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，而且能够积极地寻找人类认为是剧毒的环境？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是一个谜。预测微生物如何对环境变化作出反应的能力，或者对发生在细胞内外的各种反应的了解，都远远不够。在很大程度上，这是由于鉴定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物景观限制了对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关键作用的微生物过程的理解。在这项工作中，将使用最先进的技术来发现和表征到目前为止研究人员基本上看不见的代谢物。这项工作将为本科生和研究生提供极好的培训机会，特别是来自印第安人等代表性不足的群体的培训机会，以及热生物学研究所的一系列讲座，这些讲座为有效的推广提供了机会，并使公众了解微生物的重要性。本项目以革兰氏阴性土壤细菌农杆菌（Agrobacterium tumefaciens）菌株5A为模型，重点发现细菌产生的未知微生物代谢物。这种细菌是了解微生物如何代谢砷的模型，砷是一种在受污染的土壤和供水中发现的关键环境毒素，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到目前为止的研究。因此，微生物产生的砷的表征是该项目的重点，该项目将采用最先进的核磁共振（NMR）和质谱（MS）代谢组学技术来鉴定未知的微生物化合物，包括砷（即甲基化物种、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。该项目将极大地提高研究人员探索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。将瘤胃芽孢杆菌作为一个模型系统，将有助于鉴定和表征新型有机砷化合物和砷脂。这些研究的结果将为微生物-砷相互作用领域带来革命性的知识，这些知识与旨在预测砷如何原位破坏/改变细菌代谢的科学研究相关，对微生物必须处理砷时自然界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.