Collaborative Research: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments

海洋沉积物是世界上最大的有机碳储存库，了解微生物如何分解这些碳对于了解全球碳循环至关重要。然而，关于微生物网络如何共同完成海洋沉积物中有机碳的完全分解，长期存在的问题仍然存在。沉积物微生物以无数种方式相互作用，将它们的代谢与有机碳的分解结合起来，包括共享代谢产物。越来越多的证据进一步表明，一些微生物可以通过将电子直接传递给其他不相关的微生物来相互作用。这种能力发生在不同的微生物中，似乎在生物圈中广泛存在，特别是在海洋沉积物等厌氧环境中。该项目解决了在天然厌氧海洋和河口沉积物中共同工作以分解有机碳的微生物之间的身份和代谢联系的新问题。研究人员通过关注关键细菌对其周围微生物群落的影响来解决这些问题。“电缆细菌”是最近发现的一组长丝状细菌，它们在水生沉积物中充当电导体，通过厘米级的电子传输过程，为电子从较深的硫化物沉积物转移到表层氧层提供管道。自从6年前被发现以来，这些细菌已经在广泛的沉积环境中被观察到，通常是在极高的细胞密度下。在这些细菌丰富的地方，如沿海海洋泥中，它们会引起局部pH值的剧烈变化，并强烈影响矿物循环。本研究探讨了电缆菌对相关微生物代谢活性的直接和间接影响。该项目还促进了两名早期职业研究者、两名博士生和本科生的教育和培训。从这些博士研究项目中获得的技能和专业知识将使学生在学术追求和与私营企业相关的生物信息学和技术应用方面具有竞争力。从这项工作中产生的科学发现正在被纳入海洋微生物生态学的本科和研究生水平的课程。研究小组将通过举办公共讲座来促进对环境微生物生态学的更好理解，从而接触到更广泛的社区。提出的工作是研究电缆细菌在构建沉积物微生物群落中的作用。由于其生长策略和形态，电缆细菌特别适合实验操作，为更好地了解自然和复杂厌氧环境中微生物之间的群落相互作用提供了绝佳的机会。研究人员将通过控制电缆细菌的生长和活性，并量化由此产生的微生物群落反应，探索电缆细菌与其相关微生物群落之间的相互作用和关系。具体而言，该项目旨在(1)识别由电缆细菌促进生长的微生物，(2)使用超转录组学识别与电缆细菌活性相关的代谢过程，(3)使用dna稳定同位素探测（SIP）方法测试沉积物微生物与电缆细菌活性之间的特定代谢联系，以及(4)使用显微镜视觉确认与电缆细菌相关的关键微生物的身份和量化。随着对缺氧沉积物中微生物代谢联系的特性和机制的了解越来越多，我们将能够更好地理解和预测微生物在其环境中如何发挥作用以及如何在生物工程系统中利用它们。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Marine sediments represent the world's largest repository of stored organic carbon, and understanding how microorganisms break down this carbon is an imperative for understanding global carbon cycling. Yet long-standing questions remain regarding how networks of microorganisms work together to accomplish the complete breakdown of organic carbon in marine sediments. Sediment microbes interact in a myriad of ways that couple their metabolism to the break down of organic carbon, including by sharing products of metabolism. Accumulating evidence further suggests that some microorganisms can interact by transferring electrons directly to other unrelated microorganisms. This ability occurs across diverse microorganisms and appears to be widespread in the biosphere, particularly in anaerobic environments such as marine sediments. This project addresses emerging questions about the identity and metabolic linkages between microorganisms that work together in natural anaerobic marine and estuarine sediments to break down organic carbon. The investigators approach these questions by focussing on the influence of a keystone bacterium on its surrounding microbial community. "Cable bacteria" are a recently discovered group of long filamentous bacteria that act as electrical conductors in aquatic sediments providing a conduit for electrons to commute from deeper sulfidic sediments up to the surface oxygen layer by the process of centimeter-scale electron transport. Since their discovery about 6 years ago, these bacteria have been observed in a wide range of depositional sedimentary environments, often at extremely high cell densities. Where these bacteria are abundant, such as in coastal marine muds, they drive intense localized changes in pH and strongly influence the mineral cycling. This research explorew the direct and indirect influence of cable bacteria on the metabolic activity of associated microorganisms. This project also advance the education and training of two early-career investigators, two PhD students, and undergraduate students. The skills and expertise gained from these PhD research projects will enable the students to be competitive in academic pursuits and in bioinformatics and technology applications relevant to private industry. The scientific discoveries emerging from this work is being incorporated into undergraduate and graduate level courses in marine microbial ecology. The research team will reach out to the broader community by hosting public lectures promoting a better understanding of environmental microbial ecology. The proposed work is to investigate the role of cable bacteria in structuring sediment microbial communities. Due to their growth strategy and morphology, cable bacteria are particularly amenable to experimental manipulation, providing an outstanding opportunity to better understand community interactions among microorganisms in a natural and complex anaerobic environment. The investigators will explore the interactions and relationships between cable bacteria and their associated microbial community by manipulating the growth and activity of cable bacteria and quantifying the resultant microbial community response. Specifically, this project aims to (1) identify microorganisms whose growth is enhanced by cable bacteria, (2) identify metabolic processes linked with cable bacteria activity using metatranscriptomics, (3) test specific metabolic links between sediment microorganisms and cable bacteria activity using a DNA-stable isotope probing (SIP) approach, and (4) visually confirm the identity and quantify key microorganisms associated with cable bacteria using microscopy. As more is learned about the identity and the mechanisms by which microorganisms are metabolically linked in anoxic sediments, we will be better able to understand and make predictions about how microorganisms function in their environment and how they can be utilized in bioengineered systems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.