Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level.

BACKGROUND: Magnetotactic bacteria (MTB) are a unique group of microorganisms that sense and navigate through the geomagnetic field by biomineralizing magnetic nanoparticles. MTB from the phylum Nitrospirota (previously known as Nitrospirae) thrive in diverse aquatic ecosystems. They are of great interest due to their production of hundreds of magnetite (Fe3O4) magnetosome nanoparticles per cell, which far exceeds that of other MTB. The morphological, phylogenetic, and genomic diversity of Nitrospirota MTB have been extensively studied. However, the metabolism and ecophysiology of Nitrospirota MTB are largely unknown due to the lack of cultivation techniques. METHODS: Here, we established a method to link the morphological, genomic, and metabolic investigations of an uncultured Nitrospirota MTB population (named LHC-1) at the single-cell level using nanoscale secondary-ion mass spectrometry (NanoSIMS) in combination with rRNA-based in situ hybridization and target-specific mini-metagenomics. RESULTS: We magnetically separated LHC-1 from a freshwater lake and reconstructed the draft genome of LHC-1 using genome-resolved mini-metagenomics. We found that 10 LHC-1 cells were sufficient as a template to obtain a high-quality draft genome. Genomic analysis revealed that LHC-1 has the potential for CO2 fixation and NO3- reduction, which was further characterized at the single-cell level by combining stable-isotope incubations and NanoSIMS analyses over time. Additionally, the NanoSIMS results revealed specific element distributions in LHC-1, and that the heterogeneity of CO2 and NO3- metabolisms among different LHC-1 cells increased with incubation time. CONCLUSIONS: To our knowledge, this study provides the first metabolic measurements of individual Nitrospirota MTB cells to decipher their ecophysiological traits. The procedure constructed in this study provides a promising strategy to simultaneously investigate the morphology, genome, and ecophysiology of uncultured microbes in natural environments. Video Abstract.

Intrinsic and extrinsic determinants of conditional localization of Mms6 to magnetosome organelles in Magnetospirillum magneticum AMB-1.

Magnetotactic bacteria are a diverse group of microbes that use magnetic particles housed within intracellular lipid-bounded magnetosome organelles to guide navigation along geomagnetic fields. The development of magnetosomes and their magnetic crystals in Magnetospirillum magneticum AMB-1 requires the coordinated action of numerous proteins. Most proteins are thought to localize to magnetosomes during the initial stages of organelle biogenesis, regardless of environmental conditions. However, the magnetite-shaping protein Mms6 is only found in magnetosomes that contain magnetic particles, suggesting that it might conditionally localize after the formation of magnetosome membranes. The mechanisms for this unusual mode of localization to magnetosomes are unclear. Here, using pulse-chase labeling, we show that Mms6 translated under non-biomineralization conditions translocates to pre-formed magnetosomes when cells are shifted to biomineralizing conditions. Genes essential for magnetite production, namely mamE, mamM, and mamO, are necessary for Mms6 localization, whereas mamN inhibits Mms6 localization. MamD localization was also investigated and found to be controlled by similar cellular factors. The membrane localization of Mms6 is dependent on a glycine-leucine repeat region, while the N-terminal domain of Mms6 is necessary for retention in the cytosol and impacts conditional localization to magnetosomes. The N-terminal domain is also sufficient to impart conditional magnetosome localization to MmsF, altering its native constitutive magnetosome localization. Our work illuminates an alternative mode of protein localization to magnetosomes in which Mms6 and MamD are excluded from magnetosomes by MamN until biomineralization initiates, whereupon they translocate into magnetosome membranes to control the development of growing magnetite crystals.IMPORTANCEMagnetotactic bacteria (MTB) are a diverse group of bacteria that form magnetic nanoparticles surrounded by membranous organelles. MTB are widespread and serve as a model for bacterial organelle formation and biomineralization. Magnetosomes require a specific cohort of proteins to enable magnetite formation, but how those proteins are localized to magnetosome membranes is unclear. Here, we investigate protein localization using pulse-chase microscopy and find a system of protein coordination dependent on biomineralization-permissible conditions. In addition, our findings highlight a protein domain that alters the localization behavior of magnetosome proteins. Utilization of this protein domain may provide a synthetic route for conditional functionalization of magnetosomes for biotechnological applications.

Nitric oxide sensor NsrR is the key direct regulator of magnetosome formation and nitrogen metabolism in Magnetospirillum.

Nitric oxide (NO) plays an essential role as signaling molecule in regulation of eukaryotic biomineralization, but its role in prokaryotic biomineralization is unknown. Magnetospirillum gryphiswaldense MSR-1, a model strain for studies of prokaryotic biomineralization, has the unique ability to form magnetosomes (magnetic organelles). We demonstrate here that magnetosome biomineralization in MSR-1 requires the presence of NsrRMg (an NO sensor) and a certain level of NO. MSR-1 synthesizes endogenous NO via nitrification-denitrification pathway to activate magnetosome formation. NsrRMg was identified as a global transcriptional regulator that acts as a direct activator of magnetosome gene cluster (MGC) and nitrification genes but as a repressor of denitrification genes. Specific levels of NO modulate DNA-binding ability of NsrRMg to various target promoters, leading to enhancing expression of MGC genes, derepressing denitrification genes, and repressing nitrification genes. These regulatory functions help maintain appropriate endogenous NO level. This study identifies for the first time the key transcriptional regulator of major MGC genes, clarifies the molecular mechanisms underlying NsrR-mediated NO signal transduction in magnetosome formation, and provides a basis for a proposed model of the role of NO in the evolutionary origin of prokaryotic biomineralization processes.

Exploring the host range for genetic transfer of magnetic organelle biosynthesis.

Magnetosomes produced by magnetotactic bacteria have great potential for application in biotechnology and medicine due to their unique physicochemical properties and high biocompatibility. Attempts to transfer the genes for magnetosome biosynthesis into non-magnetic organisms have had mixed results. Here we report on a systematic study to identify key components needed for magnetosome biosynthesis after gene transfer. We transfer magnetosome genes to 25 proteobacterial hosts, generating seven new magnetosome-producing strains. We characterize the recombinant magnetosomes produced by these strains and demonstrate that denitrification and anaerobic photosynthesis are linked to the ability to synthesize magnetosomes upon the gene transfer. In addition, we show that the number of magnetosomes synthesized by a foreign host negatively correlates with the guanine-cytosine content difference between the host and the gene donor. Our findings have profound implications for the generation of magnetized living cells and the potential for transgenic biogenic magnetic nanoparticle production.

Effects of static magnetic field on the sulfate metabolic pathway involved in Magnetospirillum magneticum AMB-1 cell growth and magnetosome formation.

AIMS: Magnetotactic bacteria (MTB) can use their unique intracellular magnetosome organelles to swim along the Earth's magnetic field. They play important roles in the biogeochemical cycles of iron and sulfur. Previous studies have shown that the applied magnetic fields could affect the magnetosome formation and antioxidant defense systems in MTB. However, the molecular mechanisms by which magnetic fields affect MTB cells remain unclear. We aim to better understand the dark at 28°C-29°C for 20 h, as shownthe interactions between magnetic fields and cells, and the mechanism of MTB adaptation to magnetic field at molecular levels. METHODS AND RESULTS: We performed microbiological, transcriptomic, and genetic experiments to analyze the effects of a weak static magnetic field (SMF) exposure on the cell growth and magnetosome formation in the MTB strain Magnetospirillum magneticum AMB-1. The results showed that a 1.5 mT SMF significantly promoted the cell growth but reduced magnetosome formation in AMB-1, compared to the geomagnetic field. Transcriptomic analysis revealed decreased expression of genes primarily involved in the sulfate reduction pathway. Consistently, knockout mutant lacking adenylyl-sulfate kinase CysC did no more react to the SMF and the differences in growth and Cmag disappeared. Together with experimental findings of increased reactive oxidative species in the SMF-treated wild-type strain, we proposed that cysC, as a key gene, can participate in the cell growth and mineralization in AMB-1 by SMF regulation. CONCLUSIONS: This study suggests that the magnetic field exposure can trigger a bacterial oxidative stress response involved in AMB-1 growth and magnetosome mineralization by regulating the sulfur metabolism pathway. CysC may serve as a pivotal enzyme in mediating sulfur metabolism to synchronize the impact of SMF on both growth and magnetization of AMB-1.

Phylogenetics and biomineralization of a novel magnetotactic Gammaproteobacterium from a freshwater lake in Beijing, China.

Magnetotactic bacteria (MTB) have the remarkable capability of producing intracellularly membrane-enveloped magnetic nanocrystals (i.e. magnetosomes) and swimming along geomagnetic field lines. Despite more than 50 years of research, bacterial diversity and magnetosome biomineralization within MTB are relatively less known in the Gammaproteobacteria class than other groups. This is incompatible with the status of Gammaproteobacteria as the most diverse class of gram-negative bacteria with a number of ecologically important bacteria. Here, we identify a novel MTB strain YYHR-1 affiliated with the Gammaproteobacteria class of the Pseudomonadota phylum from a freshwater lake. In YYHR-1, most magnetosome crystals are organized into a long chain aligned along the cell long axis; unusually, a few small superparamagnetic crystals are located at the side of the chain, off the main chain axis. Micromagnetic simulations indicate that magnetostatic interactions among adjacent crystals within a chain reduce the Gibbs energy to enhance chain stability. Genomic analysis suggests that duplication of magnetosome gene clusters may result in off-chain magnetosomes formation. By integrating available genomic data from Gammaproteobacteria, the phylogenetic position of MTB in this class is reassigned here. Our new findings expand knowledge about MTB diversity and magnetosome biomineralization, and deepen understanding of the phylogenetics of the Gammaproteobacteria.

Experimental analysis of diverse actin-like proteins from various magnetotactic bacteria by functional expression in Magnetospirillum gryphiswaldense.

IMPORTANCE: To efficiently navigate within the geomagnetic field, magnetotactic bacteria (MTB) align their magnetosome organelles into chains, which are organized by the actin-like MamK protein. Although MamK is the most highly conserved magnetosome protein common to all MTB, its analysis has been confined to a small subgroup owing to the inaccessibility of most MTB. Our study takes advantage of a genetically tractable host where expression of diverse MamK orthologs together with a resurrected MamK LUCA and uncharacterized actin-like Mad28 proteins from deep-branching MTB resulted in gradual restoration of magnetosome chains in various mutants. Our results further indicate the existence of species-specific MamK interactors and shed light on the evolutionary relationships of one of the key proteins associated with bacterial magnetotaxis.

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.

Lipid membrane modulated control of magnetic nanoparticles within bacterial systems.

Bacterial magnetosomes synthesized by the magnetotactic bacterium Magnetospirillum magneticum are suitable for biomedical and biotechnological applications because of their high level of chemical purity of mineral with well-defined morphological features and a biocompatible lipid bilayer coating. However, utilizations of native magnetosomes are not sufficient for maximum effectiveness in many applications as the appropriate particle size differs. In this study, a method to control magnetosome particle size is developed for integration into targeted technological applications. The size and morphology of magnetosome crystals are highly regulated by the complex interactions of magnetosome synthesis-related genes; however, these interactions have not been fully elucidated. In contrast, previous studies have shown a positive correlation between vesicle and crystal sizes. Therefore, control of the magnetosome vesicle size is tuned by modifying the membrane lipid composition. Exogenous phospholipid synthesis pathways have been genetically introduced into M. magneticum. The experimental results show that these phospholipids altered the properties of the magnetosome membrane vesicles, which yielded larger magnetite crystal sizes. The genetic engineering approach presented in this study is shown to be useful for controlling magnetite crystal size without involving complex interactions of magnetosome synthesis-related genes.

Identifying magnetosome-associated genes in the extended CtrA regulon in Magnetospirillum magneticum AMB-1 using a combinational approach.

Magnetotactic bacteria (MTB) are worth studying because of magnetosome biomineralization. Magnetosome biogenesis in MTB is controlled by multiple genes known as magnetosome-associated genes. Recent advances in bioinformatics provide a unique opportunity for studying functions of magnetosome-associated genes and networks that they are involved in. Furthermore, various types of bioinformatics analyses can also help identify genes associated with magnetosome biogenesis. To predict novel magnetosome-associated genes in the extended CtrA regulon, we analyzed expression data of Magnetospirillum magneticum AMB-1 in the GSE35625 dataset in NCBI GEO. We identified 10 potential magnetosome-associated genes using a combinational approach of differential expression analysis, Gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analysis, protein-protein interaction network analysis and weighted gene co-expression network analysis. Meanwhile, we also discovered and compared two co-expression modules that most known magnetosome-associated genes belong to. Our comparison indicated the importance of energy on regulating co-expression module structures for magnetosome biogenesis. At the last stage of our research, we predicted at least four real magnetosome-associated genes out of 10 potential genes, based on a comparison of evolutionary trees between known and potential magnetosome-associated genes. Because of the discovery of common subtrees that the stressed species are enriched in, we proposed a hypothesis that multiple types of environmental stress can trigger magnetosome evolution in different waters, and therefore its evolution can recur at different times in various locations on earth. Overall, our research provides useful information for identifying new MTB species and understanding magnetosome biogenesis.

Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium.

Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.

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.

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 1100-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.

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.

A Magnetosome-Based Platform for Flow Biocatalysis.

Biocatalysis in flow reactor systems is of increasing importance for the transformation of the chemical industry. However, the necessary immobilization of biocatalysts remains a challenge. We here demonstrate that biogenic magnetic nanoparticles, so-called magnetosomes, represent an attractive alternative for the development of nanoscale particle formulations to enable high and stable conversion rates in biocatalytic flow processes. In addition to their intriguing material characteristics, such as high crystallinity, stable magnetic moments, and narrow particle size distribution, magnetosomes offer the unbeatable advantage over chemically synthesized nanoparticles that foreign protein "cargo" can be immobilized on the enveloping membrane via genetic engineering and thus, stably presented on the particle surface. To exploit these advantages, we develop a modular connector system in which abundant magnetosome membrane anchors are genetically fused with SpyCatcher coupling groups, allowing efficient covalent coupling with complementary SpyTag-functionalized proteins. The versatility of this approach is demonstrated by immobilizing a dimeric phenolic acid decarboxylase to SpyCatcher magnetosomes. The functionalized magnetosomes outperform similarly functionalized commercial particles by exhibiting stable substrate conversion during a 60 h period, with an average space-time yield of 49.2 mmol L-1 h-1. Overall, our results demonstrate that SpyCatcher magnetosomes significantly expand the genetic toolbox for particle surface functionalization and increase their application potential as nano-biocatalysts.

Magnetotactic bacteria: concepts, conundrums, and insights from a novel in situ approach using digital holographic microscopy (DHM).

Magnetotactic bacteria (MTB) are a diverse group of highly motile Gram-negative microorganisms with the common ability to orient along magnetic field lines, a behavior known as magnetotaxis. Ubiquitous in aquatic sediment environments, MTB are often microaerophilic and abundant at the oxic/anoxic interface. Magnetic field sensing is accomplished using intracellular, membrane-encased, iron-containing minerals known as magnetosomes. The chemistry, morphology and arrangement of magnetosomes differs substantially among different MTB. Although magnetic field sensing mechanisms, genetic bases and protein functions have been elucidated in select model organisms such as the Magnetospirillum strains and Desulfovibrio RS-1, not all findings are applicable to diverse clades of MTB. As the number of identified species has increased, it has become evident that many of the characteristics and mechanisms once presumed to be prototypical of MTB are in fact not universal. Here we present a general overview of the current state of MTB research for readers outside of the realm of prokaryotic research, focusing on recent discoveries, knowledge gaps and future directions. In addition, we report new insights acquired using holographic technology to observe and quantify microbial responses in magnetic fields that are earth-strength or weaker, providing a new ecophysiological approach to in situ MTB research.

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.

Conservation of magnetite biomineralization genes in all domains of life and implications for magnetic sensing.

Animals use geomagnetic fields for navigational cues, yet the sensory mechanism underlying magnetic perception remains poorly understood. One idea is that geomagnetic fields are physically transduced by magnetite crystals contained inside specialized receptor cells, but evidence for intracellular, biogenic magnetite in eukaryotes is scant. Certain bacteria produce magnetite crystals inside intracellular compartments, representing the most ancient form of biomineralization known and having evolved prior to emergence of the crown group of eukaryotes, raising the question of whether magnetite biomineralization in eukaryotes and prokaryotes might share a common evolutionary history. Here, we discover that salmonid olfactory epithelium contains magnetite crystals arranged in compact clusters and determine that genes differentially expressed in magnetic olfactory cells, contrasted to nonmagnetic olfactory cells, share ancestry with an ancient prokaryote magnetite biomineralization system, consistent with exaptation for use in eukaryotic magnetoreception. We also show that 11 prokaryote biomineralization genes are universally present among a diverse set of eukaryote taxa and that nine of those genes are present within the Asgard clade of archaea Lokiarchaeota that affiliates with eukaryotes in phylogenomic analysis. Consistent with deep homology, we present an evolutionary genetics hypothesis for magnetite formation among eukaryotes to motivate convergent approaches for examining magnetite-based magnetoreception, molecular origins of matrix-associated biomineralization processes, and eukaryogenesis.

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.