Final Report Summary - 3D SWARMING (Complex Dynamics of Swarming Bacteria in Three Dimensions)
Research
This grant enabled me to provide new and innovative insights on several aspects of collectively moving bacteria. I tend to divide the research into four main topics.
1. In the first part we have studied the collective dynamics of swimming bacteria in culture drops. The cells, of the Gram-negative species Serratia marcescens, were grown overnight in liquid bulk, and formed a dense culture of spherical cells. In drops taken from the culture and deposited on glass slides the cells migrated to the upper surface of the drop and moved in coherent structures of whirls and jets. The interesting and innovative point of this study was that the collective motion of these self-propelled cells was obtained for spherical particles and not rod-shaped cells as is mostly found and argued to be the only optional possibility. This is because of the steric – excluded volume – interactions, which are very weak in spherical objects. The results indicated that steric forces are not mandatory, although better be there, for the generation of collective motion of self-propelled particles.
2. In the second part of the research we have studied the dynamics of Bacillus subtilis swarming bacteria (rod-shaped cells) on agar plates, where antibiotics was systematically added to some of the plates in order to see how the collective dynamics depends on stress. While past work demonstrated that most swarming species under adverse conditions such as starvation, dryness and oxygen depletion, exhibit Normal statistics, we have found that antibiotics affects the swarm differently. To do so we have used optical flow analyses of the swarming flow and generated velocity and vorticity fields. From these we have extracted the velocity and vorticity distributions and spatio-temporal correlation functions. We have found that under normal conditions the statistics is normal with Gaussian distributions of the velocity and vorticity fields. In addition, the correlation functions were found to decay exponentially. These results supported the fact that at normal conditions the statistics in Normal – as was found in similar studies. However, when kanamycin was added, the velocity and vorticity distributions shifted towards an exponential distribution with large kurtosis, and the correlation was found to decay in a more intricate way. A mathematical model we have built was found to reveal that the swarm is composed of two populations – non-affected cells and motility defective cells generated by kanamycin. Interactions between the two populations formed this anomalous statistics. Additional experiments with a mix of two populations were performed to support the model and the results of the entire research have shown that while kanamycin affects some of the cells, they segregate into clusters to avoid jamming and allow fast expansion and territory acquisition.
3. In the third part of the research we have focused on the dynamics of individual bacteria that move in the swarm. The main point was to observe and analyze the trajectories of the cells while they are pushed by their neighbors in the dense swarm. Fluorescent microscopy of swarming Bacillus subtilis colonies, of mixed wild type and RFP labeled (but still have the motility of the wild type) cells, demonstrated that the cells are performing super-diffusion, consistent with Levy walk. Levy walks are characterized by trajectories that have straight stretches for extended lengths whose variance is infinite. The evidence of super-diffusion consistent with Levy walks in bacteria suggests that this strategy may have evolved considerably earlier than previously thought. Most importantly, we have shown that the bacteria examined in this study can use the collective dynamics of the swarm to fundamentally change the statistical properties of their dynamics from run-tumble in sparse liquid bulks to Levy walk in swarm.
4. In the fourth part of the research we have focused on the interactions, or links, between the swarming cells as a group and the motion of the individuals in it. Namely, we asked how independent is the motion of the single cell embedded in the swarm; does it follow the flow or perhaps it is able to “decide” and move on its own will. To do so we have embedded fluorescently labelled cells in a non-labelled swarm and obtained two fields: phase contrast (“bright-field”) for the swarm and fluorescent for the labelled cells (two cameras and a special optical technique were used). The experiments were performed in two different rod-shaped species (Bacillus subtilis, and Serratia marcescens that form rod-shaped cells on agar) to strengthen the conclusions. The results indicated that the wild type cells do not necessarily follow their own flow. They tend to move to almost any direction, even perpendicular to the flow, and also not be aligned with the flow (their main axis, regardless the direction of motions, was not parallel to the flow). On the other hand, immotile cells that were embedded in the active swarm, and served as tracers, did follow the flow and their orientation was mostly parallel to the flow. The results demonstrate how the motile cells can maneuver or switch between local streams and jets to enhance spreading and dissemination.
Career development
The grant assisted me in establishing my career as a researcher, a mentor and a teacher. During the past four years I have mentored six students and collaborated with many faculty members in Europe (mostly Germany and France), the US and Israel. I have developed new courses about the topic of this study and I am giving them not only in my Department but also in other Departments of my university in order to spread the knowledge. I am often invited to give talks about the topic of this research; for instance, next year I will be participating in a summer school on this topic in Institut d’Etudes Scientifiques de Cargèse.
The grant assisted us in obtaining great data that was eventually the topic of seven publications (with two more currently under consideration). Among these, stand out two significant works, one in PRL (114, 018105 (2015)) and the second one in Nat Comm (6, 8396 (2015)).
The most important outcome of the research was a conference I have organized in Israel on May 2016. “Collective dynamics in microorganisms and cellular systems”, Sede-Boqer, May 22-26, 2016. Please see the conference website http://swarming-in-israel.weebly.com
This wonderful and successful international conference took place in our campus, Sede Boqer. It included 28 talks that were all plenary talks, 16 of them were given by invited scientists from other countries (USA, France, Germany, Netherland, Hong Kong), and 12 were given by Israelis (TAU, BIU, Weizmann Inst, BGU, U Haifa, HUJI). Most speakers were senior researchers who are leaders in their respective fields. We also had a session with 11 shorter talks (ignite talks) which were given by students and postdocs, and a poster session that included 8 presentations. The scientific scope was multidisciplinary; we have had microbiologists, physicists and mathematicians, all speaking on similar topics but using different approaches. We aimed at building bridges and collaborations between the physics and the biology, and we are already aware of new collaborations that were initiated among the visitors.
The conference lasted almost four full days. There were several sessions divided between experimental physicists, theoretical physicists and mathematicians, and biologists. Talks covered a wide spectrum of collective dynamics in microorganisms including bacteria, cancer cells, blood cells, amoeba, yeast, fungus and more. Two special sessions addressed more general topics that are also related to the main scope of the conference, such as, collective phenomenon in other species, bio-physics and pattern formation. All speakers were hosted at the same hotel (Ramon Inn). The conference covered all accommodation, meals and coffee break costs. In order to strengthen the interaction between people, two social activities were held, one in Sede Boqer and the other one in Mitzpe Ramon.
The scientific and organizing committees consisted of Prof. Rasika Harshey from UT Austin (microbiology), Dr. Gil Ariel from BIU Israel (Mathematics), and myself (Dr. Avraham Be’er from Ben Gurion University). The budget for the conference was obtained mostly from the Marie Curie CIG grant.
This grant enabled me to provide new and innovative insights on several aspects of collectively moving bacteria. I tend to divide the research into four main topics.
1. In the first part we have studied the collective dynamics of swimming bacteria in culture drops. The cells, of the Gram-negative species Serratia marcescens, were grown overnight in liquid bulk, and formed a dense culture of spherical cells. In drops taken from the culture and deposited on glass slides the cells migrated to the upper surface of the drop and moved in coherent structures of whirls and jets. The interesting and innovative point of this study was that the collective motion of these self-propelled cells was obtained for spherical particles and not rod-shaped cells as is mostly found and argued to be the only optional possibility. This is because of the steric – excluded volume – interactions, which are very weak in spherical objects. The results indicated that steric forces are not mandatory, although better be there, for the generation of collective motion of self-propelled particles.
2. In the second part of the research we have studied the dynamics of Bacillus subtilis swarming bacteria (rod-shaped cells) on agar plates, where antibiotics was systematically added to some of the plates in order to see how the collective dynamics depends on stress. While past work demonstrated that most swarming species under adverse conditions such as starvation, dryness and oxygen depletion, exhibit Normal statistics, we have found that antibiotics affects the swarm differently. To do so we have used optical flow analyses of the swarming flow and generated velocity and vorticity fields. From these we have extracted the velocity and vorticity distributions and spatio-temporal correlation functions. We have found that under normal conditions the statistics is normal with Gaussian distributions of the velocity and vorticity fields. In addition, the correlation functions were found to decay exponentially. These results supported the fact that at normal conditions the statistics in Normal – as was found in similar studies. However, when kanamycin was added, the velocity and vorticity distributions shifted towards an exponential distribution with large kurtosis, and the correlation was found to decay in a more intricate way. A mathematical model we have built was found to reveal that the swarm is composed of two populations – non-affected cells and motility defective cells generated by kanamycin. Interactions between the two populations formed this anomalous statistics. Additional experiments with a mix of two populations were performed to support the model and the results of the entire research have shown that while kanamycin affects some of the cells, they segregate into clusters to avoid jamming and allow fast expansion and territory acquisition.
3. In the third part of the research we have focused on the dynamics of individual bacteria that move in the swarm. The main point was to observe and analyze the trajectories of the cells while they are pushed by their neighbors in the dense swarm. Fluorescent microscopy of swarming Bacillus subtilis colonies, of mixed wild type and RFP labeled (but still have the motility of the wild type) cells, demonstrated that the cells are performing super-diffusion, consistent with Levy walk. Levy walks are characterized by trajectories that have straight stretches for extended lengths whose variance is infinite. The evidence of super-diffusion consistent with Levy walks in bacteria suggests that this strategy may have evolved considerably earlier than previously thought. Most importantly, we have shown that the bacteria examined in this study can use the collective dynamics of the swarm to fundamentally change the statistical properties of their dynamics from run-tumble in sparse liquid bulks to Levy walk in swarm.
4. In the fourth part of the research we have focused on the interactions, or links, between the swarming cells as a group and the motion of the individuals in it. Namely, we asked how independent is the motion of the single cell embedded in the swarm; does it follow the flow or perhaps it is able to “decide” and move on its own will. To do so we have embedded fluorescently labelled cells in a non-labelled swarm and obtained two fields: phase contrast (“bright-field”) for the swarm and fluorescent for the labelled cells (two cameras and a special optical technique were used). The experiments were performed in two different rod-shaped species (Bacillus subtilis, and Serratia marcescens that form rod-shaped cells on agar) to strengthen the conclusions. The results indicated that the wild type cells do not necessarily follow their own flow. They tend to move to almost any direction, even perpendicular to the flow, and also not be aligned with the flow (their main axis, regardless the direction of motions, was not parallel to the flow). On the other hand, immotile cells that were embedded in the active swarm, and served as tracers, did follow the flow and their orientation was mostly parallel to the flow. The results demonstrate how the motile cells can maneuver or switch between local streams and jets to enhance spreading and dissemination.
Career development
The grant assisted me in establishing my career as a researcher, a mentor and a teacher. During the past four years I have mentored six students and collaborated with many faculty members in Europe (mostly Germany and France), the US and Israel. I have developed new courses about the topic of this study and I am giving them not only in my Department but also in other Departments of my university in order to spread the knowledge. I am often invited to give talks about the topic of this research; for instance, next year I will be participating in a summer school on this topic in Institut d’Etudes Scientifiques de Cargèse.
The grant assisted us in obtaining great data that was eventually the topic of seven publications (with two more currently under consideration). Among these, stand out two significant works, one in PRL (114, 018105 (2015)) and the second one in Nat Comm (6, 8396 (2015)).
The most important outcome of the research was a conference I have organized in Israel on May 2016. “Collective dynamics in microorganisms and cellular systems”, Sede-Boqer, May 22-26, 2016. Please see the conference website http://swarming-in-israel.weebly.com
This wonderful and successful international conference took place in our campus, Sede Boqer. It included 28 talks that were all plenary talks, 16 of them were given by invited scientists from other countries (USA, France, Germany, Netherland, Hong Kong), and 12 were given by Israelis (TAU, BIU, Weizmann Inst, BGU, U Haifa, HUJI). Most speakers were senior researchers who are leaders in their respective fields. We also had a session with 11 shorter talks (ignite talks) which were given by students and postdocs, and a poster session that included 8 presentations. The scientific scope was multidisciplinary; we have had microbiologists, physicists and mathematicians, all speaking on similar topics but using different approaches. We aimed at building bridges and collaborations between the physics and the biology, and we are already aware of new collaborations that were initiated among the visitors.
The conference lasted almost four full days. There were several sessions divided between experimental physicists, theoretical physicists and mathematicians, and biologists. Talks covered a wide spectrum of collective dynamics in microorganisms including bacteria, cancer cells, blood cells, amoeba, yeast, fungus and more. Two special sessions addressed more general topics that are also related to the main scope of the conference, such as, collective phenomenon in other species, bio-physics and pattern formation. All speakers were hosted at the same hotel (Ramon Inn). The conference covered all accommodation, meals and coffee break costs. In order to strengthen the interaction between people, two social activities were held, one in Sede Boqer and the other one in Mitzpe Ramon.
The scientific and organizing committees consisted of Prof. Rasika Harshey from UT Austin (microbiology), Dr. Gil Ariel from BIU Israel (Mathematics), and myself (Dr. Avraham Be’er from Ben Gurion University). The budget for the conference was obtained mostly from the Marie Curie CIG grant.