Fe(II) oxidation by metabolically flexible phototrophs under complex geochemical conditions

过去几十年的工作表明，环境中铁矿物的微生物形成对全球生物地球化学循环具有至关重要的影响。然而，我们对微生物矿物质形成过程的许多基本理解都来自于纯微生物培养的实验。通常，这些实验只用一种能量或碳基质进行，浓度高得不自然。然而，在环境中，许多不同来源的底物通常同时存在，通常浓度较低。关于铁矿物形成细菌在这些低、混合底物条件下的行为，存在着一个基本的知识缺口。在研究具有高度代谢灵活性的微生物类型时，这是一个特别的问题，这些微生物可以使用许多不同的能源和碳源。在这个项目中，我们提出了一种多学科的方法来确定竞争底物对代谢最灵活的矿质形成细菌--厌氧光营养Fe(II)-氧化菌氧化Fe(II)的速率和程度的影响。我们的目标是建立一个基本的理解，即这些细菌留下的矿物学和生化标记是如何受到铁以外的底物(即铁(II)、醋酸盐、葡萄糖、氢)的影响的。为了实现这一点，我们将广泛地表征各种产生缺氧的光养Fe(II)氧化菌在与环境相关的底物浓度(通常在10s-100s微米量级)下的底物选择性。然后，我们将对这些细菌留下的矿物学和生化标记进行表征。这将包括使用穆斯堡尔光谱、微型背散射穆斯堡尔光谱(MIMOS II)、X射线衍射、共聚焦激光扫描显微镜(CLSM)、低温聚焦离子束扫描电子显微镜(CRYO-FIB-SEM)和Zeta电位对“矿物指纹”(即矿物和形成的细胞-矿物聚集体)进行广泛的表征。我们将用蛋白质组学补充矿物学分析，以确定细胞在不同混合底物条件下的生物化学变化。这将使我们能够为Fe(II)的氧化过程建立与环境相关的“分子指纹”。最后，我们将在海洋沉积物微宇宙中结合这些矿物学和微生物学的方法，以确定竞争底物浓度对发现它们的自然环境之一的光养Fe(II)氧化活性的影响。最终，这种矿物学和分子方法的独特结合将提供对环境相关条件下Fe(III)矿物形成的控制的彻底了解，并开发一套标记，用于识别自然环境中光养Fe(II)氧化细菌的贡献。

Decades of previous work have demonstrated that the microbial formation of iron minerals in the environment has a crucial impact on global biogeochemical cycling. However, much of our fundamental understanding of microbial mineral-forming processes comes from experiments with pure cultures of microorganisms. Typically, these experiments are conducted with only one energy or carbon substrate at unnaturally high concentrations. In the environment, however, many different sources of substrate are commonly present at the same time, often with low concentrations. A fundamental knowledge gap exists as to how iron mineral-forming bacteria behave under these low, mixed substrate conditions. This is a particular problem when studying types of microorganisms with high metabolic flexibility which can use many different energy and carbon sources. In this project, we propose a multi-disciplinary approach to determine the effect of competing substrates on rates and extent of Fe(II) oxidation by the most metabolically flexible type of mineral-forming bacteria, anoxygenic phototrophic Fe(II)-oxidizers. We aim to develop a fundamental understanding of how both mineralogical and biochemical markers left by these bacteria are affected by the presence of substrates other than iron (i.e. Fe(II), acetate, glucose, H2). To achieve this, we will extensively characterize the substrate preference of a variety of anoxygenic phototrophic Fe(II)-oxidizers at environmentally relevant substrate concentrations (typically on the order of 10s-100s micrometer). We will then characterize the mineralogical and biochemical markers left by these bacteria. This will include extensive characterization of the “mineral fingerprint” (i.e. minerals and cell-mineral aggregates formed) using Mössbauer spectroscopy, miniaturized backscatter Mössbauer spectroscopy (MIMOS II), X-ray diffraction, confocal laser scanning microscopy (CLSM), cryogenic focussed ion beam scanning electron microscopy (cryo-FIB-SEM) and zeta potentials. We will complement this mineralogical analysis with proteomics to determine how the biochemistry of the cells varies under different mixed substrate conditions. This will enable us to establish an environmentally-relevant “molecular fingerprint” for the process of Fe(II) oxidation. Finally, we will combine both these mineralogical and microbiological approaches in marine sediment microcosms in order to determine the effect of competing substrate concentration on the activity of phototrophic Fe(II) oxidation in one of the natural environments in which they are found. Ultimately this unique combination of mineralogical and molecular approaches will provide a thorough understanding of the controls on Fe(III) mineral formation at environmentally relevant conditions, and develop a suite of markers with which to identify the contribution of phototrophic Fe(II)-oxidizing bacteria in the natural environment.