Solidesulfovibrio magneticus

Solidesulfovibrio magneticus
Scientific classification
Domain:	Bacteria
Phylum:	Thermodesulfobacteriota
Class:	Desulfovibrionia
Order:	Desulfovibrionales
Family:	Desulfovibrionaceae
Genus:	Solidesulfovibrio
Species:	S. magneticus
Binomial name
	Solidesulfovibrio magneticus; (Sakaguchi et al. 2002) Waite et al. 2020

Last updated April 30, 2024

Solidesulfovibrio magneticus is an anaerobic, Gram-negative, sulfate-reducing bacteria originally sourced from freshwater sediments in Wakayama, Japan but have also been found in the deep sea, indicating their ability to thrive in aquatic environments.^[1]^[2]S. magneticus are classified as magnetotactic bacteria with the ability to produce magnetite particles Since its discovery, further research has revealed the importance of S. magneticus and the magnetosomes they produce in the development of medical devices, reduction of nutrient-rich dead zones, and fossilization methods.^[1]^[3]^[4]^[5] Originally described under Desulfovibrio , it was reassigned to Solidesulfovibrio by Waite et al. in 2020.^[6]

Taxonomy

Solidesulfovibrio magneticus is a magnetotactic bacteria. Unlike most other magnetotactic bacteria, S. magneticus is not a member of the α-Proteobacteria phylum.^[1] Instead, this bacteria belongs to the Proteobacteria phylum, the Deltaproteobacteria class, and the Solidesulfovibrio genus.^[1] With further testing and analysis, S. magneticus was also taxonomically classified as a member of the Desulfovibrionaceae family and the Desulfovibrionales order.^[7]

Phylogenetics

Upon comparison of 1540 bases of 16S rDNA for the RS-1^T strain, the strain identified as S. magneticus, it was found that the organism is most phylogenetically related to Desulfovibrio burkinesis, with a similarity of approximately 98%.^[1] Although increasingly similar, the two species were further tested against each other using DNA-DNA hybridization to confirm they were not identical organisms.^[1] With this analysis, they were found to be related by only 51%, indicating that they are not identical and carry significant differences in their nitrogenous base compositions.^[1] The next two phylogenetically close species to S. magneticus are Desulfovibrio alcoholivorans and Desulfovibrio fructosivorans, which have 95% and 94% similarities to the RS-1^T strain, respectively.^[1] Further investigation of the similarity between S. magneticus and other existing magnetotactic bacteria, including those belonging to species of the Magnetospirillum genus, revealed large differences in the metabolism and morphology of the sulfate-reducing bacterium, indicating that magnetotactic bacteria did not all originate and evolve from the same source.^[1]

Discovery

Solidesulfovibrio magneticus was discovered by Toshifumi Sakaguchi, Atsushi Arakaki, and Tadashi Matsunaga from Tokyo University of Agriculture and Technology in January of 2002.^[1] The sample was found in the Kameno River waterway in the freshwater sediment in Wakayama, Japan, and they separated a specific strain called RS-1^T in the organism via non-magnetic enrichment after they were incubated anaerobically.^[1] The non-magnetic enrichment method that was utilized to isolate the RS-1^T strain consisted of incubating and enriching the growth of the magnetic organism in a specific medium, and separating the colonies after the magnetic bacteria growth was further amplified.^[8] Once isolation procedures were complete, DNA was extracted from the organism to remove the 16s rDNA fragment.^[1] Copies of 16s rDNA fragments, a section of DNA that is often used to identify rare species, were then amplified via Polymerase Chain Reaction, and analyzed further.^[9]^[1] GenBank, DDBJ databases, and FASTA software were used to find other sequences similar to the RS-1^T 16s rDNA sequences.^[1] Identified 16s rDNA sequences similar to the RS-1^T strain were compared to further analyze the genetic profile of the organism.^[1] Finally, a tree topology was created using the Neighbor Joining algorithm method.^[1]

Morphology

Solidesulfovibrio magneticus is a vibrio-shaped, Gram-negative cell with no spores and moves with a single polar flagellum.^[1] It is 3 to 5 micrometers in length and 1 micrometer in width, and it is a motile organism.^[1]

Ecology

Solidesulfovibrio magneticus were originally found in freshwater sediments in Japan.^[7] It is seen that the general magnetotactic bacterias typically thrive in sediments or water columns that have been chemically stratified.^[10] However, magnetotactic bacterias have also been recorded to survive in various aquatic habitats including intertidal sediments and the deep sea.^[2]

Genomics

After analyzing the whole genome sequence of S. magneticus RS-1 strain, it was found the genome is a circular chromosome that is 5,248,049 base pairs long, which is around 1.5 million base pairs larger than other Desulfovibrio strains.^[11] The genome also consists of two circular plasmids called pDMC1 and pDMC2.^[11] Within the circular chromosome, there are 4629 open reading frames (ORF), while pDMC1 contains 65 and pDMC2 contains 10 ORFs. There were several long genomic segments found in this strain, with the longest segment being 115 kilobases long.^[11] It was also observed that the average guanine and cytosine content in each of the genomic segments was lower than the total guanine and cytosine content seen in the entire chromosome.^[11] Within the chromosome sequence, 55 insertion sequence elements were found mainly in the genomic segments with low guanine and cytosine content and in pDMC1.^[11] These genomic characteristics of S. magneticus have suggested the idea that a majority of their DNA has been acquired from distantly related organisms through horizontal gene transfers.^[11]

Metabolism

S. magneticus is an anaerobic microbe nutritionally powered by using organic carbon as both the energy and carbon source for growth of its population. They also utilize chemical reactions by accepting and donating electrons to obtain energy. More specifically, the bacterium is a chemoorganotroph that can use organic carbon sources such as lactate, pyruvate, and glycerol as carbon sources and as electron donors as well.^[1] Additional electron acceptors for the bacterium’s growth include sulfate, thiosulfate, and fumarate.^[1] Different combinations of specific electron donors and acceptors corresponding to S. magneticus can produce a varying amount of magnetite particles. According to the Sakaguchi, Arakaki, and Matsunaga, six magnetite particles were produced when a combination of pyruvate and fumarate were used.^[1]

Importance

Use in healthcare settings

Solidesulfovibrio magneticus is a magnetotactic bacteria, which produces an important form of crystallized organelle called magnetosomes.^[10] A magnetosome is a well organized chain organelle that is surrounded by a lipid bilayer membrane that consists of a nano-sized crystallization of a magnetic iron mineral.^[10] Since magnetosomes have magnetic properties that can be useful for certain biomedical practices, magnetosomes have been utilized in certain processes such as Magnetic resonance imaging (MRI), drug delivery, separating of molecules, immobilization, gene therapeutics, and hyperthermia therapeutics.^[3] Additionally, many types of magnetosomes have been observed to have similar morphologies with smaller size variations, good dispersion properties, and more compatible with biomaterials in medical devices, which led researchers to apply this crystallized organelle in more medical practices.^[3]

Potential in reducing eutrophication in aquatic systems

Magnetotactic bacteria, which is one of the classifications of Solidesulfovibrio magneticus, have been observed to be involved in cycling of iron, sulfur, phosphorus, carbon, and nitrogen on Earth.^[5] They have also been discovered to be capable of isolating heavy metal elements such as selenium, cadmium, and tellurium.^[5] With their ability to cycle and isolate both essential and heavy metal trace elements, scientists have found magnetotactic bacteria to have the potential to decontaminate aquatic pollution.^[5] Since magnetotactic bacteria are also involved in the earth’s cycling of certain essential elements, it is also seen as a potential microorganism that can reduce eutrophication in aquatic environments. Eutrophication is the process where a large build-up of nutrients in an aquatic environment causes an overgrowth of algae that kills aquatic plants by blocking the sunlight.^[4] Additionally, the decomposition of the algae growth kills the animals in the environment by depleting their oxygen source which causes further harm to the aquatic system.^[4] The process of eutrophication and the creation of dead zones lead to global warming, so the utilization of magnetotactic bacteria as a potential tool to reduce eutrophication can help slow down climate change.^[5]

Use as magnetofossils

As a magnetotactic bacteria, Desulfovibrio magneticus can be used to record paleoenvironmental change and track geomagnetic field history after their death by creating fossil magnetosome magnetic nanoparticles, also known as magnetofossils.^[5] This occurs because magnetofossils can be preserved in rocks and sediments, and can be used to trace evolutionary magnetotactic bacteria for up to 1.9 Ga, or one billion years ago.^[5] However, the use of microbial fossils to study geological history has been seen as controversial in the field, as there have been several cases where the interpretations and purity of the fossils have been questioned.^[12] For example, there was a controversial paper published about the discovery of Apex chert fossils which were stated to be the oldest evidence of life, but was uncovered to be a form of graphite mineral that have been formed through non-biological processes.^[12] Although the use of microbiotic fossils for the study of geological history has been controversial, the use of magnetofossils are still regarded as a promising tool to record and trace geomagnetic field history.^[5]

Related Research Articles

Bacillus is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum Bacillota, with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural Bacilli is the name of the class of bacteria to which this genus belongs. Bacillus species can be either obligate aerobes which are dependent on oxygen, or facultative anaerobes which can survive in the absence of oxygen. Cultured Bacillus species test positive for the enzyme catalase if oxygen has been used or is present.

Ureaplasma urealyticum is a bacterium belonging to the genus Ureaplasma and the family Mycoplasmataceae in the order Mycoplasmatales. This family consists of the genera Mycoplasma and Ureaplasma. Its type strain is T960. There are two known biovars of this species; T960 and 27. These strains of bacteria are commonly found as commensals in the urogenital tracts of human beings, but overgrowth can lead to infections that cause the patient discomfort. Unlike most bacteria, Ureaplasma urealyticum lacks a cell wall making it unique in physiology and medical treatment.

Magnetosomes are membranous structures present in magnetotactic bacteria (MTB). They contain iron-rich magnetic particles that are enclosed within a lipid bilayer membrane. Each magnetosome can often contain 15 to 20 magnetite crystals that form a chain which acts like a compass needle to orient magnetotactic bacteria in geomagnetic fields, thereby simplifying their search for their preferred microaerophilic environments. Recent research has shown that magnetosomes are invaginations of the inner membrane and not freestanding vesicles. Magnetite-bearing magnetosomes have also been found in eukaryotic magnetotactic algae, with each cell containing several thousand crystals.

Magnetotaxis is a process implemented by a diverse group of Gram-negative bacteria that involves orienting and coordinating movement in response to Earth's magnetic field. This process is mainly carried out by microaerophilic and anaerobic bacteria found in aquatic environments such as salt marshes, seawater, and freshwater lakes. By sensing the magnetic field, the bacteria are able to orient themselves towards environments with more favorable oxygen concentrations. This orientation towards more favorable oxygen concentrations allows the bacteria to reach these environments faster as opposed to random movement through Brownian motion.

Magnetospirillum is a Gram-negative, microaerophilic genus of magnetotactic bacteria, first isolated from pond water by the microbiologist R. P. Blakemore in 1975. They have a spiral (helical) shape and are propelled by a polar flagellum at each end of their cells. The three main species identified are M. magnetotacticum strain MS-1, M. griphiswaldense strain MSR-1, and M. magneticum strain AMB-1.

<span class="mw-page-title-main">Magnetotactic bacteria</span> Polyphyletic group of bacteria

Magnetotactic bacteria are a polyphyletic group of bacteria that orient themselves along the magnetic field lines of Earth's magnetic field. Discovered in 1963 by Salvatore Bellini and rediscovered in 1975 by Richard Blakemore, this alignment is believed to aid these organisms in reaching regions of optimal oxygen concentration. To perform this task, these bacteria have organelles called magnetosomes that contain magnetic crystals. The biological phenomenon of microorganisms tending to move in response to the environment's magnetic characteristics is known as magnetotaxis. However, this term is misleading in that every other application of the term taxis involves a stimulus-response mechanism. In contrast to the magnetoreception of animals, the bacteria contain fixed magnets that force the bacteria into alignment—even dead cells are dragged into alignment, just like a compass needle.

Mycobacterium bohemicum is a species of the phylum Actinomycetota, belonging to the genus Mycobacterium.

<span class="mw-page-title-main">16S ribosomal RNA</span> RNA component

16S ribosomal RNA is the RNA component of the 30S subunit of a prokaryotic ribosome. It binds to the Shine-Dalgarno sequence and provides most of the SSU structure.

Magnetofossils are the fossil remains of magnetic particles produced by magnetotactic bacteria (magnetobacteria) and preserved in the geologic record. The oldest definitive magnetofossils formed of the mineral magnetite come from the Cretaceous chalk beds of southern England, while magnetofossil reports, not considered to be robust, extend on Earth to the 1.9-billion-year-old Gunflint Chert; they may include the four-billion-year-old Martian meteorite ALH84001.

Nitratidesulfovibrio vulgaris is a species of Gram-negative sulfate-reducing bacteria in the Desulfovibrionaceae family. It is also an anaerobic sulfate-reducing bacterium that is an important organism involved in the bioremediation of heavy metals in the environment. Nitratidesulfovibrio vulgaris is often used as a model organism for sulfur-reducing bacteria and was the first of such bacteria to have its genome sequenced. It is ubiquitous in nature and has also been implicated in a variety of human bacterial infections, although it may only be an opportunistic pathogen. This microbe also has the ability to endure high salinity environments, which is done through the utilization of osmoprotectants and efflux systems.

Bacterial phyla constitute the major lineages of the domain Bacteria. While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla.

Desulfosporosinus is a genus of strictly anaerobic, sulfate-reducing bacteria, often found in soil.

Sulfurimonas is a bacterial genus within the class of Campylobacterota, known for reducing nitrate, oxidizing both sulfur and hydrogen, and containing Group IV hydrogenases. This genus consists of four species: Sulfurimonas autorophica, Sulfurimonas denitrificans, Sulfurimonas gotlandica, and Sulfurimonas paralvinellae. The genus' name is derived from "sulfur" in Latin and "monas" from Greek, together meaning a “sulfur-oxidizing rod”. The size of the bacteria varies between about 1.5-2.5 μm in length and 0.5-1.0 μm in width. Members of the genus Sulfurimonas are found in a variety of different environments which include deep sea-vents, marine sediments, and terrestrial habitats. Their ability to survive in extreme conditions is attributed to multiple copies of one enzyme. Phylogenetic analysis suggests that members of the genus Sulfurimonas have limited dispersal ability and its speciation was affected by geographical isolation rather than hydrothermal composition. Deep ocean currents affect the dispersal of Sulfurimonas spp., influencing its speciation. As shown in the MLSA report of deep-sea hydrothermal vents Campylobacterota, Sulfurimonas has a higher dispersal capability compared with deep sea hydrothermal vent thermophiles, indicating allopatric speciation.

Desulfovibrio gracilis is a moderately halophilic bacteria. It is sulfate-reducing, mesophilic and motile. Its type strain is SRL6146^T.

Thermotoga petrophila is a hyperthermophilic, anaerobic, non-spore-forming, rod-shaped, fermentative heterotroph, with type strain RKU-1^T. T. petrophila was first discovered and isolated from an oil reservoir off of the coast of Japan and was deemed genetically distinct from its sister clades. Because these organism are found in deep, hot aquatic settings, they have become of great interest for biotechnology due to their enzymes functioning at high temperatures and pressures.

Desulfovibrio desulfuricans is a Gram-negative sulfate-reducing bacteria. It is generally found in soil, water, and the stools of animals, although in rare cases it has been found to cause infection in humans. It is particularly noted for its ability to produce methyl mercury. The reductive glycine pathway, a seventh route for organisms to capture CO₂, was discovered in this species. Since these bacteria are killed by exposure to atmospheric oxygen, the environmental niches most frequently occupied by these bacteria are anaerobic. Desulfovibrio desulfuricans 27774 was reported to produce gene transfer agents.

Microbial oxidation of sulfur is the oxidation of sulfur by microorganisms to build their structural components. The oxidation of inorganic compounds is the strategy primarily used by chemolithotrophic microorganisms to obtain energy to survive, grow and reproduce. Some inorganic forms of reduced sulfur, mainly sulfide (H₂S/HS⁻) and elemental sulfur (S⁰), can be oxidized by chemolithotrophic sulfur-oxidizing prokaryotes, usually coupled to the reduction of oxygen (O₂) or nitrate (NO₃⁻). Anaerobic sulfur oxidizers include photolithoautotrophs that obtain their energy from sunlight, hydrogen from sulfide, and carbon from carbon dioxide (CO₂).

Thermodesulfobacterium hveragerdense is a bacterial species belonging to genus Thermodesulfobacterium, which are thermophilic sulfate-reducing bacteria. This species is found in aquatic areas of high temperature, and lives in freshwater like most, but not all Thermodesulfobacterium species It was first isolated from hotsprings in Iceland.

Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The three-domain system of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and the microscopic archaea, while everything else, the eukaryotes, become the third domain.

Magnetobacterium bavaricum is a species of bacterium.

References

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Sakaguchi T, Arakaki A, Matsunaga T (2002). "Desulfovibrio magneticus sp. nov., a novel sulfate-reducing bacterium that produces intracellular single-domain-sized magnetite particles". International Journal of Systematic and Evolutionary Microbiology . 52 (Pt 1): 215–21. doi: 10.1099/00207713-52-1-215 . PMID 11837306.
1 2 Chen, Si; Yu, Min; Zhang, Wenyan; He, Kuang; Pan, Hongmiao; Cui, Kaixuan; Zhao, Yicong; Zhang, Xiao-Hua; Xiao, Tian; Zhang, Wuchang; Wu, Long-Fei (2022). "Metagenomic and Microscopic Analysis of Magnetotactic Bacteria in Tangyin Hydrothermal Field of Okinawa Trough". Frontiers in Microbiology. 13. doi: 10.3389/fmicb.2022.887136 . ISSN 1664-302X. PMC 9226615 . PMID 35756025.
1 2 3 Ren, Gang; Zhou, Xia; Long, Ruimin; Xie, Maobin; Kankala, Ranjith Kumar; Wang, Shibin; Zhang, Yu Shrike; Liu, Yuangang (2023). "Biomedical applications of magnetosomes: State of the art and perspectives". Bioactive Materials. 28: 27–49. doi:10.1016/j.bioactmat.2023.04.025. ISSN 2452-199X. PMC 10200801 . PMID 37223277.
1 2 3 Harper, David (1992), Harper, David (ed.), "What is eutrophication?", Eutrophication of Freshwaters: Principles, problems and restoration, Dordrecht: Springer Netherlands, pp. 1–28, doi:10.1007/978-94-011-3082-0_1, ISBN 978-94-011-3082-0 , retrieved 2024-04-26
1 2 3 4 5 6 7 8 Goswami, Pranami; He, Kuang; Li, Jinhua; Pan, Yongxin; Roberts, Andrew P.; Lin, Wei (2022). "Magnetotactic bacteria and magnetofossils: ecology, evolution and environmental implications". npj Biofilms and Microbiomes. 8 (1): 43. doi:10.1038/s41522-022-00304-0. ISSN 2055-5008. PMC 9160268 . PMID 35650214.
↑ "Species: Solidesulfovibrio magneticus". lpsn.dsmz.de. Retrieved 2024-04-29.
1 2 Shimoshige, Hirokazu; Kobayashi, Hideki; Shimamura, Shigeru; Mizuki, Toru; Inoue, Akira; Maekawa, Toru (2021). "Isolation and cultivation of a novel sulfate-reducing magnetotactic bacterium belonging to the genus Desulfovibrio". PLOS ONE. 16 (3): e0248313. Bibcode:2021PLoSO..1648313S. doi: 10.1371/journal.pone.0248313 . ISSN 1932-6203. PMC 7951924 . PMID 33705469.
↑ Sakaguchi, Toshifumi; Tsujimura, Noriyuki; Matsunaga, Tadashi (1996). "A novel method for isolation of magnetic bacteria without magnetic collection using magnetotaxis". Journal of Microbiological Methods. 26 (1): 139–145. doi:10.1016/0167-7012(96)00905-0. ISSN 0167-7012.
↑ Clarridge, Jill E. (2004). "Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases". Clinical Microbiology Reviews. 17 (4): 840–862. doi:10.1128/CMR.17.4.840-862.2004. ISSN 0893-8512. PMC 523561 . PMID 15489351.
1 2 3 Lefèvre, Christopher T.; Bazylinski, Dennis A. (2013). "Ecology, Diversity, and Evolution of Magnetotactic Bacteria". Microbiology and Molecular Biology Reviews. 77 (3): 497–526. doi:10.1128/MMBR.00021-13. ISSN 1092-2172. PMC 3811606 . PMID 24006473.
1 2 3 4 5 6 Nakazawa, Hidekazu; Arakaki, Atsushi; Narita-Yamada, Sachiko; Yashiro, Isao; Jinno, Koji; Aoki, Natsuko; Tsuruyama, Ai; Okamura, Yoshiko; Tanikawa, Satoshi; Fujita, Nobuyuki; Takeyama, Haruko; Matsunaga, Tadashi (2009). "Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria". Genome Research. 19 (10): 1801–1808. doi:10.1101/gr.088906.108. ISSN 1088-9051. PMC 2765288 . PMID 19675025.
1 2 Schopf, J. William; Kudryavtsev, Anatoliy B. (2012). "Biogenicity of Earth's earliest fossils: A resolution of the controversy". Gondwana Research. 22 (3): 761–771. Bibcode:2012GondR..22..761S. doi:10.1016/j.gr.2012.07.003. ISSN 1342-937X.