Ecology and biogeochemical impacts of DNA and RNA viruses throughout the global oceans

DNA 和 RNA 病毒对全球海洋的生态和生物地球化学影响

• 批准号: 1829831
• 负责人: Matthew Sullivan
• 金额: $ 105.29万
• 依托单位: Ohio State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1829831&HistoricalAwards=false
• 关键词: Ecology; biogeochemical; impacts; DNA; RNA

In the oceans, microbial life sits at the base of the food chain, but microbes also control the flow of nutrients and energy. While our knowledge of microbial impacts on the oceans is rapidly advancing, we remain far behind in studying the impact of viruses. Decades of experiments and global surveys that have focused on common ocean viruses (double-stranded DNA viruses) suggest that they kill many cells, change the genes that cells encode in their genomes, and reprogram how cells function during infection. This project seeks to create a metabolic map of the global oceans and quantify which of these microbial processes common viruses manipulate. Further, this project will expand to other types of viruses (RNA viruses) that are less well studied, as well as advance our knowledge of both DNA and RNA viruses with respect to global patterns and distributions to assess viral activity. Such analyses are critical to better understand how viruses of all types alter microbial processes and thereby drive nutrient cycling in the oceans. Beyond the science, this project will train two postdocs, a graduate student and five undergraduate students, as well as conduct outreach through Columbus-area seminars and lecture series and provide a training workshop for researchers in each years 1 and 3. Microbial metabolisms alter nutrients and energy flow in ways that impact global ocean biogeochemistry, but associated viruses modulate these metabolic impacts through mortality, horizontal gene transfer and metabolic reprogramming. The latter impact is particularly understudied due to being a largely manual process, though early data hints that it likely impacts photosynthesis, central carbon metabolism, and nitrogen and sulfur cycling. Further, though eukaryotes are likely most commonly infected by RNA viruses and RNA viruses are thought to represent about half of viral particles in seawater, very little information on RNA virus diversity or ecology exists. Finally, particles are not the ?active? form of viruses, which begs for the development of new approaches to assess activity using the newly-available reference genomes against expression (e.g., metatranscriptomic) datasets. This project seeks to leverage extensive organismal, physical, and chemical datasets from the global Tara Oceans expedition to (i) advance from surveying dsDNA viral biodiversity towards inferring their metabolic impacts and active infection ecology, and (ii) build a parallel RNA virus biodiversity inventory from which to establish foundational ecological understanding of drivers and community structure. Scientifically, these efforts will evaluate more than a dozen hypotheses and establish countless more hypotheses about viral roles in marine microbial ecology and biogeochemistry. The project will train two postdocs, a graduate student and five undergraduate students, some through engagement with international Tara Oceans Consortium meetings, as well as provide public outreach through classroom and seminar visits at a Columbus area school (~240 students), a local chapter of the MIT Alumni club, an OSU Center for RNA Biology ?Science Sundays? lecture series, and seminars and interactive activities with Canada?s indigenous people. A viromics training workshop will be held in each years 1 and 3 to maximize research community involvement and engagement.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

在海洋中，微生物位于食物链的底部，但微生物也控制着营养物质和能量的流动。 虽然我们对微生物对海洋影响的了解正在迅速发展，但我们在研究病毒影响方面仍然远远落后。数十年针对常见海洋病毒（双链 DNA 病毒）的实验和全球调查表明，它们会杀死许多细胞，改变细胞在基因组中编码的基因，并重新编程细胞在感染期间的功能。该项目旨在创建全球海洋的代谢图，并量化常见病毒操纵的这些微生物过程。此外，该项目还将扩展到研究较少的其他类型的病毒（RNA 病毒），并增进我们对 DNA 和 RNA 病毒在全球模式和分布方面的了解，以评估病毒活动。此类分析对于更好地了解所有类型的病毒如何改变微生物过程并从而驱动海洋中的营养循环至关重要。除了科学之外，该项目还将培训两名博士后、一名研究生和五名本科生，并通过哥伦布地区研讨会和系列讲座进行推广，并在每年第一年和第三年为研究人员提供培训研讨会。微生物代谢以影响全球海洋生物地球化学的方式改变营养物和能量流，但相关病毒通过死亡率、水平基因转移和代谢来调节这些代谢影响 重新编程。由于主要是手动过程，后一种影响尤其未被充分研究，尽管早期数据暗示它可能会影响光合作用、中央碳代谢以及氮和硫循环。此外，尽管真核生物可能最常被RNA病毒感染，并且RNA病毒被认为代表了海水中大约一半的病毒颗粒，但关于RNA病毒多样性或生态学的信息却很少。最后，粒子不是“活性的”？病毒的形式，这就需要开发新的方法来使用新可用的参考基因组针对表达（例如元转录组）数据集来评估活动。该项目旨在利用来自全球塔拉海洋探险的广泛有机、物理和化学数据集，以（i）从调查 dsDNA 病毒生物多样性转向推断其代谢影响和活跃感染生态学，以及（ii）建立平行的 RNA 病毒生物多样性清单，从中建立对驱动因素和群落结构的基础生态理解。从科学角度来看，这些努力将评估十多个假设，并建立无数关于病毒在海洋微生物生态学和生物地球化学中的作用的假设。该项目将培训两名博士后、一名研究生和五名本科生，其中一些学生参加国际塔拉海洋联盟会议，并通过在哥伦布地区学校（约 240 名学生）、麻省理工学院校友俱乐部当地分会、俄勒冈州立大学 RNA 生物学中心“科学周日”的课堂和研讨会访问来提供公众宣传。系列讲座、研讨会以及与加拿大原住民的互动活动。每年第一年和第三年将举办一次病毒组学培训研讨会，以最大限度地提高研究界的参与度。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

• DOI: 10.1016/j.cell.2019.10.014
• 发表时间: 2019-11-14
• 期刊: CELL
• 影响因子: 64.5
• 作者: Salazar, Guillem;Paoli, Lucas;Wincker, Patrick
• 通讯作者: Wincker, Patrick

Global Trends in Marine Plankton Diversity across Kingdoms of Life

• DOI: 10.1016/j.cell.2019.10.008
• 发表时间: 2019-11-14
• 期刊: CELL
• 影响因子: 64.5
• 作者: Ibarbalz, Federico M.;Henry, Nicolas;Zinger, Lucie
• 通讯作者: Zinger, Lucie

Genome‐resolved viral ecology in a marine oxygen minimum zone

基因组解析了海洋最低氧气区的病毒生态学

• DOI: 10.1111/1462-2920.15313
• 发表时间: 2020
• 期刊: Environmental Microbiology
• 影响因子: 5.1
• 作者: Vik, Dean;Gazitúa, Maria Consuelo;Sun, Christine L.;Zayed, Ahmed A.;Aldunate, Montserrat;Mulholland, Margaret R.;Ulloa, Osvaldo;Sullivan, Matthew B.
• 通讯作者: Sullivan, Matthew B.

Diversity and ecological footprint of Global Ocean RNA viruses

• DOI: 10.1126/science.abn6358
• 发表时间: 2022-06-10
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Dominguez-Huerta, Guillermo;Zayed, Ahmed A.;Sullivan, Matthew B.
• 通讯作者: Sullivan, Matthew B.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

• DOI: 10.1093/nar/gkaa621
• 发表时间: 2020-09-18
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Shaffer, Michael;Borton, Mikayla A.;Wrighton, Kelly C.
• 通讯作者: Wrighton, Kelly C.