Microbial Dark Matter: Forging New Discoveries in Metabolism

是什么因素使单细胞微生物不仅能够生存，而且还能主动寻找人类认为具有高毒性的环境？科学家们已经了解了这些微小生物的功能，促进了医学，能源和生物修复科学的突破。 然而，对微生物如何在恶劣环境中生长和繁荣的理解在很大程度上仍然笼罩在神秘之中。 预测微生物将如何对环境变化作出反应的能力，或者对细胞内外发生的反应类型的了解，都远远不够。在很大程度上，这是由于识别微生物产生和消耗的小分子（代谢物）的能力有限。 这种未知的微生物代谢产物景观限制了对微生物过程的理解，这些过程在生物地球化学循环，生物修复，生物能源生产以及人类微生物组的调节中发挥着关键作用。在这项工作中，最先进的技术将被用来寻找和表征代谢物，到目前为止，研究人员在很大程度上看不到。 这项工作将为本科生和研究生提供极好的培训机会，特别是来自美洲原住民等代表性不足的群体，以及热生物学研究所的一系列讲座，为有效的推广提供机会，并让公众了解微生物的重要性。本项目以土壤中的革兰氏阴性杆菌Agrobacterium tumefaciens strain 5A为模型，重点研究了由细菌产生的未知微生物代谢产物。这种细菌是了解微生物如何代谢砷的模型，砷是在受污染的土壤和水源中发现的一种重要的环境毒素，也是生物修复工作的重中之重。关注微生物如何代谢砷是很重要的，因为微生物影响砷的毒性和生物利用度在每一个环境中，迄今为止研究。因此，表征微生物产生的砷是该项目的重点，该项目将采用最先进的核磁共振（NMR）和质谱（MS）代谢组学技术来识别未知的微生物化合物，包括砷（即甲基化物质，砷脂，砷糖）。 重要的是，在这个项目中开发的分析方法将适用于生物学的许多方面。该项目将大大提高研究人员探测微生物代谢组丰富性的能力，并更好地了解微生物未知小分子的多样性。聚焦A.根癌农杆菌作为一个模型系统将能够识别和结构表征的新的有机砷化合物和砷脂。这些研究的结果将为与科学研究相关的微生物-砷相互作用领域带来变革性的知识，这些科学研究旨在预测砷如何破坏/改变原位细菌代谢，当微生物必须处理砷时，对自然界中的生物地球化学碳和氮循环具有更广泛的影响。

What factors allow single-celled microbial organisms to not only survive, but actively seek out environments that humans consider highly toxic? Scientists have learned much about how these tiny living creatures function, facilitating breakthroughs in medical, energy, and bioremediation sciences. However, the understanding of how microorganisms grow and thrive in harsh environments remains largely cloaked in mystery. The ability to predict how microorganisms will respond to environmental changes or the knowledge of the types of reactions that occur inside and outside their cells is vastly under-represented. In a large part, this is due to the limited ability to identify the small molecules produced and consumed by microbes (metabolites). This unknown microbial metabolite landscape limits the understanding of the microbial processes playing key roles in the regulation of biogeochemical cycles, bioremediation, bioenergy production, as well as the human microbiome. In this work, state of the art techniques will be used to find and characterize metabolites that up until now have been largely invisible to researchers. The work will result in excellent training opportunities for undergraduate and graduate students, especially from under-represented groups such as Native Americans, as well as a series of lectures at the Thermal Biology Institute that provide an opportunity for effective outreach and give the public a view of the importance of microbes. This project focuses on the discovery of unknown microbial metabolites produced by bacteria using the Gram-negative soil bacterium Agrobacterium tumefaciens strain 5A as model. This bacterium is a model for understanding how microbes metabolize arsenic, a critical environmental toxin found in contaminated soils and water supplies, and a top priority for bioremediation efforts. Focusing on how microbes metabolize arsenic is important because microorganisms influence arsenic toxicity and bioavailability in every environment thus far studied. Thus, characterization of arsenicals produced by microbes are a focal point of this project that will employ state-of-the-art nuclear magnetic resonance (NMR) and mass spectrometry (MS) metabolomics technology to identify unknown microbial compounds, including arsenicals (i.e. methylated species, arsenolipids, arsenosugars). Importantly, the analytical approaches developed in this project will be applicable to many facets of biology. The project will greatly enhance researchers' abilities to probe the richness of the metabolomes of microbes, and to gain a much better appreciation for the diversity of microbial unknown small molecules. Focusing on A. tumefaciens as a model system will enable the identification and structural characterization of novel organo-arsenic compounds and arsenolipids. Results from these studies will bring transformative knowledge to the field of microbe-arsenic interactions relevant to scientific research aimed at predicting how arsenic disrupts/alters bacterial metabolism in situ, with broader implications for biogeochemical carbon and nitrogen cycling in nature when microbes must deal with arsenic.