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

摘要：长期以来，人们一直认为硝化作用的第一步和限速步骤氨氧化仅限于细菌领域的少数类群，因此氨氧化古菌（AOA）的发现严重挑战了我们对微生物生态学和氮循环生物地球化学的理解。AOA是地球上最丰富的微生物类群之一（现在称为Thaumarchaeota）。AOA目前被认为是海洋中大部分硝化作用的原因，并且在海洋水柱中分为两个不同的类群，即水柱群A （WCA）和水柱群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的分类定义及其观测到的分布是否对应于不同的生态位和生物地球化学位。为了填补这一关键的知识空白，该项目将研究生态型特异性古菌氨单加氧酶（amoA）基因丰度和表达模式与蒙特雷湾时间序列（MBTS）内多个深度（0-500m）和两个站点的15n硝化速率之间的联系。在两年的时间里，每个月从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，将对古细菌氨氧化和AOA生态类型动力学如何受到海洋条件变化的影响产生有价值的新见解。知识价值：AOA的发现重新引起了人们对海洋硝化作用的关注；然而，对海洋氨氧化速率的直接测量仍然少得惊人。由于缺乏数据，很难准确量化硝化作用对全球海洋初级生产的支持程度。该项目的一个主要目标是确定在沿海海洋中AOA基因和转录本的丰度与瞬时硝化速率之间是否存在定量关系。先前的合作表明，蒙特雷湾北部地表水中15n基硝化速率与古细菌amoA基因拷贝之间存在很强的相关性。本研究将通过将这些测量作为MBTS的一部分，对这种关系进行更全面的理解，不仅在光带深度-硝化作用的生物地球化学重要性正在激烈辩论-而且在中上层的双光和无光水域。通过将这项研究作为23年MBTS的一部分进行，所得数据集将被纳入更大的海洋学框架。这些努力也将直接与MBTS的目标联系起来，即通过对光区再生氮生产过程提供新的定量见解，确定新的和再生的初级生产的时空模式。此外，通过本研究产生的微生物序列和生物地球化学数据的广泛收集将为科学界提供宝贵的资源，并最终有助于揭示有关海洋中硝化的生态学和调节因素的新信息，大大提高我们在当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：海洋水体中的硝化作用的影响范围从对浮游植物群落（即初级生产者）的结构和活动的局部影响延伸到对含氮营养物的形态和氧化亚氮（N2O，一种强效温室气体）的产生的更广泛的影响，所有这些都具有重要的社会影响。该项目将提供关于蒙特利湾（全球海洋中最具生产力和生物多样性的地区之一）复杂和波动的环境条件如何影响潜在AOA群落的多样性、丰度和活动的关键信息。该项目将培养和指导一名研究生（斯坦福大学）和一名博士后研究员（MBARI）。受训者将与两位pi进行广泛的互动，他们共同代表不同的职业阶段和科学观点，涵盖微生物生态学，生物地球化学和海洋学。这个项目将由本科生和高中实习生参与。该项目的各个方面也将纳入为期四周的霍普金斯微生物学课程，重点关注蒙特利湾作为研究海洋微生物生态学、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.