Magneto-aerotaxis in marine coccoid bacteria

Genomic and metabolic characterisation of a novel species Magnetominusculus dajiuhuensis DJH-1Ts sp. nov. from an acidic peatland

Magnetotactic bacteria (MTB) are recognised widely for their ability to synthesise intracellular magnetite (Fe3O4) and/or greigite (Fe3S4) nanocrystals and align with Earth's magnetic field. They are crucial for understanding prokaryotic organelle biogenesis. MTB members of the Nitrospirota phylum (previously known as the Nitrospirae phylum) are of interest due to their important ecological roles in the biogeochemical cycling of iron and sulphur. Here, we introduce Magnetominusculus dajiuhuensis DJH-1Ts, a newly discovered Nitrospirota MTB species that thrives in the acidic Dajiuhu Peatland of central China. By combining electron microscopy, 16S rRNA gene-based analysis and genome-resolved metagenomics, we elucidate its distinctive morphology, genomic features, and metabolic functions. The metagenome-assembled genome, assigned to the genus Magnetominusculus, family Magnetobacteriaceae, order Thermodesulfovibrionales, class Thermodesulfovibrionia according to the GTDB taxonomy, reveals an obligate anaerobe that lives in central China's largest wetland. We propose the formal name Magnetominusculus dajiuhuensis DJH-1Ts sp. nov., following the SeqCode system. Genomic and metabolic characterisation of this novel species suggests its potential role in nitrogen, sulphur, and carbon metabolism in aquatic biogeochemistry, particularly in peatlands. The genome of this novel strain indicates that it harnesses the Wood-Ljungdahl pathway for carbon fixation and acetate metabolism in anaerobic conditions, while its potential role in nitrogen cycling is characterised by denitrification and nitrogen fixation. It also participates in reduction of sulphate to sulphide, indicating a role in sulphur cycling in its ecological niche. Taken together, the discovery and characterisation of Magnetominusculus dajiuhuensis DJH-1Ts provide new insights into MTB diversity and ecological functions, particularly in peatland biogeochemistry.

Revealing the diversity of bacterial and archaeal organelles via comparative genomics

Like eukaryotes, bacteria and archaea rely on intracellular organelles to manage biological activities. Despite their prevalence, the understanding of the diversity of these organelles and the molecular mechanisms governing their function remain limited. In this review, we examine the potential of genomics and metagenomics to augment classical approaches for the study and discovery of microbial organelles. First, we highlight how the intimate interplay between model system studies and metagenomics have been critical in illuminating the function, diversity, and ancient evolutionary origins of the lipid-bounded magnetosome organelles of magnetotactic bacteria. We next discuss the central role of open genome databases and mechanistic studies in identification and characterization of protein-bounded encapsulin organelles with novel roles in sulfur metabolism and other cellular processes. Finally, we focus on the mostly uncultured Asgard archaea superphylum, whose metagenomes are challenging our views on organelle evolution and eukaryogenesis.

Synergistic mechanism of magneto-optical sensing mediated by magnetic response protein Amb0994 and LOV-like protein Amb2291 in Magnetospirillum magneticum AMB-1

Magnetotactic bacteria (MTB), known for their precision in navigating along magnetic fields, also exhibit light-sensitive behaviors. In Magnetospirillum magneticum AMB-1, the photoreceptor Amb2291 is involved in phototaxis regulation and magnetosome synthesis, particularly under oxidative stress. The magnetoreceptor Amb0994 modulates flagellar activity in response to magnetic field changes. Our study used a magneto-optical system to analyze the U-turn motility of north-seeking AMB-1 wild type (WT), amb2291 and amb0994 mutants under reversed magnetic fields and controlled light conditions. The results showed that WT strains consistently executed U-turns in response to magnetic fields, regardless of light variations. The diameters of U-turn of amb0994 mutant were smaller than those of the WT control. When illuminated with blue light in a direction opposite to the magnetic field, Δamb0994 exhibited slower U-turns with diameters similar to WT. In contrast, the Δamb2291 strain exhibited exaggerated U-turn movements under blue light, characterized by larger movement diameters and times compared to the WT, particularly whatever the light propagation direction is the same or opposite to the magnetic field in the initial state of motility. Gene expression analysis revealed that long-term exposure to blue light and magnetic fields led to a significant upregulation of amb2291 in Δamb0994 mutant strains and amb0994 in Δamb2291 mutant strains. These indicate a potential cooperative role of amb2291 and amb0994 in modulating bacterial motility under blue light. This research enhances our understanding of photoreception in MTB and its impact on magnetotaxis, shedding light on how environmental factors interact with microorganisms.

Isolation and cultivation of a novel freshwater magnetotactic coccus FCR-1 containing unchained magnetosomes

Magnetotactic bacteria are ubiquitous aquatic prokaryotes that have the ability to biomineralize magnetite (Fe3O4) and/or greigite (Fe3S4) nanoparticles called magnetosomes. Magnetotactic cocci belonging to the class "Ca. Magnetococcia" are most frequently identified in freshwater habitats, but remain uncultivated. Here, we report for the first time axenic cultivation of freshwater magnetotactic coccus FCR-1 isolated from Chichijima, Japan. Strain FCR-1 grows microaerophilically in a semi-solid gellan gum medium. We find that strain FCR-1 biomineralizes Fe3O4 nanoparticles, which are not chained, into a cell. Based on phylogenomic analysis, compared with strains of the class "Ca. Magnetococcia", strain FCR-1 represents a novel genus of candidate family "Ca. Magnetaquicoccaceae" within the class "Ca. Magnetococcia" and we tentatively name this novel genus "Ca. Magnetaquiglobus chichijimensis". Our isolate provides a promising tool for elucidating the functions of unchained magnetosomes, the global distribution of magnetotactic bacteria and the origin of magnetotaxis.

On the backward excursions in the free-swimming magnetotactic multicellular prokaryote 'Candidatus Magnetoglobus multicellularis'

Magnetotactic bacteria align to magnetic field lines while swimming in a behavior known as magnetotaxis. They are diverse phylogenetically and morphologically and include both unicellular and multicellular morphologies. The magnetotactic multicellular prokaryote (MMP) 'Candidatus Magnetoglobus multicellularis' has been extensively studied, even though it remains uncultured up to now. It swims back and forth along magnetic field lines, exhibiting a preferential swimming direction that is usually south-seeking, as described for most magnetotactic microorganisms from the Southern Hemisphere. In order to understand the effects of the magnetic field intensity on the backward excursions of 'Ca. M. multicellularis', we applied magnetic fields ranging from 0.09 to 3.4 mT and recorded their movements. Each microorganism was followed frame by frame generating position coordinates, which were used to calculate the frequency of reversal events, as well as the time, distance, and velocity. The velocities in forward movements before and after backward excursions are similar, but no relation was found with the velocity in backward movements. The shapes of the trajectories are distinct in forward and backward movements. In addition, the backward velocities are usually higher. The sharp changes in direction (approximately 180°) indicate that reversal of the flagella rotation direction is the probable mechanism for swimming backward. In conclusion, the backward excursions provide additional freedom of movement to the microorganism, especially when it is constrained by magnetic fields stronger than the Earth's. Backward movements integrate the 'Ca. M. multicellularis' behavioral toolbox, which includes also negative phototaxis, photokinesis, magnetotaxis and possibly helical klinotaxis.

Three-dimensional reconstruction of Magnetofaba australis strain IT-1: Magnetosome chain position with respect to flagella

Magnetotactic bacteria (MTB) are a broad and diverse group of Gram-negative prokaryotes that biomineralize magnetosomes, organelles composed of a magnetic nanocrystal of magnetite (Fe3O4) or greigite (Fe3S4) and enveloped by a biological membrane. Magnetosomes are arranged in one or more chains intracellularly, which impart a magnetic moment to the cell. These structures permit a passive orientation of the MTB with the geomagnetic field lines (GML), which, when associated with swimming propelled by flagella, originate a phenomenon called magneto-aerotaxis, an important life strategy in a chemical stratified environment. There is a classical model based on elongated cells as vibrios and rods that tries to explain the magneto-aerotaxis. Still, this model raises questions when applied to other morphologies other than elongated cells. Here, we observe the spatial disposition of magnetosomes, motility behavior, and influence of magneto-aerotaxis in Magnetofaba australis strain IT-1, an MTB that achieves high swimming speeds and has some peculiarity in its motility. The three-dimensional reconstruction showed that Mf. australis strain IT-1's magnetosome chain is misaligned with the swimming axis, which makes it impossible to use the classical model to explain magneto-aerotaxis in this MTB. Despite this, Mf. australis strain IT-1 was capable of swimming aligned to the GML. Also, this work studied the influence of the magnetosome and magneto-aerotaxis between populations of Mf. australis strain IT-1 with and without magnetosomes. Our results indicated that the magnetosome presence not only positively influences the movement in Mf.australis strain IT-1 but also can positively impact population growth in these MTB.

Combined response of polar magnetotaxis to oxygen and pH: Insights from hanging drop assays and microcosm experiments

Magnetotactic bacteria (MTB) combine passive alignment with the Earth magnetic field with a chemotactic response (magneto-chemotaxis) to reach their optimal living depth in chemically stratified environments. Current magneto-aerotaxis models fail to explain the occurrence of MTB far below the oxic-anoxic interface and the coexistence of MTB cells with opposite magnetotactic polarity at depths that are unrelated with the redox gradient. Here we propose a modified model of polar magnetotaxis which explains these observations, as well as the distinct concentration profiles and magnetotactic advantages of two types of MTB inhabiting a freshwater sediment: a group of unidentified cocci (MC), and a giant rod-shaped bacterium (MB) apparently identical to M. bavaricum (MB). This model assumed that magnetotactic polarity is set by a threshold mechanism in counter gradients of oxygen and a second group of repellents, with, in case of MB, includes H+ ions. MTB possessing this type of polar magnetotaxis can shuttle between two limit depths across the redox gradient (redox taxis), as previously postulated for M. bavaricum and other members of the Nitrospirota group. The magnetotaxis of MB and MC is predominantly dipolar whenever the presence of a magnetic field ensures a magnetotactic advantage. In addition, MB can overcome unfavorable magnetic field configurations through a temporal sensing mechanism. The availability of threshold and temporal sensing mechanisms of different substances can generate a rich variety of responses by different types of MTB, enabling them to exploit multiple ecological niches.

Escape motility of multicellular magnetotactic prokaryotes

Microorganisms often actively respond to multiple external stimuli to navigate toward their preferred niches. For example, unicellular magnetotactic bacteria integrate both oxygen sensory information and the Earth's geomagnetic field to help them locate anoxic conditions in a process known as magneto-aerotaxis. However, for multicellular magnetotactic prokaryotes (MMPs), the colonial structure of 4-16 cells places fundamental constraints on collective sensing, colony motility and directed swimming. To investigate how colonies navigate environments with multiple stimuli, we performed microfluidic experiments of MMPs with opposing magnetic fields and oxygen gradients. These experiments reveal unusual back-and-forth excursions called 'escape motility', in which colonies shuttle along magnetic field lines, punctuated by abrupt-yet highly coordinated-changes in collective ciliary beating. Through cell tracking and numerical simulations, we demonstrate that escape motility can arise through a simple magneto-aerotaxis mechanism, which includes the effect of magnetic torques and chemical sensing. At sufficiently high densities of MMPs, we observe the formation of dynamic crystal structures, whose stability is governed by the magnetic field strength and near-field hydrodynamic interactions. The results shed light on how some of the earliest multicellular organisms navigate complex physico-chemical landscapes.

Detecting life by behavior, the overlooked sensitivity of behavioral assays

Detecting life has driven research and exploration for centuries, but recent attempts to compile and generate a framework that summarizes life features, aimed to develop strategies for life detection missions beyond planet Earth, have disregarded a key life feature: behavior. Yet, some behaviors such as biomineralization or motility have occasionally been proposed as biosignatures to detect life. Here, we capitalize on a specific taxis' motility behavior, magnetotaxis, to experimentally provide insights in support of behavior as an unambiguous, sensitive biosignature, and magnetic forces as a prescreening option. Using a magnetotactic bacterial species, Magnetospirillum magneticum, we conducted a lab sensitivity experiment comparing PCR with the hanging drop behavioral assay, using a dilution series. The hanging drop behavioral assay visually shows the motility of MTB toward magnetic poles. Our findings reveal that the behavioral assay exhibits higher sensitivity in the detection of M. magneticum when compared to the established PCR protocol. While both methods present similar detection sensitivities at high concentrations, at ≥ 10-7 fold dilutions, the behavioral method proved more sensitive. The behavioral method can detect bacteria even when samples are diluted at 10-9. Comparable results were obtained with environmental samples from the Hula Valley. We propose behavioral cues as valuable biosignatures in the ongoing efforts of life detection in unexplored aquatic habitats on Earth and to stimulate and support discussions about how to detect extant life beyond Earth. Generic and robust behavioral assays can represent a methodological revolution.

Migration of surface-associated microbial communities in spaceflight habitats

Astronauts are spending longer periods locked up in ships or stations for scientific and exploration spatial missions. The International Space Station (ISS) has been inhabited continuously for more than 20 years and the duration of space stays by crews could lengthen with the objectives of human presence on the moon and Mars. If the environment of these space habitats is designed for the comfort of astronauts, it is also conducive to other forms of life such as embarked microorganisms. The latter, most often associated with surfaces in the form of biofilm, have been implicated in significant degradation of the functionality of pieces of equipment in space habitats. The most recent research suggests that microgravity could increase the persistence, resistance and virulence of pathogenic microorganisms detected in these communities, endangering the health of astronauts and potentially jeopardizing long-duration manned missions. In this review, we describe the mechanisms and dynamics of installation and propagation of these microbial communities associated with surfaces (spatial migration), as well as long-term processes of adaptation and evolution in these extreme environments (phenotypic and genetic migration), with special reference to human health. We also discuss the means of control envisaged to allow a lasting cohabitation between these vibrant microscopic passengers and the astronauts.

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.

Collective magnetotaxis of microbial holobionts is optimized by the three-dimensional organization and magnetic properties of ectosymbionts

Over the last few decades, symbiosis and the concept of holobiont-a host entity with a population of symbionts-have gained a central role in our understanding of life functioning and diversification. Regardless of the type of partner interactions, understanding how the biophysical properties of each individual symbiont and their assembly may generate collective behaviors at the holobiont scale remains a fundamental challenge. This is particularly intriguing in the case of the newly discovered magnetotactic holobionts (MHB) whose motility relies on a collective magnetotaxis (i.e., a magnetic field-assisted motility guided by a chemoaerotaxis system). This complex behavior raises many questions regarding how magnetic properties of symbionts determine holobiont magnetism and motility. Here, a suite of light-, electron- and X-ray-based microscopy techniques [including X-ray magnetic circular dichroism (XMCD)] reveals that symbionts optimize the motility, the ultrastructure, and the magnetic properties of MHBs from the microscale to the nanoscale. In the case of these magnetic symbionts, the magnetic moment transferred to the host cell is in excess (102 to 103 times stronger than free-living magnetotactic bacteria), well above the threshold for the host cell to gain a magnetotactic advantage. The surface organization of symbionts is explicitly presented herein, depicting bacterial membrane structures that ensure longitudinal alignment of cells. Magnetic dipole and nanocrystalline orientations of magnetosomes were also shown to be consistently oriented in the longitudinal direction, maximizing the magnetic moment of each symbiont. With an excessive magnetic moment given to the host cell, the benefit provided by magnetosome biomineralization beyond magnetotaxis can be questioned.

Live-Cell Fluorescence Imaging of Magnetosome Organelle for Magnetotaxis Motility

The assessment of intracellular dynamics is crucial for understanding the function and formation process of bacterial organelle, just as it is for the inquisition of their eukaryotic counterparts. The methods for imaging magnetosome organelles in a magnetotactic bacterial cell using live-cell fluorescence imaging by highly inclined and laminated optical sheet (HILO) microscopy are presented in this chapter. Furthermore, we introduce methods for pH imaging in magnetosome lumen as an application of fluorescence magnetosome imaging.

Precisely Navigated Biobot Swarms of Bacteria Magnetospirillum magneticum for Water Decontamination

Hybrid biological robots (biobots) prepared from living cells are at the forefront of micro-/nanomotor research due to their biocompatibility and versatility toward multiple applications. However, their precise maneuverability is essential for practical applications. Magnetotactic bacteria are hybrid biobots that produce magnetosome magnetite crystals, which are more stable than synthesized magnetite and can orient along the direction of earth's magnetic field. Herein, we used Magnetospirillum magneticum strain AMB-1 (M. magneticum AMB-1) for the effective removal of chlorpyrifos (an organophosphate pesticide) in various aqueous solutions by naturally binding with organic matter. Precision control of M. magneticum AMB-1 was achieved by applying a magnetic field. Under a programed clockwise magnetic field, M. magneticum AMB-1 exhibit swarm behavior and move in a circular direction. Consequently, we foresee that M. magneticum AMB-1 can be applied in various environments to remove and retrieve pollutants by directional control magnetic actuation.

Collective Behaviors of Active Matter Learning from Natural Taxes Across Scales

Taxis orientation is common in microorganisms, and it provides feasible strategies to operate active colloids as small-scale robots. Collective taxes involve numerous units that collectively perform taxis motion, whereby the collective cooperation between individuals enables the group to perform efficiently, adaptively, and robustly. Hence, analyzing and designing collectives is crucial for developing and advancing microswarm toward practical or clinical applications. In this review, natural taxis behaviors are categorized and synthetic microrobotic collectives are discussed as bio-inspired realizations, aiming at closing the gap between taxis strategies of living creatures and those of functional active microswarms. As collective behaviors emerge within a group, the global taxis to external stimuli guides the group to conduct overall tasks, whereas the local taxis between individuals induces synchronization and global patterns. By encoding the local orientations and programming the global stimuli, various paradigms can be introduced for coordinating and controlling such collective microrobots, from the viewpoints of fundamental science and practical applications. Therefore, by discussing the key points and difficulties associated with collective taxes of different paradigms, this review potentially offers insights into mimicking natural collective behaviors and constructing intelligent microrobotic systems for on-demand control and preassigned tasks.

Interaction between marine protists and bacteria results in magnetotaxis and iron recycling

Marine protists are eukaryotic trophic linkers that play a crucial role in iron recycling. Some marine protists have the ability of magnetotaxis, which they gain by consuming their ectosymbiotic bacteria. They graze and internalize the magnetotactic bacteria along with their magnetosome chains. Through egestion, marine protists avoid iron toxicity. Colloidal iron digestion by protists produces bioavailable iron for other marine organisms, passing to phytoplankton and mesozooplankton through the mesotrophic system. Indeed, ectosymbiotic bacteria and their protistan host form a microbial holobiont acting as an ecological unit. Some of the genetic mechanisms influencing the biosynthesis of magnetite in both prokaryotes and eukaryotes appear to be common. The recorded history of the magnetoreception ability of some marine protists goes back to the study by F.F. Torres de Araujo in 1986. After research over 35 years or more, it is safe to record that magnetotaxis in marine protists is yet to be fully understood, and might be similar to that of free-living magnetotactic bacteria. However, the attainment of magnetotaxis by protistan grazers through bacterivory and its role in iron recycling in the marine ecosystem is very interesting. The present article aims to provide an account of such interesting facts.

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.

Actuators for Implantable Devices: A Broad View

The choice of actuators dictates how an implantable biomedical device moves. Specifically, the concept of implantable robots consists of the three pillars: actuators, sensors, and powering. Robotic devices that require active motion are driven by a biocompatible actuator. Depending on the actuating mechanism, different types of actuators vary remarkably in strain/stress output, frequency, power consumption, and durability. Most reviews to date focus on specific type of actuating mechanism (electric, photonic, electrothermal, etc.) for biomedical applications. With a rapidly expanding library of novel actuators, however, the granular boundaries between subcategories turns the selection of actuators a laborious task, which can be particularly time-consuming to those unfamiliar with actuation. To offer a broad view, this study (1) showcases the recent advances in various types of actuating technologies that can be potentially implemented in vivo, (2) outlines technical advantages and the limitations of each type, and (3) provides use-specific suggestions on actuator choice for applications such as drug delivery, cardiovascular, and endoscopy implants.

Microbial diversity and geochemistry of groundwater impacted by steel slag leachates

To understand long-term impacts of steel slag material on aquifer geochemistry and microbial communities, we conducted four sampling campaigns in the Gier alluvial groundwater (Loire, France). In its northern part, the aquifer flows under a 200,000 m³ steel slag exhibiting high levels of chromium and molybdenum. Geochemical analyses of the water table revealed the existence of water masses with different chemical signatures. They allowed us to identify an area particularly contaminated by leachates from the slag heap, whatever the sampling period. Water samples from this area were compared to non-contaminated samples, with geochemical characteristics similar to the river samples. To follow changes in microbial communities, the V3-V4 region of 16 s rRNA gene was sequenced. Overall, we observed lower diversity indices in contaminated areas, with higher relative abundances of Verrucomicrobiota and Myxococcota phyla, while several Proteobacteria orders exhibited lower relative abundances. In particular, one single genus among the Verrucomicrobiota, Candidatus Omnitrophus, represented up to 36 % of total taxon abundance in areas affected by steel slag leachates. A large proportion of taxa identified in groundwater were also detected in the upstream river, indicating strong river-groundwater interactions. Our findings pave the way for future research work on C. Omnitrophus remediation capacities.

Periplasmic Bacterial Biomineralization of Copper Sulfide Nanoparticles

Metal sulfides are a common group of extracellular bacterial biominerals. However, only a few cases of intracellular biomineralization are reported in this group, mostly limited to greigite (Fe3 S4 ) in magnetotactic bacteria. Here, a previously unknown periplasmic biomineralization of copper sulfide produced by the magnetotactic bacterium Desulfamplus magnetovallimortis strain BW-1, a species known to mineralize greigite (Fe3 S4 ) and magnetite (Fe3 O4 ) in the cytoplasm is reported. BW-1 produces hundreds of spherical nanoparticles, composed of 1-2 nm substructures of a poorly crystalline hexagonal copper sulfide structure that remains in a thermodynamically unstable state. The particles appear to be surrounded by an organic matrix as found from staining and electron microscopy inspection. Differential proteomics suggests that periplasmic proteins, such as a DegP-like protein and a heavy metal-binding protein, could be involved in this biomineralization process. The unexpected periplasmic formation of copper sulfide nanoparticles in BW-1 reveals previously unknown possibilities for intracellular biomineralization that involves intriguing biological control and holds promise for biological metal recovery in times of copper shortage.

Fundidesulfovibrio magnetotacticus sp. nov., a sulphate-reducing magnetotactic bacterium, isolated from sediments and freshwater of a pond

A sulphate-reducing magnetotactic bacterium, designated strain FSS-1T, was isolated from sediments and freshwater of Suwa Pond located in Hidaka, Saitama, Japan. Strain FSS-1T was a motile, Gram-negative and curved rod-shaped bacterium that synthesizes bullet-shaped magnetite (Fe3O4) nanoparticles in each cell. Strain FSS-1T was able to grow in the range of pH 6.5–8.0 (optimum, pH 7.0), 22–34 °C (optimum, 28 °C) and with 0–8.0 g l−1 NaCl (optimum, 0–2.0 g l−1 NaCl). Strain FSS-1T grew well in the presence of 50 µM ferric quinate as an iron source. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The major menaquinone was MK-7 (H2). Strain FSS-1T contained desulfoviridin, cytochrome c 3 and catalase, but did not contain oxidase. Strain FSS-1T used fumarate, lactate, pyruvate, malate, formate/acetate, succinate, tartrate, ethanol, 1-propanol, peptone, soytone and yeast extract as electron donors, while the strain used sulphate, thiosulphate and fumarate as electron acceptors. Fumarate was fermented in the absence of electron acceptors. Analysis of the 16S rRNA gene sequence showed that strain FSS-1T is a member of the genus Fundidesulfovibrio . The gene sequence showed 96.7, 95.0, 92.0, 91.2 and 91.4% similarities to the most closely related members of the genera Fundidesulfovibrio putealis B7-43T, Fundidesulfovibrio butyratiphilus BSYT, Desulfolutivibrio sulfoxidireducens DSM 107105T, Desulfolutivibrio sulfodismutans ThAc01T and Solidesulfovibrio magneticus RS-1T, respectively. The DNA G+C content of strain FSS-1T was 67.5 mol%. The average nucleotide identity value between strain FSS-1T and F. putealis B7-43T was 80.7 %. Therefore, strain FSS-1T represents a novel species within the genus Fundidesulfovibrio , for which the name Fundidesulfovibrio magnetotacticus sp. nov. is proposed (=JCM 32405T=DSM 110007T).

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.

Direct measurement of the aerotactic response in a bacterial suspension

Aerotaxis is the ability of motile cells to navigate toward oxygen. A key question is the dependence of the aerotactic velocity with the local oxygen concentration c. Here we combine simultaneous bacteria tracking and local oxygen concentration measurements using Ruthenium encapsulated in micelles to characterize the aerotactic response of Burkholderia contaminans, a motile bacterium ubiquitous in the environment. In our experiments, an oxygen gradient is produced by the bacterial respiration in a sealed glass capillary permeable to oxygen at one end, producing a bacterial band traveling toward the oxygen source. We compute the aerotactic response χ(c) both at the population scale, from the drift velocity in the bacterial band, and at the bacterial scale, from the angular modulation of the run times. Both methods are consistent with a power-law χ∝c^{-2}, in good agreement with existing models based on the biochemistry of bacterial membrane receptors.

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 advantage in stable sediment by long-term observations of magnetotactic bacteria in Earth’s field, zero field and alternating field

Magnetotactic bacteria (MTB) rely on magnetotaxis to effectively reach their preferred living habitats, whereas experimental investigation of magnetotactic advantage in stable sediment is currently lacking. We studied two wild type MTB (cocci and rod-shaped M. bavaricum) in sedimentary environment under exposure to geomagnetic field in the laboratory, zero field and an alternating field whose polarity was switched every 24 hours. The mean concentration of M. bavaricum dropped by ~50% during 6 months in zero field, with no clear temporal trend suggesting an extinction. Cell numbers recovered to initial values within ~1.5 months after the Earth’s field was reset. Cocci displayed a larger temporal variability with no evident population changes in zero field. The alternating field experiment produced a moderate decrease of M. bavaricum concentrations and nearby extinction of cocci, confirming the active role of magnetotaxis in sediment and might point to a different magnetotactic mechanism for M. bavaricum which possibly benefited them to survive field reversals in geological periods. Our findings provide a first quantification of magnetotaxis advantage in sedimentary environment.

Biogeochemical Niche of Magnetotactic Cocci Capable of Sequestering Large Polyphosphate Inclusions in the Anoxic Layer of the Lake Pavin Water Column

Magnetotactic bacteria (MTB) are microorganisms thriving mostly at oxic–anoxic boundaries of aquatic habitats. MTB are efficient in biomineralising or sequestering diverse elements intracellularly, which makes them potentially important actors in biogeochemical cycles. Lake Pavin is a unique aqueous system populated by a wide diversity of MTB with two communities harbouring the capability to sequester not only iron under the form of magnetosomes but also phosphorus and magnesium under the form of polyphosphates, or calcium carbonates, respectively. MTB thrive in the water column of Lake Pavin over a few metres along strong redox and chemical gradients representing a series of different microenvironments. In this study, we investigate the relative abundance and the vertical stratification of the diverse populations of MTB in relation to environmental parameters, by using a new method coupling a precise sampling for geochemical analyses, MTB morphotype description, and in situ measurement of the physicochemical parameters. We assess the ultrastructure of MTB as a function of depth using light and electron microscopy. We evidence the biogeochemical niche of magnetotactic cocci, capable of sequestering large PolyP inclusions below the oxic–anoxic transition zone. Our results suggest a tight link between the S and P metabolisms of these bacteria and pave the way to better understand the implication of MTB for the P cycle in stratified environmental conditions.

Global Analysis of Biomineralization Genes in Magnetospirillum magneticum AMB-1

Magnetotactic bacteria (MTB) are a phylogenetically diverse group of bacteria remarkable for their ability to biomineralize magnetite (Fe₃O₄) or greigite (Fe₃S₄) in organelles called magnetosomes. The majority of genes required for magnetosome formation are encoded by a magnetosome gene island (MAI). Most previous genetic studies of MTB have focused on the MAI, using screens to identify key MAI genes or targeted genetics to isolate specific genes and their function in one specific growth condition. This is the first study that has taken an unbiased approach to look at many different growth conditions to reveal key genes both inside and outside the MAI. Here, we conducted random barcoded transposon mutagenesis (RB-TnSeq) in Magnetospirillum magneticum AMB-1. We generated a library of 184,710 unique strains in a wild-type background, generating ∼34 mutant strains for each gene. RB-TnSeq also allowed us to determine the essential gene set of AMB-1 under standard laboratory growth conditions. To pinpoint novel genes that are important for magnetosome formation, we subjected the library to magnetic selection screens under varied growth conditions. We compared biomineralization under standard growth conditions to biomineralization under high-iron and anaerobic conditions, respectively. Strains with transposon insertions in the MAI gene mamT had an exacerbated biomineralization defect under both high-iron and anaerobic conditions compared to standard conditions, adding to our knowledge of the role of MamT in magnetosome formation. Mutants in an ex-MAI gene, amb4151, are more magnetic than wild-type cells under anaerobic conditions. All three of these phenotypes were validated by creating a markerless deletion strain of the gene and evaluating with TEM imaging. Overall, our results indicate that growth conditions affect which genes are required for biomineralization and that some MAI genes may have more nuanced functions than was previously understood. IMPORTANCE Magnetotactic bacteria (MTB) are a group of bacteria that can form nano-sized crystals of magnetic minerals. MTB are likely an important part of their ecosystems, because they can account for up to a third of the microbial biomass in an aquatic habitat and consume large amounts of iron, potentially impacting the iron cycle. The ecology of MTB is relatively understudied; however, the cell biology and genetics of MTB have been studied for decades. Here, we leverage genetic studies of MTB to inform environmental studies. We expand the genetic toolset for studying MTB in the lab and identify novel genes, or functions of genes, that have an impact on biomineralization.

A Novel Magnetotactic Alphaproteobacterium Producing Intracellular Magnetite and Calcium-Bearing Minerals

Magnetotactic bacteria (MTB) are prokaryotes that form intracellular magnetite (Fe₃O₄) or greigite (Fe₃S₄) nanocrystals with tailored sizes, often in chain configurations. Such magnetic particles are each surrounded by a lipid bilayer membrane, called a magnetosome, and provide a model system for studying the formation and function of specialized internal structures in prokaryotes. Using fluorescence-coupled scanning electron microscopy, we identified a novel magnetotactic spirillum, XQGS-1, from freshwater Xingqinggong Lake, Xi'an City, Shaanxi Province, China. Phylogenetic analyses based on 16S rRNA gene sequences indicate that strain XQGS-1 represents a novel genus of the Alphaproteobacteria class in the Proteobacteria phylum. Transmission electron microscopy analyses reveal that strain XQGS-1 forms on average 17 ± 3 magnetite magnetosome particles with an ideal truncated octahedral morphology, with an average length and width of 88.3 ± 11.7 nm and 83.3 ± 11.0 nm, respectively. They are tightly organized into a single chain along the cell long axis close to the concave side of the cell. Intrachain magnetic interactions likely result in these large equidimensional magnetite crystals behaving as magnetically stable single-domain particles that enable bacterial magnetotaxis. Combined structural and chemical analyses demonstrate that XQGS-1 cells also biomineralize intracellular amorphous calcium phosphate (2 to 3 granules per cell; 90.5- ± 19.3-nm average size) and weakly crystalline calcium carbonate (2 to 3 granules per cell; 100.4- ± 21.4-nm average size) in addition to magnetite. Our results expand the taxonomic diversity of MTB and provide evidence for intracellular calcium phosphate biomineralization in MTB. IMPORTANCE Biomineralization is a widespread process in eukaryotes that form shells, teeth, or bones. It also occurs commonly in prokaryotes, resulting in more than 60 known minerals formed by different bacteria under wide-ranging conditions. Among them, magnetotactic bacteria (MTB) are remarkable because they might represent the earliest organisms that biomineralize intracellular magnetic iron minerals (i.e., magnetite [Fe₃O₄] or greigite [Fe₃S₄]). Here, we report a novel magnetotactic spirillum (XQGS-1) that is phylogenetically affiliated with the Alphaproteobacteria class. In addition to magnetite crystals, XQGS-1 cells form intracellular submicrometer calcium carbonate and calcium phosphate granules. This finding supports the view that MTB are also an important microbial group for intracellular calcium carbonate and calcium phosphate biomineralization.

Occurrence of south- and north-seeking multicellular magnetotactic prokaryotes in a coastal lagoon in the South Hemisphere

Magnetotactic bacteria (MTB) response to the magnetic field can be classified into north-seeking (NS) and south-seeking (SS), which usually depends on their inhabiting site in the North and South Hemisphere, respectively. However, uncommon inverted polarity was observed on both hemispheres. Here, we studied magnetotactic multicellular prokaryotes (MMPs) from a coastal lagoon in Brazil collected in April and August 2014. MMPs from the first sampling period presented both magnetotactic behaviors, while MMPs collected in August/2014 were only SS. Phylogenetic analysis based on the 16S rRNA coding gene showed that these organisms belong to the Deltaproteobacteria class. The 16S rRNA gene sequences varied among MMPs regardless of the sampling period, and similarity values were not related to the type of magnetotactic response presented by the microorganisms. Therefore, differences in the magnetotactic behavior might result from the physiological state of MMPs, the availability of resources, or the instability of the chemical gradient in the environment. This is the first report of NS magnetotactic behavior on MMPs from the South Hemisphere.

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.

Identification and Genomic Characterization of Two Previously Unknown Magnetotactic Nitrospirae

Magnetotactic bacteria (MTB) are a group of microbes that biomineralize membrane-bound, nanosized magnetite (Fe3O4), and/or greigite (Fe3S4) crystals in intracellular magnetic organelle magnetosomes. MTB belonging to the Nitrospirae phylum can form up to several hundreds of Fe3O4 magnetosome crystals and dozens of sulfur globules in a single cell. These MTB are widespread in aquatic environments and sometimes account for a significant proportion of microbial biomass near the oxycline, linking these lineages to the key steps of global iron and sulfur cycling. Despite their ecological and biogeochemical importance, our understanding of the diversity and ecophysiology of magnetotactic Nitrospirae is still very limited because this group of MTB remains unculturable. Here, we identify and characterize two previously unknown MTB populations within the Nitrospirae phylum through a combination of 16S rRNA gene-based and genome-resolved metagenomic analyses. These two MTB populations represent distinct morphotypes (rod-shaped and coccoid, designated as XYR, and XYC, respectively), and both form more than 100 bullet-shaped magnetosomal crystals per cell. High-quality draft genomes of XYR and XYC have been reconstructed, and they represent a novel species and a novel genus, respectively, according to their average amino-acid identity values with respect to available genomes. Accordingly, the names Candidatus Magnetobacterium cryptolimnobacter and Candidatus Magnetomicrobium cryptolimnococcus for XYR and XYC, respectively, were proposed. Further comparative genomic analyses of XYR, XYC, and previously reported magnetotactic Nitrospirae reveal the general metabolic potential of this MTB group in distinct microenvironments, including CO2 fixation, dissimilatory sulfate reduction, sulfide oxidation, nitrogen fixation, or denitrification processes. A remarkably conserved magnetosome gene cluster has been identified across Nitrospirae MTB genomes, indicating its putative important adaptive roles in these bacteria. Taken together, the present study provides novel insights into the phylogenomic diversity and ecophysiology of this intriguing, yet poorly understood MTB group.

Identification and characterization of magnetotactic Gammaproteobacteria from a salt evaporation pool, Bohai Bay, China

Magnetotactic bacteria (MTB) are phylogenetically diverse prokaryotes that can produce intracellular chain-assembled nanocrystals of magnetite (Fe₃ O₄ ) or greigite (Fe₃ S₄ ). Compared with their wide distribution in the Alpha-, Eta- and Delta-proteobacteria classes, few MTB strains have been identified in the Gammaproteobacteria class, resulting in limited knowledge of bacterial diversity and magnetosome biomineralization within this phylogenetic branch. Here, we identify two magnetotactic Gammaproteobacteria strains (tentatively named FZSR-1 and FZSR-2 respectively) from a salt evaporation pool in Bohai Bay, at the Fuzhou saltern, Dalian City, eastern China. Phylogenetic analysis indicates that strain FZSR-2 is the same species as strains SHHR-1 and SS-5, which were discovered previously from brackish and hypersaline environments respectively. Strain FZSR-1 represents a novel species. Compared with strains FZSR-2, SHHR-1 and SS-5 in which magnetite particles are assembled into a single chain, FZSR-1 cells form relatively narrower magnetite nanoparticles that are often organized into double chains. We find a good relationship between magnetite morphology within strains FZSR-2, SHHR-1 and SS-5 and the salinity of the environment in which they live. This study expands the bacterial diversity of magnetotactic Gammaproteobacteria and provides new insights into magnetosome biomineralization within magnetotactic Gammaproteobacteria.

Isolation and cultivation of a novel sulfate-reducing magnetotactic bacterium belonging to the genus Desulfovibrio

Magnetotactic bacteria (MTB) synthesize magnetosomes composed of membrane-enveloped magnetite (Fe₃O₄) and/or greigite (Fe₃S₄) nanoparticles in the cells. It is known that the magnetotactic Deltaproteobacteria are ubiquitous and inhabit worldwide in the sediments of freshwater and marine environments. Mostly known MTB belonging to the Deltaproteobacteria are dissimilatory sulfate-reducing bacteria that biomineralize bullet-shaped magnetite nanoparticles, but only a few axenic cultures have been obtained so far. Here, we report the isolation, cultivation and characterization of a dissimilatory sulfate-reducing magnetotactic bacterium, which we designate “strain FSS-1”. We found that the strain FSS-1 is a strict anaerobe and uses casamino acids as electron donors and sulfate as an electron acceptor to reduce sulfate to hydrogen sulfide. The strain FSS-1 produced bullet-shaped magnetite nanoparticles in the cells and responded to external magnetic fields. On the basis of 16S rRNA gene sequence analysis, the strain FSS-1 is a member of the genus Desulfovibrio, showing a 96.7% sequence similarity to Desulfovibrio putealis strain B7-43^T. Futhermore, the magnetosome gene cluster of strain FSS-1 was different from that of Desulfovibrio magneticus strain RS-1. Thus, the strain FSS-1 is considered to be a novel sulfate-reducing magnetotactic bacterium belonging to the genus Desulfovibrio.

Mass collection of magnetotactic bacteria from the permanently stratified ferruginous Lake Pavin, France

Obtaining high biomass yields of specific microorganisms for culture-independent approaches is a challenge faced by scientists studying organism's recalcitrant to laboratory conditions and culture. This difficulty is highly decreased when studying magnetotactic bacteria (MTB) since their unique behaviour allows their enrichment and purification from other microorganisms present in aquatic environments. Here, we use Lake Pavin, a permanently stratified lake in the French Massif Central, as a natural laboratory to optimize collection and concentration of MTB that thrive in the water column and sediments. A method is presented to separate MTB from highly abundant abiotic magnetic particles in the sediment of this crater lake. For the water column, different sampling approaches are compared such as in situ collection using a Niskin bottle and online pumping. By monitoring several physicochemical parameters of the water column, we identify the ecological niche where MTB live. Then, by focusing our sampling at the peak of MTB abundance, we show that the online pumping system is the most efficient for fast recovering of large volumes of water at a high spatial resolution, which is necessary considering the sharp physicochemical gradients observed in the water column. Taking advantage of aerotactic and magnetic MTB properties, we present an efficient method for MTB concentration from large volumes of water. Our methodology represents a first step for further multidisciplinary investigations of the diversity, metagenomic and ecology of MTB populations in Lake Pavin and elsewhere, as well as chemical and isotopic analyses of their magnetosomes.

Biodiversity of magnetotactic bacteria in the tropical marine environment of Singapore revealed by metagenomic analysis

Most studies on the diversity of magnetotactic bacteria (MTB) have been conducted on samples obtained from the Northern or the Southern hemispheres. The diversity of MTB in tropical Asia near the geo-equator, with a close-to-zero geomagnetic inclination, weak magnetic field and constantly high seawater temperature has never been explored. This study aims to decipher the diversity of MTB in the marine environment of Singapore through shotgun metagenomics. Although MTB has been acknowledged to be ubiquitous in aquatic environments, we did not observe magnetotactic behaviour in the samples. However, we detected the presence and determined the diversity of MTB through bioinformatic analyses. Metagenomic analysis suggested majority of the MTB in the seafloor sediments represents novel MTB taxa that cannot be classified at the species level. The relative abundance of MTB (~0.2-1.69%) in the samples collected from the marine environment of Singapore was found to be substantially lower than studies for other regions. In contrast to other studies, the genera Magnetovibrio and Desulfamplus, but not Magnetococcus, were the dominant MTB. Additionally, we recovered 3 MTB genomic bins that are unclassified at the species level, with Magnetovibrio blakemorei being the closest-associated genome. All the recovered genomic bins contain homologs of at least 5 of the 7 mam genes but lack homologs for mamI, a membrane protein suggested to take part in the magenetosome invagination. This study fills in the knowledge gap of MTB biodiversity in the tropical marine environment near the geo-equator. Our findings will facilitate future research efforts aiming to unravel the ecological roles of MTB in the tropical marine environments as well as to bioprospecting novel MTB that have been adapted to tropical marine environments for biotechnological applications.

The Biology and Evolution of Calcite and Aragonite Mineralization in Octocorallia

Octocorallia (class Anthozoa, phylum Cnidaria) is a group of calcifying corals displaying a wide diversity of mineral skeletons. This includes skeletal structures composed of different calcium carbonate polymorphs (aragonite and calcite). This represents a unique feature among anthozoans, as scleractinian corals (subclass Hexacorallia), main reef builders and focus of biomineralization research, are all characterized by an aragonite exoskeleton. From an evolutionary perspective, the presence of aragonitic skeletons in Octocorallia is puzzling as it is observed in very few species and has apparently originated during a Calcite sea (i.e., time interval characterized by calcite-inducing seawater conditions). Despite this, octocorals have been systematically overlooked in biomineralization studies. Here we review what is known about octocoral biomineralization, focusing on the evolutionary and biological processes that underlie calcite and aragonite formation. Although differences in research focus between octocorals and scleractinians are often mentioned, we highlight how strong variability also exists between different octocoral groups. Different main aspects of octocoral biomineralization have been in fact studied in a small set of species, including the (calcitic) gorgonian Leptogorgia virgulata and/or the precious coral Corallium rubrum. These include descriptions of calcifying cells (scleroblasts), calcium transport and chemistry of the calcification fluids. With the exception of few histological observations, no information on these features is available for aragonitic octocorals. Availability of sequencing data is also heterogeneous between groups, with no transcriptome or genome available, for instance, for the clade Calcaxonia. Although calcite represents by far the most common polymorph deposited by octocorals, we argue that studying aragonite-forming could provide insight on octocoral, and more generally anthozoan, biomineralization. First and foremost it would allow to compare calcification processes between octocoral groups, highlighting homologies and differences. Secondly, similarities (exoskeleton) between Heliopora and scleractinian skeletons, would provide further insight on which biomineralization features are driven by skeleton characteristics (shared by scleractinians and aragonitic octocorals) and those driven by taxonomy (shared by octocorals regardless of skeleton polymorph). Including the diversity of anthozoan mineralization strategies into biomineralization studies remains thus essential to comprehensively study how skeletons form and evolved within this ecologically important group of marine animals.

Expanding magnetic organelle biogenesis in the domain Bacteria

BACKGROUND

The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis.

RESULTS

Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria.

CONCLUSIONS

These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle. Video Abstract.

A Compass To Boost Navigation: Cell Biology of Bacterial Magnetotaxis

Magnetotactic bacteria are aquatic or sediment-dwelling microorganisms able to take advantage of the Earth's magnetic field for directed motility. The source of this amazing trait is magnetosomes, unique organelles used to synthesize single nanometer-sized crystals of magnetic iron minerals that are queued up to build an intracellular compass. Most of these microorganisms cannot be cultivated under controlled conditions, much less genetically engineered, with only few exceptions. However, two of the genetically amenable Magnetospirillum species have emerged as tractable model organisms to study magnetosome formation and magnetotaxis. Recently, much has been revealed about the process of magnetosome biogenesis and dedicated structures for magnetosome dynamics and positioning, which suggest an unexpected cellular intricacy of these organisms. In this minireview, we summarize new insights and place the molecular mechanisms of magnetosome formation in the context of the complex cell biology of Magnetospirillum spp. First, we provide an overview on magnetosome vesicle synthesis and magnetite biomineralization, followed by a discussion of the perceptions of dynamic organelle positioning and its biological implications, which highlight that magnetotactic bacteria have evolved sophisticated mechanisms to construct, incorporate, and inherit a unique navigational device. Finally, we discuss the impact of magnetotaxis on motility and its interconnection with chemotaxis, showing that magnetotactic bacteria are outstandingly adapted to lifestyle and habitat.

Limnobacter alexandrii sp. nov., a thiosulfate-oxidizing, heterotrophic and EPS-bearing Burkholderiaceae isolated from cultivable phycosphere microbiota of toxic Alexandrium catenella LZT09

A novel Gram-negative, aerobic, motile and short rod-shaped bacterium with exopolysaccharides production, designated as LZ-4^T, was isolated from cultivable phycosphere microbiota of harmful algal blooms-causing marine dinoflagellate Alexandrium catenella LZT09 which produces paralytic shellfish poisoning toxins. Strain LZ-4^T was able to use thiosulfate (optimum concentration 10 mM) as energy source for bacterial growth. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LZ-4^T belonged to the genus Limnobacter, showing high 16S rRNA gene sequences similarities with L. thiooxidans DSM 13612^T (99.4%), L. humi NBRC 11650^T (98.2%) and L. litoralis NBRC 105857^T (97.2%), respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between LZ-4^T and L. thiooxidans DSM 13612^T were 78.9 and 21.9%, respectively. Both values were far lower than the thresholds (95-96% for ANI and 70% for dDDH) generally accepted for new species delineation. The respiratory quinone of strain LZ-4^T was Q-8. The dominant cellular fatty acids were determined as summed feature 3 (C_16:1 ω6c/ω7c), summed feature 8 (C_18:1 ω6c/ω7c) and C_16:0. Polar lipids profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids and three unidentified polar lipids. The genomic DNA G+C content of strain LZ-4^T was 52.5 mol%. Based on polyphasic characterization, strain LZ-4^T represents a novel species of the genus Limnobacter, for which the name Limnobacter alexandrii sp. nov. is proposed. The type strain is LZ-4^T (=CCTCC AB 2019004^T  =KCTC 72281^T).

Bacteriophytochrome from Magnetospirillum magneticum affects phototactic behavior in response to light

Phytochromes are a class of photoreceptors found in plants and in some fungi, cyanobacteria, and photoautotrophic and heterotrophic bacteria. Although phytochromes have been structurally characterized in some bacteria, their biological and ecological roles in magnetotactic bacteria remain unexplored. Here, we describe the biochemical characterization of recombinant bacteriophytochrome (BphP) from magnetotactic bacteria Magnetospirillum magneticum AMB-1 (MmBphP). The recombinant MmBphP displays all the characteristic features, including the property of binding to biliverdin (BV), of a genuine phytochrome. Site-directed mutagenesis identified that cysteine-14 is important for chromophore covalent binding and photoreversibility. Arginine-240 and histidine-246 play key roles in binding to BV. The N-terminal photosensory core domain of MmBphP lacking the C-terminus found in other phytochromes is sufficient to exhibit the characteristic red/far-red-light-induced fast photoreversibility of phytochromes. Moreover, our results showed MmBphP is involved in the phototactic response, suggesting its conservative role as a stress protectant. This finding provided us a better understanding of the physiological function of this group of photoreceptors and photoresponse of magnetotactic bacteria.

Iron-biomineralizing organelle in magnetotactic bacteria: function, synthesis and preservation in ancient rock samples

Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that incorporate iron from their environment to synthesize intracellular nanoparticles of magnetite (Fe₃ O₄ ) or greigite (Fe₃ S₄ ) in a genetically controlled manner. Magnetite and greigite magnetic phases allow MTB to swim towards redox transition zones where they thrive. MTB may represent some of the oldest microorganisms capable of synthesizing minerals on Earth and have been proposed to significantly impact the iron biogeochemical cycle by immobilizing soluble iron into crystals that subsequently fossilize in sedimentary rocks. In the present article, we describe the distribution of MTB in the environment and discuss the possible function of the magnetite and greigite nanoparticles. We then provide an overview of the chemical mechanisms leading to iron mineralization in MTB. Finally, we update the methods used for the detection of MTB crystals in sedimentary rocks and present their occurrences in the geological record.

Active dipolar spheroids in shear flow and transverse field: Population splitting, cross-stream migration, and orientational pinning

We study the steady-state behavior of active, dipolar, Brownian spheroids in a planar channel subjected to an imposed Couette flow and an external transverse field, applied in the "downward" normal-to-flow direction. The field-induced torque on active spheroids (swimmers) is taken to be of magnetic form by assuming that they have a permanent magnetic dipole moment, pointing along their self-propulsion (swim) direction. Using a continuum approach, we show that a host of behaviors emerges over the parameter space spanned by the particle aspect ratio, self-propulsion and shear/field strengths, and the channel width. The cross-stream migration of the model swimmers is shown to involve a regime of linear response (quantified by a linear-response factor) in weak fields. For prolate swimmers, the weak-field behavior crosses over to a regime of full swimmer migration to the bottom half of the channel in strong fields. For oblate swimmers, a counterintuitive regime of reverse migration arises in intermediate fields, where a macroscopic fraction of swimmers reorient and swim to the top channel half at an acute "upward" angle relative to the field axis. The diverse behaviors reported here are analyzed based on the shear-induced population splitting (bimodality) of the swim orientation, giving two distinct, oppositely polarized, swimmer subpopulations (albeit very differently for prolate/oblate swimmers) in each channel half. In strong fields, swimmers of both types exhibit net upstream currents relative to the laboratory frame. The onsets of full migration and net upstream current depend on the aspect ratio, enabling efficient particle separation strategies in microfluidic setups.

Targeted drug delivery therapies inspired by natural taxes

A taxis is the movement responding to a stimulus of an organism. This behavior helps organisms to migrate, to find food or to avoid dangers. By mimicking and using natural taxes, many bio-inspired and bio-hybrid drug delivery systems have been synthesized. Under the guidance of physical and chemical stimuli, drug-loaded carriers are led to a target, for example tumors, then locally release the drug, inducing a therapeutic effect without influencing other parts of the body. On the other hand, for moving targets, for example metastasis cancer cells or bacteria, taking advantage of their taxes behavior is a solution to capture and to eliminate them. For instance, several traps and ecological niches have been fabricated to attract cancer cells by releasing chemokines. Cancer cells are then eliminated by drug loaded inside the trap, by radiotherapy focusing on the trap location or by simply removing the trap. Further research is needed to deeply understand the taxis behavior of organisms, which is essential to ameliorate the performance of taxes-inspired drug delivery application.

Bacteria as genetically programmable producers of bioactive natural products

Next to plants, bacteria account for most of the biomass on Earth. They are found everywhere, although certain species thrive only in specific ecological niches. These microorganisms biosynthesize a plethora of both primary and secondary metabolites, defined, respectively, as those required for the growth and maintenance of cellular functions and those not required for survival but offering a selective advantage for the producer under certain conditions. As a result, bacterial fermentation has long been used to manufacture valuable natural products of nutritional, agrochemical and pharmaceutical interest. The interactions of secondary metabolites with their biological targets have been optimized by millions of years of evolution and they are, thus, considered to be privileged chemical structures, not only for drug discovery. During the last two decades, functional genomics has allowed for an in-depth understanding of the underlying biosynthetic logic of secondary metabolites. This has, in turn, paved the way for the unprecedented use of bacteria as programmable biochemical workhorses. In this Review, we discuss the multifaceted use of bacteria as biological factories in diverse applications and highlight recent advances in targeted genetic engineering of bacteria for the production of valuable bioactive compounds. Emphasis is on current advances to access nature's abundance of natural products.

Flagella and Swimming Behavior of Marine Magnetotactic Bacteria

Marine environments are generally characterized by low bulk concentrations of nutrients that are susceptible to steady or intermittent motion driven by currents and local turbulence. Marine bacteria have therefore developed strategies, such as very fast-swimming and the exploitation of multiple directional sensing–response systems in order to efficiently migrate towards favorable places in nutrient gradients. The magnetotactic bacteria (MTB) even utilize Earth’s magnetic field to facilitate downward swimming into the oxic–anoxic interface, which is the most favorable place for their persistence and proliferation, in chemically stratified sediments or water columns. To ensure the desired flagella-propelled motility, marine MTBs have evolved an exquisite flagellar apparatus, and an extremely high number (tens of thousands) of flagella can be found on a single entity, displaying a complex polar, axial, bounce, and photosensitive magnetotactic behavior. In this review, we describe gene clusters, the flagellar apparatus architecture, and the swimming behavior of marine unicellular and multicellular magnetotactic bacteria. The physiological significance and mechanisms that govern these motions are discussed.