高春辉在 ISME Communications 期刊发表论文

发表论文 最新动态

Chun-Hui Gao, Hui Cao, Feng Ju, Ke-Qing Xiao, Peng Cai, Yichao Wu & Qiaoyun Huang.  Emergent transcriptional adaption facilitates convergent succession within a synthetic community.ISME Communications  volume 1, Article number: 46 (2021)

Abstract

Taxonomic convergence is common in bacterial communities but its underlying molecular mechanism remains largely unknown. We thus conducted a time-series transcriptional analysis of a convergent two-species synthetic community that grew in a closed broth-culture system. By analyzing the gene expression and monitoring the community structure, we found that gene expression mainly changed in the early stage, whereas community structure significantly changed in the late stage. The significant change of gene expression occurred even at the very beginning, which was designated as “0 h effect”, suggesting the effect of species interaction on gene expression was inevitable. Besides, the effect of interaction on gene expression has a “population effect”, which means that majority species have greater impact on gene expressions of minority species than vice versa. Furthermore, gene set enrichment analysis revealed that among a total of 63 unique pathways (occupying about 50% of all the metabolic pathways in both species), 40 (63%) were consistently suppressed, 16 (25%) were conditionally expressed, and only 7 (11%) were consistently activated. Overall, they were strictly regulated by both time and initial structures. Therefore, we proposed that microorganism responses and the induced gene expression changes play important roles in the process of community succession.

该工作在菌群种间互作与代谢能力调控模式新发现的基础上(The ISME Journal,2020),完整重现了菌群的收敛过程,并揭示了该过程中基因表达调控的核心特征。菌群收敛是指具有不同组成与多样性的微生物群落经历一段时间演化后,结构和功能趋于一致的现象,普遍存在于自然界微生物群落演化过程中。在土壤生态系统中,以生物膜形式存在的微生物聚集体通常只包含少数几种微生物,但是内部却存在着复杂的微生物互作。因此,认识菌群收敛过程与机制,不仅是理解微生物群落组装、演化的前提,也是构建土壤生物膜调控体系的关键。近年来,少量研究发现,外部因素如环境pH、外源养分等在调节菌群收敛中发挥重要作用,但是对于细菌内在因素对收敛过程的作用还知之甚少,特别是细菌内部适应性的基因表达调控网络在菌群收敛中的作用机制尚不清楚。

本研究发现,在由两个模式生物膜细菌(大肠杆菌E. coli和恶臭假单胞菌P. putida)按照一定比例构建的多个合成菌群中,尽管其初始结构指标相差 100 万倍,但是在 24 h 内各个菌群在群落结构和基因表达变化两个方面即可完成收敛,并且收敛过程主要是由细菌内在的适应性所驱动。此外,菌群的群落结构在初期变化相对较小,而基因表达的变化则非常显著,具有明显的 “涌现性” 特征。

图  合成菌群中两个物种基因表达的收敛过程

通过对群落基因表达变化的深入分析,论文进一步揭示了菌群收敛过程中涌现性基因表达具有三个典型特征:① 零时效应。群落中各物种内部的基因表达自群落形成就开始显现,且初期更加明显;② 群体数量效应。菌群中数目多的物种对数目小的物种影响更大;③ 严谨调控效应。菌群中基因表达受到精准调控,细菌能够通过自身的调控网络优化生存策略,促成菌群收敛。

该工作对于理解土壤生物膜群落的决定性装配过程,破译土壤微生物互作和生物膜功能间的联系具有重要的科学意义。

华中农业大学农业微生物学国家重点实验室、资源与环境学院博士后高春辉为论文第一作者,蔡鹏教授为通讯作者,西湖大学鞠峰研究员,英国利兹大学肖可青博士参与该研究。该研究得到了国家自然科学基金、牛顿高级学者基金、国家重点研发计划、以及华中农业大学自主创新基金等项目的资助。

 

相关研究:

https://www.nature.com/articles/s43705-021-00049-5

https://www.nature.com/articles/s41396-020-00751-7