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

浮游海洋微生物群落由细菌、古生菌、病毒、原生生物（浮游植物和原生动物）和小型动物（后生动物）组成。 总体而言，这些鱼种负责几乎所有海洋中上层初级生产，它们构成食物网的基础，并进行大部分呼吸过程。 微生物的相互作用包括传统的捕食作用，但最近的研究认识到寄生，共生和病毒感染的重要性。 描述浮游微生物群落和过程对环境影响的反应是理解和模拟海洋中碳流动和能源利用的基础，但很少有研究试图在同一研究中研究所有这些组合。 该项目包括在圣佩德罗海洋时间序列（SPOT）站点进行长期（每月）和短期（每日）取样。 对所得数据集的分析研究了微生物分类群的共现模式（例如，原生生物-病毒和原生生物-原核生物相互作用，阳性和阴性），表明哪些物种始终共现并可能相互作用，然后检查基因表达以帮助定义潜在的机制。 这项研究增加了20年来对该地点微生物丰度、多样性和速率的基线研究，并将能够检测微生物组成和潜在生态相互作用的低频变化，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，并在当地K-12学校，博物馆，水族馆和该地区的非正式学习中心进行PI演示。此外，PI还在地方、县和州一级提供有关沿海海水水质的建议。该研究项目的独特之处在于，它是一项关于微生物物种多样性和生态活动的整体研究（包括从病毒到小型后生动物的所有微生物），在加州南部海岸的SPOT现场进行。 在同时研究所有微生物的过程中，这项工作旨在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。 本研究包括（1）广泛分析原核生物（古生菌和细菌）和真核生物（2）通过真核生物和原核生物研究整个群落的基因表达，以鉴定微生物群体的关键功能特征和检测活性病毒感染，和（3）病毒和细菌的宏基因组分析，以帮助使用基因组编码的信息解释转录组分析。 该项目包括探索性的元转录组学分析的理解不足的无光和缺氧区原生生物，以检查他们的分层，功能和假设的原核生物共生。

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.