Starter Grant: Uncovering the Phylogenetic And Physiological Diversity of Soil Acidobacteria

酸杆菌门的细菌在土壤中普遍存在且数量丰富。尽管如此，我们对土壤酸杆菌知之甚少；只有一小部分的遗传多样性在门内被调查和酸杆菌分类群的系统发育关系尚未得到充分解决。此外，酸杆菌的生理特性及其在土壤中的生态作用在很大程度上仍然未知。其中一个主要原因是酸杆菌在土壤培养收集中表现不佳，因为它们难以使用传统的计算策略进行培养。本项目有两个目的：1)调查和描述土壤酸杆菌的遗传多样性；2)改进土壤酸杆菌的体外培养方法，以评估其生理特性。为了实现这些目标，我们将从美国各地收集六种不同的土壤，并从提取的DNA中建立酸杆菌特异性克隆文库，以描述土壤酸杆菌的系统发育多样性。然后，我们将使用基于pcr的筛选方法来确定从土壤中最有效培养酸杆菌的特定条件或条件集。我们的目标是分离和培养那些从土壤克隆文库的结果中发现在收集的土壤样品中数量丰富的酸杆菌。由于我们之前的工作表明土壤酸杆菌是强烈的寡营养，我们期望酸杆菌可以在营养贫乏的培养基和延长的孵育时间中最有效地培养。一旦成功地分离和培养了油酸杆菌，就可以对其生理特性进行深入的评估。通过这个项目，我们将大大扩展我们目前对土壤酸杆菌的了解；我们将描述这个未被调查的分类群的遗传多样性，并且通过获得纯培养分离物，我们可以开始研究土壤酸杆菌的生态作用。该项目将为研究生提供传统微生物学（菌株分离和培养）和分子微生物学（rDNA序列分析）的培训。

Bacteria belonging to the phylum Acidobacteria are ubiquitous and abundant insoil. Despite this, we know very little about soil Acidobacteria; only a smallportion of the genetic diversity within the phylum has been surveyed and thephylogenetic relationships of acidobacterial taxa have not been adequately resolved. Inaddition, the physiological characteristics of Acidobacteria and their ecological roles insoil remain largely unknown. One major reason for this is that Acidobacteria are poorlyrepresented in soil culture collections as they are difficult to culture using traditionalculturing strategies. This project has two objectives: 1) to survey and describe thegenetic diversity of soil Acidobacteria, and 2) to improve methods for the cultivation ofsoil Acidobacteria in vitro so their physiological characteristics can be assessed. Tomeet these objectives, we will collect six distinct soils from across the United States andbuild acidobacterial-specific clone libraries from extracted DNA to describe thephylogenetic diversity of soil Acidobacteria. We will then use a PCR-based screeningapproach to identify the specific conditions, or set of conditions, under whichAcidobacteria are most efficiently cultivated from soil. Our goal is to isolate and culturethose Acidobacteria which, from the results of the soil clone libraries, are found to benumerically abundant in the collected soil samples. Since our previous work suggeststhat soil Acidobacteria are strongly oligotrophic, we expect that Acidobacteria can bemost effectively cultured with nutrient-poor media and prolonged incubation times. Oncesoil Acidobacteria can be successfully isolated and cultured in vitro, their physiologicalcharacteristics can be assessed in-depth. With this project, we will significantly expandwhat we currently know about soil Acidobacteria; we will describe the genetic diversity ofthis under-surveyed taxa and, by obtaining pure culture isolates, we can begin toinvestigate the ecological roles of soil Acidobacteria. This project will provide a graduatestudent with training in both conventional microbiology (strain isolation and cultivation)and molecular microbiology (rDNA sequence analysis).