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过程，它影响细菌在长时间范围内的进化，以及在短时间尺度上影响抗生素耐药性等特征的传播。最近，公众更加关注基因工程生物向土著生物转移基因的风险及其后果。许多环境微生物在其生命周期中的很大一部分时间是在自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，地下也为不同的细菌菌株提供了一个混合区，每一种细菌都在水相和固相之间进行分配。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-分离动力学，以及通过接合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，以在受控微型模型实验中量化接合基因转移的速率。预计基因转移将受到宿主细胞和受体细胞在固体表面的一对停留时间的限制，因此这些一对停留时间的分布和基因转移时间的分布将从微观模型实验中得到。这些数据的模型将通过结合有偏的Levy运动和细菌在多孔介质中传输的漂移，以及附着在表面的停留时间的α稳定随机变量，以及用于从宿主到受体的基因转移的非马尔科夫反应动力学模型来构建。该项目的智力价值来自于具有水文学、微生物学、分子生物学、应用数学和物理学专业知识的人员的协调合作，以(1)采用遗传分析和显微镜方面的新工具，在分子水平上研究微流动室中的微生物活动和基因交换，以及(2)使用数学来推断结果，以了解地下更高尺度的过程。通过实验和理论的结合，我们也许能够确定成功的基因转移的主要要求。该项目的更广泛影响来自于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、污染物补救和进化生物学。所有这些现象都涉及到这里研究的过程，其中许多是在多孔介质(地下或生物)中。在教育方面，该项目提供了一个场所，通过这个场所，合作研究的结果可以被纳入到PI的微生物学、工程学和数学的本科和研究生课程中。PI还通过普渡大学的MARC/AIM项目和加州大学戴维斯分校的女性工程(NEE‘Women Engineering Link)项目，在让少数族裔和女性参与研究方面有着坚实的记录，这一习惯将在这个项目中继续下去。

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.