Targeted and comparative viral community genomics of the Eastern North Pacific

北太平洋东部（ENP）具有两个重要的气候和生物地球化学特征。该地区是地球上最大的含氧量最低的地区之一，每年浮游植物大量繁殖，导致一些最高的二甲基硫化物（DMS）浓度被观察到。氧最小带（OMZs）在海洋生物地球化学循环中发挥着不可或缺的作用，是氮的主要汇和气候活性微量气体（包括甲烷和氧化亚氮）的主要来源。越来越多的证据表明，预估的海洋变暖和环流变化正在降低ENP沿海和内陆地区的溶解氧浓度，导致OMZ横向和垂直扩张。这将对沿海底栖生物生态系统和海洋渔业生产力产生直接影响，并可能产生积极的气候反馈。此外，ENP中产生的DMS通过其在大气云形成中的作用是大气变暖的潜在负反馈，同时它也占地球总生物硫通量的大约一半。该项目的PI自2008年6月起与Steven Hallam博士（UBC）合作，将病毒群落DNA存档，与微生物生物量的高分子量基因组DNA（自2006年6月起）和丰富的天气海洋学元数据集配对，并在ENP中定义氧化还原梯度，作为加拿大资助的Line P时间序列计划的一部分。病毒样本集中在开放海洋站OSP，跨越表层水、缺氧内层和上下缺氧过渡带。微生物调查自2006年以来一直在进行，研究了ENP本地微生物群的群落多样性和种群结构。时间序列分析揭示了动态的季节变化，与光照、温度和营养条件的变化相一致。然而，关于共同发生的病毒群落在调节微生物群落动态以及对水柱缺氧和大量DMS产生和硫循环的反应中的作用，人们知之甚少。通过分解微生物细胞，海洋病毒负责海洋中最大的碳通量，同时也编码“宿主”代谢基因。以海洋蓝藻为例，噬菌体通过编码地表水光系统中~60%的核心反应中心基因，直接影响全球碳循环。了解ENP的病毒、微生物和生物地球化学耦合过程对于理解、预测或有朝一日可能减轻与OMZ扩张和DMS产量变化相关的生产力和微量气体循环变化至关重要。该项目将通过在ENP中沿定义的时空梯度采样的病毒宏基因组来研究病毒群落的多样性和代谢能力。通过DOE JGI社区测序计划和摩尔基金会病毒测序计划，已经获得了对20个病毒宏基因组及其共同发生的微生物群落进行高系统发育分辨率的16S高变序列标记的资金支持。该项目将确定具有深远生态和进化后果的病毒-宿主相互作用的相关模式。更广泛的影响：微生物和病毒采样工作将由博士后和研究生在50多年的海洋学采样工作的背景下进行，使这些受训者看到“调查”海洋群落所需的大量生物地球化学和物理海洋学测量。该项目将通过直接参与研究、生物圈2号“动手取样训练”和图森高中一门名为“海洋病毒：从分离到基因组和元基因组”的新课程，使本科生和高中生接触到实地海洋学研究的兴奋之处。

Two climatically and biogeochemically important features characterize the Eastern North Pacific (ENP). This region encompasses one of the planet's largest oxygen minimum zones, and annually hosts a phytoplankton bloom that leads to some of the highest dimethyl sulfide (DMS) concentrations observed. Oxygen minimum zones (OMZs) play integral roles in marine biogeochemical cycles, as major sinks for nitrogen and sources for climatologically active trace gases including methane and nitrous oxide. There is increasing evidence that projected ocean warming and circulation changes is decreasing dissolved oxygen concentrations within the coastal and interior regions of the ENP, causing lateral and vertical OMZ expansion. This will have a direct effect on coastal benthic ecosystems and the productivity of marine fisheries, as well as potentially positive climatalogical feedbacks. In addition, the DMS produced in the ENP is a potential negative feedback for atmospheric warming through its role in atmospheric cloud formation, while it also accounts for approximately half of the planet's total biogenic sulfur flux. The PI of this project has collaborated with Dr. Steven Hallam (UBC) since June 2008 to archive viral community DNA, paired with high molecular weight genomic DNA from microbial biomass (since June 2006) and a rich synoptic oceanographic metadataset, along defined redox gradients in the ENP as part of the Canadian-funded Line P time series program. The viral samples focus on open-ocean station OSP and span surface waters, hypoxic interior, and upper and lower oxichypoxic transition zones. Microbial investigations, ongoing since 2006, have examined community diversity and population structure of indigenous microbial groups in the ENP. Time-series analyses have revealed dynamic seasonal changes, consistent with changing light, temperature, and nutrient conditions. However, little is known about the role that co-occurring viral communities play in modulating microbial community dynamics and responses to both water column hypoxia and massive DMS production and sulfur cycling. Marine viruses are responsible for the largest flux of carbon in the oceans by lysing microbial cells, while also encoding "host" metabolic genes. In the case of marine cyanobacteria, phage directly impact global carbon cycling by encoding ~60% of the core reaction center genes in surface water photosystems. Understanding coupled viral, microbiological and biogeochemical processes the ENP is critical to understand, predict, or one day possibly mitigate changes in productivity and trace gas cycling associated with OMZ expansion and changing DMS production. This project will investigate viral community diversity and metabolic capacity through viral metagenomes sampled along defined spatiotemporal gradients in the ENP. The endeavor is highly leveraged with funding already secured for sequencing 20 viral metagenomes, and their co-occurring microbial communities at high phylogenetic resolution using 16S hypervariable sequence tagging through the DOE JGI Community Sequencing Program and the Moore Foundation viral sequencing initiative. This project will identify relevant patterns of viral-host interaction with profound ecological and evolutionary consequences.Broader impacts: The microbial and viral sampling effort will be performed by post-docs and graduate students in the context of a 50+ year oceanographic sampling effort that allows these trainees see the vast biogeochemical and physical oceanographic measurements required to "survey" an ocean community. This project will expose undergraduates and high school students to the excitement of field-based oceanographic research through a combination of direct involvement in research, a Biosphere 2 "hands-on sampling training", and a new course at Tucson High School entitled "Ocean viruses: From isolates to genomes and metagenomes".