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

摘要概述：由于硝化的第一步和限速步骤，氨氧化，长期以来被认为是限制在细菌领域内的少数群体，氨氧化古菌（AOA）-地球上最丰富的微生物群体之一（现在称为Thaumarchaeota）的成员-的发现严重挑战了我们对氮循环的微生物生态学和生物地球化学的理解。AOA被认为是海洋中硝化作用的主要原因，并且在海洋水柱中作为两个分类学上不同的组出现，即水柱组A（WCA）和B（WCB）生态型。WCA和WCB的分类学定义及其观测分布是否对应于不同的生态和海洋地球化学生态位是海洋地球化学中的一个悬而未决的问题。为了填补这一关键的知识空白，该项目将研究特定生态类型的古细菌氨单加氧酶（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- 500米）和两个站点的15 N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性数据，在两年的时间里每两个月一次，将产生有价值的新见解，了解古细菌氨氧化和AOA生态类型动态如何受到海洋条件变化的影响。智力优势：AOA的发现使人们重新关注海洋中的硝化作用;然而，海洋氨氧化速率的直接测量数量仍然少得惊人。由于数据的缺乏，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AOA基因和转录本的丰度和瞬时硝化速率之间是否存在定量关系。先前的合作表明，在北方蒙特雷湾的表面沃茨中，基于15 N的硝化速率和古菌amoA基因拷贝之间存在很强的相关性。这项研究将获得一个更全面的了解这种关系，通过执行这些测量的一部分，MBTS，不仅在真光层的深度-硝化作用的地球化学的重要性是激烈的辩论-但也在diphotic和无光沃茨的中层。通过将这项研究作为23年MBTS的一部分进行，所得到的数据集将被纳入一个更大的海洋学框架。这些努力也将直接连接到MBTS的目标，以确定时空模式，在新的和再生的初级生产提供新的定量见解负责再生氮生产过程中的透光区。此外，通过这项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硝化作用的生态和因素的新信息，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物种形成和一氧化二氮（N2 O，一种强效温室气体）的产生的更广泛影响，所有这些都具有重要的社会影响。该项目将提供关键信息，了解底层AOA群落的多样性，丰度和活动如何受到蒙特雷湾复杂和波动的环境条件的影响-蒙特雷湾是全球海洋中最具生产力和生物多样性的地区之一。该项目将培训和指导一名研究生（斯坦福大学）和一名博士后研究员（MBARI）。学员将与两个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。本科生将参加这个项目，以及高中实习生。该项目的各个方面也将纳入为期4周的霍普金斯微生物学课程，重点是蒙特雷湾作为一个天然实验室，用于研究生态学，生理学和海洋微生物的进化。

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.