CAREER: The impact of spatial-positioning mechanisms on the metabolic interactions and emergent properties of synthetic bacterial communities

职业：空间定位机制对合成细菌群落代谢相互作用和新兴特性的影响

• 批准号: 1749489
• 负责人: James McKinlay
• 金额: $ 114.9万
• 依托单位: Indiana University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-01-01 至 2024-12-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1749489&HistoricalAwards=false
• 关键词: CAREER; impact; spatial; positioning; mechanisms

Microbes constitute a large portion of the Earth's biomass. In the majority of environments, microbes live as interacting communities. However, not much is known regarding how microbial worlds communicate, evolve, share resources, and interact with other organisms. This project will address how bacteria position themselves within microbial communities to cooperatively trade nutrients with neighboring cells or alternatively steal nutrients from neighbors. Such cross-feeding interactions influence important processes, including human health and element cycling. Cross-feeding communities can also be harnessed to degrade pollutants and convert renewable resources into useful products, such as biofuels. The results from this project will thus have broad benefits by informing on natural microbial interactions of environmental and medical relevance and by generating principles for the engineering of bacterial communities as a technology to benefit society. This research will involve direct participation of regional high school students, including underrepresented minorities. Additional high school students will gain research experiences through a collaboration between the research team and high school teachers, which will bring experiments to classrooms. This project will also generate an innovative storytelling platform that will provide an intuitive framework upon which to communicate detail-intensive and traditionally unpopular topics in metabolism and biochemistry to learners of all ages. This project will examine how bacteria optimize their location within cross-feeding communities that pit cooperative cells against exploitive (cheater) cells. Current theory indicates that clustering of cooperative cells can keep cheaters at bay. However, this theory does not take into account mechanisms that bacteria use to sense and swim towards nutrients and to adhere to surfaces and other cells. A lack of knowledge on how motility and adhesion influence metabolic interactions and community structure hampers not only our general understanding of microbial community behavior but also our ability to design useful synthetic communities. The objective of this project is to determine the impact of motility and adhesion on subpopulation dynamics in cross-feeding communities and on emergent properties, such as hydrogen biofuel production. The objective will be achieved using both experimental and computationally-simulated communities. One community will pair ammonium-excreting cooperators and ammonium-consuming cheaters of a single species, Rhodopseudomonas palustris. A second community will pair R. palustris with Escherichia coli in an obligate cross-feeding relationship wherein ammonium from R. palustris is exchanged for carbon nutrients from E. coli. This mutualism will also be challenged with an R. palustris cheater. In each case, the effects of motility and adhesion on cooperator and cheater fitness and community structure will be determined using environmental and genetic conditions that either permit or restrict motility and adhesion. This project will thus provide a much-needed molecular understanding of spatial bacterial community behaviors of environmental, medical, and industrial relevance.

微生物构成了地球生物量的很大一部分。在大多数环境中，微生物作为相互作用的社区生活。然而，关于微生物世界如何交流，进化，共享资源以及与其他生物相互作用的知之甚少。该项目将研究细菌如何在微生物群落中定位，与相邻细胞合作交换营养物质，或者从邻居那里窃取营养物质。这种交叉喂养的相互作用影响重要的过程，包括人类健康和元素循环。还可以利用交叉喂养社区来降解污染物，并将可再生资源转化为有用的产品，如生物燃料。因此，该项目的结果将通过提供环境和医学相关性的自然微生物相互作用的信息，以及通过产生细菌群落工程的原则，作为造福社会的技术，从而产生广泛的利益。这项研究将涉及地区高中学生的直接参与，包括代表性不足的少数民族。更多的高中学生将通过研究团队和高中教师之间的合作获得研究经验，这将把实验带到课堂上。该项目还将产生一个创新的讲故事平台，将提供一个直观的框架，在此基础上向所有年龄段的学习者传达新陈代谢和生物化学中的细节密集型和传统上不受欢迎的主题。该项目将研究细菌如何优化它们在交叉喂养社区中的位置，使合作细胞与剥削（作弊）细胞相对抗。目前的理论表明，合作细胞的集群可以阻止作弊者。然而，这一理论没有考虑到细菌用来感知和游向营养物质以及粘附在表面和其他细胞上的机制。缺乏关于运动性和粘附性如何影响代谢相互作用和群落结构的知识不仅阻碍了我们对微生物群落行为的一般理解，而且也阻碍了我们设计有用的合成群落的能力。该项目的目标是确定在交叉喂养的社区和新兴的属性，如氢生物燃料生产的亚群动态的运动和粘附的影响。这一目标将通过实验和计算模拟社区来实现。其中一个群落会将同一物种的排氨合作者和耗氨作弊者配对，即沼泽红蜻蜓。第二个社区将配对R。palustris与大肠杆菌的专性交叉喂养关系，其中铵从R。palustris从E.杆菌这种互惠关系也将受到R的挑战。沼泽骗子在每种情况下，运动和粘附对合作者和作弊者的健身和社区结构的影响将使用环境和遗传条件，允许或限制运动和粘附。因此，该项目将提供一个急需的空间细菌群落行为的环境，医疗和工业相关性的分子理解。

项目成果

Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community

• DOI: 10.1038/s41396-020-00737-5
• 发表时间: 2020-08-12
• 期刊: ISME JOURNAL
• 影响因子: 11
• 作者: Fritts, Ryan K.;Bird, Jordan T.;McKinlay, James B.
• 通讯作者: McKinlay, James B.

I have a kit and I create worlds: synthetic ecology from synthetic genomes

我有一个工具包，我可以创造世界：来自合成基因组的合成生态学

• DOI: 10.1111/1758-2229.12883
• 发表时间: 2020
• 期刊: Environmental Microbiology Reports
• 影响因子: 3.3
• 作者: McKinlay, James B.

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

• DOI: 10.1128/aem.01741-23
• 发表时间: 2023-12-11
• 期刊: APPLIED AND ENVIRONMENTAL MICROBIOLOGY
• 影响因子: 4.4
• 作者: LaSarre，Breah;Morlen，Ryan;McKinlay，James B.
• 通讯作者: McKinlay，James B.

Phototrophic Lactate Utilization by Rhodopseudomonas palustris Is Stimulated by Coutilization with Additional Substrates

• DOI: 10.1128/aem.00048-19
• 发表时间: 2019-06-01
• 期刊: APPLIED AND ENVIRONMENTAL MICROBIOLOGY
• 影响因子: 4.4
• 作者: Govindaraju, Alekhya;McKinlay, James B.;LaSarre, Breah
• 通讯作者: LaSarre, Breah

A purine salvage bottleneck leads to bacterial adenine cross-feeding.

• DOI: pii: 2023.10.17.562681. doi: 10.1101/2023.10.17.562681
• 发表时间: 2023-10-17
• 期刊: bioRxiv : the preprint server for biology
• 作者: Chuang YC;Haas NW;Pepin R;Behringer M;Oda Y;LaSarre B;Harwood CS;McKinlay JB
• 通讯作者: McKinlay JB