Dominating role of an unusual magnetotactic bacterium in the microaerobic zone of a freshwater sediment

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

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

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

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

Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes

The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (https://gtdb.ecogenomic.org). In the case of union of taxa, GTDB names were applied based on the priority of publication. The division of taxa or change in rank led to the formation of new Latin names above the rank of genus that were only made publicly available via the GTDB website without associated published taxonomic descriptions. This has sometimes led to confusion in the literature and databases. A number of the provisional GTDB names were later published in other studies, while many still lack authorships. To reduce further confusion, here we propose names and descriptions for 329 GTDB-defined prokaryotic taxa, 223 of which are suitable for validation under the International Code of Nomenclature of Prokaryotes (ICNP) and 49 under the Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode). For the latter, we designated 23 genomes as type material. An additional 57 taxa that do not currently satisfy the validation criteria of either code are proposed as Candidatus.

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.

First insights into the prokaryotic community structure of Lake Cote, Costa Rica: Influence on nutrient cycling

Prokaryotic diversity in lakes has been studied for many years mainly focusing on community structure and how the bacterial assemblages are driven by physicochemical conditions such as temperature, oxygen, and nutrients. However, little is known about how the composition and function of the prokaryotic community changes upon lake stratification. To elucidate this, we studied Lake Cote in Costa Rica determining prokaryotic diversity and community structure in conjunction with physicochemistry along vertical gradients during stratification and mixing periods. Of the parameters measured, ammonium, oxygen, and temperature, in that order, were the main determinants driving the variability in the prokaryotic community structure of the lake. Distinct stratification of Lake Cote occurred (March 2018) and the community diversity was compared to a period of complete mixing (March 2019). The microbial community analysis indicated that stratification significantly altered the bacterial composition in the epi-meta- and hypolimnion. During stratification, the Deltaproteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Euryarchaeota were dominant in the hypolimnion yet largely absent in surface layers. Among these taxa, strict or facultative anaerobic bacteria were likely contributing to the lake nitrogen biogeochemical cycling, consistent with measurements of inorganic nitrogen measurements and microbial functional abundance predictions. In general, during both sampling events, a higher abundance of Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and Cyanobacteria was found in the oxygenated layers. Lake Cote had a unique bacterial diversity, with 80% of Amplicon Sequence Variant (ASV) recovered similar to unclassified/uncultured strains and exhibits archetypal shallow lake physicochemical but not microbial fluctuations worthy of further investigation. This study provides an example of lake hydrodynamics impacts to microbial community and their function in Central American lakes with implications for other shallow, upland, and oligotrophic lake systems.

Biosensors and Drug Delivery in Oncotheranostics Using Inorganic Synthetic and Biogenic Magnetic Nanoparticles

Magnetic nanocarriers have attracted attention in translational oncology due to their ability to be employed both for tumor diagnostics and therapy. This review summarizes data on applications of synthetic and biogenic magnetic nanoparticles (MNPs) in oncological theranostics and related areas. The basics of both types of MNPs including synthesis approaches, structure, and physicochemical properties are discussed. The properties of synthetic MNPs and biogenic MNPs are compared with regard to their antitumor therapeutic efficiency, diagnostic potential, biocompatibility, and cellular toxicity. The comparative analysis demonstrates that both synthetic and biogenic MNPs could be efficiently used for cancer theranostics, including biosensorics and drug delivery. At the same time, reduced toxicity of biogenic particles was noted, which makes them advantageous for in vivo applications, such as drug delivery, or MRI imaging of tumors. Adaptability to surface modification based on natural biochemical processes is also noted, as well as good compatibility with tumor cells and proliferation in them. Advances in the bionanotechnology field should lead to the implementation of MNPs in clinical trials.

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.

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.

Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications

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

A Novel Isolate of Spherical Multicellular Magnetotactic Prokaryotes Has Two Magnetosome Gene Clusters and Synthesizes Both Magnetite and Greigite Crystals

Multicellular magnetotactic prokaryotes (MMPs) are a unique group of magnetotactic bacteria that are composed of 10–100 individual cells and show coordinated swimming along magnetic field lines. MMPs produce nanometer-sized magnetite (Fe3O4) and/or greigite (Fe3S4) crystals—termed magnetosomes. Two types of magnetosome gene cluster (MGC) that regulate biomineralization of magnetite and greigite have been found. Here, we describe a dominant spherical MMP (sMMP) species collected from the intertidal sediments of Jinsha Bay, in the South China Sea. The sMMPs were 4.78 ± 0.67 μm in diameter, comprised 14–40 cells helical symmetrically, and contained bullet-shaped magnetite and irregularly shaped greigite magnetosomes. Two sets of MGCs, one putatively related to magnetite biomineralization and the other to greigite biomineralization, were identified in the genome of the sMMP, and two sets of paralogous proteins (Mam and Mad) that may function separately and independently in magnetosome biomineralization were found. Phylogenetic analysis indicated that the sMMPs were affiliated with Deltaproteobacteria. This is the first direct report of two types of magnetosomes and two sets of MGCs being detected in the same sMMP. The study provides new insights into the mechanism of biomineralization of magnetosomes in MMPs, and the evolutionary origin of MGCs.

Comparative Genomics on Cultivated and Uncultivated Freshwater and Marine "Candidatus Manganitrophaceae" Species Implies Their Worldwide Reach in Manganese Chemolithoautotrophy

Chemolithoautotrophic manganese oxidation has long been theorized but only recently demonstrated in a bacterial coculture. The majority member of the coculture, “Candidatus Manganitrophus noduliformans,” is a distinct but not yet isolated lineage in the phylum Nitrospirota (Nitrospirae). Here, we established two additional MnCO₃-oxidizing cultures using inocula from Santa Barbara (California) and Boetsap (South Africa). Both cultures were dominated by strains of a new species, designated “Candidatus Manganitrophus morganii.” The next most abundant members differed in the available cultures, suggesting that while “Ca. Manganitrophus” species have not been isolated in pure culture, they may not require a specific syntrophic relationship with another species. Phylogeny of cultivated “Ca. Manganitrophus” and related metagenome-assembled genomes revealed a coherent taxonomic family, “Candidatus Manganitrophaceae,” from both freshwater and marine environments and distributed globally. Comparative genomic analyses support this family being Mn(II)-oxidizing chemolithoautotrophs. Among the 895 shared genes were a subset of those hypothesized for Mn(II) oxidation (Cyc2 and PCC_1) and oxygen reduction (TO_1 and TO_2) that could facilitate Mn(II) lithotrophy. An unusual, plausibly reverse complex 1 containing 2 additional pumping subunits was also shared by the family, as were genes for the reverse tricarboxylic acid carbon fixation cycle, which could enable Mn(II) autotrophy. All members of the family lacked genes for nitrification found in Nitrospira species. The results suggest that “Ca. Manganitrophaceae” share a core set of candidate genes for the newly discovered manganese-dependent chemolithoautotrophic lifestyle and likely have a broad, global distribution.

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.

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.

Rock-Hosted Subsurface Biofilms: Mineral Selectivity Drives Hotspots for Intraterrestrial Life

The continental deep subsurface is likely the largest reservoir of biofilm-based microbial biomass on Earth, but the role of mineral selectivity in regulating its distribution and diversity is unclear. Minerals can produce hotspots for intraterrestrial life by locally enhancing biofilm biomass. Metabolic transformations of minerals by subsurface biofilms may occur widely with the potential to significantly impact subsurface biogeochemical cycles. However, the degree of impact depends upon the amount of biofilm biomass and its relationship to host rock mineralogy, estimates that are currently loosely constrained to non-existent. Here, we use in situ cultivation of biofilms on native rocks and coupled microscopy/spectroscopy to constrain mineral selectivity by biofilms in a deep continental subsurface setting: the Deep Mine Microbial Observatory (DeMMO). Through hotspot analysis and spatial modeling approaches we find that mineral distributions, particularly those putatively metabolized by microbes, indeed drive biofilm distribution at DeMMO, and that bioleaching of pyrite may be a volumetrically important process influencing fluid geochemistry at this site when considered at the kilometer scale. Given the ubiquity of iron-bearing minerals at this site and globally, and the amount of biomass they can support, we posit that rock-hosted biofilms likely contribute significantly to subsurface biogeochemical cycles. As more data becomes available, future efforts to estimate biomass in the continental subsurface should incorporate host rock mineralogy.

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.

Lists of names of prokaryotic Candidatus taxa

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

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.

A species of magnetotactic deltaproteobacterium was detected at the highest abundance during an algal bloom

Magnetotactic bacteria (MTB) are a group of microorganisms that have the ability to synthesize intracellular magnetic crystals (magnetosomes). They prefer microaerobic or anaerobic aquatic sediments. Thus, there is growing interest in their ecological roles in various habitats. In this study we found co-occurrence of a large rod-shaped deltaproteobacterial magnetotactic bacterium (tentatively named LR-1) in the sediment of a brackish lagoon with algal bloom. Electron microscopy observations showed that they were ovoid to slightly curved rods having a mean length of 6.3 ± 1.1 μm and a mean width of 4.1 ± 0.4 μm. Each cell had a single polar flagellum. They contained hundreds of bullet-shaped intracellular magnetite magnetosomes. Phylogenetic analysis revealed that they were most closely related to Desulfamplus magnetovallimortis strain BW-1, and belonged to the Deltaproteobacteria. Our findings indicate that LR-1 may be a new species of MTB. We propose that deltaproteobacterial MTB may play an important role in iron cycling and so may represent a reservoir of iron, and be an indicator species for monitoring algal blooms in such eutrophic ecosystems. These observations provide new clues to the cultivation of magnetotactic Deltaproteobacteria and the control of algal blooms, although further studies are needed.

Single-cell determination of iron content in magnetotactic bacteria: implications for the iron biogeochemical cycle

Magnetotactic bacteria (MTB) are ubiquitous aquatic microorganisms that mineralize dissolved iron into intracellular magnetic crystals. After cell death, these crystals are trapped into sediments that remove iron from the soluble pool. MTB may significantly impact the iron biogeochemical cycle, especially in the ocean where dissolved iron limits nitrogen fixation and primary productivity. A thorough assessment of their impact has been hampered by a lack of methodology to measure the amount of, and variability in, their intracellular iron content. We quantified the iron mass contained in single MTB cells of Magnetospirillum magneticum strain AMB-1 using a time-resolved inductively coupled plasma-mass spectrometry methodology. Bacterial iron content depends on the external iron concentration, and reaches a maximum value of ~10^-6 ng of iron per cell. From these results, we calculated the flux of dissolved iron incorporation into environmental MTB populations and conclude that MTB may mineralize a significant fraction of dissolved iron into crystals.

Identification of novel species of marine magnetotactic bacteria affiliated with Nitrospirae phylum

Magnetotactic bacteria (MTB) are a group of Gram-negative bacteria characterized by synthesizing magnetosomes and swimming along geomagnetic field lines. Phylogenetically, they belong to different taxonomic lineages including Proteobacteria, Nitrospirae, Omnitrophica, Latescibacteria and Planctomycetes phyla on the phylogenetic tree. To date, six Nitrospirae MTB phylotypes have been identified from freshwater or low-salinity environments and described in the literature. Here, we report the identification of two Nitrospirae MTB phylotypes collected, for the first time, from the marine environment. Both have a spherical morphology with a cell size of ~ 5 μM and similar motility but are different colours (black-brown and ivory-white) under the optic microscope. They synthesized bullet-shaped iron-oxide magnetosomes that were arranged in multiple bundles of chains. Moreover, the cytoplasm of the black-brown Nitrospirae MTB contained sulphur inclusions that conferred on cells a rough, granular appearance. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that they are two novel species and cluster with the previously reported MTB affiliated with the phylum Nitrospirae, thus extending the distribution of Nitrospirae MTB from freshwater to the marine environment.

On the origin of microbial magnetoreception

A broad range of organisms, from prokaryotes to higher animals, have the ability to sense and utilize Earth's geomagnetic field—a behavior known as magnetoreception. Although our knowledge of the physiological mechanisms of magnetoreception has increased substantially over recent decades, the origin of this behavior remains a fundamental question in evolutionary biology. Despite this, there is growing evidence that magnetic iron mineral biosynthesis by prokaryotes may represent the earliest form of biogenic magnetic sensors on Earth. Here, we integrate new data from microbiology, geology and nanotechnology, and propose that initial biomineralization of intracellular iron nanoparticles in early life evolved as a mechanism for mitigating the toxicity of reactive oxygen species (ROS), as ultraviolet radiation and free-iron-generated ROS would have been a major environmental challenge for life on early Earth. This iron-based system could have later been co-opted as a magnetic sensor for magnetoreception in microorganisms, suggesting an origin of microbial magnetoreception as the result of the evolutionary process of exaptation.

Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution

The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe₃O₄) or greigite (Fe₃S₄) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and "Candidatus Lambdaproteobacteria" classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe₃O₄ and Fe₃S₄) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB.

Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus "Candidatus Sulfobium"

Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. Here we present a metaproteogenomic analysis of Nitrospirae bacterium Nbg-4 as a representative of this clade. Its genome was assembled from replicated metagenomes of rice paddy soil that was used to grow rice in the presence and absence of gypsum (CaSO₄·2H₂O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression of this pathway in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics. In addition, Nbg-4 encoded the full pathway of dissimilatory nitrate reduction to ammonia (DNRA), with expression of its first step being detected in bulk soil without gypsum amendment. The relative abundances of Nbg-4 were similar under both treatments, indicating that Nbg-4 maintained stable populations while shifting its energy metabolism. Whether Nbg-4 is a strict sulfate reducer or can couple sulfur oxidation to DNRA by operating the pathway of dissimilatory sulfate reduction in reverse could not be resolved. Further genome reconstruction revealed the potential to utilize butyrate, formate, H₂, or acetate as an electron donor; the Wood-Ljungdahl pathway was expressed under both treatments. Comparison to publicly available Nitrospirae genome bins revealed the pathway for dissimilatory sulfate reduction also in related Nitrospirae recovered from groundwater. Subsequent phylogenomics showed that such microorganisms form a novel genus within the Nitrospirae, with Nbg-4 as a representative species. Based on the widespread occurrence of this novel genus, we propose for Nbg-4 the name “Candidatus Sulfobium mesophilum,” gen. nov., sp. nov.

IMPORTANCE Rice paddies are indispensable for the food supply but are a major source of the greenhouse gas methane. If it were not counterbalanced by cryptic sulfur cycling, methane emission from rice paddy fields would be even higher. However, the microorganisms involved in this sulfur cycling are little understood. By using an environmental systems biology approach with Italian rice paddy soil, we could retrieve the population genome of a novel member of the phylum Nitrospirae. This microorganism encoded the full pathway of dissimilatory sulfate reduction and expressed it in anoxic paddy soil under sulfate-enriched conditions. Phylogenomics and comparison to the results of environmental surveys showed that such microorganisms are actually widespread in freshwater and marine environments. At the same time, they represent an undiscovered genus within the little-explored phylum Nitrospirae. Our results will be important for the design of enrichment strategies and postgenomic studies to further understanding of the contribution of these novel Nitrospirae spp. to the global sulfur cycle.

Morphological and cellular diversity of magnetotactic bacteria: A review

Magnetotactic bacteria (MTB) are getting much attention in the recent years due to the biomineralization in their magnetosomes (MS). MS are unique organelles that are bio-mineralized due to MTB. MS contains nanosized crystal minerals of magnetite or greigite covered by bilayer lipid membrane, which are originated from cytoplasmic membrane (CM). MS are organized as an ordered chain into the cell which acts as a miniature compass needle. Furthermore, the biodiversity of MTB and their distribution is principally linked with the characteristics and growths of the MS. MTB are often considered as a part of the bacterial biomass from all of the aquatic environments. There have been a lot of genes that control the functions of MTB by accumulating as clusters of genomes such as magnetosomes genomic island (MAI). Therefore, in the present review, the function of the genes and proteins has been highlighted, which are mainly associated with the construction and formation of MS. In addition, the biodiversity, morphology and cell biology of MTB is discussed in greater detail to understand the formation of MS crystals by MTB.

The symbiotic magnetic-sensing hypothesis: do Magnetotactic Bacteria underlie the magnetic sensing capability of animals?

The ability to sense Earth's magnetic field has evolved in various taxa. However, despite great efforts to find the 'magnetic-sensor' in vertebrates, the results of these scientific efforts remain inconclusive. A few decades ago, it was found that bacteria, known as magnetotactic bacteria (MTB), can move along a magnetic field using nanometric chain-like structures. Still, it is not fully clear why these bacteria evolved to have this capacity. Thus, while for MTB the 'magnetic-sensor' is known but the adaptive value is still under debate, for metazoa it is the other way around. In the absence of convincing evidence for any 'magnetic-sensor' in metazoan species sensitive to Earth's magnetic field, we hypothesize that a mutualism between these species and MTB provides one. In this relationship the host benefits from a magnetotactic capacity, while the bacteria benefit a hosting environment and dispersal. We provide support for this hypothesis using existing literature, demonstrating that by placing the MTB as the 'magnetic-sensor', previously contradictory results are now in agreement. We also propose plausible mechanisms and ways to test the hypothesis. If proven correct, this hypothesis would shed light on the forces driving both animal and bacteria magnetotactic abilities.

Diversity and ecology of and biomineralization by magnetotactic bacteria

Magnetotactic bacteria (MTB) biomineralize intracellular, membrane-bounded crystals of magnetite (Fe₃ O₄ ) and/or greigite (Fe₃ S₄ ) called magnetosomes. MTB play important roles in the geochemical cycling of iron, sulfur, nitrogen and carbon. Significantly, they also represent an intriguing model system not just for the study of microbial biomineralization but also for magnetoreception, prokaryotic organelle formation and microbial biogeography. Here we review current knowledge on the ecology of and biomineralization by MTB, with an emphasis on more recent reports of unexpected ecological and phylogenetic findings regarding MTB. In this study, we conducted a search of public metagenomic databases and identified six novel magnetosome gene cluster-containing genomic fragments affiliated with the Deltaproteobacteria and Gammaproteobacteria classes of the Proteobacteria phylum, the Nitrospirae phylum and the Planctomycetes phylum from the deep subseafloor, marine oxygen minimum zone, groundwater biofilm and estuary sediment, thereby extending our knowledge on the diversity and distribution of MTB as well deriving important information as to their ecophysiology. We point out that the increasing availability of sequence data will facilitate researchers to systematically explore the ecology and biomineralization of MTB even further.

Respiring cellular nano-magnets

Magnetotactic bacteria provide an interesting example for the biosynthesis of magnetic (Fe₃O₄ or Fe₃S₄) nanoparticles, synthesized through a process known as biologically controlled mineralization, resulting in complex monodispersed, and nanostructures with unique magnetic properties. In this work, we report a novel aerobic bacterial strain isolated from sludge of an oil refinery. Microscopic and staining analysis revealed that it was a gram positive rod with the capability to thrive in a medium (9K) supplemented, with Fe²⁺ ions at an acidic pH (~3.2). The magnetic behaviour of these cells was tested by their alignment towards a permanent magnet, and later on confirmed by magnetometry analysis. The X-ray diffraction studies proved the cellular biosynthesis of magnetite nanoparticles inside the bacteria. This novel, bio-nano-magnet, could pave the way for green synthesis of magnetic nanoparticles to be used in industrial and medical applications such as MRI, magnetic hyperthermia and ferrofluids.

Crystallizing the function of the magnetosome membrane mineralization protein Mms6

The literature on the magnetosome membrane (MM) protein, magnetosome membrane specific6 (Mms6), is reviewed. Mms6 is native to magnetotactic bacteria (MTB). These bacteria take up iron from solution and biomineralize magnetite nanoparticles within organelles called magnetosomes. Mms6 is a small protein embedded on the interior of the MM and was discovered tightly associated with the formed mineral. It has been the subject of intensive research as it is seen to control the formation of particles both in vivo and in vitro. Here, we compile, review and discuss the research detailing Mms6’s activity within the cell and in a range of chemical in vitro methods where Mms6 has a marked effect on the composition, size and distribution of synthetic particles, with approximately 21 nm in size for solution precipitations and approximately 90 nm for those formed on surfaces. Furthermore, we review and discuss recent work detailing the structure and function of Mms6. From the evidence, we propose a mechanism for its function as a specific magnetite nucleation protein and summaries the key features for this action: namely, self-assembly to display a charged surface for specific iron binding, with the curvature of the surfaces determining the particle size. We suggest these may aid design of biomimetic additives for future green nanoparticle production.

Single-Cell Resolution of Uncultured Magnetotactic Bacteria via Fluorescence-Coupled Electron Microscopy

Magnetotactic bacteria (MTB) form intracellular chain-assembled nanocrystals of magnetite or greigite termed magnetosomes. The characterization of magnetosome crystals requires electron microscopy due to their nanoscopic sizes. However, electron microscopy does not provide phylogenetic information for MTB. We have developed a strategy for the simultaneous and rapid phylogenetic and biomineralogical characterization of uncultured MTB at the single-cell level. It consists of four steps: (i) enrichment of MTB cells from an environmental sample, (ii) 16S rRNA gene sequencing of MTB, and (iii) fluorescence in situ hybridization analyses coordinated with (iv) transmission or scanning electron microscopy of the probe-hybridized cells. The application of this strategy identified a magnetotactic Gammaproteobacteria strain, SHHR-1, from brackish sediments collected from the Shihe River estuary in Qinhuangdao City, China. SHHR-1 magnetosomes are elongated prismatic magnetites which can be idealized as hexagonal prisms. Taxonomic groups of uncultured MTB were also identified in freshwater sediments from Lake Miyun in northern Beijing via this novel coordinated fluorescence and scanning electron microscopy method based on four group-specific rRNA-targeted probes. Our analyses revealed that major magnetotactic taxonomic groups can be accurately determined only with coordinated scanning electron microscopy observations on fluorescently labeled single cells due to limited group coverage and specificity for existing group-specific MTB fluorescence in situ hybridization (FISH) probes. Our reported strategy is simple and efficient, offers great promise toward investigating the diversity and biomineralization of MTB, and may also be applied to other functional groups of microorganisms.

IMPORTANCE Magnetotactic bacteria (MTB) are phylogenetically diverse and biomineralize morphologically diverse magnetic nanocrystals of magnetite or greigite in intracellular structures termed magnetosomes. However, many uncultured MTB strains have not been phylogenetically identified or structurally investigated at the single-cell level, which limits our comprehensive understanding of the diversity of MTB and their role in biomineralization. We developed a fluorescence-coupled electron microscopy method for the rapid phylogenetic and biomineralogical characterization of uncultured MTB at the single-cell level. Using this novel method, we successfully identified taxonomic groups of several uncultured MTB and one novel magnetotactic Gammaproteobacteria strain, SHHR-1, from natural environments. Our analyses further indicate that strain SHHR-1 forms elongated prismatic magnetites. Our findings provide a promising strategy for the rapid characterization of phylogenetic and biomineralogical properties of uncultured MTB at the single-cell level. Furthermore, due to its simplicity and generalized methodology, this strategy can also be useful in the study of the diversity and biomineralization properties of microbial taxa involved in other mineralization processes.

Magnetotactic Coccus Strain SHHC-1 Affiliated to Alphaproteobacteria Forms Octahedral Magnetite Magnetosomes

Magnetotactic bacteria (MTB) are morphologically and phylogenetically diverse prokaryotes. They can form intracellular chain-assembled magnetite (Fe₃O₄) or greigite (Fe₃S₄) nanocrystals each enveloped by a lipid bilayer membrane called a magnetosome. Magnetotactic cocci have been found to be the most abundant morphotypes of MTB in various aquatic environments. However, knowledge on magnetosome biomineralization within magnetotactic cocci remains elusive due to small number of strains that have been cultured. By using a coordinated fluorescence and scanning electron microscopy method, we discovered a unique magnetotactic coccus strain (tentatively named SHHC-1) in brackish sediments collected from the estuary of Shihe River in Qinhuangdao city, eastern China. It phylogenetically belongs to the Alphaproteobacteria class. Transmission electron microscopy analyses reveal that SHHC-1 cells formed many magnetite-type magnetosomes organized as two bundles in each cell. Each bundle contains two parallel chains with smaller magnetosomes generally located at the ends of each chain. Unlike most magnetotactic alphaproteobacteria that generally form magnetosomes with uniform crystal morphologies, SHHC-1 magnetosomes display a more diverse variety of crystal morphology even within a single cell. Most particles have rectangular and rhomboidal projections, whilst others are triangular, or irregular. High resolution transmission electron microscopy observations coupled with morphological modeling indicate an idealized model-elongated octahedral crystals, a form composed of eight {111} faces. Furthermore, twins, multiple twins and stack dislocations are frequently observed in the SHHC-1 magnetosomes. This suggests that biomineralization of strain SHHC-1 magnetosome might be less biologically controlled than other magnetotactic alphaproteobacteria. Alternatively, SHHC-1 is more sensitive to the unfavorable environments under which it lives, or a combination of both factors may have controlled the magnetosome biomineralization process within this unique MTB.

Origin of microbial biomineralization and magnetotaxis during the Archean

Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event. Magnetotaxis likely evolved due to environmental pressures conferring an evolutionary advantage to navigation via the geomagnetic field. Earth's dynamo must therefore have been sufficiently strong to sustain microbial magnetotaxis in the Archean, suggesting that magnetotaxis coevolved with the geodynamo over geological time.

Biomagnetic Recovery and Bioaccumulation of Selenium Granules in Magnetotactic Bacteria

Using microorganisms to remove waste and/or neutralize pollutants from contaminated water is attracting much attention due to the environmentally friendly nature of this methodology. However, cell recovery remains a bottleneck and a considerable challenge for the development of this process. Magnetotactic bacteria are a unique group of organisms that can be manipulated by an external magnetic field due to the presence of biogenic magnetite crystals formed within their cells. In this study, we demonstrated an account of accumulation and precipitation of amorphous elemental selenium nanoparticles within magnetotactic bacteria alongside and independent of magnetite crystal biomineralization when grown in a medium containing selenium oxyanion (SeO3 (2-)). Quantitative analysis shows that magnetotactic bacteria accumulate the largest amount of target molecules (Se) per cell compared with any other previously reported nonferrous metal/metalloid. For example, 2.4 and 174 times more Se is accumulated than Te taken up into cells and Cd(2+) adsorbed onto the cell surface, respectively. Crucially, the bacteria with high levels of Se accumulation were successfully recovered with an external magnetic field. The biomagnetic recovery and the effective accumulation of target elements demonstrate the potential for application in bioremediation of polluted water.

IMPORTANCE

The development of a technique for effective environmental water remediation is urgently required across the globe. A biological remediation process of waste removal and/or neutralization of pollutant from contaminated water using microorganisms has great potential, but cell recovery remains a bottleneck. Magnetotactic bacteria synthesize magnetic particles within their cells, which can be recovered by a magnetic field. Herein, we report an example of accumulation and precipitation of amorphous elemental selenium nanoparticles within magnetotactic bacteria independent of magnetic particle synthesis. The cells were able to accumulate the largest amount of Se compared to other foreign elements. More importantly, the Se-accumulating bacteria were successfully recovered with an external magnetic field. We believe magnetotactic bacteria confer unique advantages of biomagnetic cell recovery and of Se accumulation, providing a new and effective methodology for bioremediation of polluted water.

Isolation and characterization of Magnetospirillum from saline lagoon

Magnetotactic bacteria (MTB) are aquatic prokaryotes that orient themselves to earth's magnetic field with the help of intracellular organelle magnetosomes. Although many species of MTB have been identified, the isolation of MTB is a challenging task due to the lack of systematic isolation procedure and/or commercial media. In this study, we are reporting the isolation of magnetotactic spirillum from the Pulicat lagoon, India using a systematic and selective procedure. Sampling site was chosen on the basis of physicochemical properties of the ecosystem and the catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) analysis of sediment samples. In the current study, a combination of techniques including 'capillary racetrack' Purification and gradient cultivation resulted in the isolation of magnetotactic spirilla from aquatic sediments. Based on the 16S rRNA gene sequence analysis, the strain was identified as Magnetospirillum and was designated as Magnetospirillum sp. VITRJS1. The genes responsible for magnetosome formation (mamA, B, E, F, K, M, O, P, Q, T) were successfully detected using PCR amplification. The presence of cbbM gene confirmed that the isolate is chemolithoautotroph and utilises reduced sulphur as an electron source. Furthermore, magnetosomes extracted from VITRJS1 found to be cubo-octahedral in shape and 45 nm in size. Our results indicate that the systematic procedure using sediment analysis, CARD-FISH, and a combination of isolation methods enables the selective and rapid isolation of MTB from aquatic sediment sample.

Microscopic observation of magnetic bacteria in the magnetic field of a rotating permanent magnet

Magnetotactic bacteria are ubiquitous and can be found in both freshwater and marine environments. Due to intracellular chains of magnetic single domain particles, they behave like swimming compass needles. In external magnetic fields like the Earth's magnetic field, a torque is acting on the chain. This will cause the bacterium to be rotated and aligned with the external field. The swimming direction of magnetotactic bacteria can be controlled with external magnetic fields, which makes it convenient to study them under a light microscope. Usually, a special set of coils arranged around a light microscope is used to control the swimming magnetotactic bacteria. Here, we present a simple mechanical system with a permanent magnet, which produces a rotating magnetic field of nearly constant amplitude in the focal plane of a light microscope. The device is placed beside the light microscope and easily adaptable to almost any microscope and thus convenient for field experiments. To describe the trajectories qualitatively, a theoretical model of the trajectories is presented. This device can be used to control the swimming direction of magnetotactic bacteria and also for studying their magnetic and hydrodynamic properties.

Crystal growth of bullet-shaped magnetite in magnetotactic bacteria of the Nitrospirae phylum

Magnetotactic bacteria (MTB) are known to produce single-domain magnetite or greigite crystals within intracellular membrane organelles and to navigate along the Earth's magnetic field lines. MTB have been suggested as being one of the most ancient biomineralizing metabolisms on the Earth and they represent a fundamental model of intracellular biomineralization. Moreover, the determination of their specific crystallographic signature (e.g. structure and morphology) is essential for palaeoenvironmental and ancient-life studies. Yet, the mechanisms of MTB biomineralization remain poorly understood, although this process has been extensively studied in several cultured MTB strains in the Proteobacteria phylum. Here, we show a comprehensive transmission electron microscopy (TEM) study of magnetic and structural properties down to atomic scales on bullet-shaped magnetites produced by the uncultured strain MYR-1 belonging to the Nitrospirae phylum, a deeply branching phylogenetic MTB group. We observed a multiple-step crystal growth of MYR-1 magnetite: initial isotropic growth forming cubo-octahedral particles (less than approx. 40 nm), subsequent anisotropic growth and a systematic final elongation along [001] direction. During the crystal growth, one major {111} face is well developed and preserved at the larger basal end of the crystal. The basal {111} face appears to be terminated by a tetrahedral-octahedral-mixed iron surface, suggesting dimensional advantages for binding protein(s), which may template the crystallization of magnetite. This study offers new insights for understanding magnetite biomineralization within the Nitrospirae phylum.

Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes

While magnetosome biosynthesis within the magnetotactic Proteobacteria is increasingly well understood, much less is known about the genetic control within deep-branching phyla, which have a unique ultrastructure and biosynthesize up to several hundreds of bullet-shaped magnetite magnetosomes arranged in multiple bundles of chains, but have no cultured representatives. Recent metagenomic analysis identified magnetosome genes in the genus 'Candidatus Magnetobacterium' homologous to those in Proteobacteria. However, metagenomic analysis has been limited to highly abundant members of the community, and therefore only little is known about the magnetosome biosynthesis, ecophysiology and metabolic capacity in deep-branching MTB. Here we report the analysis of single-cell derived draft genomes of three deep-branching uncultivated MTB. Single-cell sorting followed by whole genome amplification generated draft genomes of Candidatus Magnetobacterium bavaricum and Candidatus Magnetoovum chiemensis CS-04 of the Nitrospirae phylum. Furthermore, we present the first, nearly complete draft genome of a magnetotactic representative from the candidate phylum Omnitrophica, tentatively named Candidatus Omnitrophus magneticus SKK-01. Besides key metabolic features consistent with a common chemolithoautotrophic lifestyle, we identified numerous, partly novel genes most likely involved in magnetosome biosynthesis of bullet-shaped magnetosomes and their arrangement in multiple bundles of chains.

Molecular identification of the occurrence of magnetotactic bacteria in fresh water sediments (Czech Republic)

Magnetotactic bacteria (MTB) are of considerable interest because of their importance in the manufacture of various bioinspired materials. In order to find out the status of magnetotactic bacteria at three different sediment in Czech Republic, samples collected from both standing and running freshwaters were subjected to molecular diversity analysis by using 16S rRNA gene approach. Total community DNA from sediment sample was isolated and used for PCR, cloning and sequence analysis. Of the 24 analyzed sequences, six clones are closely related to Magnetobacterium sp. affiliated with the Nitrospira phylum which showed the dominance of Magnetobacterium phylotypes in the sample. This study will provide useful insight about the community structure of MTB in this particular geographical region. However more detailed and specific studies are warranted in order to properly assess the community structure of MTB’s in fresh water sediments.

Novel co-enrichment method for isolation of magnetotactic bacteria

A novel co-enrichment technique was designed for enrichment of magnetotactic bacteria from soil, water, and sediments. Delayed addition of iron uptake inducer and the iron source proved amenable to induce magnetosome synthesis by MTB followed by their separation from consortium using magnetic flux. We successfully enriched and isolated both North seeking as well as South seeking magnetotactic bacteria from Lonar Lake (Buldhana), Moti Lake (Jalna), Ghanewadi Lake (Jalna), Ganesh Lake (Miraj), Rankala Lake (Kolhapur), and industrial metal-contaminated glaying soils (Jalna) and a soil (Karad), (MS, India) exposed to high-voltage electric current. The hanging drop preparations and growth under magnetic stress on low-agar media allowed conformation of magnetotactic behavior of the isolates. Both Gram positive and Gram negative MTB were isolated with diverse morphologies. South seeking population was more predominant. The soil inhabitants showed little dwelling property which was more prominent in case of aquatic inhabitants. The use of in situ pH and salt concentrations during enrichment and isolation found suited. The simultaneous growth of whole consortium in the system ensured the in situ simulation of microenvironment needful for proper growth of fastidious MTB.

Microbes: mini iron factories

Microbes have flourished in extreme habitats since beginning of the Earth and have played an important role in geological processes like weathering, mineralization, diagenesis, mineral formation and destruction. Biotic mineralization is one of the most fascinating examples of how microbes have been influencing geological processes. Iron oxidizing and reducing bacteria are capable of precipitating wide varieties of iron oxides (magnetite), carbonates (siderite) and sulphides (greigite) via controlled or induced mineralization processes. Microbes have also been considered to play an important role in the history of evolution of sedimentary rocks on Earth from the formation of banded iron formations during the Archean to modern biotic bog iron and ochre deposits. Here, we discuss the role that microbes have been playing in precipitation of iron and the role and importance of interdisciplinary studies in the field of geology and biology in solving some of the major geological mysteries.

Characterization of uncultured giant rod-shaped magnetotactic Gammaproteobacteria from a freshwater pond in Kanazawa, Japan

Magnetotactic bacteria (MTB) are widespread aquatic bacteria, and are a phylogenetically, physiologically and morphologically heterogeneous group, but they all have the ability to orientate and move along the geomagnetic field using intracellular magnetic organelles called magnetosomes. Isolation and cultivation of novel MTB are necessary for a comprehensive understanding of magnetosome formation and function in divergent MTB. In this study, we enriched a giant rod-shaped magnetotactic bacterium (strain GRS-1) from a freshwater pond in Kanazawa, Japan. Cells of strain GRS-1 were unusually large (~13×~8 µm). They swam in a helical trajectory towards the south pole of a bar magnet by means of a polar bundle of flagella. Another striking feature of GRS-1 was the presence of two distinct intracellular biomineralized structures: large electron-dense granules composed of calcium and long chains of magnetosomes that surround the large calcium granules. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that this strain belongs to the Gammaproteobacteria and represents a new genus of MTB.

Sub-micrometer-scale mapping of magnetite crystals and sulfur globules in magnetotactic bacteria using confocal Raman micro-spectrometry

The ferrimagnetic mineral magnetite Fe3O4 is biomineralized by magnetotactic microorganisms and a diverse range of animals. Here we demonstrate that confocal Raman microscopy can be used to visualize chains of magnetite crystals in magnetotactic bacteria, even though magnetite is a poor Raman scatterer and in bacteria occurs in typical grain sizes of only 35-120 nm, well below the diffraction-limited optical resolution. When using long integration times together with low laser power (<0.25 mW) to prevent laser induced damage of magnetite, we can identify and map magnetite by its characteristic Raman spectrum (303, 535, 665 cm(-1)) against a large autofluorescence background in our natural magnetotactic bacteria samples. While greigite (cubic Fe3S4; Raman lines of 253 and 351 cm(-1)) is often found in the Deltaproteobacteria class, it is not present in our samples. In intracellular sulfur globules of Candidatus Magnetobacterium bavaricum (Nitrospirae), we identified the sole presence of cyclo-octasulfur (S8: 151, 219, 467 cm(-1)), using green (532 nm), red (638 nm) and near-infrared excitation (785 nm). The Raman-spectra of phosphorous-rich intracellular accumulations point to orthophosphate in magnetic vibrios and to polyphosphate in magnetic cocci. Under green excitation, the cell envelopes are dominated by the resonant Raman lines of the heme cofactor of the b or c-type cytochrome, which can be used as a strong marker for label-free live-cell imaging of bacterial cytoplasmic membranes, as well as an indicator for the redox state.

Isolation and Characterization of a Novel Magnetotactic Bacterium From Iran: Iron Uptake and Producing Magnetic Nanoparticles in Alphaproteobacterium MTB-KTN90

Background:

Magnetotactic bacteria (MTB) have the ability to biomineralize unique intracellular magnetic nanosize particles. These bacteria and their magnetosomes are under special attraction because of their great useful potential in nano-biotechnological and biomedical applications. MTB are ubiquitous in aquatic environments, but their isolation and axenic cultivation in pure culture is very difficult and only a limited number of them have been isolated in pure culture.

Objectives:

The main goal of this study was screening, isolation and cultivation of a new strain of these fastidious bacteria in pure culture from Iran to use them and their magnetosomes.

Materials and Methods:

Thirty samples were collected from various aquatic habitats. Most important physicochemical environmental factors that are involved in growth of MTB in the microcosms were investigated using inductively coupled plasma atomic emission spectroscopy (ICP-AES), portable dissolved oxygen meter, etc. Capillary racetrack technique and magnetic separation were used to purify and enrich MTB. Various isolation media were simultaneously used for isolation of a new magnetotactic bacterium in pure culture. Two imaging techniques were used to visualize the characterizations and cell division: transmission electron microscopy (TEM) and field-emission scanning electron microscopy (FESEM). Polymerase chain reaction (PCR), ChromasPro software and MEGA5 were applied for sequence analysis of the 16S rRNA gene.

Results:

The results revealed a correlation of important physicochemical factors such as pH and iron with growth and blooms of these bacteria in the microcosms. New strain MTB-KTN90 was isolated in a modified isolation medium at microaerophilic zone from Anzali lagoon, Iran and cultured in a modified growth medium subsequently. The phylogenetic analysis showed that the strain belongs to Alphaproteobacteria. Growth and iron uptake studies indicated an important role by this bacterium in the iron biogeochemical cycle. For the first time, this paper introduced a cultured magnetotactic Alphaproteobacterium, able to synthesize magnetosomes in the temperatures above 30°C and reduce selenate oxyanion.

Conclusions:

This paper may serve as a guide to screening, isolation, and cultivation of more new MTB. The new isolated strain opens up good opportunities for biotechnological applications such as medicine to bioremediation processes due to its unique abilities.

Magneto-chemotaxis in sediment: first insights

Magnetotactic bacteria (MTB) use passive alignment with the Earth magnetic field as a mean to increase their navigation efficiency in horizontally stratified environments through what is known as magneto-aerotaxis (M-A). Current M-A models have been derived from MTB observations in aqueous environments, where a >80% alignment with inclined magnetic field lines produces a one-dimensional search for optimal living conditions. However, the mean magnetic alignment of MTB in their most widespread living environment, i.e. sediment, has been recently found to be <1%, greatly reducing or even eliminating the magnetotactic advantage deduced for the case of MTB in water. In order to understand the role of magnetotaxis for MTB populations living in sediment, we performed first M-A observations with lake sediment microcosms. Microcosm experiments were based on different combinations of (1) MTB position with respect to their preferred living depth (i.e. above, at, and below), and (2) magnetic field configurations (i.e. correctly and incorrectly polarized vertical fields, horizontal fields, and zero fields). Results suggest that polar magnetotaxis is more complex than implied by previous experiments, and revealed unexpected differences between two types of MTB living in the same sediment. Our main findings are: (1) all investigated MTB benefit of a clear magnetotactic advantage when they need to migrate over macroscopic distances for reaching their optimal living depth, (2) magnetotaxis is not used by all MTB under stationary, undisturbed conditions, (3) some MTB can rely only on chemotaxis for macroscopic vertical displacements in sediment while other cannot, and (4) some MTB use a fixed polar M-A mechanisms, while other can switch their M-A polarity, performing what can be considered as a mixed polar-axial M-A. These observations demonstrate that sedimentary M-A is controlled by complex mechanical, chemical, and temporal factors that are poorly reproduced in aqueous environments.