Comparative genomic analysis of magnetotactic bacteria from the Deltaproteobacteria provides new insights into magnetite and greigite magnetosome genes required for magnetotaxis

Ecology, diversity, and evolution of magnetotactic bacteria

Magnetotactic bacteria (MTB) are widespread, motile, diverse prokaryotes that biomineralize a unique organelle called the magnetosome. Magnetosomes consist of a nano-sized crystal of a magnetic iron mineral that is enveloped by a lipid bilayer membrane. In cells of almost all MTB, magnetosomes are organized as a well-ordered chain. The magnetosome chain causes the cell to behave like a motile, miniature compass needle where the cell aligns and swims parallel to magnetic field lines. MTB are found in almost all types of aquatic environments, where they can account for an important part of the bacterial biomass. The genes responsible for magnetosome biomineralization are organized as clusters in the genomes of MTB, in some as a magnetosome genomic island. The functions of a number of magnetosome genes and their associated proteins in magnetosome synthesis and construction of the magnetosome chain have now been elucidated. The origin of magnetotaxis appears to be monophyletic; that is, it developed in a common ancestor to all MTB, although horizontal gene transfer of magnetosome genes also appears to play a role in their distribution. The purpose of this review, based on recent progress in this field, is focused on the diversity and the ecology of the MTB and also the evolution and transfer of the molecular determinants involved in magnetosome formation.

Structure and evolution of the magnetochrome domains: no longer alone

Magnetotactic bacteria (MTB) can swim along Earth's magnetic field lines, thanks to the alignment of dedicated cytoplasmic organelles. These organelles, termed magnetosomes, are proteolipidic vesicles filled by a 35–120 nm crystal of either magnetite or greigite. The formation and alignment of magnetosomes are mediated by a group of specific genes, the mam genes, encoding the magnetosome-associated proteins. The whole process of magnetosome biogenesis can be divided into four sequential steps; (i) cytoplasmic membrane invagination, (ii) magnetosomes alignment, (iii) iron crystal nucleation and (iv) species-dependent mineral size and shape control. Since both magnetite and greigite are a mix of iron (III) and iron (II), iron redox state management within the magnetosome vesicle is a key issue. Recently, studies have started pointing out the importance of a MTB-specific c-type cytochrome domain found in several magnetosome-associated proteins (MamE, P, T, and X). This magnetochrome (MCR) domain is almost always found in tandem, and this tandem is either found alone (MamT), in combination with a PDZ domain (MamP), a domain of unknown function (MamX) or with a trypsin combined to one or two PDZ domains (MamE). By taking advantage of new genomic data available on MTB and a recent structural study of MamP, which helped define the MCR domain boundaries, we attempt to retrace the evolutionary history within and between the different MCR-containing proteins. We propose that the observed tandem repeat of MCR is the result of a convergent evolution and attempt to explain why this domain is rarely found alone.

Isolation, cultivation and genomic analysis of magnetosome biomineralization genes of a new genus of South-seeking magnetotactic cocci within the Alphaproteobacteria

Although magnetotactic bacteria (MTB) are ubiquitous in aquatic habitats, they are still considered fastidious microorganisms with regard to growth and cultivation with only a relatively low number of axenic cultures available to date. Here, we report the first axenic culture of an MTB isolated in the Southern Hemisphere (Itaipu Lagoon in Rio de Janeiro, Brazil). Cells of this new isolate are coccoid to ovoid in morphology and grow microaerophilically in semi-solid medium containing an oxygen concentration ([O₂]) gradient either under chemoorganoheterotrophic or chemolithoautotrophic conditions. Each cell contains a single chain of approximately 10 elongated cuboctahedral magnetite (Fe₃O₄) magnetosomes. Phylogenetic analysis based on the 16S rRNA gene sequence shows that the coccoid MTB isolated in this study represents a new genus in the Alphaproteobacteria; the name Magnetofaba australis strain IT-1 is proposed. Preliminary genomic data obtained by pyrosequencing shows that M. australis strain IT-1 contains a genomic region with genes involved in biomineralization similar to those found in the most closely related magnetotactic cocci Magnetococcus marinus strain MC-1. However, organization of the magnetosome genes differs from M. marinus.

Phylogenetic significance of composition and crystal morphology of magnetosome minerals

Magnetotactic bacteria (MTB) biomineralize magnetosomes, nano-scale crystals of magnetite or greigite in membrane enclosures that comprise a permanent magnetic dipole in each cell. MTB control the mineral composition, habit, size, and crystallographic orientation of the magnetosomes, as well as their arrangement within the cell. Studies involving magnetosomes that contain mineral and biological phases require multidisciplinary efforts. Here we use crystallographic, genomic and phylogenetic perspectives to review the correlations between magnetosome mineral habits and the phylogenetic affiliations of MTB, and show that these correlations have important implications for the evolution of magnetosome synthesis, and thus magnetotaxis.

The magnetosome model: insights into the mechanisms of bacterial biomineralization

Though the most ready example of biomineralization is the calcium phosphate of vertebrate bones and teeth, many bacteria are capable of creating biominerals inside their cells. Because of the diversity of these organisms and the minerals they produce, their study may reveal aspects of the fundamental mechanisms of biomineralization in more complex organisms. The best-studied case of intracellular biomineralization in bacteria is the magnetosome, an organelle produced by a diverse group of aquatic bacteria that contains single-domain crystals of the iron oxide magnetite (Fe₃O₄) or the iron sulfide greigite (Fe₃S₄). Here, recent advances in our understanding of the mechanisms of bacterial magnetite biomineralization are discussed and used as a framework for understanding less-well studied examples, including the bacterial intracellular biomineralization of cadmium, selenium, silver, nickel, uranium, and calcium carbonate. Understanding the molecular mechanisms underlying the biological formation of these minerals will have important implications for technologies such as the fabrication of nanomaterials and the bioremediation of toxic compounds.

Deciphering unusual uncultured magnetotactic multicellular prokaryotes through genomics

Candidatus Magnetoglobus multicellularis (Ca. M. multicellularis) is a member of a group of uncultured magnetotactic prokaryotes that possesses a unique multicellular morphology. To better understand this organism's physiology, we used a genomic approach through pyrosequencing. Genomic data analysis corroborates previous structural studies and reveals the proteins that are likely involved in multicellular morphogenesis of this microorganism. Interestingly, some detected protein sequences that might be involved in cell adhesion are homologues to phylogenetically unrelated filamentous multicellular bacteria proteins, suggesting their contribution in the early development of multicellular organization in Bacteria. Genes related to the behavior of Ca. M. multicellularis (chemo-, photo- and magnetotaxis) and its metabolic capabilities were analyzed. On the basis of the genomic-physiologic information, enrichment media were tested. One medium supported chemoorganoheterotrophic growth of Ca. M. multicellularis and allowed the microorganisms to maintain their multicellular morphology and cell cycle, confirming for the first time that the entire life cycle of the MMP occurs in a multicellular form. Because Ca. M. multicellularis has a unique multicellular life style, its cultivation is an important achievement for further studies regarding the multicellular evolution in prokaryotes.

Evolution of the bacterial organelle responsible for magnetotaxis

There are few examples of protein- and lipid-bounded organelles in bacteria that are encoded by conserved gene clusters and lead to a specific function. The magnetosome chain represents one of these rare examples and is responsible for magnetotaxis in magnetotactic bacteria (MTB), a behavior thought to aid in finding their optimal growth conditions. The origin and evolution of the magnetotaxis is still a matter of debate. Recent breakthroughs in isolation, cultivation, single-cell separation, and whole-genome sequencing have generated abundant data that give new insights into the biodiversity and evolution of MTB.