The dynamics of evolution - how horizontal gene transfer drives the diversification and adaptation of complex microbial communities in marine ecosystems

进化动态——水平基因转移如何驱动海洋生态系统中复杂微生物群落的多样化和适应

• 批准号: 324709907
• 负责人: Dr. Bernd Wemheuer
• 金额: --
• 依托单位: Abteilung Genomische und Angewandte Mikrobiologie
• 依托单位国家: 德国
• 项目类别: Research Fellowships
• 财政年份: 2016
• 资助国家: 德国
• 起止时间: 2015-12-31 至 2018-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/324709907?language=en
• 关键词: dynamics; evolution; how; horizontal; gene

Marine bacteria and archaea represent the major part of the total biodiversity on Earth. These microorganisms are main drivers of biogeochemical cycles in the marine realm and thus play an integral role in ecosystem stability and functioning. Several recent studies targeted the diversity of marine microorganisms and their response to changing environmental conditions. However, our knowledge about genetic diversification of natural microbial communities and their genomic adaptation to environmental stresses is still rather limited. The aim of this project is to understand the dynamics of microbial evolution in marine ecosystems. As horizontal gene transfer is thought to be the major driver of microbial evolution, the main question to be answered is how horizontal gene transfer drives the diversification of complex microbial communities in marine ecosystems and their adaptation to prevailing environmental stresses. To assess microbial community dynamics, samples will be taken repeatedly in three coastal areas of Australia, where microbial communities are threatened by various stressors including risen water temperatures and agricultural run-offs. Data on environmental properties will be measured simultaneously. Environmental DNA will be extracted from obtained sampling material. As horizontal gene transfer is likely to occur in dense microbial communities, DNA isolated from host-associated microbial communities including the seaweed holobiont will be subjected to next-generation sequencing, and obtained metagenomic datasets will be subsequently mined for mobile genetic elements transferred by horizontal gene transfer. In addition to data on environmental properties and horizontal gene transfer, changes in taxonomic composition as well as species richness of free-living, host-associated and sediment microbial communities will be assessed by sequencing of 16S rRNA genes amplified from environmental DNA. The generated data will be statistically evaluated to decipher the dynamics of microbial evolution in marine ecosystems with emphasis on microbial diversification and adaptation. The final outcome of this project will provide insights into short-term genetic diversification of complex microbial communities and the relation to environmental adaptation. This is important as it will define the adaptability of microorganisms and microbial communities to environmental stressors and will allow a prediction of how these systems will respond to current and future ecosystem changes, e.g., induced by pollution and global warming, respectively.

海洋细菌和古细菌是地球生物多样性的主要组成部分。这些微生物是海洋领域生物地球化学循环的主要驱动力，因此在生态系统的稳定和功能中发挥着不可或缺的作用。最近的几项研究针对海洋微生物的多样性及其对不断变化的环境条件的反应。然而，我们对天然微生物群落的遗传多样性及其基因组对环境胁迫的适应性的认识仍然相当有限。该项目的目的是了解海洋生态系统中微生物进化的动态。由于水平基因转移被认为是微生物进化的主要驱动力，需要回答的主要问题是水平基因转移如何驱动海洋生态系统中复杂微生物群落的多样化及其对当前环境胁迫的适应。为了评估微生物群落动态，将在澳大利亚的三个沿海地区反复采集样本，那里的微生物群落受到各种压力因素的威胁，包括水温上升和农业径流。同时测量环境属性的数据。将从获得的取样材料中提取环境DNA。由于水平基因转移可能发生在密集的微生物群落中，从宿主相关微生物群落（包括海藻全息生物）中分离的DNA将进行下一代测序，并获得宏基因组数据集，随后将挖掘通过水平基因转移转移的可移动遗传元件。除了环境特性和水平基因转移数据外，还将通过从环境DNA中扩增的16S rRNA基因测序来评估自由生活、宿主相关和沉积物微生物群落的分类组成和物种丰富度的变化。生成的数据将进行统计评估，以破译海洋生态系统中微生物进化的动态，重点是微生物的多样化和适应。该项目的最终结果将为复杂微生物群落的短期遗传多样性及其与环境适应的关系提供见解。这很重要，因为它将定义微生物和微生物群落对环境压力源的适应性，并将允许预测这些系统将如何应对当前和未来的生态系统变化，例如分别由污染和全球变暖引起的变化。

项目成果

MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

• DOI: 10.1186/s40168-019-0649-y
• 发表时间: 2019-03-04
• 期刊: MICROBIOME
• 影响因子: 15.5
• 作者: Song, Weizhi;Wemheuer, Bernd;Thomas, Torsten
• 通讯作者: Thomas, Torsten

Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes

• DOI: 10.3390/microorganisms7020037
• 发表时间: 2019-01
• 期刊: Microorganisms
• 影响因子: 4.5
• 作者: B. Wemheuer;T. Thomas;F. Wemheuer

Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota

• DOI: 10.1128/msystems.00288-19
• 发表时间: 2019-07
• 期刊: mSystems
• 影响因子: 6.4
• 作者: Sha Zhang;Weizhi Song;B. Wemheuer;J. Reveillaud;N. Webster;T. Thomas

Modularity and predicted functions of the global sponge-microbiome network

• DOI: 10.1038/s41467-019-08925-4
• 发表时间: 2019-03-01
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Lurgi, Miguel;Thomas, Torsten;Montoya, Jose M.
• 通讯作者: Montoya, Jose M.

Tax4Fun2: a R-based tool for the rapid prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene marker gene sequences

• DOI: 10.1101/490037
• 发表时间: 2018-12
• 期刊: bioRxiv
• 作者: F. Wemheuer;Jessica A. Taylor;R. Daniel;E. Johnston;P. Meinicke;T. Thomas;B. Wemheuer