Viruses in Marine Food Webs

浮游病毒是海洋中最丰富的生物实体，主要通过与微生物的相互作用对生物地球化学和生态过程产生巨大的潜在影响。然而，数据表明，真正的影响存在很大的变异性，原因尚不清楚。最可能的因素似乎与病毒及其宿主在空间和时间上的多样性变化有关，因为病毒被认为具有狭窄的宿主范围。模型和一些有限的现场数据表明，病毒可以对微生物多样性产生实质性的控制，这也意味着宿主多样性对病毒活性有反馈作用，从而影响生物地球化学过程。通过传统的培养方法研究这种多样性是极其困难的，但在过去的几年里，我们通过几种主要依赖于16S rRNA序列变异的分子生物学方法，在研究微生物多样性方面取得了显著的进展。此外，就在过去的几个月里，一种基于病毒基因组总长度调查海洋系统中病毒多样性的方法已经公布。该项目将使用这些方法研究主要来自南加州的自然和实验海洋微生物系统，目的是确定病毒和宿主多样性之间的相互作用以及对一般病毒和原核过程的影响。具体的研究地点包括洛杉矶和圣卡塔利纳岛之间的新海洋时间序列站，由南加州大学瑞格利环境研究所的A·迈克尔斯运营。样本也将来自圣莫尼卡码头(相对丰富的沿海海水)和南加州大学卡特琳娜海洋实验室的码头(原始和相对营养较少的沿海水域)。作为该项目观察或探索部分的一部分，样本将在两年内每月通过一系列方法进行分析，包括温度、盐度、无机营养物质、叶绿素和溶解氧的基本时间序列参数。调查人员将增加细菌和病毒直接计数、感染细菌频率、细菌产量、初级产量、蓝藻的流式细胞仪计数，以及病毒DNA的脉冲场凝胶电泳法，以及变性梯度凝胶电泳法、末端限制性片段长度多态性、长度异质性聚合酶链式反应和荧光原位杂交的原核生物多样性分析。短期、更频繁的抽样和中观系统将被用来检查世代时间尺度上的种群动态。各种方法各有优缺点，将提供有关细菌和病毒活性及其多样性在自然界中相互作用的数据，适用于检验病毒多样性和总体活性与原核生物群落多样性有关的假设。该项目的实验部分包括：检测病毒对改变在过滤海水中生长的本地细菌之间竞争结果的影响的实验，测试自然混合群落中的哪些类群容易受到它们的共生病毒的感染，以及测量克隆培养病毒的宿主范围(包括混合自然群落中的非栽培宿主)。该项目具有附加值，即在一个容易到达的海洋地点具有独特的微生物多样性时间序列，适合于进一步分析，例如审查海洋微生物多样性和稳定性之间的联系。

Planktonic viruses are the most abundant biological entities in the sea and have a tremendous potential impact on biogeochemical and ecological processes, primarily via their interactions with microorganisms. However, the data suggest a great deal of variability of the true impacts, and the reasons for this are unknown. The most likely factor seems to relate to the spatial and temporal variations in diversity of both the viruses and their hosts, because viruses are thought to have a narrow host range. Models and some limited field data suggest that viruses can exert substantial control over microbial diversity, and this also implies that host diversity has a feedback to viral activity and hence biogeochemical processes. Such diversity has been extremely difficult to study via traditional cultivation methods, but the past few years have seen remarkable strides in our ability to investigate microbial diversity, via several molecular biological methods that rely primarily on variations in 16S rRNA sequences. Also, just within the past few months a method has been published to investigate viral diversity in marine systems based upon total viral genome lengths. This project will use these approaches to study natural and experimental marine microbial systems, primarily from Southern California, with the goal of determining the interactions between virus and host diversity and the effects on general viral and prokaryotic processes. The specific study sites include the new oceanographic time-series station midway between Los Angeles and Santa Catalina Island, run by A. Michaels of the USC Wrigley Institute for Environmental Studies. Samples will also come from Santa Monica Pier (relatively rich coastal seawater) and the dock at the USC Marine Lab on Catalina (pristine and relatively oligotrophic coastal waters). As part of the observation, or exploratory, component of the project, samples would be analyzed monthly for 2 years by a battery of methods, including the basic time series parameters of temperature, salinity, inorganic nutrients, chlorophyll, and dissolved oxygen. The investigators will add measurements of bacterial and viral direct counts, frequency of infected bacteria, bacterial production, primary production, flow cytometry counts of cyanobacteria, as well as pulsed field gel electrophoresis of viral DNA for viral diversity, and prokaryote diversity assays with denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and fluorescent in situ hybridizations. Short-term, more frequent sampling and mesocosms will be used to examine population dynamics on the generation time scale. The various methods, each with its own advantages and shortcomings, will provide data on the interplay in nature between bacterial and virus activities and their diversity, suitable to test the hypotheses that viral diversity and overall activity are related to the diversity of the prokaryotic community. The experimental component of the project includes experiments examining the effect of viruses on altering the outcome of competition between native bacteria grown in filtered seawater, testing which taxa in natural mixed communities are susceptible to infection by their co-occurring viruses, and measuring the host range of clonal cultivated viruses (including noncultivated hosts in mixed natural communities). The project has the added value of a unique time series of microbial diversity at an easily accessible marine site, suitable for further analysis such as examining the links between diversity and stability in marine microbes.