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

PI：Taylor提案：0120677 达特茅斯学院的罗纳德泰勒的项目得到了环境中生物复杂性项目、基因组环境科学与工程子项目（BE GEN-EN）的支持。异养细菌在浮游营养物质循环中起着关键作用，因为它们在有机物质沉出系统之前将其分解。可能影响矿化率的两个关键细菌行为是休眠和附着于浮游生物。这两种行为在表型上都是可塑的，使细菌能够对环境的变化做出反应。例如，高休眠率（30-95%）表明细菌群落具有巨大的能力，能够迅速响应环境条件的变化，从而触发向代谢活性状态的转变。相反，很少有人知道的潜在影响的细菌生活在生态系统processes.The研究项目的目标是休眠和附着行为之间的相互作用使用的焦点物种（霍乱弧菌）在对比的环境条件下，在现场和实验室的全基因组表达谱。我们特别感兴趣的是确定（1）在现实环境条件下休眠和附着可能共同调节的程度，以及（2）这些行为如何被人类活动（如土地利用变化或有机污染）改变。我们将进行三个相互关联的研究，每一个使用微阵列，这将使我们的理解，煽动活跃和休眠状态之间的转换和unattached和attached states.Aim之间的遗传过程的重大贡献1对比的时间动态的基因表达在unattached和attached细菌在有利与不利的环境条件下超过两个星期的时间。这将是第一次全面分析休眠和SRB的遗传共同调控。目标2将确定四个关键环境参数（温度，盐度，pH值和营养物质）对暴露于三种不同微生境（未附着，附着于浮游动物，附着于浮游植物）的细菌基因表达的直接影响和相互作用。这将是第一个多因素的实验与微阵列，并将需要引进新的方法来分析微阵列数据。目标3将量化基因表达的季节性变化的领域条件下使用原位培养的细菌在孟加拉国池塘对比人为影响。因此，这将是第一个使用微阵列在自然系统中而不是在实验室条件下评估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选择：它存在于全世界的浮游生物群落中，是细菌大家族的代表。（弧菌科），并且具有完全测序和充分研究的基因组，这使得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大的医学重要性。 这项研究将由一个跨学科的国际研究人员团队完成，他们专门从事生态学，微生物学，遗传学和统计学。我们计划公开所有的微阵列结果，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.