Quorum-sensing and the Carbon Cycle: Identifying Cell-density Dependent Organic Carbon Degradation among Marine Bacteria in Sinking Particles

绝大多数在海洋表层形成的下沉有机碳在通过水柱的运输过程中被降解，而下沉颗粒上的异养菌是这一过程的重要因素。最近的工作表明，这些细菌有能力通过群体感应(QS)相互交流来调节有机碳降解代谢。QS是细菌使用细胞-细胞信号来测量其环境中相关细胞的密度，以协调这些相关细胞之间的代谢反应的过程。在这项研究中，伍兹霍尔海洋研究所和海洋生物实验室的研究人员将检验这一假设，即基于AHL的QS系统通过捕获下沉的颗粒来活跃地下沉海洋颗粒，并分析它们以寻找对活跃的QS具有诊断作用的细胞-细胞信号分子。下沉的海洋颗粒中含有丰富的变形杆菌。这组细菌利用一类名为酰化高丝氨酸内酯(AHL)的QS分子，该团队此前已为其开发了新的预浓缩和质谱分析方法，用于分析下沉颗粒中的AHL。此外，该团队还将通过构建下沉颗粒的基因组DNA文库并筛选这些文库来生产AHL，来测试这一假设，即下沉颗粒中受基于AHL的QS调控的基因编码有机物降解的酶。这将使含有AHL调节基因的基因组DNA片段能够被挑选出来，并进一步分析编码水解酶的基因，而不需要依赖于序列数据库搜索。最后，他们将应用“功能基因表达”策略来明确限制水解酶是否真的是这些AHL调控基因的产物。在之前的工作中，研究小组发现，一些海洋细菌也会分泌酶来降解AHL；因此，他们将使用功能基因表达分析和基于培养的实验来检查这是否发生在下沉颗粒上。这项关于下沉颗粒群体感应的研究有可能揭示细菌群落组成和颗粒通量衰减之间以前未知的联系。提出这项研究的主要理由是，法定人数感应就是这样一种联系。QS已经在生物医学文献中得到了很好的描述，因此，在海洋环境中进行探索的时机已经成熟。更广泛的影响：该项目将支持两名研究生，其中一人对从事博士后职业生涯特别感兴趣，这将在很大程度上依赖本科生进行的研究。

The vast majority of sinking organic carbon formed within the surface layer of the ocean is degraded in transit through the water column, and heterotrophic bacteria on sinking particles are important agents of this process. Recent work suggests that these bacteria have the ability to regulate organic carbon degrading metabolisms by communicating with one another via quorum sensing (QS). QS is a process where bacteria use cell-cell signaling to gauge the density of related cells in their environment for the purpose of coordinating metabolic responses among these related cells. In this study, researchers at the Woods Hole Oceanography Institution and the Marine Biological Laboratory will test the hypothesis that AHL-based QS systems are active in sinking marine particles by trapping sinking particles, and analyzing them for cell-cell signaling molecules that are diagnostic for active QS. Sinking marine particles contain abundant Proteobacteria. This group of bacteria utilizes a class of QS molecules called acylated homoserine lactones (AHL) for which the team has previously developed new pre-concentration and mass spectrometry methods for analyzing AHLs in sinking particles. Additionally, the team will also test the hypothesis that that genes regulated by AHL-based QS in sinking particles encode enzymes for organic matter degradation by constructing libraries of genomic DNA from sinking particles and screening these libraries for AHL production. This should enable sections of genomic DNA that contain AHL-regulated genes to be singled out and analyzed further for genes encoding hydrolytic enzymes without relying on sequence database searches. Finally, they will apply a "functional gene expression" strategy to definitively constrain whether hydrolytic enzymes are indeed the products of these AHL-regulated genes. In previous work, the research team found that some marine bacteria also secrete enzymes to degrade AHLs; consequently, they will will examine whether this is occurring on sinking particles using both functional gene expression assays and incubation-based experiments. This study of quorum sensing in sinking particles has the potential to reveal previously uncharacterized linkages between bacterial community composition and particle flux attenuation. The primary justification for the proposed study is that quorum sensing is one such connection. QS has been well-characterized in the biomedical literature, and, as such, is ripe for exploration in marine environments. Broader impacts: The project will support two graduate students, one of whom is specifically interested in pursuing a postdoctoral career path that will depend heavily on research conducted by undergraduates.