行，根际区域被分为五个1毫米厚的层。基于变性梯度凝胶电泳分析以及细菌和古菌16S rRNA基因测序，重建了预测的宏基因组。PAHs降解过程中，水稻根际的微生物群落受PAHs浓度和距根表面距离的影响。相关网络分析表明古菌在PAHs降解中起重要作用。预测的宏基因组可分为分别具有高和低PAHs降解潜力的两组。具有高PAHs降解潜力的样本中，防御机制、复制、重组和修复相关基因的相对丰度显著更高。水稻根表面附近双加氧酶基因的相对丰度更大。然而，在距根表面不同距离的根际土壤中，醛缩酶和脱氢酶的丰度是恒定的。
距根表面的距离和PAHs浓度影响水稻根际的微生物群落和宏基因组。宏基因组中与PAHs降解相关的双加氧酶基因的丰度反映了水稻根际的PAHs降解潜力。
我们的研究结果表明，从16S rRNA标记基因序列重建的预测宏基因组为生物修复过程中发生的微生物功能的空间变化和动态提供了进一步的见解。
