Editing Thiomargarita namibiensis

{{Short description|Species of bacterium}}
{{Use dmy dates|date=April 2020}}
{{Speciesbox
| image = Sulphide bacteria crop.jpg
| image_caption = Stained micrograph of ''Thiomargarita namibiensis''
| taxon = Thiomargarita namibiensis
| authority = Schulz ''et al.'', 1999
}}

'''''Thiomargarita namibiensis''''' is a [[gram-negative]], [[Facultative anaerobic organism|facultative anaerobic]], [[coccus|coccoid]] [[bacterium]] found in South America's ocean sediments of the [[continental shelf]] of [[Namibia]].<ref name="WHOI 1999 Giant Sulfur Bacteria Discovered">{{cite press release |title=Giant Sulfur Bacteria Discovered off African Coast |url=https://www.whoi.edu/press-room/news-release/giant-sulfur-bacteria-discovered-off-african-coast/ |publisher=Woods Hole Oceanographic Institution |date=16 April 1999 }}</ref> 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.<ref name=":3" /> The cells are each covered in a mucus sheath aligned in a chain, resembling loose strings of pearls.<ref name="Schulz Brinkhoff Ferdelman et al 1999">{{cite journal |last1=Schulz |first1=H. N. |last2=Brinkhoff |first2=T. |last3=Ferdelman |first3=T. G. |last4=Mariné |first4=M. Hernández |last5=Teske |first5=A. |last6=Jørgensen |first6=B. B. |title=Dense Populations of a Giant Sulfur Bacterium in Namibian Shelf Sediments |journal=Science |date=16 April 1999 |volume=284 |issue=5413 |pages=493–495 |doi=10.1126/science.284.5413.493 |pmid=10205058 |bibcode=1999Sci...284..493S }}</ref> The species name ''namibiensis'' means "of Namibia".<ref name="WHOI 1999 Giant Sulfur Bacteria Discovered"/> 

It is the second largest [[bacterium]] ever discovered, at {{convert|0.1|-|0.3|mm|µm
|abbr=on}} in diameter on average, but can attain up to {{convert|0.75|mm|µm|abbr=on}},<ref name="Max Planck 1999 The largest Bacterium">{{cite press release |publisher=Max Planck Institute for Marine Microbiology |date=8 April 1999 |title=The largest Bacterium: Scientist discovers new bacterial life form off the African coast |url=http://www.mpg.de/english/illustrationsDocumentation/documentation/pressReleases/1999/news17_99.htm |url-status=dead |archive-url=https://web.archive.org/web/20100120043846/http://www.mpg.de/english/illustrationsDocumentation/documentation/pressReleases/1999/news17_99.htm |archive-date=20 January 2010 }}</ref><ref>{{cite web |work = List of Prokaryotic names with Standing in Nomenclature | title = Genus Thiomargarita |url=https://lpsn.dsmz.de/genus/thiomargarita}}</ref> making it large enough to be visible to the naked eye. ''Thiomargarita namibiensis'' is nonpathogenic. 

''Thiomargarita namibiensis'' is categorized as a [[mesophile]]<ref name="Schulz 2006 The Genus Thiomargarita">{{cite book |doi=10.1007/0-387-30746-X_47 |chapter=The Genus Thiomargarita |title=The Prokaryotes |date=2006 |last1=Schulz |first1=Heide N. |pages=1156–1163 |isbn=978-0-387-25496-8 }}</ref> because it prefers moderate temperatures, which typically range between 20-45 degrees Celsius. The organism shows neutrophilic characteristics by favoring environments with neutral pH levels like 6.5-7.5.<ref name="Schulz Jørgensen 2001">{{cite journal |last1=Schulz |first1=Heide N. |last2=Jørgensen |first2=Bo Barker |title=Big Bacteria |journal=Annual Review of Microbiology |date=October 2001 |volume=55 |issue=1 |pages=105–137 |doi=10.1146/annurev.micro.55.1.105 |pmid=11544351 }}</ref>

== 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]].<ref name=Wuethrich1999/> It was discovered in coastal sediments on the Namibian coast of West Africa. Schulz and her colleagues were off the coast of Namibia in search of ''[[Beggiatoa]]'' and ''[[Thioploca]]'', two microbes which had previously been discovered off the South American Pacific coast in 1842 and 1906, respectively. They chose to conduct further research off the Namibian coast due to the similar [[hydrography]] of these coasts; both have strong and deep ocean currents which can stir-up various nutrients for the deep sea organisms to feast.<ref name=":3">{{cite press release |title=Biggest Bacteria Ever Found -- May Play Underrated Role In The Environment |url=https://www.sciencedaily.com/releases/1999/04/990416081113.htm |work=ScienceDaily |publisher=American Association For The Advancement Of Science |date=16 April 1999 }}</ref> Schulz's team found small quantities of ''Beggiatoa'' and ''Thioploca'' in sediment samples, but large quantities of the previously undiscovered ''Thiomargarita namibiensis''.<ref name=Amos2022>{{cite news |last1=Amos |first1=Jonathan |title=Record bacterium discovered as long as human eyelash |url=https://www.bbc.com/news/science-environment-61911817 |work=BBC News |date=23 June 2022 }}</ref><ref name="Max Planck 1999 The largest Bacterium"/> Researchers suggested the species be named ''Thiomargarita namibiensis'', which means "sulfur pearl of Namibia", which was fitting as the bacteria appeared a blue-green, white color, as well as spheres strung together.<ref name="WHOI 1999 Giant Sulfur Bacteria Discovered"/><ref name=":3" /> The previously largest known bacterium was ''[[Epulopiscium fishelsoni]]'', at 0.5 mm long.<ref>{{cite news |last1=Randerson |first1=James |title=Record breaker |url=https://www.newscientist.com/article/mg17423461-600-record-breaker/ |work=New Scientist |date=8 June 2002 }}</ref> The current largest known bacterium is ''[[Thiomargarita magnifica]],'' described in 2022, at an average length of 10&nbsp;mm.<ref name=Amos2022/><ref>{{cite news |last1=Devlin |first1=Hannah |title=Scientists discover world's largest bacterium, the size of an eyelash |url=https://www.theguardian.com/science/2022/jun/23/scientists-discover-world-largest-bacterium-thiomargarita-magnifica-bacteria |work=The Guardian |date=23 June 2022 }}</ref>

[[File:DistributionThiomargaritaNamibiensisNamibia.jpg|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.<ref name="Girnth Grünke Lichtschlag et al 2011">{{cite journal |last1=Girnth |first1=Anne-Christin |last2=Grünke |first2=Stefanie |last3=Lichtschlag |first3=Anna |last4=Felden |first4=Janine |last5=Knittel |first5=Katrin |last6=Wenzhöfer |first6=Frank |last7=de Beer |first7=Dirk |last8=Boetius |first8=Antje |title=A novel, mat-forming Thiomargarita population associated with a sulfidic fluid flow from a deep-sea mud volcano |journal=Environmental Microbiology |date=February 2011 |volume=13 |issue=2 |pages=495–505 |doi=10.1111/j.1462-2920.2010.02353.x |pmid=20946529 |bibcode=2011EnvMi..13..495G }}</ref> 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.<ref name="Kalanetra_2005" />

== Occurrence ==
''Thiomargarita namibiensis'' was found in the continental shelf off the coast of [[Namibia]], an area with high plankton productivity and low oxygen concentrations between 0-3 μM, and nitrate concentrations of 5-28 μM.<ref name="Schulz Brinkhoff Ferdelman et al 19994">{{cite journal |last1=Schulz |first1=H. N. |last2=Brinkhoff |first2=T. |last3=Ferdelman |first3=T. G. |last4=Mariné |first4=M. Hernández |last5=Teske |first5=A. |last6=Jørgensen |first6=B. B. |date=16 April 1999 |title=Dense Populations of a Giant Sulfur Bacterium in Namibian Shelf Sediments |journal=Science |volume=284 |issue=5413 |pages=493–495 |bibcode=1999Sci...284..493S |doi=10.1126/science.284.5413.493 |pmid=10205058}}</ref> ''Thiomargarita namibiensis'' is most prevalent in the Walvis Bay area at 300 feet deep,<ref name="WHOI 1999 Giant Sulfur Bacteria Discovered32">{{cite press release |title=Giant Sulfur Bacteria Discovered off African Coast |date=16 April 1999 |publisher=Woods Hole Oceanographic Institution |url=https://www.whoi.edu/press-room/news-release/giant-sulfur-bacteria-discovered-off-african-coast/}}</ref> but they are distributed along the coast of Namibia from Palgrave Point to Lüderitzbucht.<ref>{{cite web |date=29 October 2007 |title=Distribution of Thiomargarita namibiensis along the namibian coast |url=https://commons.wikimedia.org/wiki/File:DistributionThiomargaritaNamibiensisNamibia.jpg}}{{self-published inline|date=April 2024}}</ref> ''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.<ref name="Schulz 2006 The Genus Thiomargarita2">{{cite book |last1=Schulz |first1=Heide N. |title=The Prokaryotes |date=2006 |isbn=978-0-387-25496-8 |pages=1156–1163 |chapter=The Genus Thiomargarita |doi=10.1007/0-387-30746-X_47}}</ref> The most bacteria were obtained from the upper 3cm of sediment in the sample, with concentrations decreasing exponentially past this point.<ref name="Schulz Schulz 20052">{{cite journal |last1=Schulz |first1=Heide N. |last2=Schulz |first2=Horst D. |date=21 January 2005 |title=Large Sulfur Bacteria and the Formation of Phosphorite |journal=Science |volume=307 |issue=5708 |pages=416–418 |bibcode=2005Sci...307..416S |doi=10.1126/science.1103096 |pmid=15662012}}</ref> 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.<ref name=":32">{{cite press release |title=Biggest Bacteria Ever Found -- May Play Underrated Role In The Environment |date=16 April 1999 |publisher=American Association For The Advancement Of Science |url=https://www.sciencedaily.com/releases/1999/04/990416081113.htm |work=ScienceDaily}}</ref> In this section of sediment, there were sulfide concentrations of 100-800 μM.<ref name="Schulz Brinkhoff Ferdelman et al 19994" />

Although previously undiscovered, ''T. namibiensis'' is not uncommon in its environment. It is by far the most common [[benthos]] bacterium of the Namibian shelf, comprising almost 0.8% of the sediment volume.<ref>{{cite journal |last=Schulz |first=Heide |date=March 2002 |title=Thiomargarita namibiensis: Giant microbe holding its breath |url=https://www.researchgate.net/publication/256398005 |journal=ASM News |volume=68 |issue=3 |pages=122–127}}</ref> About 8% of the shelf with diatomaceous mud has free gases are present in shallow depths.<ref name="Schulz 2006 The Genus Thiomargarita2" /> When the gas is released from the sediment, sulfide is released into the water column. ''T. namibiensis'' is more prevalent in areas with free gas, suggesting that the presence of suspended sulfide is beneficial to the bacteria. ''T. namibiensis'' will oxidize the hydrogen sulfide (H2S) from the sediment into sulfur and sulfide, thus allowing less sulfide into the water column and detoxifying the water.<ref name="Winkel Salman-Carvalho Woyke et al 20162">{{cite journal |last1=Winkel |first1=Matthias |last2=Salman-Carvalho |first2=Verena |last3=Woyke |first3=Tanja |last4=Richter |first4=Michael |last5=Schulz-Vogt |first5=Heide N. |last6=Flood |first6=Beverly E. |last7=Bailey |first7=Jake V. |last8=Mußmann |first8=Marc |date=21 June 2016 |title=Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions |journal=Frontiers in Microbiology |volume=7 |page=964 |doi=10.3389/fmicb.2016.00964 |pmc=4914600 |pmid=27446006 |doi-access=free}}</ref><ref name=":8" /> However, the supply of sulfide produced by the underlying sediment can be too much for the cell to oxidize all of it, and sulfide still enters the water column. The Namibian coastal environmental experiences strong upwelling, resulting in low oxygen levels with large amounts of plankton. The lower waters lack oxygen due to the multitude of microorganisms releasing carbon dioxide while they perform heterotrophic respiration to generate energy.<ref name="Schulz Brinkhoff Ferdelman et al 19994" />

Since the ''Thiomargarita namibiensis'' are immobile, they are unable to seek a more ideal environment when sulfide and nitrate levels are low in this environment.<ref name="Girnth Grünke Lichtschlag et al 2011" /> They simply remain in position and wait for levels to increase once again so that they can undergo respiration and other processes.<ref name="WHOI 1999 Giant Sulfur Bacteria Discovered" /> This is possible because ''T. namibiensis'' have the ability to store large supplies of sulfur and nitrate.<ref name="Max Planck 1999 The largest Bacterium" /> The organism also has a direct impact on its environment. [[Apatite]], a mineral high in [[phosphorite]], is correlated with the abundance of ''T. namibiensis'' through phosphogenesis.<ref name=":8">{{cite journal |last1=Auer |first1=Gerald |last2=Hauzenberger |first2=Christoph A. |last3=Reuter |first3=Markus |last4=Piller |first4=Werner E. |title=Orbitally paced phosphogenesis in M editerranean shallow marine carbonates during the middle M iocene M onterey event |journal=Geochemistry, Geophysics, Geosystems |date=April 2016 |volume=17 |issue=4 |pages=1492–1510 |doi=10.1002/2016GC006299 |pmid=27570497 |pmc=4984836 |bibcode=2016GGG....17.1492A }}</ref> 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.<ref name="Schulz Schulz 2005">{{cite journal |last1=Schulz |first1=Heide N. |last2=Schulz |first2=Horst D. |date=21 January 2005 |title=Large Sulfur Bacteria and the Formation of Phosphorite |journal=Science |volume=307 |issue=5708 |pages=416–418 |bibcode=2005Sci...307..416S |doi=10.1126/science.1103096 |pmid=15662012}}</ref> The Mexican strain was primarily found in the top centimeter of sediment sampled from cold seeps in the Gulf of Mexico. The top 3cm of sediment from the Gulf of Mexico locations contained sulfide concentrations of 200-1900 μM.<ref name="Kalanetra_2005" />[[File:ThiomargaritaFeeding.jpg|thumb|250px|''Thiomargarita namibiensis'', collecting nitrate and oxygen in water above the bottom in case of being resuspended and collecting sulfide in the sediments]]

== Physiology ==

=== Morphology ===
Although ''Thiomargarita'' are closely related to ''[[Thioploca]]'' and ''[[Beggiatoa]]'' in function, their structures are different. ''Thioploca'' and ''Beggiatoa'' cells are much smaller and grow tightly stacked on each other in long filaments.<ref name="Schulz Schulz 2005" /> Their shape is necessary for them to shuttle down into the ocean sediments to find more [[sulfide]] and [[nitrate]].<ref>{{cite journal |last1=Brüchert |first1=Volker |last2=Jørgensen |first2=Bo Barker |last3=Neumann |first3=Kirsten |last4=Riechmann |first4=Daniela |last5=Schlösser |first5=Manfred |last6=Schulz |first6=Heide |title=Regulation of bacterial sulfate reduction and hydrogen sulfide fluxes in the central namibian coastal upwelling zone |journal=Geochimica et Cosmochimica Acta |date=December 2003 |volume=67 |issue=23 |pages=4505–4518 |doi=10.1016/S0016-7037(03)00275-8 |bibcode=2003GeCoA..67.4505B }}</ref> In contrast, ''Thiomargarita'' grow in rows of separate single spherical cells, so they lack the range of motility that ''Thioploca'' and ''Beggiota'' have.<ref name="Schulz Schulz 2005" /> ''Thiomargarita'' can also grow in barrel-like shapes. The cocci shaped ''Thiomargarita'' can join together to create chains of 4-20 cells, while the bacillus shaped ''Thiomargarita'' can form chains of more than 50 cells.<ref>{{cite journal |last1=Brock |first1=Jörg |last2=Schulz-Vogt |first2=Heide N |title=Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain |journal=The ISME Journal |date=1 March 2011 |volume=5 |issue=3 |pages=497–506 |doi=10.1038/ismej.2010.135 |pmid=20827290 |pmc=3105714 |bibcode=2011ISMEJ...5..497B }}</ref> These chains are not linked together by filaments, but connected by a mucus sheath.<ref name="Schulz 2006 The Genus Thiomargarita" /> Each cell appears reflective and white as a result of their sulfur content.<ref>{{cite news |last1=Johnson |first1=C. |title=Monster microbes found |url=https://www.abc.net.au/science/articles/1999/04/16/22180.htm |work=ABC News (Australia) |date=16 April 1999 }}</ref>

Scientists did not previously believe these large bacteria could exist because bacteria rely on [[chemiosmosis]] and cellular transport processes across their membranes to make [[Adenosine triphosphate|ATP]].<ref>{{Citation |last=Ahmad |first=Maria |title=Biochemistry, Electron Transport Chain |date=2024 |work=StatPearls |url=https://pubmed.ncbi.nlm.nih.gov/30252361/ |access-date=2024-11-21 |place=Treasure Island (FL) |publisher=StatPearls Publishing |pmid=30252361 |last2=Wolberg |first2=Adam |last3=Kahwaji |first3=Chadi I.}}</ref> As the cell size increases, they make proportionately less ATP, thus energy production limits their size.<ref name="Schulz Brinkhoff Ferdelman et al 1999" /> ''Thiomargarita'' are an exception to this size constraint, as their cytoplasm forms along the periphery of the cell, while the nitrate-storing vacuoles occupy the center of the cell.<ref name="Ahmad Kalanetra Nelson 2006" /> These vacuoles make up most of the cell. As these vacuoles swell, the cell grows considerably which is the primary factor contributing to the record sizes of ''Thiomargarita'' cells. ''T.'' ''namibiensis'' holds the record for the world's second largest bacterium, with a volume three million times more than that of average bacteria.<ref>{{cite web |date=October 2001 |title=The World's Largest Bacteria |url=https://www.whoi.edu/page.do?pid=14958&tid=282&cid=46727 |archive-url=https://web.archive.org/web/20160304195221/https://www.whoi.edu/page.do?pid=14958&tid=282&cid=46727 |archive-date=4 March 2016 |work=Woods Hole Oceanographic Institution}}</ref>

=== 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.<ref>{{cite journal | pmid=20827290 | date=2011 | last1=Brock | first1=J. | last2=Schulz-Vogt | first2=H. N. | title=Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain | journal=The ISME Journal | volume=5 | issue=3 | pages=497–506 | doi=10.1038/ismej.2010.135 | pmc=3105714 | bibcode=2011ISMEJ...5..497B }}</ref> 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.<ref name=":7">{{cite journal |last1=Salman |first1=Verena |last2=Amann |first2=Rudolf |last3=Girnth |first3=Anne-Christin |last4=Polerecky |first4=Lubos |last5=Bailey |first5=Jake V. |last6=Høgslund |first6=Signe |last7=Jessen |first7=Gerdhard |last8=Pantoja |first8=Silvio |last9=Schulz-Vogt |first9=Heide N. |title=A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria |journal=Systematic and Applied Microbiology |date=June 2011 |volume=34 |issue=4 |pages=243–259 |doi=10.1016/j.syapm.2011.02.001 |pmid=21498017 |bibcode=2011SyApM..34..243S }}</ref> Other large sulfur bacteria found in the same sediment samples as ''T. namibiensis'' with different structures, such as ''Thioploca'' and ''Beggiota,'' have gliding motility.<ref name=":7" /> However, ''Thiomargarita'' cells do not have gliding motility due to their shape.<ref name=":7" /> The vacuoles give ''T. namibiensis'' cells the ability to stay immobile, waiting for nitrate-rich waters to sweep over them once again.<ref name="Ahmad Kalanetra Nelson 2006"/> These vacuoles are what account for the size that scientists had previously thought impossible, and account for roughly 98% of the cell volume.<ref name="Mendell Clements Choat et al 2008">{{cite journal |last1=Mendell |first1=Jennifer E. |last2=Clements |first2=Kendall D. |last3=Choat |first3=J. Howard |last4=Angert |first4=Esther R. |title=Extreme polyploidy in a large bacterium |journal=Proceedings of the National Academy of Sciences |date=6 May 2008 |volume=105 |issue=18 |pages=6730–6734 |doi=10.1073/pnas.0707522105 |pmid=18445653 |pmc=2373351 |doi-access=free }}</ref> 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.<ref name="Mendell Clements Choat et al 2008" /> The cytoplasm contains small bubbles of [[sulfur]], [[polyphosphate]], and [[glycogen]]. These bubbles give the cytoplasm a “sponge-like” resemblance.<ref name="Schulz 2006 The Genus Thiomargarita"/>

As areas of nitrate and hydrogen sulfide do not mix together and ''T. namibiensis'' cells are immobile, the storage vacuoles in the cell provide a solution to this problem.<ref name="Ahmad Kalanetra Nelson 2006" /> Because of these storage vacuoles, cells are able to stay viable without growing (or dividing), with low relative amounts of cellular protein, and large amounts of nitrogen in the vacuoles. The storage vacuoles provide a novel solution which allows cells to wait for changing conditions while staying alive.<ref name="Schulz Brinkhoff Ferdelman et al 1999" /> These vacuoles are packed with sulfur granules that can be used for energy and contribute to their [[Lithotroph|chemolithotrophic]] metabolism. The [[vacuole]]s of ''Thiomargarita namibiensis'' contribute to their gigantism, allowing them to store nutrients for [[asexual reproduction]] of their complex [[genome]].<ref>{{cite journal |last1=Brüchert |first1=Volker |last2=Jørgensen |first2=Bo Barker |last3=Neumann |first3=Kirsten |last4=Riechmann |first4=Daniela |last5=Schlösser |first5=Manfred |last6=Schulz |first6=Heide |title=Regulation of bacterial sulfate reduction and hydrogen sulfide fluxes in the central namibian coastal upwelling zone |journal=Geochimica et Cosmochimica Acta |date=December 2003 |volume=67 |issue=23 |pages=4505–4518 |doi=10.1016/S0016-7037(03)00275-8 |bibcode=2003GeCoA..67.4505B }}</ref>

== Size Adaption ==
Bacteria, on average, are significantly smaller in size than ''Thiomargarita namibiensis.'' The smaller the size of a cell, the quicker it can reproduce and diffuse nutrients, and the higher the likelihood the biomolecule will almost immediately reach its site of activity.<ref name=":0" /> Despite the large size of ''T. namibiensis,'' its primary mechanism for nutrient uptake is still through normal diffusion.<ref name=":2">{{Cite web |title=Thiomargarita namibiensis - microbewiki |url=https://microbewiki.kenyon.edu/index.php/Thiomargarita_namibiensis#:~:text=Thiomargarita%20namibiensis%20was%20discovered%20in%20oceanic%20sediments%20off%20the%20Namibian |access-date=2024-09-13 |website=microbewiki.kenyon.edu}}</ref> ''T. namibiensis'' can perform normal diffusion due to the reduced amount of cytoplasm as a result of its large vacuoles.<ref name="Kalanetra_2005" /> These large central vacuoles, which act as reserves, are the source of the large size of ''T. namibiensis''.<ref name=":2" /> Because of its reserves, ''Thiomargarita namibiensis'' can survive in its environment where nutrients are infrequently available.<ref name=":2" /> The reserves allow ''T. namibiensis'' to store the required nutrients to sustain the cell for extended periods of nutrient deficiency in its environment. Another adaptation advanced by the large size of ''T. namibiensis'' is its ability to survive without growing.<ref name="Schulz Brinkhoff Ferdelman et al 1999" /> Collected and stored sediment samples were found to have surviving ''T. namibiensis'' cells after over two years.<ref name="Schulz Brinkhoff Ferdelman et al 1999" /> The cells had no access to any added sulfide or nitrate during this time. In the surviving cells, there was a notable size decrease.<ref name="Schulz Brinkhoff Ferdelman et al 1999" /> To survive without growing the cells depended on the nutrient stores of the central vacuoles. The consistent reliance on the nutrient stores without replenishment caused the cells to lose size; however, the cells were able to continue surviving. The displayed durability of these cells reveals the impressive functionality of the large vacuoles in ''T. namibiensis'' cells.<ref name="Schulz Brinkhoff Ferdelman et al 1999" /> The storage capacity of these vacuoles can allow ''T. namibiensis'' cells to survive for prolonged lengths of time without access to nutrients.<ref name=":2" />

== Metabolism ==
''Thiomargarita namibiensis'' is chemolithotrophic and is capable of using [[nitrate]] as the terminal electron acceptor in the [[electron transport chain]].<ref name="Bailey Flood Ricci 2014">{{cite conference |last1=Bailey |first1=J. |last2=Flood |first2=B. |last3=Ricci |first3=E. |title=Metabolism in the Uncultivated Giant Sulfide-Oxidizing Bacterium Thiomargarita Namibiensis Assayed Using a Redox-Sensitive Dye |conference=American Geophysical Union, Fall Meeting |date=December 2014 |volume=2014 |id=abstract id. B14C-02 |bibcode=2014AGUFM.B14C..02B }}</ref> [[Chemotroph|Chemo]] refers to the way the microbe obtains its energy, which is done by using oxidation-reduction reactions of compounds.<ref name="Schulz Schulz 2005"/> [[Lithotroph|Litho]] defines an organism's way of getting energy, which is done by using inorganic molecules as a source of electrons. This would be useful in an environment deficient in nutrients, such as soil or in an area with lots of sulfur. The final part of this metabolism characterization is how the bacterium obtains carbon, which in this case is done so in an [[Auxotrophy|autotrophic]] way. This means the organism uses carbon dioxide (CO<sub>2</sub>) from its environment as a carbon source and then synthesizes organic compounds from it.<ref name="Girnth Grünke Lichtschlag et al 2011"/>  ''Thiomargarita namibiensis'' uses what is known as the reverse or reductive TCA cycle to convert CO<sub>2</sub> into usable energy.<ref name="Schulz Jørgensen 2001"/> This adaptation shows how the bacterium has learned to survive in specific environments where usual metabolic pathways might not work well enough. There is still much unknown about the metabolism and phylogeny of the sulfur bacteria.<ref name="Bailey Flood Ricci 2014"/>

The bacterium is [[Facultative anaerobic organism|facultatively anaerobic]] rather than obligately anaerobic, and thus capable of respiring with oxygen if it is plentiful and without oxygen when it is minimal or absent.<ref name=":9">{{cite journal |last1=Schulz |first1=Heide N. |last2=de Beer |first2=Dirk |title=Uptake Rates of Oxygen and Sulfide Measured with Individual Thiomargarita namibiensis Cells by Using Microelectrodes |journal=Applied and Environmental Microbiology |date=November 2002 |volume=68 |issue=11 |pages=5746–5749 |doi=10.1128/AEM.68.11.5746-5749.2002 |pmid=12406774 |pmc=129903 |bibcode=2002ApEnM..68.5746S }}</ref> 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.<ref name="Wuethrich1999">{{cite journal |last1=Wuethrich |first1=Bernice |title=Giant Sulfur-Eating Microbe Found |journal=Science |date=16 April 1999 |volume=284 |issue=5413 |pages=415 |id={{Gale|A54515055}} {{ProQuest|213556653}} |doi=10.1126/science.284.5413.415 |pmid=10232982 }}</ref> This bacterium often uses anaerobic respiration due to its environment not supplying ample oxygen.<ref name="Schulz Jørgensen 2001" /> 

Sulfur oxidation is the main energy source for ''Thiomargarita namibiensis''.<ref name=":0">{{cite journal | vauthors = Levin PA, Angert ER | title = Small but Mighty: Cell Size and Bacteria | journal = Cold Spring Harbor Perspectives in Biology | volume = 7 | issue = 7 | pages = a019216 | date = June 2015 | pmid = 26054743 | pmc = 4484965 | doi = 10.1101/cshperspect.a019216 }}</ref> Sulfide is the electron donor for this bacterium. ''T. namibiensis'' will oxidize [[hydrogen sulfide]] (H<sub>2</sub>S) into elemental [[sulfur]] (S).<ref name="Schulz Schulz 2005" /> This is deposited as granules in its periplasm.<ref name="Bailey Flood Ricci 2014" /> Nitrate is the electron acceptor in this oxidation-reduction reaction. Large amounts of nitrogen must be stored as a terminal electron acceptor in the electron transport chain.<ref name="Ahmad Kalanetra Nelson 2006" /> The large vacuole mainly stores nitrate for sulfur oxidation.<ref name=":0" /> Because of this and the organism's size, large amounts of sulfur are required which are stored as cyclooctasulfur.<ref name="Ahmad Kalanetra Nelson 2006">{{cite journal |last1=Ahmad |first1=Azeem |last2=Kalanetra |first2=Karen M |last3=Nelson |first3=Douglas C |title=Cultivated Beggiatoa spp. define the phylogenetic root of morphologically diverse, noncultured, vacuolate sulfur bacteria |journal=Canadian Journal of Microbiology |date=1 June 2006 |volume=52 |issue=6 |pages=591–598 |doi=10.1139/w05-154 |pmid=16788728 }}</ref> 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.<ref name=":9" /> However, this bacterium is predominantly located in environments of very minimal to no oxygen availability; therefore, nitrate will be the standard electron acceptor for the oxidation-reduction reaction. However, when oxygen is available in its environment ''Thiomargarita namibiensis'' is able to utilize it as the electron acceptor in place of nitrate.<ref name=":9" />

While sulfide is available in the surrounding sediment, produced by other bacteria from dead [[microalgae]] that sank down to the sea bottom, the nitrate comes from the above seawater. Since the bacterium is [[Sessility (zoology)|sessile]], and the concentration of available nitrate fluctuates considerably over time, it stores nitrate at high concentration (up to 0.8 [[molarity|molar]]<ref name="Schulz Brinkhoff Ferdelman et al 1999" />) in a large [[vacuole]], which is responsible for about 80% of its size.<ref name="Kalanetra_2005">{{cite journal | vauthors = Kalanetra KM, Joye SB, Sunseri NR, Nelson DC | title = Novel vacuolate sulfur bacteria from the Gulf of Mexico reproduce by reductive division in three dimensions | journal = Environmental Microbiology | volume = 7 | issue = 9 | pages = 1451–1460 | date = September 2005 | pmid = 16104867 | doi = 10.1111/j.1462-2920.2005.00832.x | bibcode = 2005EnvMi...7.1451K | doi-access = free }}</ref> 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.<ref>{{cite journal |last1=Girnth |first1=Anne-Christin |last2=Grünke |first2=Stefanie |last3=Lichtschlag |first3=Anna |last4=Felden |first4=Janine |last5=Knittel |first5=Katrin |last6=Wenzhöfer |first6=Frank |last7=de Beer |first7=Dirk |last8=Boetius |first8=Antje |title=A novel, mat-forming Thiomargarita population associated with a sulfidic fluid flow from a deep-sea mud volcano |journal=Wiley |date=15 October 2010 |volume=13 |issue=2 |pages=495–505 |doi=10.1111/j.1462-2920.2010.02353.x |pmid=20946529 |bibcode=2011EnvMi..13..495G |url=https://enviromicro-journals.onlinelibrary.wiley.com/doi/abs/10.1111/j.1462-2920.2010.02353.x}}</ref> The non-motility of ''Thiomargarita'' cells is compensated by its large cellular size.<ref name="Schulz 2006 The Genus Thiomargarita" /> This immobility suggests that they rely on shifting chemical conditions.<ref name="Winkel Salman-Carvalho Woyke et al 2016">{{cite journal |last1=Winkel |first1=Matthias |last2=Salman-Carvalho |first2=Verena |last3=Woyke |first3=Tanja |last4=Richter |first4=Michael |last5=Schulz-Vogt |first5=Heide N. |last6=Flood |first6=Beverly E. |last7=Bailey |first7=Jake V. |last8=Mußmann |first8=Marc |date=21 June 2016 |title=Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions |journal=Frontiers in Microbiology |volume=7 |page=964 |doi=10.3389/fmicb.2016.00964 |pmc=4914600 |pmid=27446006 |doi-access=free}}</ref>

[[Cyclooctasulfur]] is stored in the globules of sulfur in the vacuoles of ''T. namibiensis'', aiding in their metabolism.<ref name="Prange Chauvistré Modrow et al 2002">{{cite journal |last1=Prange |first1=Alexander |last2=Chauvistré |first2=Reinhold |last3=Modrow |first3=Hartwig |last4=Hormes |first4=Josef |last5=Trüper |first5=Hans G |last6=Dahl |first6=Christiane |title=Quantitative speciation of sulfur in bacterial sulfur globules: X-ray absorption spectroscopy reveals at least three different species of sulfur |journal=Microbiology |date=2002 |volume=148 |issue=1 |pages=267–276 |doi=10.1099/00221287-148-1-267 |doi-access=free |pmid=11782519 }}</ref> After the oxidation of sulfide, ''T. namibiensis'' stores sulfur as cyclooctasulfur, the most thermodynamically stable form of sulfur at standard temperature and pressure.<ref name="Girnth Grünke Lichtschlag et al 2011"/> With these sulfur globules in the cell, the organism uses it as storage of elemental sulfur in usually anoxic conditions to reduce the toxicity of various sulfur compounds (can also survive in atmospheric oxygen conditions as it is not toxic). The sulfur globules are stored in the thin outer layer of the cytoplasm, presumably after their use as a source of electrons in the electron transport chain through oxidation of sulfide.<ref name="Prange Chauvistré Modrow et al 2002"/> The ability to oxidize hydrogen sulfide provides nutrients to other organisms living near it.<ref name=":1">{{cite book |doi=10.1007/978-3-030-47384-6_1 |chapter=Contribution of Human and Animal to the Microbial World and Ecological Balance |title=Gut Microbiome and Its Impact on Health and Diseases |date=2020 |last1=Tabashsum |first1=Zajeba |last2=Alvarado-Martinez |first2=Zabdiel |last3=Houser |first3=Ashley |last4=Padilla |first4=Joselyn |last5=Shah |first5=Nishi |last6=Young |first6=Alana |pages=1–18 |isbn=978-3-030-47383-9 }}</ref>

== 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.<ref name="Schulz Brinkhoff Ferdelman et al 1999" /> ''T. namibiensis'' reproduces mainly through binary fission.<ref name="Winkel Salman-Carvalho Woyke et al 2016"/> Reproduction of ''T. namibiensis'' occurs on a single plane; the [[Coccus|cocci]] (a spherical bacterial cell) divide into a [[diplococcus]] or streptococcus arrangement.<ref name="Kalanetra_2005" /><ref>{{Cite web |date=2016-03-01 |title=2.1: Sizes, Shapes, and Arrangements of Bacteria |url=https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(Kaiser)/Unit_1%3A_Introduction_to_Microbiology_and_Prokaryotic_Cell_Anatomy/2%3A_The_Prokaryotic_Cell_-_Bacteria/2.1%3A_Sizes_Shapes_and_Arrangements_of_Bacteria |access-date=2024-04-18 |website=Biology LibreTexts |language=en}}</ref> A diplococcus is a pair of cocci cells that can form chains, and streptococcus is a grape-like cluster of cells.<ref>{{cite web |title=Diplococcus {{!}} bacteria |url=https://www.britannica.com/science/diplococcus |website=Britannica }}</ref> 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.<ref name=":0" /> During the process of [[Fission (biology)|binary fission]], a single bacterial cell divides into two identical daughter cells, representing a comparatively basic form of [[asexual reproduction]].<ref name="Girnth Grünke Lichtschlag et al 2011"/> The cells that make up the filamentous chain may then separate into smaller segments, and each of those segments may go on to produce a new filament.<ref>{{cite journal |last1=Shih |first1=Yu-Ling |last2=Rothfield |first2=Lawrence |title=The Bacterial Cytoskeleton |journal=Microbiology and Molecular Biology Reviews |date=September 2006 |volume=70 |issue=3 |pages=729–754 |doi=10.1128/MMBR.00017-06 |pmid=16959967 |pmc=1594594 }}</ref> In a laboratory setting, the number of cells doubled over a period of 1 to 2 weeks when both nitrate and sulfide were available.<ref name="Schulz Brinkhoff Ferdelman et al 1999" />

== Genome ==
''Thiomargarita namibiensis'' has a distinct genetic architecture because of its remarkable cell size and [[environmental niche]]. The DNA of ''T. namibiensis'' is dispersed over nucleoid areas situated under the cell membrane, in contrast to normal bacteria, which have a concentrated nucleoid. This peripheral design provides efficient cellular activities by lowering the distance over which chemical signals and metabolites must travel despite the huge cell volume.<ref name=":4">{{Cite journal |last1=Schulz |first1=Heide N. |last2=Jørgensen |first2=Bo Barker |date=October 2001 |title=Big Bacteria |url=https://www.annualreviews.org/doi/10.1146/annurev.micro.55.1.105 |journal=Annual Review of Microbiology |language=en |volume=55 |issue=1 |pages=105–137 |doi=10.1146/annurev.micro.55.1.105 |pmid=11544351 |issn=0066-4227}}</ref><ref name=":5">{{Cite journal |last=Angert |first=Esther R. |date=March 2005 |title=Alternatives to binary fission in bacteria |url=https://www.nature.com/articles/nrmicro1096 |journal=Nature Reviews Microbiology |language=en |volume=3 |issue=3 |pages=214–224 |doi=10.1038/nrmicro1096 |pmid=15738949 |issn=1740-1534}}</ref> A whole genome sequence of ''T. namibiensis'' is unavailable because it is difficult to culture and extract sufficient DNA. However, ''T. namibiensis'' is [[Polyploidy|polyploid]], which means many copies of the genome are distributed throughout the cytoplasm. <ref>{{Cite journal |last1=Mußmann |first1=Marc |last2=Hu |first2=Fen Z. |last3=Richter |first3=Michael |last4=Beer |first4=Dirk de |last5=Preisler |first5=André |last6=Jørgensen |first6=Bo B. |last7=Huntemann |first7=Marcel |last8=Glöckner |first8=Frank Oliver |last9=Amann |first9=Rudolf |last10=Koopman |first10=Werner J. H. |last11=Lasken |first11=Roger S. |last12=Janto |first12=Benjamin |last13=Hogg |first13=Justin |last14=Stoodley |first14=Paul |last15=Boissy |first15=Robert |date=2007-08-28 |title=Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments |journal=PLOS Biology |language=en |volume=5 |issue=9 |pages=e230 |doi=10.1371/journal.pbio.0050230 |doi-access=free |issn=1545-7885 |pmc=1951784 |pmid=17760503}}</ref><ref>{{Cite journal |last=Angert |first=Esther R. |date=2012-10-13 |title=DNA Replication and Genomic Architecture of Very Large Bacteria |url=https://www.annualreviews.org/doi/10.1146/annurev-micro-090110-102827 |journal=Annual Review of Microbiology |language=en |volume=66 |issue=1 |pages=197–212 |doi=10.1146/annurev-micro-090110-102827 |pmid=22994492 |issn=0066-4227}}</ref> 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 sediment|marine sediments]] because of its gene involved in sulfur [[Oxidation state|oxidation]] and nitrate reduction. <ref name=":4" /><ref name=":6">{{Cite journal |last1=Winkel |first1=Matthias |last2=Salman-Carvalho |first2=Verena |last3=Woyke |first3=Tanja |last4=Richter |first4=Michael |last5=Schulz-Vogt |first5=Heide N. |last6=Flood |first6=Beverly E. |last7=Bailey |first7=Jake V. |last8=Mußmann |first8=Marc |date=2016-06-21 |title=Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions |journal=Frontiers in Microbiology |language=English |volume=7 |page=964 |doi=10.3389/fmicb.2016.00964 |doi-access=free |issn=1664-302X |pmc=4914600 |pmid=27446006}}</ref> Single-cell genomic investigations revealed that it has identified genes that might provide adaptability to dynamic [[redox]] circumstances. <ref name=":6" /><ref>{{Cite journal |last1=Schulz |first1=Heide N. |last2=Schulz |first2=Horst D. |date=2005-01-21 |title=Large Sulfur Bacteria and the Formation of Phosphorite |url=https://www.science.org/doi/10.1126/science.1103096 |journal=Science |language=en |volume=307 |issue=5708 |pages=416–418 |doi=10.1126/science.1103096 |pmid=15662012 |bibcode=2005Sci...307..416S |issn=0036-8075}}</ref>

== 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]].<ref name=":1" /> Therefore, ''T. nambiensis'' acts as a detoxifier that removes poisonous gas from the water. This keeps the environment affable for fish and other marine living beings as well as providing [[sulfide]], a crucial nutrient for marine organisms.<ref name=":1" /> These bacteria also play an essential role in the [[phosphorus cycle]] of the sediment. ''T. namibiensis'' can release [[phosphate]] in anoxic sediments at high rates which contribute to the spontaneous [[precipitation]] of phosphorus-containing material. This plays an important role in the removal of phosphorus in the [[biosphere]].<ref name="Schulz 2006 The Genus Thiomargarita"/>

== See also ==
* ''[[Valonia ventricosa]]'' – a large, 5 centimetre-wide unicellular species of algae
* ''[[Thiomargarita magnifica]]'' – the current largest bacterium in the world, closely related to this organism

== References ==
{{Reflist}}

== External links ==
* [https://schaechter.asmblog.org/schaechter/2012/02/the-three-faces-of-thiomargarita.html Macrophotos of ''Thiomargarita namibiensis'']

{{Taxonbar|from=Q132118}}

[[Category:Thiotrichales]]
[[Category:Bacteria described in 1999]]