Thiomargarita namibiensis is a gram-negative, facultative anaerobic, coccoid bacterium found in South Africa's ocean sediments of the continental shelf of Namibia. The genus name Thiomargarita means "sulfur pearl." This refers to the cells' appearance as they contain microscopic elemental sulfur granules just below the cell wall that refract light creating a pearly iridescent luster. The species name namibiensis means "of Namibia". making it large enough to be visible to the naked eye. Thiomargarita namibiensis is nonpathogenic.
Thiomargarita namibiensis is categorized as a mesophile because it prefers moderate temperatures between 20 and 45 degrees Celsius. The organism shows neutrophilic characteristics by favoring environments with neutral pH levels like 6.5-7.5.
Discovery
The species Thiomargarita namibiensis was collected in 1997 and discovered in 1999 by Heide N. Schulz and her colleagues from the Max Planck Institute for Marine Microbiology. Schulz's team found small quantities of Beggiatoa and Thioploca in sediment samples, but large quantities of the previously undiscovered Thiomargarita namibiensis. The current largest known bacterium is Thiomargarita magnifica, described in 2022, at an average length of 10 mm.
thumb|Distribution of Thiomargarita namibiensis in Namibia
In 2002 a strain exhibiting 99% identity with Thiomargarita namibiensis was found in sediment cores taken from the Gulf of Mexico during a research expedition. This similar strain either occurs in single cells or clusters of 2, 4, and 8 cells, as opposed to the Namibian strain which occurs in single chains of cells separated by a thin mucus sheath. Thiomargarita namibiensis is most prevalent in the Walvis Bay area at 300 feet deep, but they are distributed along the coast of Namibia from Palgrave Point to Lüderitzbucht. T. namibiensis is not found across the entire shelf, it is only found within a specific sediment type, diatomaceous mud, which is composed mainly of dead diatoms. Diatomaceous mud has high sulfate reduction rates and high levels of organic material. The most bacteria were obtained from the upper 3 cm of sediment in the sample, with concentrations decreasing exponentially past this point. Here, Thiomargarita namibiensis is easily suspended in moving ocean currents due to the sheath around the cells, which makes it easy for the bacteria to passively float. In this section of sediment, there were sulfide concentrations of 100-800 μM. About 8% of the shelf with diatomaceous mud has free gases are present in shallow depths. Internal polyphosphate and nitrate are used as external electron acceptors in the presence of acetate, releasing enough phosphate to cause precipitation. While the amount directly created by T. namibiensis cannot be calculated, it is a significant contribution to the large amounts of hydroxyapatite in solid-phase shelf sediment. In contrast, Thiomargarita grow in rows of separate single spherical cells, so they lack the range of motility that Thioploca and Beggiota have. These chains are not linked together by filaments, but connected by a mucus sheath.
Scientists did not previously believe these large bacteria could exist because bacteria rely on chemiosmosis and cellular transport processes across their membranes to make ATP. As the cell size increases, they make proportionately less ATP, thus energy production limits their size.
Motility
With their lack of movement, Thiomargarita have adapted by evolving the very large nitrate-storing bubbles vacuoles, allowing them to survive long periods of nitrate and sulfide starvation. Studies have shown that although there are no present motility features, the individual spherical cells can move slightly in a "slow jerky rolling motion," but this does not give them the range of motion traditional motility features would. Other large sulfur bacteria found in the same sediment samples as T. namibiensis with different structures, such as Thioploca and Beggiota, have gliding motility. Because of the vast size of the liquid central vacuole, the cytoplasm separating the vacuole and the cell membrane is a very thin layer reported to be around 0.5-2 micrometers thick. This cytoplasm, however, is non-homogenous. T. namibiensis can perform normal diffusion due to the reduced amount of cytoplasm as a result of its large vacuoles. Chemo refers to the way the microbe obtains its energy, which is done by using oxidation-reduction reactions of compounds. While not much is known about the exact metabolism the bacterium performs, it is known to exist in environments of high sulfur and little to no oxygen present. This bacterium often uses anaerobic respiration due to its environment not supplying ample oxygen. Sulfide is the electron donor for this bacterium. T. namibiensis will oxidize hydrogen sulfide (H<sub>2</sub>S) into elemental sulfur (S). Both sulfide and nitrate are essential to the function of energy production in this bacterium.
Studies show that in some cases T. namibiensis can use oxygen as the electron acceptor in the oxidation of sulfur. When nitrate concentrations in the environment are low, T. namibiensis uses the contents of its vacuole for respiration. T. namibiensis cells possess elevated nitrate concentrations giving them the capacity to absorb oxygen both when nitrate is present and when it is not. Thus, the presence of a central vacuole in its cells enables a prolonged survival in sulfidic sediments and nitrate starvation. This allows the bacteria cells to safely wait for shifts in environmental conditions. The non-motility of Thiomargarita cells is compensated by its large cellular size. After the oxidation of sulfide, T. namibiensis stores sulfur as cyclooctasulfur, the most thermodynamically stable form of sulfur at standard temperature and pressure.
Reproduction
Thiomargarita namibiensis has an ability to survive in nutrient-poor environments due to stored nitrate and sulfur, which enables the cells to stay alive without reproducing. When the cells are unable to reproduce, most cells shorten to cocci or diplococcus arrangement. A diplococcus is a pair of cocci cells that can form chains, and streptococcus is a grape-like cluster of cells. In the case of T. namibiensis, a diplococci structure is observed. Despite this, its cells remain connected, forming chains within a common mucus matrix. In addition to helping with essential functions including food exchange and cell-to-cell communication, this matrix can give the bacteria protection and structural support. In a laboratory setting, the number of cells doubled over a period of 1 to 2 weeks when both nitrate and sulfide were available. A whole genome sequence of T. namibiensis is unavailable because it is difficult to culture and extract sufficient DNA. However, T. namibiensis is polyploid, which means many copies of the genome are distributed throughout the cytoplasm. This genetic redundancy helped its metabolic requirements and improved its capacity to repair damaged DNA by environmental stresses. T. namibiensis's genomic architecture is like that of other big bacteria, such as Epulopiscium fishelsoni. Both species have DNA distributed around the cell periphery to promote localized gene expression and effective cellular responses in big cells. This structure helps to overcome the constraints based on their size, allowing them to adapt quickly to environmental changes. The T. namibiensis genome is important because it is involved in biogeochemical cycles including sulfur and nitrogen cycling. T. namibiensis is found in sulfide-rich, oxygen-poor marine sediments because of its gene involved in sulfur oxidation and nitrate reduction. Single-cell genomic investigations revealed that it has identified genes that might provide adaptability to dynamic redox circumstances.
Significance
T. namibiensis plays a vital role in the sulfur and nitrogen cycles. In their sulfur rich environment, oxygen is scarcely available and cannot be used as an electron acceptor. In turn, T. namibiensis uses nitrate as the electron acceptor, which they consume at the sediment surface and condense in a vacuole. From this, they can oxidize the toxic hydrogen sulfide that inhabits the sediment into sulfide.