DIMENSIONS: COLLABORATIVE RESEARCH: The phylogenetic and functional diversity of extracellular electron transfer across all three domains of life

所有的细胞都需要能量。这一事实在植物和动物的生物多样性研究中多少被认为是理所当然的，但却处于发现新的微生物生物多样性的前沿。当电荷流过细胞中的能量转移分子时，它与ATP分子的产生（类似于给电池充电）或其他对生命功能至关重要的化合物的产生相结合。直到最近，人们还认为所有的细胞都需要可溶于水的电子能量转移分子，这样它们才能被带入细胞。然而，科学家们发现，一些细菌能够利用位于细胞外的固体金属，如铁锈（氧化铁）作为能量来源。它们通过能量转移分子将电荷传递给环境中的金属沉积物，将电子从细胞内部传送到细胞外部。换句话说，这些微生物的部分能量生产途径已经进化到细胞外。这个过程被称为细胞外电子转移（EET），它改变了我们对细胞生命的看法，特别是微生物如何影响维持地球上生命的全球元素循环。该研究小组将对所有三个生命领域（细菌、古生菌和真核生物）的EET多样性进行首次广泛评估。该计划亦会透过发展互动式博物馆展览，向公众展示微生物的EET，以加深公众对微生物生命的认识。项目调查人员将与《生命百科全书》合作，在其数据库和学校课程中扩大微生物的代表性。该项目还通过教育课程，吸引中学生参与跨学科的EET研究，以及为学生和博士后学者提供进行跨学科研究的教学培训和实验室交流计划，加强行业和学术渠道。与DIMENSIONS计划的目标一致，本提案旨在确定核糖型和基因型与功能和活性相关的程度。这也是环境微生物学的一个巨大挑战，我们使用生物电化学系统选择性地靶向电活性群落的能力为选择性地分离和表征具有细胞外电子转移（EET）能力的微生物提供了独特的机会。为此，本提案的总体目标是全面评估和关联所有三个生命领域中参与EET的微生物的系统发育多样性，遗传/基因组多样性和功能多样性。工作计划包括：1)对自然生境中eet激活微生物的系统发育多样性进行首次广泛、系统的评估；2)利用这些数据的结果确定20个具有代表性的群落，进行宏基因组、亚转录组和生物地球化学特征的联合注册，以针对与EET相关的差异表达转录物以及这些群落介导的生物地球化学过程；3)表征电活性表面上常见的培养但未表征的微生物的遗传、生化和生物物理特性；4)整合这些结果，以更好地预测自然界电活性群落的生理和生物地球化学影响；5)将这些数据存档在健壮的数据库中，以便其他人将项目的发现与他们的数据联系起来。这些努力将首次提供一个综合的数据集，将系统发育数据（16S, 18S）与功能潜力（基因组学）、生理平衡（转录组学）和代谢活动（地球化学测量）联系起来，这将在生物多样性科学之外有许多应用。例如，组学和速率测量的结合将使研究人员能够限制EET对自然界生物地球化学循环的贡献程度。转座子突变和生物物理研究反过来将帮助研究人员了解常见但特征不明确的微生物进行EET的方法。虽然每一项提议的努力都具有重要的价值，但这些活动的协调能够真正整合这些发现，从而为系统发育、基因组和生理多样性之间的关系提供一个全面的视角。

All cells require energy. This fact is somewhat taken for granted in biodiversity studies of plants and animals, but is at the forefront of discovering novel microbial biodiversity. As an electrical charge flows through energy transfer molecules in a cell, it is coupled to the production of ATP molecules (akin to charging the battery that powers the cell) or the production of other compounds that are critical for life function. Until recently, it was thought that all cells require electron energy transfer molecules that are soluble in water, so that they can be brought into the cell. However, scientists discovered that some bacteria are able to use solid metals such as rust (iron oxides) located outside the cell as an energy source. They do so by shuttling electrons from the inside of the cell to the outside of the cell, via energy transfer molecules that deliver electrical charge to metal deposits in the environment. In other words, part of these microbes' energy production pathways have evolved to be outside of the cell. This process, termed extracellular electron transfer (EET), transformed how we think about cellular life and in particular how microbes may impact the global elemental cycles that sustain life on Earth. This research team will conduct the first wide-ranging assessment of the diversity of EET across all three domains of life (Bacteria, Archaea and Eukarya). The project will also broaden public understanding about microbial life through developing interactive museum exhibits that present microbial EET to the public. Project investigators will work with the Encyclopedia of Life to broaden the representation of microbes in their databases and in school curricula. The project is also uniquely poised to strengthen industry and academic pipelines through educational curriculum that engages middle school students in interdisciplinary EET research, and a pedagogical training and lab exchange program that affords students and postdoctoral scholars an opportunity to conduct interdisciplinary research. Consistent with the objectives of the DIMENSIONS program, this proposal aims to establish the degree to which ribotypes and genotypes relate to function and activity. This is also a grand challenge in environmental microbiology, and our ability to use bioelectrochemical systems to selectively target electroactive communities affords a unique opportunity to selectively isolate and characterize microbes capable of extracellular electron transfer (EET). To these ends, the overarching goal of this proposal is to comprehensively assess and relate the phylogenetic diversity, genetic/genomic diversity, and functional diversity of microorganisms engaged in EET across all three domains of life. The work plan includes: 1) conducting the first broad, systematic assessment of the phylogenetic diversity of EET-enabled microbes in natural habitats; 2) using the results of these data to identify 20 "representative" communities for co-registered metagenomic, metatranscriptomic, and biogeochemical characterization to target differentially expressed transcripts associated with EET and the biogeochemical processes that are mediated by these communities; 3) characterizing the genetic, biochemical and biophysical attributes of cultivated but uncharacterized microbes commonly found on electroactive surfaces; 4) integrating these results to develop a better capacity to predict the physiologies and biogeochemical impacts of electroactive communities in nature; and 5) archiving these data in robust databases to allow others to relate the project's findings to their data. These efforts will provide, for the first time, a comprehensive dataset linking phylogenetic data (16S, 18S) with functional potential (genomics), physiological poise (transcriptomics) and metabolic activity (geochemical measurements) that will have many applications to beyond biodiversity science. For example, the combined 'omics and rate measurements will allow the investigators to constrain the extent to which EET contributes to biogeochemical cycles in nature. The transposon mutagenesis and biophysical studies, in turn, will help researchers understand the means by which common but poorly characterized microbes carry out EET. While the value of each of the proposed efforts is significant, the coordination of these activities enables true integration of these findings to provide a comprehensive perspective on the relationships among phylogenetic, genomic and physiological diversity.