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

DNA测序技术的进步使我们对微生物多样性的了解有了前所未有的提高，但我们对功能性状与生物多样性的关系或与基因组中发现的基因含量的关系缺乏清晰的认识。正因为如此，我们还不清楚两种生物的DNA序列有多相似，我们才能称它们为同一种生物。这在进行生态推断时具有重要的影响。研究人员已经开发出一种新的方法，通过跟踪独特的“条形码”的频率，快速确定哪些微生物在不同的环境条件下生长良好，这些条形码已被遗传地插入到96个自然生长在植物叶子上的天然分离细菌的面板中。研究人员还将能够追踪不同菌株的微生物如何聚集成群落，这将阐明哪些菌株可以稳定共存。这项工作最终将阐明性状的系统发育保护，这些性状与基因组变化的关联，以及这些性状对微生物间遗传交换的影响程度。推广到K-12学生将导致微生物遗传和功能多样性的公众更大的赞赏。研究人员将重点研究甲基细菌属，这是一个由50个已命名的物种组成的集合，以使用植物衍生的甲醇作为其生长基质之一而闻名。该团队最近发现，当镧系元素存在时，甲基细菌会刺激大豆的生长；因此，有机会将群落多样性与重要的生态系统功能联系起来。该团队的新型条形码系统将完成传统16S rRNA扩增子测序无法完成的两件事：消除PCR偏差，以及在任何混合物中同时跟踪数十个分离株的能力，即使它们具有相同的16S rRNA。该提案利用数据以前所未有的深度和效率开发甲基细菌属的图片，以检查性状的系统发育保护，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，这可以确定一个丰富的具有相同16S rRNA序列的菌株群是否代表了一个成功的基因组云，它们在生态上是相互中立的，还是一组生态多样化的菌株，它们进化出了不同的特征，允许共存。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值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.