Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series

圣佩德罗海洋时间序列中的原生生物、原核生物和病毒过程

• 批准号: 1737409
• 负责人: Jed Fuhrman
• 金额: $ 152.88万
• 依托单位: University of Southern California
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2023-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1737409&HistoricalAwards=false
• 关键词: Protistan; prokaryotic; viral; processes; San

Planktonic marine microbial communities consist of a diverse collection of bacteria, archaea, viruses, protists (phytoplankton and protozoa) and small animals (metazoan). Collectively, these species are responsible for virtually all marine pelagic primary production where they form the basis of food webs and carry out a large fraction of respiratory processes. Microbial interactions include the traditional role of predation, but recent research recognizes the importance of parasitism, symbiosis and viral infection. Characterizing the response of pelagic microbial communities and processes to environmental influences is fundamental to understanding and modeling carbon flow and energy utilization in the ocean, but very few studies have attempted to study all of these assemblages in the same study. This project is comprised of long-term (monthly) and short-term (daily) sampling at the San Pedro Ocean Time-series (SPOT) site. Analysis of the resulting datasets investigates co-occurrence patterns of microbial taxa (e.g. protist-virus and protist-prokaryote interactions, both positive and negative) indicating which species consistently co-occur and potentially interact, followed by examination gene expression to help define the underlying mechanisms. This study augments 20 years of baseline studies of microbial abundance, diversity, rates at the site, and will enable detection of low-frequency changes in composition and potential ecological interactions among microbes, and their responses to changing environmental forcing factors. These responses have important consequences for higher trophic levels and ocean-atmosphere feedbacks. The broader impacts of this project include training graduate and undergraduate students, providing local high school student with summer lab experiences, and PI presentations at local K-12 schools, museums, aquaria and informal learning centers in the region. Additionally, the PIs advise at the local, county and state level regarding coastal marine water quality.This research project is unique in that it is a holistic study (including all microbes from viruses to small metazoa) of microbial species diversity and ecological activities, carried out at the SPOT site off the coast of southern California. In studying all microbes simultaneously, this work aims to identify important ecological interactions among microbial species, and identify the basis(es) for those interactions. This research involves (1) extensive analyses of prokaryote (archaean and bacterial) and eukaryote (protistan and micro-metazoan) diversity via the sequencing of marker genes, (2) studies of whole-community gene expression by eukaryotes and prokaryotes in order to identify key functional characteristics of microorganismal groups and the detection of active viral infections, and (3) metagenomic analysis of viruses and bacteria to aid interpretation of transcriptomic analyses using genome-encoded information. The project includes exploratory metatranscriptomic analysis of poorly-understood aphotic and hypoxic-zone protists, to examine their stratification, functions and hypothesized prokaryotic symbioses.

浮游海洋微生物群落由细菌、古菌、病毒、原生动物(浮游植物和原生动物)和小动物(后生动物)组成。总体而言，这些物种负责几乎所有海洋中上层初级生产，在那里它们构成食物网的基础，并执行很大一部分呼吸过程。微生物相互作用包括捕食的传统作用，但最近的研究认识到寄生、共生和病毒感染的重要性。描述海洋微生物群落和过程对环境影响的响应是理解和模拟海洋碳流和能量利用的基础，但很少有研究试图在同一项研究中研究所有这些组合。该项目包括圣佩德罗海洋时间序列(SPOT)站点的长期(每月)和短期(每日)采样。对所得数据集的分析调查微生物分类群的共生模式(例如，原生生物与病毒和原生生物与原核生物的积极和消极相互作用)，表明哪些物种持续共存并可能相互作用，然后检查基因表达，以帮助确定潜在的机制。这项研究补充了20年来对现场微生物丰度、多样性、速率的基线研究，并将能够检测微生物组成的低频变化和潜在的生态相互作用，以及它们对不断变化的环境强迫因素的反应。这些反应对更高的营养水平和海洋-大气反馈具有重要影响。该项目的更广泛影响包括培训研究生和本科生，为当地高中生提供暑期实验室体验，以及在当地K-12学校、博物馆、水族馆和非正式学习中心进行PI演示。这项研究项目的独特之处在于，它是对微生物物种多样性和生态活动的全面研究(包括从病毒到小型后生动物的所有微生物)，在加利福尼亚州南部海岸的现场进行。在同时研究所有微生物的过程中，这项工作的目的是确定微生物物种之间重要的生态相互作用，并确定这些相互作用的基础。这项研究涉及(1)通过标记基因测序对原核生物(古生物和细菌)和真核生物(原生动物和微型后生动物)多样性的广泛分析；(2)真核生物和原核生物整个群落基因表达的研究，以确定微生物群体的关键功能特征和检测活跃的病毒感染；以及(3)病毒和细菌的元基因组分析，以帮助利用基因组编码信息解释转录分析。该项目包括对知之甚少的缺氧区和缺氧区原生生物进行探索性的后转录分析，以检查它们的层化、功能和假设的原核生物共生。

项目成果

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

• DOI: 10.1038/s41467-019-09106-z
• 发表时间: 2019-03
• 期刊: Nature Communications
• 影响因子: 16.6
• 作者: Ella T. Sieradzki;J. C. Ignacio-Espinoza;D. Needham;E. Fichot;J. Fuhrman

Long-term stability and Red Queen-like strain dynamics in marine viruses

• DOI: 10.1038/s41564-019-0628-x
• 发表时间: 2020-02-01
• 期刊: NATURE MICROBIOLOGY
• 影响因子: 28.3
• 作者: Ignacio-Espinoza, J. Cesar;Ahlgren, Nathan A.;Fuhrman, Jed A.
• 通讯作者: Fuhrman, Jed A.

Using DNA to Predict How Fast Bacteria can Grow

使用 DNA 预测细菌的生长速度

• DOI: 10.3389/frym.2022.714713
• 发表时间: 2022
• 期刊: Frontiers for Young Minds
• 作者: Weissman, Jake L.;Hou, Shengwei;Fuhrman, Jed A.
• 通讯作者: Fuhrman, Jed A.