BE/GEN-EN: Marine Viromics: The Interaction of Viral Genomes with the Marine Environment

海洋病毒（主要是噬菌体）可能是地球上最丰富的生命形式。活性（裂解）病毒感染导致细胞裂解，从而控制通过海洋微生物食物网的碳流，在某些情况下引发藻华的崩溃。相反，非活性（溶原性）感染赋予对重复感染的免疫力，并导致转化为多种表型。培养的大多数海洋细菌产生某种类型的病毒样颗粒（VLP）。S)，表明溶原性的发生是广泛的。海洋病毒基因组由于体积小（通常为50-100 kb），研究起来比较经济。病毒组学的生物复杂性源于病毒基因组对环境信号的相互作用和反应。该项目将重点研究溶原性，即病毒基因组与其宿主建立稳定的相互作用。在河口环境中观察到的溶原的季节性分布表明，溶原在海洋环境中的发生是复杂的。据推测，当病毒基因对环境信号作出反应时，就会发生溶胞-溶胞性转变，初步证据表明，磷酸盐水平和pho基因可能在这种相互作用中起作用。具体的研究目标是：1)确定哪些生理和环境因素催化了培养和天然微生物群体从溶原性到溶原性的生活方式转变，2)对几种温带噬菌体的基因组进行测序，3)确定噬菌体基因如何协同作用以赋予海洋细菌的溶原性或溶原性存在，以及4)将温带噬菌体的影响纳入海洋微生物食物网模型。第一个目标将通过采用培养（蓝藻和异养细菌）和自然种群来研究可能控制“溶原决定”的线索来解决。培养物和自然种群将暴露于温度、营养、阳光、盐度和暴露于外源物的变化中，从而引起从裂解到溶生的转变，反之亦然。对于第二个目标，将对其中五个噬菌体-宿主系统进行测序。比较基因组学将用于识别共同的基因和模块。对于第三个目标，将通过northern分析对噬菌体基因表达进行量化。表达模式的差异将提供基因组对不断变化的环境条件反应的信息。如果在噬藻体中发现了保守的溶原基因，将测量其在坦帕湾天然细菌群体中的表达。最后，基于在坦帕湾为期13个月的溶原性季节性研究，将开发一个计算模型来描述温带噬菌体与海洋微生物食物网的相互作用。这项研究的更广泛影响包括在圣地亚哥州立大学以本科生研讨会的形式进行教育推广，并参与南佛罗里达大学的海洋学女孩营和海洋学项目。

ABSTRACT Marine viruses (principally bacteriophages) are perhaps the most abundant form of life on the planet. Active (lytic) viral infections cause cell to lyse and thus control carbon flow through marine microbial food webs, in some cases initiating the collapse of algal blooms. In contrast, inactive (lysogenic) infections confer immunity to superinfection and cause conversion to a diverse array of phenotypes. The majority of marine bacteria in culture produce some type of virus-like particles (VLP.s), indicating that the occurrence of lysogeny is widespread. Marine viral genomes are economical to study because of their small size (usually 50-100 kb). The biocomplexity of viromics arises from the interaction and response of viral genomes to environmental cues. This project will focus on lysogeny, whereby a viral genome establishes a stable interaction with its host. The occurrence of lysogeny in the marine environment is complex, as indicated by the seasonal distribution of lysogens observed in estuarine environments. The lytic-lsyogenic shift is hypothesized to occur when viral genes respond to environmental cues, and preliminary evidence suggests that phosphate levels and the pho genes may play a role in this interaction. Specific research objectives are to: 1) determine what physiological and environmental cues catalyze the shift from lysogenic to lytic lifestyles in cultures and natural microbial populations, 2) sequence the genomes of several temperate phages, 3) determine how phage genes work together to confer lytic or lysogenic existence in marine bacteria, and 4) incorporate the effects of temperate phage into models of the marine microbial food web. The first objective will be addressed by employing cultures (cyanobacteria and heterotrophic bacteria) and natural populations to investigate cues that might control the "lysogenic decision". Cultures and natural populations will be exposed to shifts in temperature, nutrients, sunlight, salinity, and exposure to xenobiotics to elicit shift from lytic to lysogeny and vice versa. For the second objective, five of these phage-host systems will be sequenced. Comparative genomics will be used to identify common genes and modules. For the third objective, prophage gene expression will be quantified by northern analysis. Differences in patterns of expression will yield information on genome response to shifting environmental conditions. If conserved lysogeny genes are found in cyanophage, their expression in natural bacterial populations of Tampa Bay will be measured. Finally, a computational model will be developed to describe the interaction of temperate phage with marine microbial food webs, based upon a 13 month seasonal study of lysogeny in Tampa Bay. The broader impacts of this research include educational outreach in the form of undergraduate workshops at San Diego State University, and participation in Oceanography Camp for Girls and Project Oceanography at the University of South Florida.