Genomic Assessment of Phenotypic Plasticity in an Aquatic Bacterium: Water Quality and Microhabitat Effects

PI：泰勒提案：0120677达特茅斯学院罗纳德·泰勒的这个项目得到了环境中的生物复杂性计划的支持，该子计划是由基因组使能的环境科学与工程(BE GEN)计划支持的。异养细菌在远洋营养循环中发挥着关键作用，因为它们在有机物下沉到系统之外之前重新矿化。可能影响再矿化率的两个关键细菌行为是休眠和对浮游生物的附着。这两种行为都是典型的塑料，使细菌能够对环境的变化做出反应。例如，高休眠率(30%-95%)表明细菌群落有巨大的能力对环境条件的变化做出快速反应，这些变化触发了向代谢活跃状态的转变。相比之下，生活在浮游基质上的细菌对生态系统过程的潜在影响知之甚少。本研究项目的目标是利用霍乱弧菌在野外和实验室不同环境条件下的全基因组表达谱，研究休眠和附着行为之间的相互作用。我们特别感兴趣的是确定(1)在现实环境条件下休眠和依恋可能在多大程度上受到共同调节，以及(2)这些行为可能如何被土地利用变化或有机污染等人为活动改变。我们将进行三项相互关联的研究，每一项研究都使用微阵列，这将对我们理解促使活动和休眠状态之间以及独立和附着状态之间转换的遗传过程做出重大贡献。AIM 1对比了在两周的有利和不利环境条件下，独立和附着细菌中基因表达的时间动态。这将是首次对休眠和SRB的遗传共同调节进行全面分析。目的2将确定四个关键环境参数(温度、盐度、pH和营养物质)对暴露于三种不同微生境(独立、附着浮游动物和附着浮游植物)的细菌基因表达的直接影响和相互作用。这将是对微阵列进行的首批多因素实验之一，并将需要引入新的方法来分析微阵列数据。目的3将利用孟加拉国池塘中细菌的原位培养，在不同的人为影响下，量化在季节变化的田间条件下的基因表达。因此，这将是首批使用微阵列来评估自然系统中而不是实验室条件下的基因表达的项目之一。重点物种霍乱弧菌是研究这些问题的理想物种：它存在于世界各地的浮游生物群落中，是一个细菌大家族(弧菌科)的代表，并且具有完全测序和充分研究的基因组，从而能够使用微阵列技术。霍乱弧菌作为霍乱的病原体也具有相当重要的医学意义。这项研究将由一个跨学科的国际研究团队完成，他们专门从事生态学、微生物学、遗传学和统计学方面的研究。我们计划将所有的微阵列结果公之于众，并通过网站、科学会议上的演讲以及我们的本科生和研究生课程来教育科学界和公众我们的结果。

PI: Taylor Proposal: 0120677 The project by Ronald Taylor, Dartmouth College is supported by the program Biocomplexity in the Environment, subprogram Genomic-Enabled Environmental Science and Engineering (BE GEN-EN). Heterotrophic bacteria play a key role in pelagic nutrient cycling because they remineralize organic matter before it sinks out of the system. Two key bacterial behaviors that may influence remineralization rates are dormancy and attachment to plankton. Both of these behaviors are phenotypically plastic, allowing bacteria to respond to changes in their environment. For example, a high dormancy rate (30-95%) suggests that the bacterial community has a tremendous capability to respond rapidly to changes in environmental conditions that trigger the transition back to a metabolically active state. In contrast, little is known about the potential impact of bacteria living on planktonic substrates on ecosystem processes.The goal of this research project is to study the interaction between dormancy and attachment behaviors using whole-genome expression profiles for a focal species (Vibrio cholerae) under contrasting environmental conditions in both the field and laboratory. We are particularly interested in determining (1) the extent to which dormancy and attachment may be co-regulated under realistic environmental conditions and (2) how these behaviors might be altered by anthropogenic activities such as land use change or organic pollution. We will conduct three interrelated studies, each using microarrays, that will make major contributions to our understanding of the genetic processes that instigate transitions between active and dormant states and between unattached and attached states.Aim 1 contrasts the temporal dynamics of gene expression in unattached and attached bacteria under favorable vs. unfavorable environmental conditions over a two-week period. This will be the first comprehensive analysis of genetic co-regulation of dormancy and SRBs. Aim 2 will determine the direct effects and interactions of four key environmental parameters (temperature, salinity, pH, and nutrients) on gene expression in bacteria exposed to three different microhabitats (unattached, attached to zooplankton, attached to phytoplankton). This will be one of the first multi-factor experiments with microarrays, and will require introduction of new methods for analyzing microarray data. Aim 3 will quantify gene expression under seasonally varying field conditions using in situ incubations of bacteria in Bangladeshi ponds with contrasting anthropogenic impacts. As such, this will be one of the first projects to use microarrays to evaluate gene expression in a natural system rather than under laboratory conditions.The focal species, V. cholerae, is ideal for investigating these questions: it is found in plankton communities worldwide, is representative of a large family of bacteria (the Vibrionaceae), and has a fully sequenced and well-studied genome which enables the use of microarray technology. V. cholerae is also of considerable medical importance as the etiological agent of cholera. This research will be accomplished by an interdisciplinary and international team of researchers who specialize in ecology, microbiology, genetics and statistics. We plan to make all microarray results publicly available, and to educate the scientific community and the public about our results through a website, talks at scientific meetings, and our undergraduate and graduate courses.