Collaborative Research: CMG: Toward Understanding the Transfer of Genetic Information in Subsurface Hydrology

微生物之间的水平基因转移是一个关键的过程，它影响细菌在长时间内的进化，以及在短时间内抗生素耐药性等特征的传播。最近，公众对基因工程生物向本地生物转移的风险及其后果日益关注。许多环境微生物在其生存周期的很大一部分是在天然地下的多孔介质中度过的，例如土壤和含水层材料。因为它是水的天然过滤器，所以地下也为不同菌株的细菌提供了一个混合区，每个分区都在水相和固相之间。因此，为了理解自然环境中水平基因转移的后果，研究不同物种在多孔介质中经历命运和运输时的相互作用是很重要的。本项目的主要目标是评估微生物在多孔介质固体表面的附着-脱离动力学，以及通过偶联在多孔介质中水平基因转移的耦合动力学。绿色荧光蛋白（GFP）基因表达系统将用于从土壤中分离的已知宿主和受体，以定量控制微模型实验中共轭基因转移的速率。由于寄主细胞和受体细胞在固体表面的成对停留时间限制了基因的转移，因此将从微模型实验中编译这些成对停留时间的分布和基因转移时间的分布。这些数据的模型将通过将细菌在多孔介质中运输的偏置Levy运动与漂移结合起来，与附着在表面上的停留时间的α稳定随机变量结合起来，与基因从宿主转移到受体的非马尔可夫反应动力学模型结合起来。该项目的智力价值来自于水文学、微生物学、分子生物学、应用数学和物理学专业人士的协调合作，以：(1)采用遗传分析和显微镜的新工具来研究微流室中分子水平上的微生物活动和基因交换；(2)利用数学来推断研究结果，以了解地下更高尺度的过程。通过实验与理论的结合，我们也许能够确定成功的基因转移的主要要求。该项目的广泛影响源于其结果在许多领域的广泛适用性，包括人类健康、疾病传播、医学、污染物修复和进化生物学。所有这些现象都涉及这里所研究的过程，许多是在多孔介质中（地下或生物）。在教育方面，该项目提供了一个场所，通过该场所，合作研究的结果可以纳入PI的微生物学，工程学和数学的本科和研究生课程。通过普渡大学（Purdue）的MARC/AIM项目和加州大学戴维斯分校（UC Davis）的women in Engineering （nee' women Engineering Link）项目，PI在让少数族裔和女性参与研究方面也有良好的记录，这一习惯将在这个项目中延续。

Horizontal gene transfer among microorganisms is a critical process that impacts bacterial evolution over long time horizons as well as the spread of traits such as antibiotic resistance on short time scales. Recently there has been heightened public concern about the risk of gene transfer from genetically engineered organisms to indigenous organisms and its consequences. Many environmental microorganisms spend a large part of their viable life cycle in the porous medium of the natural subsurface, such as soils and aquifer materials. Because it is a natural filter for water the subsurface also provides a mixing zone for different strains of bacteria, that each partition between the aqueous and solid phases. Thus to understand the ramifications of horizontal gene transfer in the natural environment, it is important to study the interactions between different species as they undergo fate and transport in porous media. The primary goal of this project is to evaluate the kinetics of microbial attachment-detachment to porous media solid surfaces, and the coupled kinetics of horizontal gene transfer in porous media via conjugation. The green fluorescent protein (GFP) gene expression system will be used with known hosts and recipients originally isolated from soils to quantify rates of conjugative gene transfer in controlled micromodel experiments. The gene transfer is expected to be limited by the paired residence time of host and recipient cells together on solid surfaces, and so the distributions of these paired residence times and the distribution of gene transfer times will be compiled from the micromodel experiments. The model for these data will be crafted by combining a biased Levy motion with drift for the bacterial transport in the porous media, with an alpha-stable random variable for residence time attached to surfaces, with a non-Markovian reaction kinetic model for the gene transfer from host to recipient. The intellectual merit of this project arises from the coordinated collaboration of people with expertise in hydrology, microbiology, molecular biology, applied mathematics, and physics, to (1) adapt new tools in genetic analysis and microscopy to study microbial activity and gene exchange at a molecular level in micro flow chambers, and (2) use mathematics to extrapolate the findings to understand processes at higher scales in the subsurface. By combining experiment with theory we may be able to determine the major requirements for successful gene transfer. The broader impacts of this project arise from the wide applicability of the results to many areas including human health, disease propagation, medicine, contaminant remediation, and evolutionary biology. All of these phenomena involve the processes studied here, many in porous media (subsurface or biotic). Educationally the project provides the venue by which results from the collaborative study can be incorporated into the PI's undergraduate and graduate courses in microbiology, engineering, and mathematics. The PI's also have a solid record in involving minorities and women in research, via the MARC/AIM program at Purdue, and the Women In Engineering (nee' Women Engineering Link) program at UC Davis, and this habit will be continued in this project.