Ecology, diversity, and evolution of magnetotactic bacteria

Magnetic imaging of individual magnetosome chains in magnetotactic bacteria

While significant advances have been made in exploring and uncovering the promising potential of biomagnetic materials, persistent challenges remain on various fronts, notably in the characterization of individual elements. This study makes use of advanced modes of Magnetic Force Microscopy (MFM) and tailored MFM probes to characterize individual magnetotactic bacteria in different environments. The characterization of these elements posed a significant challenge, as the magnetosomes, besides presenting low magnetic signal, are embedded in bacteria of much larger size. To overcome this, customed Atomic Force Microscopy probes are developed through various strategies, enhancing sensitivity in different environments, including liquids. Furthermore, employing MFM imaging under an in-situ magnetic field provides an opportunity to gather quantitative data regarding the critical fields of these individual chains of nanoparticles. This approach marks a substantial advancement in the field of MFM for biological applications, enabling the detection of magnetosomes under different conditions.

Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.

Purification, Characterization, and Assessment of Anticancer Activity of Iron Oxide Nanoparticles Biosynthesized by Novel Thermophilic Bacillus tequilensis ASFS1‏

Magnetic nanoparticles (MNPs), particularly iron oxide nanoparticles (IONPs), are a fascinating group of nanoparticles that have been considerably investigated for biomedical applications because of their superparamagnetic properties, biodegradable nature, and biocompatibility. A novel Gram-positive moderately thermophilic bacterial strain, namely Bacillus tequilensis ASFS.1, was isolated and identified. This strain is capable of producing superparamagnetic Fe3O4 nanoparticles and exhibiting magnetotaxis behavior. This strain swimming behavior was investigated under static and dynamic environments, where it behaved very much similar to the magnetotaxis in magnetotactic bacteria. This study is the first report of a bacterium from the Bacillaceae family that has the potential to intracellular biosynthesis of IONPs. MNPs were separated by a magnetic and reproducible method which was designed for the first time for this study. In addition, UV-visible spectrophotometer, Fourier-transform infrared spectroscopy, vibrating sample magnetometer, field emission scanning electron microscopy (FESEM), X-ray diffraction, and thermal gravimetric analysis were utilized to characterize the bio-fabricated magnetite nanoparticles. Analysis of the particle size distribution pattern of the biogenic MNPs by FESEM imaging revealed the size range of 10-100 nm with the size range of 10-40 nm MNPs being the most frequent particles. VSM analysis demonstrated that biogenic MNPs displayed superparamagnetic properties with a high saturation magnetization value of 184 emu/g. After 24 h treatment of 3T3, U87, A549, MCF-7, and HT-29 cell lines with the biogenic MNPs, IC50 values were measured to be 339, 641, 582, 149, and 184 μg mL-1, respectively. This study presents the novel strain ASFS.1 capable of magnetotaxis by the aid of its magnetite nanoparticles and paving information on isolation, characterization, and in vitro cytotoxicity of its MNPs. The MNPs showed promising potential for biomedical applications, obviously subject to additional studies.

Magnetogenetics as a promising tool for controlling cellular signaling pathways

Magnetogenetics emerges as a transformative approach for modulating cellular signaling pathways through the strategic application of magnetic fields and nanoparticles. This technique leverages the unique properties of magnetic nanoparticles (MNPs) to induce mechanical or thermal stimuli within cells, facilitating the activation of mechano- and thermosensitive proteins without the need for traditional ligand-receptor interactions. Unlike traditional modalities that often require invasive interventions and lack precision in targeting specific cellular functions, magnetogenetics offers a non-invasive alternative with the capacity for deep tissue penetration and the potential for targeting a broad spectrum of cellular processes. This review underscores magnetogenetics' broad applicability, from steering stem cell differentiation to manipulating neuronal activity and immune responses, highlighting its potential in regenerative medicine, neuroscience, and cancer therapy. Furthermore, the review explores the challenges and future directions of magnetogenetics, including the development of genetically programmed magnetic nanoparticles and the integration of magnetic field-sensitive cells for in vivo applications. Magnetogenetics stands at the forefront of cellular manipulation technologies, offering novel insights into cellular signaling and opening new avenues for therapeutic interventions.

Cancer Nanovaccines: Nanomaterials and Clinical Perspectives

Cancer nanovaccines represent a promising frontier in cancer immunotherapy, utilizing nanotechnology to augment traditional vaccine efficacy. This review comprehensively examines the current state-of-the-art in cancer nanovaccine development, elucidating innovative strategies and technologies employed in their design. It explores both preclinical and clinical advancements, emphasizing key studies demonstrating their potential to elicit robust anti-tumor immune responses. The study encompasses various facets, including integrating biomaterial-based nanocarriers for antigen delivery, adjuvant selection, and the impact of nanoscale properties on vaccine performance. Detailed insights into the complex interplay between the tumor microenvironment and nanovaccine responses are provided, highlighting challenges and opportunities in optimizing therapeutic outcomes. Additionally, the study presents a thorough analysis of ongoing clinical trials, presenting a snapshot of the current clinical landscape. By curating the latest scientific findings and clinical developments, this study aims to serve as a comprehensive resource for researchers and clinicians engaged in advancing cancer immunotherapy. Integrating nanotechnology into vaccine design holds immense promise for revolutionizing cancer treatment paradigms, and this review provides a timely update on the evolving landscape of cancer nanovaccines.

Biominerals and Bioinspired Materials in Biosensing: Recent Advancements and Applications

Inspired by nature's remarkable ability to form intricate minerals, researchers have unlocked transformative strategies for creating next-generation biosensors with exceptional sensitivity, selectivity, and biocompatibility. By mimicking how organisms orchestrate mineral growth, biomimetic and bioinspired materials are significantly impacting biosensor design. Engineered bioinspired materials offer distinct advantages over their natural counterparts, boasting superior tunability, precise controllability, and the ability to integrate specific functionalities for enhanced sensing capabilities. This remarkable versatility enables the construction of various biosensing platforms, including optical sensors, electrochemical sensors, magnetic biosensors, and nucleic acid detection platforms, for diverse applications. Additionally, bioinspired materials facilitate the development of smartphone-assisted biosensing platforms, offering user-friendly and portable diagnostic tools for point-of-care applications. This review comprehensively explores the utilization of naturally occurring and engineered biominerals and materials for diverse biosensing applications. We highlight the fabrication and design strategies that tailor their functionalities to address specific biosensing needs. This in-depth exploration underscores the transformative potential of biominerals and materials in revolutionizing biosensing, paving the way for advancements in healthcare, environmental monitoring, and other critical fields.

The magneto-microbiome: A dataset of the metagenomic distribution of magnetotactic bacteria

Magnetotactic bacteria (MTB) are diverse prokaryotes characterized by their ability to generate biogenic magnetic iron crystals. MTB are ubiquitous across aquatic environments, and growing evidence has indicated they may be present in association with animal microbiomes. Unfortunately, they are difficult to culture in vitro and more studies understanding their biogeographical distribution and ecological roles are needed. To provide data regarding the patterns of diversity and distribution of MTB, we screened the entire Sequence Read Archive (SRA) from the National Center for Biotechnology Information for DNA sequencing reads matching known MTB taxa. The dataset summarizes the count of reads assigned to MTB from more than 26 million SRA accessions comprising approximately 80 petabases (7.98 × 1016) of DNA. More than 396 million DNA sequencing reads were assigned to 214 MTB taxa in 691,086 (2.65 %) SRA accessions. The final dataset can be utilized by researchers to narrow their efforts in examination of both environmental and ecological roles of specific MTB or to identify potential host organisms. These data will be instrumental to further elucidating the importance and utility of these enigmatic bacteria.

Set-up of a pharmaceutical cell bank of Magnetospirillum gryphiswaldense MSR1 magnetotactic bacteria producing highly pure magnetosomes

We report the successful fabrication of a pharmaceutical cellular bank (PCB) containing magnetotactic bacteria (MTB), which belong to the Magnetospirillum gryphiswaldense MSR1 species. To produce such PCB, we amplified MTB in a minimal growth medium essentially devoid of other heavy metals than iron and of CMR (Carcinogenic, mutagenic and reprotoxic) products. The PCB enabled to acclimate MTB to such minimal growth conditions and then to produce highly pure magnetosomes composed of more than 99.9% of iron. The qualification of the bank as a PCB relies first on a preserved identity of the MTB compared with the original strain, second on genetic bacterial stability observed over 100 generations or under cryo-preservation for 16 months, third on a high level of purity highlighted by an absence of contaminating microorganisms in the PCB. Furthermore, the PCB was prepared under high-cell load conditions (9.108 cells/mL), allowing large-scale bacterial amplification and magnetosome production. In the future, the PCB could therefore be considered for commercial as well as research orientated applications in nanomedicine. We describe for the first-time conditions for setting-up an effective pharmaceutical cellular bank preserving over time the ability of certain specific cells, i.e. Magnetospirillum gryphiswaldense MSR1 MTB, to produce nano-minerals, i.e. magnetosomes, within a pharmaceutical setting.

Ferromagnetic resonance spectra of linear magnetosome chains

The ferromagnetic resonance (FMR) spectra of oriented and non-oriented assemblies of linear magnetosome chains are calculated by solving the stochastic Landau-Lifshitz equation. The dependence of the shape of the FMR spectrum of a dilute assembly of chains on the particle diameter, the number of particles in a chain, the distance between the centers of neighboring particles, the mutual orientation of the cubic axes of particle anisotropy, and the value of the magnetic damping constant is studied. It is shown that FMR spectra of non-oriented chain assemblies depend on the average particle diameter at a fixed thickness of the lipid magnetosome membrane, as well as on the value of the magnetic damping constant. At the same time, they are practically independent of the number Np of particles in the chain under the condition Np ≥ 10. The FMR spectra of non-oriented assemblies of magnetosome chains are compared with that of random clusters of interacting spherical magnetite nanoparticles. The shape of FMR spectra of both assemblies is shown to differ appreciably even at sufficiently large values of filling density of random clusters.

Implications for nitrogen and sulphur cycles: phylogeny and niche-range of Nitrospirota in terrestrial aquifers

Increasing evidence suggests Nitrospirota are important contributors to aquatic and subsurface nitrogen and sulphur cycles. We determined the phylogenetic and ecological niche associations of Nitrospirota colonizing terrestrial aquifers. Nitrospirota compositions were determined across 59 groundwater wells. Distributions were strongly influenced by oxygen availability in groundwater, marked by a trade-off between aerobic (Nitrospira, Leptospirillum) and anaerobic (Thermodesulfovibrionia, unclassified) lineages. Seven Nitrospirota metagenome-assembled genomes (MAGs), or populations, were recovered from a subset of wells, including three from the recently designated class 9FT-COMBO-42-15. Most were relatively more abundant and transcriptionally active in dysoxic groundwater. These MAGs were analysed with 743 other Nitrospirota genomes. Results illustrate the predominance of certain lineages in aquifers (e.g. non-nitrifying Nitrospiria, classes 9FT-COMBO-42-15 and UBA9217, and Thermodesulfovibrionales family UBA1546). These lineages are characterized by mechanisms for nitrate reduction and sulphur cycling, and, excluding Nitrospiria, the Wood-Ljungdahl pathway, consistent with carbon-limited, low-oxygen, and sulphur-rich aquifer conditions. Class 9FT-COMBO-42-15 is a sister clade of Nitrospiria and comprises two families spanning a transition in carbon fixation approaches: f_HDB-SIOIB13 encodes rTCA (like Nitrospiria) and f_9FT-COMBO-42-15 encodes Wood-Ljungdahl CO dehydrogenase (like Thermodesulfovibrionia and UBA9217). The 9FT-COMBO-42-15 family is further differentiated by its capacity for sulphur oxidation (via DsrABEFH and SoxXAYZB) and dissimilatory nitrate reduction to ammonium, and gene transcription indicated active coupling of nitrogen and sulphur cycles by f_9FT-COMBO-42-15 in dysoxic groundwater. Overall, results indicate that Nitrospirota are widely distributed in groundwater and that oxygen availability drives the spatial differentiation of lineages with ecologically distinct roles related to nitrogen and sulphur metabolism.

Magnetosomes as Potential Nanocarriers for Cancer Treatment

Magnetotactic bacteria (MTBs) and their organelles, magnetosomes, are intriguing options that might fulfill the criteria of using bacterial magnetosomes (BMs). The ferromagnetic crystals contained in BMs can condition the magnetotaxis of MTBs, which is common in water storage facilities. This review provides an overview of the feasibility of using MTBs and BMs as nanocarriers in cancer treatment. More evidence suggests that MTBs and BMs can be used as natural nanocarriers for conventional anticancer medicines, antibodies, vaccine DNA, and siRNA. In addition to improving the stability of chemotherapeutics, their usage as transporters opens the possibilities for the targeted delivery of single ligands or combinations of ligands to malignant tumors. Magnetosome magnetite crystals are different from chemically made magnetite nanoparticles (NPs) because they are strong single-magnetic domains that stay magnetized even at room temperature. They also have a narrow size range and a uniform crystal morphology. These chemical and physical properties are essential for their usage in biotechnology and nanomedicine. Bioremediation, cell separation, DNA or antigen regeneration, therapeutic agents, enzyme immobilization, magnetic hyperthermia, and contrast enhancement of magnetic resonance are just a few examples of the many uses for magnetite-producing MTB, magnetite magnetosomes, and magnetosome magnetite crystals. From 2004 to 2022, data mining of the Scopus and Web of Science databases showed that most research using magnetite from MTB was carried out for biological reasons, such as in magnetic hyperthermia and drug delivery.

Phenomic and transcriptomic analyses reveal the sequential synthesis of Fe3O4 nanoparticles in Acidithiobacillus ferrooxidans BYM

IMPORTANCE

As the most important non-magnetotactic magnetosome-producing bacteria, Acidithiobacillus ferrooxidans only requires very mild conditions to produce Fe3O4 nanoparticles, thus conferring greater flexibility and potential application in biomagnetic nanoparticle production. However, the available information cannot explain the mechanism of Fe3O4 nanoparticle formation in A. ferrooxidans. In this study, we applied phenomic and transcriptomic analyses to reveal this mechanism. We found that different treatment condition factors notably affect the phenomic data of Fe3O4 nanoparticle in A. ferrooxidans. Using transcriptomic analyses, the gene network controlling/regulating Fe3O4 nanoparticle biogenesis in A. ferrooxidans was proposed, excavating the candidate hub genes for Fe3O4 nanoparticle formation in A. ferrooxidans. Based on this information, a sequential model for Fe3O4 nanoparticle synthesis in A. ferrooxidans was hypothesized. It lays the groundwork for further clarifying the feature of Fe3O4 nanoparticle synthesis.

Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing eight new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nano-scale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal non-canonical amino acid tagging (BONCAT) we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.

External magnetic field have significant effects on diversity of magnetotactic bacteria in sediments from Yangtze River, Chagan Lake and Zhalong Wetland in China

Magnetotactic bacteria (MTB) can rapidly relocate to optimal habitats by magnetotaxis, and play an important role in iron biogeochemical cycling. This study aimed to evaluate the contribution of the external magnetostatic field to the diversity of MTB in freshwater sediments from Yangtze River (Changjiang River, CJ), Chagan Lake (CGH) and Zhalong Wetland (ZL). The magnetic field intensity was tightly associated with the community richness of MTB in CJ, whereas it was closely related to the diversity of MTB in CGH and ZL (p < 0.05), elucidating a significant variation in the community composition of MTB. Magnetic exposure time appeared more significant correlation with community richness than diversity for MTB in CJ and CGH (p < 0.05), while an opposite relationship existed in ZL (p < 0.01). Herbaspirillum (93.81-96.48 %) dominated in the sediments of these surfacewatesr regardless of waterbody types, while it shifted to Magnetospirillum in ZL under 100 Gs magnetic field. The network connectivity and stability of MTB deteriorate with the increase of magnetic field intensity. Functional analysis showed that the Two-component system and ABC transporter system of MTB obviously responded to magnetic field intensity and exposure time. Our findings will pave the way to understanding the response mechanism of MTB community in freshwater sediments to the external magnetostatic field.

Biomedical applications of magnetosomes: State of the art and perspectives

Magnetosomes, synthesized by magnetotactic bacteria (MTB), have been used in nano- and biotechnological applications, owing to their unique properties such as superparamagnetism, uniform size distribution, excellent bioavailability, and easily modifiable functional groups. In this review, we first discuss the mechanisms of magnetosome formation and describe various modification methods. Subsequently, we focus on presenting the biomedical advancements of bacterial magnetosomes in biomedical imaging, drug delivery, anticancer therapy, biosensor. Finally, we discuss future applications and challenges. This review summarizes the application of magnetosomes in the biomedical field, highlighting the latest advancements and exploring the future development of magnetosomes.

Preliminary indication of the role of AHL-dependent quorum sensing systems in calcium carbonate precipitation in Gram-negative bacteria

Numerous microbial species participate in precipitation of carbonates in various natural environments, including soils, geological formations, freshwater biofilms and oceans. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and adaptive aspects remain poorly known. Many Gram-negative bacteria use cell-to-cell communication systems relying on N-acylhomoserine lactone (AHLs) signal molecules to express certain phenotypic traits in a density-dependent manner, a phenomenon referred as to quorum-sensing (QS). In this work, bacterial isolates collected from cave and rhizosphere soil were analyzed to study the occurrence of the AHL-mediated QS in bacterial calcium carbonate (CaCO3) precipitation. To test the production of AHLs signal molecules, we cross-streaked Gram-negative calcifying strains, selected among the environmental strains studied, with the AHL-negative mutant Chromobacterium subtsugae strain CV026. Only Burkholderia ambifaria LMG 11351 was able to restore violacein production in CV026 among the tested strains. The constructed AHL-negative mutant of B. ambifaria LMG 11351 could not precipitate CaCO3 on B-4 agar. Scanning Electron Microscopy (SEM) analysis on CaCO3 crystals obtained in vitro shows crystals of different morphologies, calcified biofilms and bacteria in close contact with the precipitated crystals. In the inner layers of the bioliths deposited by B. ambifaria LMG 11351, a stream-like organization of the Burkholderia imprints was not detected by SEM. Our data provide preliminary evidence that the activation of AHL-regulated genes may be a prerequisite for in vitro bacterial carbonatogenesis, in some cases, confirming the specific role of bacteria as CaCO3 precipitating agents. We enhance the understanding of bacterial CaCO3 biomineralization and its potential biotechnology implications for QS-based strategies to enhance or decrease CaCO3 precipitation through specific bacterial processes. The AHL-negative mutant of B. ambifaria LMG 11351 (a well-known plant growth-promoting bacterium) could also be used to study plant-bacteria interactions. The adaptive role of bacterial CaCO3 biomineralization was also discussed.

Micromagnetic calculation of the magnetite magnetosomal morphology control of magnetism in magnetotactic bacteria

Magnetotactic bacteria (MTB), which precisely bio-synthesize magnetosomes of magnetite or greigite nanoparticles, have attracted broad interdisciplinary interests in microbiology, magnetic materials, biotechnology and geobiology. Previous experimental and numerical investigations demonstrate a close link among MTB species, magnetosome crystal habits, and magnetic characteristics, but quantitative constraints are currently lacking. In this study, we build three-dimensional finite-element micromagnetic models of intact magnetosome chains in common MTB species and corresponding collapsed chains. Realistic numerical microstructures were constructed for the three typical biogenic magnetite crystal forms-cuboctahedron, prism and bullet. Our calculations reveal characteristic magnetic properties associated with specific magnetite crystal forms and MTB species. Cuboctahedron and bullet crystals show distinct low coercivity (less than 30 mT) and high coercivity (greater than 50 mT) clusters, respectively. Prismatic crystals have a broad range of hysteresis parameters that are strongly controlled by chain structure. This magnetic property clustering, combined with magnetic unmixing methods and electron microscopy observations, can fingerprint biogenic magnetite components in geological and environmental samples. The passive magnetic orientation efficiency of various magnetosome chains was calculated. Some bullet-shaped magnetosome chains have higher magnetic moments than those with cuboctahedron and prism magnetosomes, which may enable larger MTB cells to overcome viscous resistance for efficient magnetic navigation.

Functional expression of foreign magnetosome genes in the alphaproteobacterium Magnetospirillum gryphiswaldense

Magnetosomes of magnetotactic bacteria (MTB) consist of structurally perfect, nano-sized magnetic crystals enclosed within vesicles of a proteo-lipid membrane. In species of Magnetospirillum, biosynthesis of their cubo-octahedral-shaped magnetosomes was recently demonstrated to be a complex process, governed by about 30 specific genes that are comprised within compact magnetosome gene clusters (MGCs). Similar, yet distinct gene clusters were also identified in diverse MTB that biomineralize magnetosome crystals with different, genetically encoded morphologies. However, since most representatives of these groups are inaccessible by genetic and biochemical approaches, their analysis will require the functional expression of magnetosome genes in foreign hosts. Here, we studied whether conserved essential magnetosome genes from closely and remotely related MTB can be functionally expressed by rescue of their respective mutants in the tractable model Magnetospirillum gryphiswaldense of the Alphaproteobacteria. Upon chromosomal integration, single orthologues from other magnetotactic Alphaproteobacteria restored magnetosome biosynthesis to different degrees, while orthologues from distantly related Magnetococcia and Deltaproteobacteria were found to be expressed but failed to re-induce magnetosome biosynthesis, possibly due to poor interaction with their cognate partners within multiprotein magnetosome organelle of the host. Indeed, co-expression of the known interactors MamB and MamM from the alphaproteobacterium Magnetovibrio blakemorei increased functional complementation. Furthermore, a compact and portable version of the entire MGCs of M. magneticum was assembled by transformation-associated recombination cloning, and it restored the ability to biomineralize magnetite both in deletion mutants of the native donor and M. gryphiswaldense, while co-expression of gene clusters from both M. gryphiswaldense and M. magneticum resulted in overproduction of magnetosomes. IMPORTANCE We provide proof of principle that Magnetospirillum gryphiswaldense is a suitable surrogate host for the functional expression of foreign magnetosome genes and extended the transformation-associated recombination cloning platform for the assembly of entire large magnetosome gene cluster, which could then be transplanted to different magnetotactic bacteria. The reconstruction, transfer, and analysis of gene sets or entire magnetosome clusters will be also promising for engineering the biomineralization of magnetite crystals with different morphologies that would be valuable for biotechnical applications.

Bullet-shaped magnetosomes and metagenomic-based magnetosome gene profiles in a deep-sea hydrothermal vent chimney

Magnetosome-producing microorganisms can sense and move toward the redox gradient and have been extensively studied in terrestrial and shallow marine sediment environments. However, given the difficulty of sampling, magnetotactic bacteria (MTB) are poorly explored in deep-sea hydrothermal fields. In this study, a deep-sea hydrothermal vent chimney from the Southern Mariana Trough was collected using a remotely operated submersible. The mineralogical and geochemical characterization of the vent chimney sample showed an internal iron redox gradient. Additionally, the electron microscopy of particles collected by magnetic separation from the chimney sample revealed MTB cells with bullet-shaped magnetosomes, and there were minor occurrences of cuboctahedral and hexagonal prismatic magnetosomes. Genome-resolved metagenomic analysis was performed to identify microorganisms that formed magnetosomes. A metagenome-assembled genome (MAG) affiliated with Nitrospinae had magnetosome genes such as mamA, mamI, mamM, mamP, and mamQ. Furthermore, a diagnostic feature of MTB genomes, such as magnetosome gene clusters (MGCs), including mamA, mamP, and mamQ, was also confirmed in the Nitrospinae-affiliated MAG. Two lines of evidence support the occurrence of MTB in a deep-sea, inactive hydrothermal vent environment.

Effect of oxic and anoxic conditions on intracellular storage of polyhydroxyalkanoate and polyphosphate in Magnetospirillum magneticum strain AMB-1

Magnetotactic bacteria (MTB) are microorganisms widely inhabiting the oxic-anoxic interface of aquatic environments. Beside biomineralizing magnetic nanocrystals, MTBs are able to sequester various chemical elements (e.g., carbon and phosphorus) for the biogenesis of intracellular granules, like polyhydroxyalkanoate (PHA) and polyphosphate (polyP), making them potentially important in biogeochemical cycling. Yet, the environmental controls of intracellular storage of carbon and phosphorus in MTB remain poorly understood. Here, we investigated the influence of oxic, anoxic and transient oxic-anoxic conditions on intracellular storage of PHA and polyP in Magnetospirillum magneticum strain AMB-1. In the incubations with oxygen, transmission electron microscopy revealed intercellular granules highly rich in carbon and phosphorus, which were further interpreted as PHA and polyP based on chemical and Energy-Dispersive X-ray spectroscopy analysis. Oxygen had a strong effect on PHA and polyP storage in AMB-1 cells, as PHA and polyP granules accounted for up to 47 ± 23% and 5.1 ± 1.7% of the cytoplasmic space, respectively, during continuous oxic conditions, while granules disappeared in anoxic incubations. Poly 3-hydroxybutyrate (PHB) and poly 3-hydroxyvalerate (PHV) accounted for 0.59 ± 0.66% and 0.0033 ± 0.0088% of dry cell weight, respectively, in anoxic incubations, while the values increased by a factor of 7 and 37 after oxygen was introduced. The results highlight a tight link between oxygen, carbon and phosphorus metabolisms in MTB, where favorable oxic growth conditions can lead to metabolic induction of polyP and PHA granule biogenesis.

Influence of protozoan grazing on magnetotactic bacteria on intracellular and extracellular iron content

Magnetotactic bacteria (MTB) ubiquitously inhabit the oxic-anoxic interface or anaerobic areas of aquatic environments. MTB biomineralize magnetite or greigite crystals and synthesize an organelle known as magnetosome. This intrinsic ability of MTB allows them to accumulate iron to levels 100-1000 times higher than those in non-magnetotactic bacteria (non-MTB). Therefore, MTB considerably contributes to the global iron cycle as primary iron suppliers in the aquatic environmental food chain. However, to the best of our knowledge, there have been no reports describing the effects of trophic interactions between MTB and their protist grazers on the iron distributions in MTB grazers and the extracellular milieu. Herein, we evaluated the effects of MTB grazing using a model species of protist (Tetrahymena pyriformis) and a model species of MTB (Magnetospirillum magneticum AMB-1). MTB-fed T. pyriformis exhibited a magnetic response and contained magnetite crystals in their vacuoles. Fluorescence imaging using a ferrous ion-specific fluorescent dye revealed that the cellular ferrous ion content was five times higher in MTB-fed T. pyriformis than in non-MTB grazers. Moreover, soluble iron concentrations in the spent media increased with time during MTB predation. This study provides experimental evidence to delineate the importance of trophic interactions of MTB on iron distributions.

Isolation, microscopic and magnetotactic characterization of Magnetospirillum moscoviense MS-24 from Banjosa Lake, Pakistan

At currently, approximately 70 species of magnetotactic bacteria have been identified; thus, there is an urgent need to identify more magnetotactic bacteria from diverse environmental sources with potential applications in industry and biotechnology. To the best of our knowledge, this is the first magnetotactic bacterial strain discovered in Pakistan. The first magnetotactic bacteria, Magnetospirillum moscoviense MS-24, was isolated from Banjosa Lake (Rawalakot), Pakistan, in the current investigation. Magnetospirillum moscoviense MS-24 was screened using the Racetrack method. The Magnetospirillum moscoviense MS-24 were physically characterised using Atomic Force Microscopy, High-Resolution Scanning Electron Microscopy, and Transmission Electron Microscopy. The current study used microscopy to illustrate the shape of bacteria and to find a very obvious chain of magnetosomes within the bacterial cell. The Magnetospirillum moscoviense MS-24 measured about 4 ± 0.04 µm in length and 600 ± 0.02 nm in diameter. The microfluidic chip experiments were also used to detect magnetotaxis behaviour in bacteria.

Insight into the metabolic potential and ecological function of a novel Magnetotactic Nitrospirota in coral reef habitat

Magnetotactic bacteria (MTB) within the Nitrospirota phylum play important roles in biogeochemical cycles due to their outstanding ability to biomineralize large amounts of magnetite magnetosomes and intracellular sulfur globules. For several decades, Nitrospirota MTB were believed to only live in freshwater or low-salinity environments. While this group have recently been found in marine sediments, their physiological features and ecological roles have remained unclear. In this study, we combine electron microscopy with genomics to characterize a novel population of Nitrospirota MTB in a coral reef area of the South China Sea. Both phylogenetic and genomic analyses revealed it as representative of a novel genus, named as Candidatus Magnetocorallium paracelense XS-1. The cells of XS-1 are small and vibrioid-shaped, and have bundled chains of bullet-shaped magnetite magnetosomes, sulfur globules, and cytoplasmic vacuole-like structures. Genomic analysis revealed that XS-1 has the potential to respire sulfate and nitrate, and utilize the Wood-Ljungdahl pathway for carbon fixation. XS-1 has versatile metabolic traits that make it different from freshwater Nitrospirota MTB, including Pta-ackA pathway, anaerobic sulfite reduction, and thiosulfate disproportionation. XS-1 also encodes both the cbb₃-type and the aa₃-type cytochrome c oxidases, which may function as respiratory energy-transducing enzymes under high oxygen conditions and anaerobic or microaerophilic conditions, respectively. XS-1 has multiple copies of circadian related genes in response to variability in coral reef habitat. Our results implied that XS-1 has a remarkable plasticity to adapt the environment and can play a beneficial role in coral reef ecosystems.

Azide click chemistry on magnetotactic bacteria: A versatile technique to attach a cargo

Adding biomolecules to living organisms and cells is the basis for creating living materials or biohybrids for robotic systems. Bioorthogonal chemistry allows covalently modifying biomolecules with functional groups not natively present under biological conditions and is therefore applicable to microorganisms and cells. Click chemistry is a biorthogonal chemistry approach that allows the study and manipulation of living entities. Incorporating the bioorthogonal click-chemistry handle, azide groups, into living microorganisms has been achieved by metabolic labeling, i.e., by culturing cells or organisms in a modified culture media having a specific natural molecular building block (e.g., amino acid, nucleotide, carbohydrate) modified with a tagged chemical analog. Here we explore the effect of the azide group incorporation into the magnetotactic bacteria Magnetospirillum gryphiswaldense (MSR-1) by adding a modified amino acid, 3-Azido-d-Alanine, during their cultivation. We show the existence of a concentration limit to effectively incorporate the azide group while maintaining the magnetic properties of the cells. We explore the use of this modification to explore the combination with versatile single-cell tagging methods.

Recovery and genome reconstruction of novel magnetotactic Elusimicrobiota from bog soil

Studying the minor part of the uncultivated microbial majority ("rare biosphere") is difficult even with modern culture-independent techniques. The enormity of microbial diversity creates particular challenges for investigating low-abundance microbial populations in soils. Strategies for selective sample enrichment to reduce community complexity can aid in studying the rare biosphere. Magnetotactic bacteria, apart from being a minor part of the microbial community, are also found in poorly studied bacterial phyla and certainly belong to a rare biosphere. The presence of intracellular magnetic crystals within magnetotactic bacteria allows for their significant enrichment using magnetic separation techniques for studies using a metagenomic approach. This work investigated the microbial diversity of a black bog soil and its magnetically enriched fraction. The poorly studied phylum representatives in the magnetic fraction were enriched compared to the original soil community. Two new magnetotactic species, Candidatus Liberimonas magnetica DUR002 and Candidatus Obscuribacterium magneticum DUR003, belonging to different classes of the relatively little-studied phylum Elusimicrobiota, were proposed. Their genomes contain clusters of magnetosome genes that differ from the previously described ones by the absence of genes encoding magnetochrome-containing proteins and the presence of unique Elusimicrobiota-specific genes, termed mae. The predicted obligately fermentative metabolism in DUR002 and lack of flagellar motility in the magnetotactic Elusimicrobiota broadens our understanding of the lifestyles of magnetotactic bacteria and raises new questions about the evolutionary advantages of magnetotaxis. The findings presented here increase our understanding of magnetotactic bacteria, soil microbial communities, and the rare biosphere.

Vanadate Bio-Detoxification Driven by Pyrrhotite with Secondary Mineral Formation

Vanadium(V) is a redox-sensitive heavy-metal contaminant whose environmental mobility is strongly influenced by pyrrhotite, a widely distributed iron sulfide mineral. However, relatively little is known about microbially mediated vanadate [V(V)] reduction characteristics driven by pyrrhotite and concomitant mineral dynamics in this process. This study demonstrated efficient V(V) bioreduction during 210 d of operation, with a lifespan about 10 times longer than abiotic control, especially in a stable period when the V(V) removal efficiency reached 44.1 ± 13.8%. Pyrrhotite oxidation coupled to V(V) reduction could be achieved by an enriched single autotroph (e.g., Thiobacillus and Thermomonas) independently. Autotrophs (e.g., Sulfurifustis) gained energy from pyrrhotite oxidation to synthesize organic intermediates, which were utilized by the heterotrophic V(V) reducing bacteria such as Anaerolinea, Bacillus, and Pseudomonas to sustain V(V) reduction. V(V) was reduced to insoluble tetravalent V, while pyrrhotite oxidation mainly produced Fe(III) and SO₄^2-. Secondary minerals including mackinawite (FeS) and greigite (Fe₃S₄) were produced synchronously, resulting from further transformations of Fe(III) and SO₄^2- by sulfate reducing bacteria (e.g., Desulfatiglans) and magnetotactic bacteria (e.g., Nitrospira). This study provides new insights into the biogeochemical behavior of V under pyrrhotite effects and reveals the previously overlooked mineralogical dynamics in V(V) reduction bioprocesses driven by Fe(II)-bearing minerals.

Large-Scale Cultivation of Magnetotactic Bacteria and the Optimism for Sustainable and Cheap Approaches in Nanotechnology

Magnetotactic bacteria (MTB), a diverse group of marine and freshwater microorganisms, have attracted the scientific community's attention since their discovery. These bacteria biomineralize ferrimagnetic nanocrystals, the magnetosomes, or biological magnetic nanoparticles (BMNs), in a single or multiple chain(s) within the cell. As a result, cells experience an optimized magnetic dipolar moment responsible for a passive alignment along the lines of the geomagnetic field. Advances in MTB cultivation and BMN isolation have contributed to the expansion of the biotechnological potential of MTB in recent decades. Several studies with mass-cultured MTB expanded the possibilities of using purified nanocrystals and whole cells in nano- and biotechnology. Freshwater MTB were primarily investigated in scaling up processes for the production of BMNs. However, marine MTB have the potential to overcome freshwater species applications due to the putative high efficiency of their BMNs in capturing molecules. Regarding the use of MTB or BMNs in different approaches, the application of BMNs in biomedicine remains the focus of most studies, but their application is not restricted to this field. In recent years, environment monitoring and recovery, engineering applications, wastewater treatment, and industrial processes have benefited from MTB-based biotechnologies. This review explores the advances in MTB large-scale cultivation and the consequent development of innovative tools or processes.

Tuning the Magnetic Response of Magnetospirillum magneticum by Changing the Culture Medium: A Straightforward Approach to Improve Their Hyperthermia Efficiency

Magnetotactic bacteria Magnetospirillum magneticum AMB-1 have been cultured using three different media: magnetic spirillum growth medium with Wolfe's mineral solution (MSGM + W), magnetic spirillum growth medium without Wolfe's mineral solution (MSGM - W), and flask standard medium (FSM). The influence of the culture medium on the structural, morphological, and magnetic characteristics of the magnetosome chains biosynthesized by these bacteria has been investigated by using transmission electron microscopy, X-ray absorption spectroscopy, and X-ray magnetic circular dichroism. All bacteria exhibit similar average size for magnetosomes, 40-45 nm, but FSM bacteria present slightly longer subchains. In MSGM + W bacteria, Co²⁺ ions present in the medium substitute Fe²⁺ ions in octahedral positions with a total Co doping around 4-5%. In addition, the magnetic response of these bacteria has been thoroughly studied as functions of both the temperature and the applied magnetic field. While MSGM - W and FSM bacteria exhibit similar magnetic behavior, in the case of MSGM + W, the incorporation of the Co ions affects the magnetic response, in particular suppressing the Verwey (∼105 K) and low temperature (∼40 K) transitions and increasing the coercivity and remanence. Moreover, simulations based on a Stoner-Wolhfarth model have allowed us to reproduce the experimentally obtained magnetization versus magnetic field loops, revealing clear changes in different anisotropy contributions for these bacteria depending on the employed culture medium. Finally, we have related how these magnetic changes affect their heating efficiency by using AC magnetometric measurements. The obtained AC hysteresis loops, measured with an AC magnetic field amplitude of up to 90 mT and a frequency, f, of 149 kHz, reveal the influence of the culture medium on the heating properties of these bacteria: below 35 mT, MSGM - W bacteria are the best heating mediators, but above 60 mT, FSM and MSGM + W bacteria give the best heating results, reaching a maximum heating efficiency or specific absorption rate (SAR) of SAR/f ≈ 12 W g^-1 kHz^-1.

Genetically Encoded Self-Assembling Protein Nanoparticles for the Targeted Delivery In Vitro and In Vivo

Targeted nanoparticles of different origins are considered as new-generation diagnostic and therapeutic tools. However, there are no targeted drug formulations within the composition of nanoparticles approved by the FDA for use in the clinic, which is associated with the insufficient effectiveness of the developed candidates, the difficulties of their biotechnological production, and inadequate batch-to-batch reproducibility. Targeted protein self-assembling nanoparticles circumvent this problem since proteins are encoded in DNA and the final protein product is produced in only one possible way. We believe that the combination of the endless biomedical potential of protein carriers as nanoparticles and the standardized protein purification protocols will make significant progress in "magic bullet" creation possible, bringing modern biomedicine to a new level. In this review, we are focused on the currently existing platforms for targeted self-assembling protein nanoparticles based on transferrin, lactoferrin, casein, lumazine synthase, albumin, ferritin, and encapsulin proteins, as well as on proteins from magnetosomes and virus-like particles. The applications of these self-assembling proteins for targeted delivery in vitro and in vivo are thoroughly discussed, including bioimaging applications and different therapeutic approaches, such as chemotherapy, gene delivery, and photodynamic and photothermal therapy. A critical assessment of these protein platforms' efficacy in biomedicine is provided and possible problems associated with their further development are described.

Exploring Microbial-Based Green Nanobiotechnology for Wastewater Remediation: A Sustainable Strategy

Water scarcity due to contamination of water resources with different inorganic and organic contaminants is one of the foremost global concerns. It is due to rapid industrialization, fast urbanization, and the low efficiency of traditional wastewater treatment strategies. Conventional water treatment strategies, including chemical precipitation, membrane filtration, coagulation, ion exchange, solvent extraction, adsorption, and photolysis, are based on adopting various nanomaterials (NMs) with a high surface area, including carbon NMs, polymers, metals-based, and metal oxides. However, significant bottlenecks are toxicity, cost, secondary contamination, size and space constraints, energy efficiency, prolonged time consumption, output efficiency, and scalability. On the contrary, green NMs fabricated using microorganisms emerge as cost-effective, eco-friendly, sustainable, safe, and efficient substitutes for these traditional strategies. This review summarizes the state-of-the-art microbial-assisted green NMs and strategies including microbial cells, magnetotactic bacteria (MTB), bio-augmentation and integrated bioreactors for removing an extensive range of water contaminants addressing the challenges associated with traditional strategies. Furthermore, a comparative analysis of the efficacies of microbe-assisted green NM-based water remediation strategy with the traditional practices in light of crucial factors like reusability, regeneration, removal efficiency, and adsorption capacity has been presented. The associated challenges, their alternate solutions, and the cutting-edge prospects of microbial-assisted green nanobiotechnology with the integration of advanced tools including internet-of-nano-things, cloud computing, and artificial intelligence have been discussed. This review opens a new window to assist future research dedicated to sustainable and green nanobiotechnology-based strategies for environmental remediation applications.

Continuous Production of Biogenic Magnetite Nanoparticles by the Marine Bacterium Magnetovibrio blakemorei Strain MV-1T with a Nitrous Oxide Injection Strategy

Magnetotactic bacteria (MTB) produce magnetosomes, which are membrane-embedded magnetic nanoparticles. Despite their technological applicability, the production of magnetite magnetosomes depends on the cultivation of MTB, which results in low yields. Thus, strategies for the large-scale cultivation of MTB need to be improved. Here, we describe a new approach for bioreactor cultivation of Magnetovibrio blakemorei strain MV-1^T. Firstly, a fed-batch with a supplementation of iron source and N₂O injection in 24-h pulses was established. After 120 h of cultivation, the production of magnetite reached 24.5 mg∙L⁻¹. The maximum productivity (16.8 mg∙L⁻¹∙day⁻¹) was reached between 48 and 72 h. However, the productivity and mean number of magnetosomes per cell decreased after 72 h. Therefore, continuous culture in the chemostat was established. In the continuous process, magnetite production and productivity were 27.1 mg∙L⁻¹ and 22.7 mg∙L⁻¹∙day⁻¹, respectively, at 120 h. This new approach prevented a decrease in magnetite production in comparison to the fed-batch strategy.

Key gene networks that control magnetosome biomineralization in magnetotactic bacteria

Magnetotactic bacteria (MTB) are a group of phylogenetically and morphologically diverse prokaryotes that have the capability of sensing Earth's magnetic field via nanocrystals of magnetic iron minerals. These crystals are enclosed within intracellular membranes or organelles known as magnetosomes and enable a sensing function known as magnetotaxis. Although MTB were discovered over half a century ago, the study of the magnetosome biogenesis and organization remains limited to a few cultured MTB strains. Here, we present an integrative genomic and phenomic analysis to investigate the genetic basis of magnetosome biomineralization in both cultured and uncultured strains from phylogenetically diverse MTB groups. The magnetosome gene contents/networks of strains are correlated with magnetic particle morphology and chain configuration. We propose a general model for gene networks that control/regulate magnetosome biogenesis and chain assembly in MTB systems.

The transcriptomic landscape of Magnetospirillum gryphiswaldense during magnetosome biomineralization

BACKGROUND

One of the most complex prokaryotic organelles are magnetosomes, which are formed by magnetotactic bacteria as sensors for navigation in the Earth's magnetic field. In the alphaproteobacterium Magnetospirillum gryphiswaldense magnetosomes consist of chains of magnetite crystals (Fe₃O₄) that under microoxic to anoxic conditions are biomineralized within membrane vesicles. To form such an intricate structure, the transcription of > 30 specific structural genes clustered within the genomic magnetosome island (MAI) has to be coordinated with the expression of an as-yet unknown number of auxiliary genes encoding several generic metabolic functions. However, their global regulation and transcriptional organization in response to anoxic conditions most favorable for magnetite biomineralization are still unclear.

RESULTS

Here, we compared transcriptional profiles of anaerobically grown magnetosome forming cells with those in which magnetosome biosynthesis has been suppressed by aerobic condition. Using whole transcriptome shotgun sequencing, we found that transcription of about 300 of the > 4300 genes was significantly enhanced during magnetosome formation. About 40 of the top upregulated genes are directly or indirectly linked to aerobic and anaerobic respiration (denitrification) or unknown functions. The mam and mms gene clusters, specifically controlling magnetosome biosynthesis, were highly transcribed, but constitutively expressed irrespective of the growth condition. By Cappable-sequencing, we show that the transcriptional complexity of both the MAI and the entire genome decreased under anaerobic conditions optimal for magnetosome formation. In addition, predominant promoter structures were highly similar to sigma factor σ⁷⁰ dependent promoters in other Alphaproteobacteria.

CONCLUSIONS

Our transcriptome-wide analysis revealed that magnetite biomineralization relies on a complex interplay between generic metabolic processes such as aerobic and anaerobic respiration, cellular redox control, and the biosynthesis of specific magnetosome structures. In addition, we provide insights into global regulatory features that have remained uncharacterized in the widely studied model organism M. gryphiswaldense, including a comprehensive dataset of newly annotated transcription start sites and genome-wide operon detection as a community resource (GEO Series accession number GSE197098).

McaA and McaB control the dynamic positioning of a bacterial magnetic organelle

Magnetotactic bacteria are a diverse group of microorganisms that use intracellular chains of ferrimagnetic nanocrystals, produced within magnetosome organelles, to align and navigate along the geomagnetic field. Several conserved genes for magnetosome formation have been described, but the mechanisms leading to distinct species-specific magnetosome chain configurations remain unclear. Here, we show that the fragmented nature of magnetosome chains in Magnetospirillum magneticum AMB-1 is controlled by genes mcaA and mcaB. McaA recognizes the positive curvature of the inner cell membrane, while McaB localizes to magnetosomes. Along with the MamK actin-like cytoskeleton, McaA and McaB create space for addition of new magnetosomes in between pre-existing magnetosomes. Phylogenetic analyses suggest that McaA and McaB homologs are widespread among magnetotactic bacteria and may represent an ancient strategy for magnetosome positioning.

Peptidoglycan as major binding motif for Uranium bioassociation on Magnetospirillum magneticum AMB-1 in contaminated waters

The U(VI) bioassociation on Magnetospirillum magneticum AMB-1 cells was investigated using a multidisciplinary approach combining wet chemistry, microscopy, and spectroscopy methods to provide deeper insight into the interaction of U(VI) with bioligands of Gram-negative bacteria for a better molecular understanding. Our findings suggest that the cell wall plays a prominent role in the bioassociation of U(VI). In time-dependent bioassociation studies, up to 95 % of the initial U(VI) was removed from the suspension and probably bound on the cell wall within the first hours due to the high removal capacity of predominantly alive Magnetospirillum magneticum AMB-1 cells. PARAFAC analysis of TRLFS data highlights that peptidoglycan is the most important ligand involved, showing a stable immobilization of U(VI) over a wide pH range with the formation of three characteristic species. In addition, in-situ ATR FT-IR reveals the predominant strong binding to carboxylic functionalities. At higher pH polynuclear species seem to play an important role. This comprehensive molecular study may initiate in future new remediation strategies on effective immobilization of U(VI). In combination with the magnetic properties of the bacteria, a simple technical water purification process could be realized not only for U(VI), but probably also for other heavy metals.

Atomic Details of Biomineralization Proteins Inspiring Protein Design and Reengineering for Functional Biominerals

Biominerals are extraordinary materials that provide organisms with a variety of functions to support life. The synthesis of biominerals and organization at the macroscopic level is a consequence of the interactions of these materials with proteins. The association of biominerals and proteins is very ancient and has sparked a wealth of research across biological, medical and material sciences. Calcium carbonate, hydroxyapatite, and silica represent widespread natural biominerals. The atomic details of the interface between macromolecules and these biominerals is very intriguing from a chemical perspective, considering the association of chemical entities that are structurally different. With this review I provide an overview of the available structural studies of biomineralization proteins, explored from the Protein Data Bank (wwPDB) archive and scientific literature, and of how these studies are inspiring the design and engineering of proteins able to synthesize novel biominerals. The progression of this review from classical template proteins to silica polymerization seeks to benefit researchers involved in various interdisciplinary aspects of a biomineralization project, who need background information and a quick update on advances in the field. Lessons learned from structural studies are exemplary and will guide new projects for the imaging of new hybrid biomineral/protein superstructures at the atomic level.

Detection of interphylum transfers of the magnetosome gene cluster in magnetotactic bacteria

Magnetosome synthesis in magnetotactic bacteria (MTB) is regarded as a very ancient evolutionary process that dates back to deep-branching phyla. Magnetotactic bacteria belonging to one of such phyla, Nitrospirota, contain the classical genes for the magnetosome synthesis (e.g., mam, mms) and man genes, which were considered to be specific for this group. However, the recent discovery of man genes in MTB from the Thermodesulfobacteriota phylum has raised several questions about the inheritance of these genes in MTB. In this work, three new man genes containing MTB genomes affiliated with Nitrospirota and Thermodesulfobacteriota, were obtained. By applying reconciliation with these and the previously published MTB genomes, we demonstrate that the last common ancestor of all Nitrospirota was most likely not magnetotactic as assumed previously. Instead, our findings suggest that the genes for magnetosome synthesis were transmitted to the phylum Nitrospirota by horizontal gene transfer (HGT), which is the first case of the interphylum transfer of magnetosome genes detected to date. Furthermore, we provide evidence for the HGT of magnetosome genes from the Magnetobacteriaceae to the Dissulfurispiraceae family within Nitrospirota. Thus, our results imply a more significant role of HGT in the MTB evolution than deemed before and challenge the hypothesis of the ancient origin of magnetosome synthesis.

Identification of sulfate-reducing magnetotactic bacteria via a group-specific 16S rDNA primer and correlative fluorescence and electron microscopy: strategy for culture-independent study

Magnetotactic bacteria (MTB) biomineralize intracellular magnetic nanocrystals and swim along geomagnetic field lines. While few axenic MTB cultures exist, living cells can be separated magnetically from natural environments for analysis. The bacterial universal 27F/1492R primer pair has been used widely to amplify nearly full-length 16S rRNA genes and to provide phylogenetic portraits of MTB communities. However, incomplete coverage and amplification biases inevitably prevent detection of some phylogenetically specific or non-abundant MTB. Here, we propose a new formulation of the upstream 390F primer that we combined with the downstream 1492R primer to specifically amplify 1,100-bp 16S rRNA gene sequences of sulfate-reducing MTB in freshwater sediments from Lake Weiyanghu, Xi'an, northwestern China. With correlative fluorescence in situ hybridization and scanning/transmission electron microscopy, three novel MTB strains (WYHR-2, WYHR-3, and WYHR-4) from the Desulfobacterota phylum were identified phylogenetically and structurally at the single cell level. Strain WYHR-2 produces bullet-shaped magnetosome magnetite, while the other two strains produce both cubic/prismatic greigite and bullet-shaped magnetite. Our results expand knowledge of bacterial diversity and magnetosome biomineralization of sulfate-reducing MTB. We also propose a general strategy for identifying and characterizing uncultured MTB from natural environments. This article is protected by copyright. All rights reserved.

Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications

Magnetotactic bacteria (MTB) are a group of phylogenetically diverse and morphologically varied microorganisms with a magnetoresponsive capability called magnetotaxis or microbial magnetoreception. MTB are a distinctive constituent of the microbiome of aquatic ecosystems because they use Earth's magnetic field to align themselves in a north or south facing direction and efficiently navigate to their favored microenvironments. They have been identified worldwide from diverse aquatic and waterlogged microbiomes, including freshwater, saline, brackish and marine ecosystems, and some extreme environments. MTB play important roles in the biogeochemical cycling of iron, sulphur, phosphorus, carbon and nitrogen in nature and have been recognized from in vitro cultures to sequester heavy metals like selenium, cadmium, and tellurium, which makes them prospective candidate organisms for aquatic pollution bioremediation. The role of MTB in environmental systems is not limited to their lifespan; after death, fossil magnetosomal magnetic nanoparticles (known as magnetofossils) are a promising proxy for recording paleoenvironmental change and geomagnetic field history. Here, we summarize the ecology, evolution, and environmental function of MTB and the paleoenvironmental implications of magnetofossils in light of recent discoveries.

Magnetic Anisotropy of Individual Nanomagnets Embedded in Biological Systems Determined by Axi-asymmetric X-ray Transmission Microscopy

Over the past few years, the use of nanomagnets in biomedical applications has increased. Among others, magnetic nanostructures can be used as diagnostic and therapeutic agents in cardiovascular diseases, to locally destroy cancer cells, to deliver drugs at specific positions, and to guide (and track) stem cells to damaged body locations in regenerative medicine and tissue engineering. All these applications rely on the magnetic properties of the nanomagnets which are mostly determined by their magnetic anisotropy. Despite its importance, the magnetic anisotropy of the individual magnetic nanostructures is unknown. Currently available magnetic sensitive microscopic methods are either limited in spatial resolution or in magnetic field strength or, more relevant, do not allow one to measure magnetic signals of nanomagnets embedded in biological systems. Hence, the use of nanomagnets in biomedical applications must rely on mean values obtained after averaging samples containing thousands of dissimilar entities. Here we present a hybrid experimental/theoretical method capable of working out the magnetic anisotropy constant and the magnetic easy axis of individual magnetic nanostructures embedded in biological systems. The method combines scanning transmission X-ray microscopy using an axi-asymmetric magnetic field with theoretical simulations based on the Stoner-Wohlfarth model. The validity of the method is demonstrated by determining the magnetic anisotropy constant and magnetic easy axis direction of 15 intracellular magnetite nanoparticles (50 nm in size) biosynthesized inside a magnetotactic bacterium.

Intracellular silicification by early-branching magnetotactic bacteria

Biosilicification-the formation of biological structures composed of silica-has a wide distribution among eukaryotes; it plays a major role in global biogeochemical cycles, and has driven the decline of dissolved silicon in the oceans through geological time. While it has long been thought that eukaryotes are the only organisms appreciably affecting the biogeochemical cycling of Si, the recent discoveries of silica transporter genes and marked silicon accumulation in bacteria suggest that prokaryotes may play an underappreciated role in the Si cycle, particularly in ancient times. Here, we report a previously unidentified magnetotactic bacterium that forms intracellular, amorphous silica globules. This bacterium, phylogenetically affiliated with the phylum Nitrospirota, belongs to a deep-branching group of magnetotactic bacteria that also forms intracellular magnetite magnetosomes and sulfur inclusions. This contribution reveals intracellularly controlled silicification within prokaryotes and suggests a previously unrecognized influence on the biogeochemical Si cycle that was operational during early Earth history.

Therapeutic Applications of Magnetotactic Bacteria and Magnetosomes: A Review Emphasizing on the Cancer Treatment

Magnetotactic bacteria (MTB) are aquatic microorganisms have the ability to biomineralize magnetosomes, which are membrane-enclosed magnetic nanoparticles. Magnetosomes are organized in a chain inside the MTB, allowing them to align with and traverse along the earth’s magnetic field. Magnetosomes have several potential applications for targeted cancer therapy when isolated from the MTB, including magnetic hyperthermia, localized medication delivery, and tumour monitoring. Magnetosomes features and properties for various applications outperform manufactured magnetic nanoparticles in several ways. Similarly, the entire MTB can be regarded as prospective agents for cancer treatment, thanks to their flagella’s ability to self-propel and the magnetosome chain’s ability to guide them. MTBs are conceptualized as nanobiots that can be guided and manipulated by external magnetic fields and are driven to hypoxic areas, such as tumor sites, while retaining the therapeutic and imaging characteristics of isolated magnetosomes. Furthermore, unlike most bacteria now being studied in clinical trials for cancer treatment, MTB are not pathogenic but might be modified to deliver and express certain cytotoxic chemicals. This review will assess the current and prospects of this burgeoning research field and the major obstacles that must be overcome before MTB can be successfully used in clinical treatments.

Construction of Recombinant Magnetospirillum Strains for Nitrate Removal from Wastewater Based on Magnetic Adsorption

Nitrate ion (NO3−) in wastewater is a major cause of pollution in aquatic environments worldwide. Magnetospirillum gryphiswaldense (MSR-1) has a complete dissimilatory denitrification pathway, converts NO3− in water into nitrogen (N2) and simultaneously removes ammonium ions (NH4+). We investigated and confirmed direct effects of regulatory protein factors Mg2046 and MgFnr on MSR-1 denitrification pathway by EMSAs and ChIP-qPCR assays. Corresponding mutant strains were constructed. Denitrification efficiency in synthetic wastewater medium during a 12-h cell growth period was significantly higher for mutant strain Δmgfnr (0.456 mmol·L−1·h−1) than for wild-type (0.362 mmol·L−1·h−1). Presence of magnetic particles (magnetosomes) in MSR-1 greatly facilitates collection and isolation of bacterial cells (and activated sludge) by addition of a magnetic field. The easy separation of magnetotactic bacteria, such as MSR-1 and Δmgfnr, from wastewater using magnetic fields is a unique feature that makes them promising candidates for practical application in wastewater treatment and sludge pretreatment.

New Insights for Biosensing: Lessons from Microbial Defense Systems

Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.

A new gene family diagnostic for intracellular biomineralization of amorphous Ca-carbonates by cyanobacteria

Cyanobacteria have massively contributed to carbonate deposition over the geological history. They are traditionally thought to biomineralize CaCO3 extracellularly as an indirect byproduct of photosynthesis. However, the recent discovery of freshwater cyanobacteria forming intracellular amorphous calcium carbonates (iACC) challenges this view. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and evolutionary history remain elusive. Here, using comparative genomics, we identify a new gene (ccyA) and protein family (calcyanin) possibly associated with cyanobacterial iACC biomineralization. Proteins of the calcyanin family are composed of a conserved C-terminal domain, which likely adopts an original fold, and a variable N-terminal domain whose structure allows differentiating 4 major types among the 35 known calcyanin homologs. Calcyanin lacks detectable full-length homologs with known function. The overexpression of ccyA in iACC-lacking cyanobacteria resulted in an increased intracellular Ca content. Moreover, ccyA presence was correlated and/or co-localized with genes involved in Ca or HCO3- transport and homeostasis, supporting the hypothesis of a functional role of calcyanin in iACC biomineralization. Whatever its function, ccyA appears as diagnostic of intracellular calcification in cyanobacteria. By searching for ccyA in publicly available genomes, we identified 13 additional cyanobacterial strains forming iACC, as confirmed by microscopy. This extends our knowledge about the phylogenetic and environmental distribution of cyanobacterial iACC biomineralization, especially with the detection of multicellular genera as well as a marine species. Moreover, ccyA was probably present in ancient cyanobacteria, with independent losses in various lineages that resulted in a broad but patchy distribution across modern cyanobacteria.

A protease-mediated switch regulates the growth of magnetosome organelles in Magnetospirillum magneticum

Biomineralization, the process by which elaborate three-dimensional structures are built out of organic and inorganic molecules, is central to health and survival of many organisms. In some magnetotactic bacteria, the growth of magnetosome membranes is closely correlated to the progression of mineral formation. However, the molecular mechanisms of such regulation are not clear. We show that the serine protease MamE links magnetosome membrane growth to the controlled production of magnetite nanoparticles through the processing of mineral-associated MamD protein. Our results indicate that membrane growth directly controls mineral growth and shed light on how an organelle’s size can determine its physiological output. Manipulation of the MamE pathway may also open the door for control of nanoparticle size in future biotechnological applications.

Magnetosomes are lipid-bound organelles that direct the biomineralization of magnetic nanoparticles in magnetotactic bacteria. Magnetosome membranes are not uniform in size and can grow in a biomineralization-dependent manner. However, the underlying mechanisms of magnetosome membrane growth regulation remain unclear. Using cryoelectron tomography, we systematically examined mutants with defects at various stages of magnetosome formation to identify factors involved in controlling membrane growth. We found that a conserved serine protease, MamE, plays a key role in magnetosome membrane growth regulation. When the protease activity of MamE is disrupted, magnetosome membrane growth is restricted, which, in turn, limits the size of the magnetite particles. Consistent with this finding, the upstream regulators of MamE protease activity, MamO and MamM, are also required for magnetosome membrane growth. We then used a combination of candidate and comparative proteomics approaches to identify Mms6 and MamD as two MamE substrates. Mms6 does not appear to participate in magnetosome membrane growth. However, in the absence of MamD, magnetosome membranes grow to a larger size than the wild type. Furthermore, when the cleavage of MamD by MamE protease is blocked, magnetosome membrane growth and biomineralization are severely inhibited, phenocopying the MamE protease-inactive mutant. We therefore propose that the growth of magnetosome membranes is controlled by a protease-mediated switch through processing of MamD. Overall, our work shows that, like many eukaryotic systems, bacteria control the growth and size of biominerals by manipulating the physical properties of intracellular organelles.