Presented here is a protocol that describes monitoring of the complete life cycle of predatory bacterium Bdellovibrio bacteriovorus using time-lapse fluorescence microscopy in combination with an agarose pad and cell-imaging dishes.
Bdellovibrio bacteriovorus is a small gram-negative, obligate predatory bacterium that kills other gram-negative bacteria, including harmful pathogens. Therefore, it is considered a living antibiotic. To apply B. bacteriovorus as a living antibiotic, it is first necessary to understand the major stages of its complex life cycle, particularly its proliferation inside prey. So far, it has been challenging to monitor successive stages of the predatory life cycle in real-time. Presented here is a comprehensive protocol for real-time imaging of the complete life cycle of B. bacteriovorus, especially during its growth inside the host. For this purpose, a system consisting of an agarose pad is used in combination with cell-imaging dishes, in which the predatory cells can move freely beneath the agarose pad while immobilized prey cells are able to form bdelloplasts. The application of a strain producing a fluorescently tagged β-subunit of DNA polymerase III further allows chromosome replication to be monitored during the reproduction phase of the B. bacteriovorus life cycle.
Bdellovibrio bacteriovorus is a small (0.3–0.5 µm by 0.5–1.4 µm) gram-negative bacterium that preys on other gram-negative bacteria, including harmful pathogens such as Klebsiella pneumoniae, Pseudomonas aeruginosa, and Shigella flexneri1,2,3. Since B. bacteriovorus kills pathogens, it is considered a potential living antibiotic that can be applied to combat bacterial infections, particularly those caused by multidrug-resistant strains.
B. bacteriovorus exhibits a peculiar life cycle consisting of two phases: a free-living non-replicative attack phase and an intracellular reproductive phase (Figure 1). In the free-living phase, this highly motile bacterium, which moves at speeds of up to 160 µm/s, searches for its prey. After attaching to the prey’s outer membrane, it enters the periplasm4,5. During the interperiplasmic reproductive phase, B. bacteriovorus uses a plethora of hydrolytic enzymes to degrade the host’s macromolecules and reuse them for its own growth. Soon after invading the periplasm, the host cell dies and bloats into a spherical structure called a bdelloplast, inside which the predatory cell elongates and replicates its chromosomes. The replication process starts at the replication origin (oriC)6 and proceeds until several copies of the chromosome have been completely synthesized7. Interestingly, replication of each chromosome is not followed by cell division. Instead, the predator elongates to form a long, multinucleoid and filamentous cell. Upon nutrient depletion, the filament undergoes synchronous septation and progeny cells are released from the bdelloplast8.
Before B. bacteriovorus can be used as a living antibiotic against bacterial infections, it is crucial to understand the major stages of its life cycle, particularly those related to its proliferation inside the prey. Live-cell imaging of B. bacteriovorus has been challenging, due to the various morphological forms of the predator and its prey during the complex life cycle. So far, the interactions between B. bacteriovorus and its host cell have been mainly studied by electron microscopy and snap-shot analysis2,9,10, both of which have limitations, especially when they are used to monitor successive stages of the predatory life cycle. These methods provide high-resolution images of B. bacteriovorus cells and enable observation of a small predator during the attack or growth phase. However, they do not allow tracking of single B. bacteriovorus cells throughout both life cycle phases.
Presented here is a comprehensive protocol for using time-lapse fluorescence microscopy (TLFM) to monitor the complete life cycle of B. bacteriovorus. A system consisting of an agarose pad is used in combination with a cell-imaging dish, in which the predatory cells can move freely beneath the agarose pad while the immobilized prey cells are able to form bdelloplasts (Figure 2). This set-up is prepared based on specific strains of both E. coli and B. bacteriovorus, but the protocol may be easily altered to fit a user’s individual strains (e.g., carrying different selection markers, proteins fused with different fluorophores, etc.).
In this case, to visualize B. bacteriovorus during the attack phase, a specific strain (HD100 DnaN-mNeonGreen/PilZ-mCherry) was constructed that expresses a fluorescently tagged version of the cytoplasmic protein, PilZ (available in our laboratory upon request)7. This strain additionally produces DnaN (the β-sliding clamp), a subunit of DNA polymerase III holoenzyme, fused with a fluorescent protein. This enables ongoing DNA replication to be monitored inside the predatory cells as they grow within bdelloplasts.
Although the described protocol and software used for image acquisition refer to an inverted microscope provided by a specific manufacturer (see Table of Materials), this technique may be adjusted for any inverted microscope equipped with an environmental chamber or other external heating holder and capable of time-lapse imaging. For data analysis, users may choose any available software compatible with the individual output formats.
Figure 1: B. bacteriovorus life cycle in E. coli as a host cell. During the attack phase, a free-swimming B. bacteriovorus cell searches for and attaches to a host E. coli cell. After the invasion, the predatory cell becomes localized in the prey’s periplasm, changing the host cell’s shape and forming a bdelloplast. The reproductive phase starts with bdelloplast formation. The predatory cell digests the prey cell and reuses simple compounds to build its own structures. B. bacteriovorus grows as a long single filament inside the host’s periplasm. When the prey cell’s resources are exhausted, the B. bacteriovorus filament synchronously septates and forms progeny cells. After the progeny cells develop their flagella, they lyse the bdelloplast. Please click here to view a larger version of this figure.
1. Preparation of B. bacteriovorus lysate for microscopic analysis
2. Preparation of host cells for B. bacteriovorus invasion
3. Set-up of the microscope (see Table of Materials)
4. Assembly of layouts for time-lapse fluorescence microscopy
Figure 2: Schematic depiction of the experimental workflow. The agarose pad is removed from the 35 mm dish and flipped so that the bottom side faces upwards. Fresh suspensions of predatory cells and overnight culture of prey cells are placed on the flipped pad to coat the “bottom” side. The agarose pad is then flipped to its original orientation and placed back in the 35 mm dish, which is mounted onto the inverted microscope stage in the microscope chamber. Please click here to view a larger version of this figure.
5. Conduction of time-lapse fluorescence microscopy
6. Processing of time-lapse images and generation of movies using Fiji software
The described TLFM-based system allows individual cells of B. bacteriovorus to be tracked in time (Figure 3, Movie 1) and provides valuable information about each stage of the complex predatory life cycle. The PilZ-mCherry fusion enables the entire predatory cell to be labeled in the attack phase as well as early stage of the growth phase (Figure 3). The transition from the attack to replicative phase was visualized not only by the host bdelloplast formation but also by the appearance of the replisome (replication machinery), which was marked by DnaN-mNeonGreen fluorescent foci (Figure 3).
As previously demonstrated, the replisome was assembled at the invading cell pole (pili-pole)7, and more than one replisome was observed within a growing B. bacteriovorus filament as the reproduction phase progressed (Figure 3). After several copies of the chromosome were synthesized, the replication was terminated (visualized as the disappearance of DnaN-mNeonGreen foci). Finally, the multinucleoid filament underwent septation, and the progeny cells were released from the bdelloplast (Figure 3).
The presented protocol describing the image processing using the Fiji software provides a step-by-step explanation of how to produce a movie for publication from the acquired time-lapse series (Movie 1).
Figure 3: B. bacteriovorus life cycle followed by time-lapse fluorescence microscopy. (A) Free-living predatory (B. bacteriovorus DnaN-mNeonGreen/PilZ-mCherry) and host (E. coli) cells. (B) Attachment of B. bacteriovorus to E. coli. (C) Bdelloplast formation. (D,E) Filamentous growth and chromosome replication. (F) Termination of chromosome replication. (G) Start of synchronous filament septation. (H) Bdelloplast lysis and release of progeny cells. Upper panels show brightfield images, lower panels represent merged brightfield and fluorescence channels. Scale bar = 1 µm, time = hh:min. Please click here to view a larger version of this figure.
Movie 1: Time-lapse imaging of B. bacteriovorus life cycle in E. coli as a host cell. Subcellular localization of DnaN-mNeonGreen (green) in strain HD100 DnaN-mNeonGreen/PilZ-mCherry. Red channel indicates labeling of the predator cells with cytoplasmic PilZ-mCherry. Grey indicates brightfield. Images were collected every 5 min. Please click here to download this video.
Due to the increased interest in using B. bacteriovorus as a living antibiotic, new tools for observing the predatory life cycle, particularly predator-pathogen interactions, are needed. The presented protocol is used to track the entire B. bacteriovorus life cycle, especially during its growth inside the host, in real-time. Moreover, the application of a strain producing fluorescently tagged beta clamp of DNA polymerase III holoenzyme enabled monitoring of chromosome replication progression throughout the reproduction phase of B. bacteriovorus.
A critical step in this method is the proper preparation of layouts in the 35 mm dish. A challenge in observing the life cycle of B. bacteriovorus under the microscope is to establish conditions that support predatory growth (involving other gram-negative bacterial cells as host cells) and provide for predatory cell motility. One of the crucial aspects of effective microscopic observations is the need for a uniform distribution of prey on the agarose pad, which is achieved by spreading the cells with an inoculating loop. The host cell density cannot be too high, and the chosen observation points should contain a sufficient number of separate host cells. Meanwhile, the Bdellovibrio cells should be motile enough to actively search for their prey. Thus, they should not be spread out or air-dried before the pad is flipped back over and placed into the dish. Sometimes greater volumes of predator suspension are needed to provide sufficient motility in a thin layer of fluid between the agarose and glass surface.
A µ-Dish is used here; however, this is not essential for the protocol. Any glass-bottom dish could be used. An advantage of the µ-Dish is the optimal height and volume of the agarose path, which enables the coculture of predatory and host to be placed on the bottom side of the agarose pad. It is also important to use fresh B. bacteriovorus cells in the experiments, as the cells lose their motility during prolonged storage. A limitation of this protocol is that, at the single field of view, users can count approximately 100 predator cells and 100 host cells, but the MOI can be estimated at 50%–60%.
Current knowledge about the Bdellovibrio cell cycle is largely based on studies that have employed E. coli or P. aeruginosa. This system allows monitoring of B. bacteriovorus preying on a variety of bacterial pathogens, including Salmonella spp., S. flexneri, Proteus mirabilis, or K. pneumoniae. Moreover, this platform may be useful in experiments involving multidrug-resistant pathogens. Thus, it may help to facilitate improvements in the genetic engineering of B. bacteriovorus as a live antibiotic in human and veterinary medicine, particularly to combat multidrug-resistant pathogens.
The authors have nothing to disclose.
This study was supported by the National Science Centre grant Opus 2018/29/B/NZ6/00539 to J.Z.C.
Centrifuge | MPW MED. INSTRUMENTS | MPW-260R | Rotor ref. 12183 |
CertifiedMolecular Biology Agarose | BIO-RAD | 161-3100 | low fluorescence agarose for agarose pad |
Fiji | ImageJ | https://imagej.net/Fiji | Open source image processing package |
Glass Bottom Dish 35 mm | ibidi | 81218-200 | uncoated glass |
Microscope | GE | DeltaVision Elite | Microtiter Stage, ultimate focus laser module, DV Elite CoolSnap HQ2 Camera, SSI assembly FP DV, kit obj. Oly 100x oil 1.4 NA, prism Nomarski 100x LWD DIC, ENV ctrl IX71 uTiter opaQ 240 V |
Minisart Filter 0.45 µm | Sartorius | 16555———-K | Cellulose Acetate, Sterile, Luer Lock Outlet |
Start SoftWoRx | GE | Manufacturer-supplied imaging software |