Dimensions: The roles of phylogeny, genome content, and functional performance traits in the evolution and assembly of a diverse Methylobacterium community

DNA测序的进展使我们对微生物多样性的理解有了前所未有的提高，但我们缺乏一个清晰的图景来说明功能特征与生物多样性或它们基因组中的基因含量是如何相关的。正因为如此，目前还不清楚两种生物的DNA序列需要有多相似才能让我们称它们为相同的东西。在做出生态推断时，这会产生重要的后果。研究人员开发了一种新的方法来快速确定哪些微生物在不同的环境条件下生长良好，方法是跟踪独特的“条形码”的频率，这些条形码已被遗传地插入到96个自然分离的细菌中，这些细菌自然生长在植物叶片上。研究人员还将能够跟踪不同菌株的微生物如何聚集成群落，这将阐明哪些微生物可以稳定共存。这项工作最终将阐明特征的系统发育保护，这些特征与基因组变化的关联，以及这些特征对微生物之间的基因交换有多大影响。对K-12学生的推广将使公众对微生物的遗传和功能多样性有更多的了解。研究人员将重点放在甲基细菌属上，这是一个由50个命名物种组成的集合，以使用植物来源的甲醇作为其生长基质之一而闻名。该团队最近发现，当有稀土元素存在时，甲基细菌可以刺激大豆的生长；因此，有机会将群落多样性与一项重要的生态系统功能联系起来。该团队新颖的条形码系统将实现传统16S rRNA扩增子测序不可能完成的两件事：消除PCR偏见，以及在任何混合物中同时跟踪数十个菌株的能力，即使它们具有相同的16S rRNA。这一建议利用数据来以前所未有的深度和效率绘制一张甲氧基乳杆菌属的图景，以检查性状的系统发育保存，将性状与基因组内容的变化联系起来，并询问这些性状对整个属的遗传交换有多大影响。最终，这可以确定具有相同16S rRNA序列的大量菌株代表的是彼此在生态上中立的成功基因组的单一云，还是进化出允许共存的独特特征的生态多样性菌株的小组。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Advances in sequencing DNA have led to an unprecedented increase in our understanding of microbial diversity, yet we lack a clear picture of how functional traits relate to organismal diversity, or to the gene content found in their genomes. Because of this, it is not clear how similar in DNA sequence two organisms need to be for us to call them the same thing. This has important consequences when making ecological inferences. The researchers have developed a novel way to rapidly determine which microbes grow well under different environmental conditions by following the frequency of unique "barcodes" that have been genetically inserted into a panel of 96 natural isolates of bacteria that naturally grow on plant leaves. The researchers will also be able to track how different strains of microbes assemble into communities, which will illuminate which ones can stably coexist. The work will ultimately shed light on the phylogenetic conservation of traits, association of those traits to changes in the genome, and how much these traits influence genetic exchange across microbes. Outreach to K-12 students will result in a greater appreciation by the public of microbial genetic and functional diversity.Researchers will focus on the genus Methylobacterium, a collection of 50 named species well known for use of plant-derived methanol as one of their growth substrates. This team recently uncovered that Methylobacterium stimulates growth of soybeans when lanthanides are present; thus, there is opportunity to connect community diversity with an important ecosystem function. The team's novel barcoding system will accomplish two things not possible with traditional 16S rRNA amplicon sequencing: elimination of PCR bias, and the ability to track dozens of isolates simultaneously in any mixture, even if they have identical 16S rRNA. This proposal leverages data to develop a picture of the genus Methylobacterium at unprecedented depth and efficiency to examine the phylogenetic conservation of traits, associate traits to changes in genome content, and ask how much these traits influence genetic exchange across the genus. Ultimately, this can establish whether an abundant group of strains with identical 16S rRNA sequences represents a single cloud of successful genomes that are ecologically neutral with regard to each other, or a panel of ecologically diverse strains that have evolved distinct traits that permit coexistence.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.