Control of magnetotactic bacterium in a micro-fabricated maze

We demonstrate the closed-loop control of a magnetotactic bacterium (MTB), i.e., Magnetospirillum magnetotacticum, within a micro-fabricated maze using a magneticbased manipulation system. The effect of the channel wall on the motion of the MTB is experimentally analyzed. This analysis is done by comparing the characteristics of the transient- and steady-states of the controlled MTB inside and outside a microfabricated maze. In this analysis, the magnetic dipole moment of our MTB is characterized using a motile technique (the u-turn technique), then used in the realization of a closed-loop control system. This control system allows the MTB to reach reference positions within a micro-fabricated maze with a channel width of 10 μm, at a velocity of 8 μm/s. Further, the control system positions the MTB within a region-of-convergence of 10 μm in diameter. Due to the effect of the channel wall, we observe that the velocity and the positioning accuracy of the MTB are decreased and increased by 71% and 44%, respectively

The behaviour of magnetotactic bacteria in changing magnetic fields

Die Beobachtung des Verhaltens von magnetotaktischen Bakterien (MTB) in wechselndeMagnetfeldern kann signifikante direkte und indirekte Informationen offenlegen über deren Merkmale und physiologische Eigenschaften. Sowohl Einzel- als auchMassenanalyse wurden in der vorliegenden Studie durchgeführt. Die Einzelzell-Experimente wurden in einem mikrofluidischen Chip mitmaßgefertigtem Design durchgeführt, in welchem die MTB fokussiert werden konnten während einMagnetfeld mittels eines permanentenMagneten angelegt wurde, welcher unter demMikroskoptisch befestigt war. Beobachtungen und Aufnahme der Reaktionen erlaubte eine offline-Analyse der Bewegungsbahnen. Diese Auswertung zeigte, dass die Zellen unterschiedlich reagierten auf Variation derMagnitude derMagnetfeldstärke. DesWeiteren konnte durch Simulationen und Experimente aufgezeigt werden, dass der Widerstand der MTB unterschätzt wurde, was zu zusätzlichen makroskopische Experimenten führte, um eine Verbindung von morphologischer Eigenschaften und Rotationswiderstandsprofilen darzulegen. Diese Experimente wurden durchgeführt in einem Gefäßmit Silikonöl unter Verwendung verschiedener 3D-gedruckter Modelle von verschiedenen ellipsoid- und spirillum-basierenden Morphologien. Die Modelle begründeten sich auf Elektronenmikroskop-Abbildungen von tatsächlichen MTB. Die Auswertung dieser Experimente konnte zur Aufklärung beitragen, dass Eigenschaften der MTB nicht in existierende Modelle des Rotationswiderstandes berücksichtigt werden. Die Massenanalyse wurde durchgeführt in einem maßangefertigtem Optischen-Dichte-Messer, spezifisch hergestellt umMagnetfeld-Orientierungen mit Photospektrometrie zu kombinieren. Von diesen Beobachtungen konnte der magnetische Gehalt von einer MTB-Kultur und Einzelproben abgeleitet werden, sowohl absolut als auch relativ. Zusätzlich wurde die Reaktionszeit einer verwendeten Charge gemessen werden umdenmagnetischen dipol-Moment mit dem Rotationswiderstand zu korrelieren. Dies erlaubte eine Unterscheidung zwischen verschiedenen Qualitäten und Quantitäten von Kulturen, als auch Langzeit- und kontinuierliche Beobachtung desWachstumsverhaltens von diesen. Trotz des Auffindens neuer Eigenschaften durch welche eine genauere Berechnung von Rotationswiderstandsprofilen möglich wurde bleibt die Länge eines Objekts weiterhin der dominierende Faktor im Zusammenspiel von magnetischem Drehmoment und Rotationswiderstandskraft. UnserModell erlaubt eine genauere Vorhersage des Rotationswiderstandes von Objekten mit ähnlichen Formen wie MTB in Schleichender Strömung als auch Zuständen von geringen Reynoldszahlen.The observation of behaviour of magnetotactic bacteria (MTB) in changing magnetic fields can give significant direct and indirect information about their traits and biophysical properties. Both single and bulk experiment and analysis were performed in this study. The single cel experimentswere performed inside custommicrofluidic chips designed to keep the MTB in focus, while a magnet field was applied using a permanent magnet mounted under a microscope stage. Observation and recording of the response allowed for off-line analysis of the trajectories. This analysis has shown that the cells respond differently to varyingmagnitudes of magnetic field strength. Furthermore, from simulations and experiments we have found that the drag of the MTB had been underestimated, which lead to additional macroscopic experiments relating morphological traits to more rotational drag profiles. These experiments were done in a vat of silicone oil using 3D-printed models of varying spheroid- and spirillum-based morphologies. The models were based on scanning electron microscope images of actualMTB. Analysis of these experiments elucidated the contribution of traits not included in existing models for rotational drag. The bulk analysis was performed in a custom made optical density meter, specifically designed to combine magnetic field orientations with photo spectrometry. From our observation we could derive the magnetic response, both absolute and relative, of a given culture or sample of MTB. Additionally, the response time of a given batch could also be measured, relating the magnetic dipole moment with the rotational drag. This allowed distinguishing between different quality and quantity of cultures, as well as long termand continuous observation of a culture in growth. In spite of having found new traits by which one can more accurately calculate the rotational drag profile, the length of an object still remains the dominate factor when balancing magnetic torque and drag force. Our model does allow for predicting more accurately the rotational drag of objects with shapes similar toMTB in Stokes flow or under low Reynolds number conditions

Closed-loop control of magnetotactic bacteria

Realization of point-to-point positioning of a magnetotactic bacterium (MTB) necessitates the application of a relatively large magnetic field gradients to decrease its velocity in the vicinity of a reference position. We investigate an alternative closed-loop control approach to position the MTB. This approach is based on the characterization of the magnetic dipole moment of the MTB and its response to a field with alternating direction. We do not only find agreement between our characterized magnetic dipole moment and previously published results, but also observe that the velocity of the MTB decreases by 37% when a field with alternating direction is applied at 85 Hz. The characterization results allow us to devise a null-space control approach which capitalizes on the redundancy of magnetic-based manipulation systems. This approach is based on two inputs. The first controls the orientation of the MTB, whereas the second generates a field with alternating direction to decrease its velocity. This control is accomplished by the redundancy of our magnetic-based manipulation system which allows for the projection of the second input onto the null-space of the magnetic force-current map of our system. A proportional–derivative control system positions the MTB at an average velocity and region of convergence of 29 μm s−1 and 20 μm, respectively, while our null-space control system achieves an average velocity and region of convergence of 15 μm s−1 and 13 μm, respectively

An integrated magnet array for trapping and manipulation of magnetotactic bacteria in microfluidics

We present a novel system for localized magnetic manipulation of magnetotactic bacteria in microfluidic systems. Where other methods require small conductive tracks directly below the sample, the new system consists of an array of permanent magnets switchable by a drive current to either trap or guide bacteria. This allows for much higher magnetic fields at reduced power consumption. Both a theoretical analysis and experimental analysis are presented. The system is scalable and is suited for integration in microfluidics

Characterization and Control of Biological Microrobots

This work addresses the characterization and control of Magnetotactic Bacterium (MTB) which can be considered as a biological microrobot. Magnetic dipole moment of the MTB and response to a field-with-alternating-direction are characterized. First, the magnetic dipole moment is characterized using four tech-niques, i.e., Transmission Electron Microscope images, flip-time, rotating-field and u-turn techniques. This characterization results in an average magnetic dipole mo-ment of 3.32×10−16 A.m2 and 3.72×10−16 A.m2 for non-motile and motile MTB, respectively. Second, the frequency response analysis of MTB shows that its ve-locity decreases by 38% for a field-with-alternating-direction of 30 rad/s. Based on the characterized magnetic dipole moment, the magnetic force produced by our magnetic system is five orders-of-magnitude less than the propulsion force gener-ated by the flagellum of the MTB. Therefore, point-to-point positioning of MTB cannot be achieved by exerting a magnetic force. A closed-loop control strategy is devised based on calculating the position tracking error, and capitalizes on the fre-quency response analysis of the MTB. Point-to-point closed-loop control of MTB is achieved for a reference set-point of 60 mm with average velocity of 20 mm/s. The closed-loop control system positions the MTB within a region-of-convergence of 10 mm diameter

Insights into the genome of large sulfur bacteria revealed by analysis of single filaments

Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. Despite their conspicuous metabolic properties and their biogeochemical importance, little is known about their genetic repertoire because of the lack of pure cultures. Here, we present a unique approach to access the genome of single filaments of Beggiatoa by combining whole genome amplification, pyrosequencing, and optical genome mapping. Sequence assemblies were incomplete and yielded average contig sizes of approximately 1 kb. Pathways for sulfur oxidation, nitrate and oxygen respiration, and CO2 fixation confirm the chemolithoautotrophic physiology of Beggiatoa. In addition, Beggiatoa potentially utilize inorganic sulfur compounds and dimethyl sulfoxide as electron acceptors. We propose a mechanism of vacuolar nitrate accumulation that is linked to proton translocation by vacuolar-type ATPases. Comparative genomics indicates substantial horizontal gene transfer of storage, metabolic, and gliding capabilities between Beggiatoa and cyanobacteria. These capabilities enable Beggiatoa to overcome non-overlapping availabilities of electron donors and acceptors while gliding between oxic and sulfidic zones. The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur and nitrogen cycling in marine sediments