Metagenomic Sequencing Reveals that the Assembly of Functional Genes and Taxa Varied Highly and Lacked Redundancy in the Earthworm Gut Compared with Soil under Vanadium Stress.
Metagenomic Sequencing Reveals that the Assembly of Functional Genes and Taxa Varied Highly and Lacked Redundancy in the Earthworm Gut Compared with Soil under Vanadium Stress.
复制标题
宏基因组测序揭示钒胁迫下蚯蚓肠道与土壤相比功能基因和类群的组装差异很大且缺乏冗余
DOI：
10.1128/msystems.01253-21
复制
发表时间：
2022-02-22
期刊：
影响因子：
6.4
通讯作者：
Hu F
中科院分区：
文献类型：
--
作者：
Xia R;Shi Y;Wang X;Wu Y;Sun M;Hu F
探索钒污染环境中土壤及蚯蚓肠道微生物群落组装的生态机制，有助于我们了解钒胁迫对微生物多样性维持及功能的影响，以及微生物缓解钒胁迫的机制。我们结合宏基因组测序和丰度分布模型，研究了蚯蚓在含梯度浓度（0至300毫克/千克）钒酸盐的土壤中暴露21天后，蚯蚓肠道细菌和原生土壤细菌的组装情况。随机过程主导了蚯蚓肠道和土壤中基因及分类群的组装。蚯蚓肠道内分类群和功能基因的组成随钒浓度变化显著，而在土壤中，只有分类群发生显著变化，功能基因则相对稳定。通过Mantel检验和相似性分析（ANOSIM）检验证实，土壤中存在功能冗余，而蚯蚓肠道中不存在。此外，携带钒解毒基因（VDG）的分类群在土壤中的多样性高于蚯蚓肠道，但丰度低于蚯蚓肠道；土壤中VDG的丰度高于蚯蚓肠道。其在土壤中更宽的生态位宽度表明，与在蚯蚓肠道中的作用相比，携带VDG的分类群在土壤中属于泛化种。这些结果表明，蚯蚓肠道微生物和土壤微生物采用了不同策略来应对钒胁迫。该研究结果从细菌分类群和遗传功能两个角度，为土壤钒胁迫对蚯蚓肠道和土壤微生物群落组装的影响提供了新的见解。
重要意义：宏基因组测序揭示了土壤和蚯蚓肠道微生物群落中功能基因随钒浓度升高的变化情况，从功能基因角度为探索钒胁迫对微生物群落组装的影响提供了新视角。我们的结果进一步证实，功能基因和分类群似乎不存在简单的对应关系。与功能基因相比，分类群更为敏感，这表明土壤中存在细菌功能冗余，而蚯蚓肠道中不存在。这些发现表明，钒胁迫下蚯蚓肠道细菌和土壤细菌具有不同的组装模式。因此，纳入遗传功能以全面理解微生物群落组装既重要又必要。
Metagenomic sequencing revealed the variation of functional genes in the microbial community in soil and earthworm gut with increasing vanadium concentrations, which provided a new insight to explore the effect of vanadium stress on microbial community assembly from the perspective of functional genes. Our results reinforced the view that functional genes and taxa do not appear to have a simple corresponding relationship. ABSTRACT Exploring the ecological mechanism of microbial community assembly in soil and the earthworm gut in a vanadium polluted environment could help us understand the effects of vanadium stress on microbial diversity maintenance and function, as well as the mechanism of microbial mitigation of vanadium stress. Combining metagenomic sequencing and abundance distribution models, we explored the assembly of earthworm intestinal bacteria and native soil bacteria after 21 days of earthworm exposure to a gradient level of vanadate (0 to 300 mg kg−1) in soil. Stochastic processes dominated the assembly of both genes and taxa in earthworm gut and soil. Both the composition of taxa and functional genes in earthworm gut varied highly with the vanadium concentration, while in soil, only the taxa changed significantly, whereas the functional genes were relatively stable. The functional redundancy in soil, but not in the earthworm gut, was confirmed by a Mantel test and analysis of similarities (ANOSIM) test. In addition, vanadium detoxifying gene (VDG)-carrying taxa were more diverse but less abundant in soil than in the worm gut; and VDGs were more abundant in soil than in the worm gut. Their wider niche breadth indicated that VDG-carrying taxa were generalists in soil, in contrast to their role in the worm gut. These results suggested that earthworm intestinal and soil microbes adopted different strategies to counteract vanadium stress. The results provide new insights into the effects of soil vanadium stress on the assembly of earthworm gut and soil microbiota from both bacterial taxa and genetic function perspectives. IMPORTANCE Metagenomic sequencing revealed the variation of functional genes in the microbial community in soil and earthworm gut with increasing vanadium concentrations, which provided a new insight to explore the effect of vanadium stress on microbial community assembly from the perspective of functional genes. Our results reinforced the view that functional genes and taxa do not appear to have a simple corresponding relationship. Taxa are more sensitive compared with functional genes, suggesting the existence of bacterial functional redundancy in soil, but not in the earthworm gut. These observations indicate different assembly patterns of earthworm intestinal and soil bacteria under vanadium stress. Thus, it is important and necessary to include genetic functions to comprehensively understand microbial community assembly.