Collaborative Research: Differential contributions of archaeal ammonia oxidizer ecotypes in relation to their changing environment

摘要概述：由于硝化的第一步，也是限速步骤，氨氧化，长期以来被认为仅限于细菌领域中的几个类群，氨氧化古生菌(AOA)的发现严重挑战了我们对氮循环微生物生态和生物地球化学的理解。AOA现在被认为是海洋中大部分硝化作用的原因，在海洋水柱中以两个不同的分类群出现，即A水柱(WCA)和B(WCB)生态型。海洋生物地球化学中的一个悬而未决的问题是，WCA和WCB的分类定义及其观察到的分布是否对应于不同的生态和生物地球化学生态位。为了填补这一关键的知识空白，该项目将研究蒙特利湾时间序列(MBTS)内多个深度(0-500米)和两个站点的生态型特定古生型氨单加氧酶(AMOA)基因丰度和表达模式与基于15N的硝化速率之间的联系。从MBTS的大量水柱样本中获取定量表达和生物地球化学活动数据，在两年的过程中每两个月一次，将对海洋条件变化如何影响古细菌氨氧化和AOA生态型动态产生有价值的新见解。智力价值：AOA的发现使人们的注意力重新集中在海洋的硝化作用上；然而，直接测量海洋氨氧化速率的数量仍然少得惊人。由于缺乏数据，很难准确量化硝化作用在多大程度上支持全球海洋的初级生产。该项目的一个主要目标是确定沿海海洋AOA基因和转录本的丰度与瞬时硝化速率之间是否存在数量关系。先前的合作表明，蒙特利湾北部表层水域基于15N的硝化速率与古菌amoA基因拷贝之间存在很强的相关性。这项研究将通过将这些测量作为MBTS的一部分进行，从而获得对这种关系的更全面的了解，不仅在真光区的深处--在那里硝化作用的生物地球化学重要性受到激烈辩论--而且还在中层海洋的疏光和非透光水域进行测量。通过将这项研究作为23年海洋科学计划的一部分进行，所产生的数据集将被纳入一个更大的海洋学框架。这些努力还将直接与MBTS的目标相联系，该目标是通过对负责光区再生氮生产的过程提供新的量化见解来确定新的和再生的初级生产中的时空模式。此外，通过这项研究产生的大量微生物序列和生物地球化学数据将为科学界提供宝贵的资源，最终有助于揭示有关海洋硝化作用的生态和调控因素的新信息，极大地提高我们在目前和未来条件下模拟其在N和C循环中的作用的能力。更广泛的影响：海洋水柱中的硝化作用对浮游植物群落(即初级生产者)的结构和活动有局部影响，对含氮营养物质的形态和一氧化二氮(一种强有力的温室气体)的产生产生更广泛的影响，所有这些都具有重要的社会影响。该项目将提供关于蒙特雷湾复杂多变的环境条件如何影响基本AOA群落的多样性、丰富度和活动的关键信息--蒙特利湾是全球海洋中生产力最高、生物多样性最丰富的区域之一。该项目将对一名研究生(斯坦福大学)和一名博士后研究员(MBARI)进行培训和指导。受训者将与这两位PI广泛互动，他们共同代表着不同的职业阶段和科学观点，横跨微生物生态学、生物地球化学和海洋学。本科生将参与这个项目，高中实习生也将参与。这个项目的方方面面也将被纳入为期4周的霍普金斯微生物学课程，重点是蒙特利湾作为研究海洋微生物的生态学、生理学和进化的天然实验室。

ABSTRACT Overview: Because the first and rate-limiting step of nitrification, ammonia oxidation, was long believed to be restricted to a few groups within the domain Bacteria, the discovery of ammonia-oxidizing archaea (AOA) - members of one of the most abundant microbial groups on the planet (now known as the Thaumarchaeota) - has seriously challenged our understanding of the microbial ecology and biogeochemistry of the nitrogen cycle. AOA are now believed to be responsible for the majority of nitrification in the sea, and occur in the marine water column as two taxonomically distinct groups, namely the Water Column Group A (WCA) and B (WCB) ecotypes. An open question in marine biogeochemistry is whether the taxonomic definition of WCA and WCB and their observed distributions correspond to distinct ecological and biogeochemical niches. To fill this critical knowledge gap, this project will examine linkages between patterns of ecotype-specific archaeal ammonia monooxygenase (amoA) gene abundance and expression and 15N-based nitrification rates across multiple depths (0-500m) and two stations within the Monterey Bay Time Series (MBTS). Acquiring quantitative expressional and biogeochemical activity data from a wide array of water column samples from the MBTS, bimonthly over the course of two years, will yield valuable new insights into how archaeal ammonia oxidation and AOA ecotype dynamics are influenced by changes in ocean conditions. Intellectual Merit: The discovery of AOA has served to refocus attention on nitrification in the ocean; however, there are still an alarmingly low number of direct measurements of oceanic ammonia oxidation rates. This paucity of data has made it difficult to accurately quantify the degree to which nitrification supports primary production in the global ocean. One major goal of this project is to ascertain whether a quantitative relationship between the abundance of AOA genes and transcripts and instantaneous rates of nitrification exists for the coastal ocean. Prior collaboration indicated a strong correlation between 15N-based nitrification rates and archaeal amoA gene copies in surface waters of northern Monterey Bay. This study will acquire a more holistic understanding of this relationship by performing these measurements as part of the MBTS, not only at depths in the euphotic zone - where the biogeochemical importance of nitrification is hotly debated - but also within disphotic and aphotic waters of the mesopelagic. By conducting this research as part of the 23 year MBTS, the resultant dataset will be incorporated into a larger oceanographic framework. These efforts will also directly connect to a goal of the MBTS to determine spatiotemporal patterns in new and regenerated primary production by providing new quantitative insights into processes responsible for regenerated nitrogen production in the photic zone. Additionally, the extensive collections of microbial sequence and biogeochemical data generated through this study will provide a valuable resource to the scientific community and, ultimately, help reveal new information about the ecology and factors regulating nitrification in the ocean, greatly advancing our ability to model its role in N and C cycles under present and future conditions. Broader Impacts: Nitrification in the oceanic water column has implications extending from local effects on the structure and activity of phytoplankton communities (i.e. primary producers) to broader-scale impacts on the speciation of nitrogenous nutrients and production of nitrous oxide (N2O, a potent greenhouse gas), all of which have important societal implications. This project will provide critical information regarding how the diversity, abundance, and activity of the underlying AOA communities are influenced by complex and fluctuating environmental conditions in Monterey Bay - one of the most productive and biologically diverse regions of the global ocean. This project will result in the training and mentorship of a graduate student (Stanford) and a postdoctoral researcher (MBARI). Trainees will interact extensively with both PIs, who together represent diverse career stages and scientific perspectives, spanning microbial ecology, biogeochemistry, and oceanography. Undergraduate students will participate in this project, as well as high school interns. Aspects of this project will also be incorporated into the 4-week Hopkins Microbiology Course, focused on Monterey Bay as a natural laboratory for examining the ecology, physiology, and evolution of marine microbes.