Editing Thiomargarita namibiensis (section)

== 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>