MagCluster: a Tool for Identification, Annotation, and Visualization of Magnetosome Gene Clusters

Magnetosome gene clusters (MGCs), which are responsible for magnetosome biosynthesis and organization in magnetotactic bacteria (MTB), are the key to deciphering the mechanisms and evolutionary origin of magnetoreception, organelle biogenesis, and intracellular biomineralization in bacteria. Here, we report the development of MagCluster, a Python stand-alone tool for efficient exploration of MGCs from large-scale (meta)genomic data.

Magnetic particle imaging of magnetotactic bacteria as living contrast agents is improved by altering magnetosome structures

ABSTRACTIron nanoparticles used as imaging contrast agents can help differentiate between normal and diseased tissue, or track cell movement and localize pathologies. Magnetic particle imaging (MPI) is an imaging modality that uses the magnetic properties of iron nanoparticles to provide specific, quantitative and sensitive imaging data. MPI signals depend on the size, structure and composition of the nanoparticles; MPI-tailored nanoparticles have been developed by modifying these properties. Magnetotactic bacteria produce magnetosomes which mimic synthetic nanoparticles, and thus comprise a living contrast agent in which nanoparticle formation can be modified by mutating genes. Specifically, genes that encode proteins critical to magnetosome formation and regulation, such as mamJ which helps with filament turnover. Deletion of mamJ in Magnetospirillum gryphiswaldense, MSR-1 led to clustered magnetosomes instead of the typical linear chains. Here we examined the effects of this magnetosome structure and revealed improved MPI signal and resolution from clustered magnetosomes compared to linear chains. Bioluminescent MSR-1 with the mamJ deletion were injected intravenously into tumor-bearing and healthy mice and imaged using both in vivo bioluminescence imaging (BLI) and MPI. BLI revealed the location and viability of bacteria which was used to validate localization of MPI signals. BLI identified the viability of MSR-1 for 24 hours and MPI detected iron in the liver and in multiple tumors. Development of living contrast agents offers new opportunities for imaging and therapy by using multimodality imaging to track the location and viability of the therapy and the resulting biological effects.

New Phenotype and Mineralization of Biogenic Iron Oxide in Magnetotactic Bacteria

Many magnetotactic bacteria (MTB) biomineralize magnetite crystals that nucleate and grow inside intracellular membranous vesicles originating from invaginations of the cytoplasmic membrane. The crystals together with their surrounding membranes are referred to as magnetosomes. Magnetosome magnetite crystals nucleate and grow using iron transported inside the vesicle by specific proteins. Here, we tackle the question of the organization of magnetosomes, which are always described as constituted by linear chains of nanocrystals. In addition, it is commonly accepted that the iron oxide nanocrystals are in the magnetite-based phase. We show, in the case of a wild species of coccus-type bacterium, that there is a double organization of the magnetosomes, relatively perpendicular to each other, and that the nanocrystals are in fact maghemite. These findings were obtained, respectively, by using electron tomography of whole mounts of cells directly from the environment and high-resolution transmission electron microscopy and diffraction. Structure simulations were performed with the MacTempas software. This study opens new perspectives on the diversity of phenotypes within MTBs and allows to envisage other mechanisms of nucleation and formation of biogenic iron oxide crystals.

Impact of Upward Oxygen Diffusion From the Oceanic Crust on the Magnetostratigraphy and Iron Biomineralization of East Pacific Ridge-Flank Sediments

Recent measurements of pore-water oxygen profiles in ridge flank sediments of the East Pacific Rise revealed an upward-directed diffusive oxygen flux from the hydrothermally active crust into the overlying sediment. This double-sided oxygenation from above and below results in a dual redox transition from an oxic sedimentary environment near the seabed through suboxic conditions at sediment mid-depth back to oxic conditions in the deeper basal sediment. The potential impact of this redox reversal on the paleo- and rock magnetic record was analyzed for three sediment cores from the Clarion-Clipperton-Zone (low-latitude eastern North Pacific). We found that the upward-directed crustal oxygen flux does not impede high quality reversal-based and relative paleointensity-refined magnetostratigraphic dating. Despite low and variable sedimentation rates of 0.1–0.8 cm/kyr, robust magnetostratigraphic core chronologies comprising the past 3.4 resp. 5.2 million years could be established. These age-models support previous findings of significant local sedimentation rate variations that are probably related to the bottom current interactions with the topographic roughness of the young ridge flanks. However, we observed some obvious paleomagnetic irregularities localized at the lower oxic/suboxic redox boundaries of the investigated sediments. When analyzing these apparently remagnetized sections in detail, we found no evidence of physical disturbance or chemical alteration. A sharp increase in single-domain magnetite concentration just below the present lower oxic/suboxic redox boundary suggests secondary magnetite biomineralization by microaerophilic magnetotactic bacteria living as a separate community in the lower, upward oxygenated part of the sediment column. We therefore postulate a two-phased post-depositional remanent magnetization of ridge flank sediments, first by a shallow and later by a deep-living community of magnetotactic bacteria. These findings are the first evidence of a second, deep population of probably inversely oriented magnetotactic bacteria residing in the inverse oxygen gradient zone of ridge flank sediments.

A review of the ecology, genetics, evolution, and magnetosome –induced behaviours of the magnetotactic bacteria

The discovery of magnetosome and magnetotaxis in its most simple form in the magnetotactic bacteria (MTB) had created the tremendous impetus. MTB, spanning multiple phyla, are distributed worldwide, and they form the organelles called magnetosomes for biomineralization. Eight phylotypes of MTB belong to Alphaproteobacteria and Nitrospirae. MTB show preference for specific redox and oxygen concentration. Magnetosome chains function as the internal compass needle and align the bacterial cells passively along the local geomagnetic field (GMF). The nature of magnetosomes produced by MTB and their phylogeny suggest that bullet-shaped magnetites appeared about 3.2 billion years ago with the first magnetosomes. All MTB contains ten genes in conserved mamAB operon for magnetosome chain synthesis of which nine genes are conserved in greigite-producing MTB. Many candidate genes identify the aero-, redox-, and perhaps phototaxis. Among the prokaryotes, the MTB possess the highest number of O2-binding proteins. Magnetofossils serve as an indicator of oxygen and redox levels of the ancient environments. Most descendants of ancestral MTB lost the magnetosome genes in the course of evolution. Environmental conditions initially favored the evolution of MTB and expansion of magnetosome-formation genes. Subsequent changes in atmospheric oxygen concentration have led to changes in the ecology of MTB, loss of magnetosome genes, and evolution of nonMTB.

Fluidic bacterial diodes rectify magnetotactic cell motility in porous environments

Directed motility enables swimming microbes to navigate their environment for resources via chemo-, photo-, and magneto-taxis. However, directed motility competes with fluid flow in porous microbial habitats, affecting biofilm formation and disease transmission. Despite this broad importance, a microscopic understanding of how directed motility impacts the transport of microswimmers in flows through constricted pores remains unknown. Through microfluidic experiments, we show that individual magnetotactic bacteria directed upstream through pores display three distinct regimes, whereby cells swim upstream, become trapped within a pore, or are advected downstream. These transport regimes are reminiscent of the electrical conductivity of a diode and are accurately predicted by a comprehensive Langevin model. The diode-like behavior persists at the pore scale in geometries of higher dimension, where disorder impacts conductivity at the sample scale by extending the trapping regime over a broader range of flow speeds. This work has implications for our understanding of the survival strategies of magnetotactic bacteria in sediments and for developing their use in drug delivery applications in vascular networks.

Functionalization of Biotinylated Polyethylene Glycol on Live Magnetotactic Bacteria Carriers for Improved Stealth Properties

The early removal of drug delivery agents before reaching the affected target remains an area of interest to researchers. Several magnetotactic bacteria (MTB) have been used as self-propelled drug delivery agents, and they can also be controlled by an external magnetic field. By attaching the PEG–biotin polymer, the bacteria are turned into a stealth material that can escape from the phagocytosis process and reach the area of interest with the drug load. In the study, we developed a potential drug carrier by attaching the PEG–biotin to the MTB-through-NHS crosslinker to form a MTB/PEG–biotin complex. The attachment stability, efficacy, and bacterial viability upon attachment of the PEG–biotin polymer were investigated. Biological applications were carried out using a cytotoxicity assay of THP-1 cells, and the results indicate that the MTB/PEG–biotin complex is less harmful to cell viability compared to MTB alone. Along with cytotoxicity, an assay for cell association was also evaluated to assess the complex as a potential stealth material. The development of these complexes focuses on an easy, time-saving, and stable technique of polymer attachment with the bacteria, without damaging the cell’s surface, so as to make it a strong and reliable delivery agent.