Thermodesulfobacteriota

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Thermodesulfobacteriota
Dvulgaris micrograph.JPG
Nitratidesulfovibrio vulgaris
Scientific classification OOjs UI icon edit-ltr.svg
Domain: Bacteria
Kingdom: Pseudomonadati
Phylum: Thermodesulfobacteriota
Garrity & Holt 2021 [1]
Classes [2]
Synonyms [2]
  • DesulfobacterotaWaite et al. 2020
  • "Ca. Dadabacteria" Hug et al. 2016
  • "Thermodesulfobacteraeota" Oren et al. 2015
  • Thermodesulfobacteria Garrity and Holt 2002

The Thermodesulfobacteriota, or Desulfobacterota, [4] are a phylum of anaerobic Gram-negative bacteria. Many representatives are sulfate-reducing bacteria, [5] others can grow by disproportionation of various sulphur species, [6] reduction or iron, [7] or even use external surfaces as electron acceptors (exoelectrogens). [8] They have highly variable morphology: vibrio, rods, cocci, [4] as well as filamentous cable bacteria. [9] Individual members of Desulfobacterota are also studied for their bacterial nanowires [10] or syntrophic relationships. [11]

Contents

Phylogenetic tree of prokaryotes based on ribosomal proteins and RNA polymerase Desulfobacterota are closely related to Pseudomonadota/Proteobacteria, Myxococcota, and Bdellovibrionota. MBE TOL.jpg
Phylogenetic tree of prokaryotes based on ribosomal proteins and RNA polymerase Desulfobacterota are closely related to Pseudomonadota/Proteobacteria, Myxococcota, and Bdellovibrionota.

Taxonomy

The bacterial phylum Desulfobacterota has been created by merging: 1) the well-established class Thermodesulfobacteria, 2) the proposed phylum Dadabacteria, and 3) various taxa separated from the abandoned non-monophyletic class "Deltaproteobacteria" alongside three other phyla: Myxococcota, Bdellovibrionota, and SAR324. [4]

Environment

In contrast to their close relatives, the aerobic phyla Myxococcota and Bdellovibrionota, Desulfobacterota are predominantly anaerobic. [4] They likely retained their anaerobic lifestyle since before the Great Oxidation Event. [13]

Three closely related classes within Desulfobacterota: Thermodesulfobacteria, Dissulfuribacteria, and Desulfofervidia, [11] as well as the more distant Deferrisomatia, are exclusively thermophilic, while most members of other classes are mesophiles [4] or even psychrophiles. [14] [15]

Metabolism

Sulfate-reducing bacteria (SRB) utilize sulfate as a terminal electron acceptor in a respiratory-type metabolism, coupled to the oxidation of organic compounds or hydrogen. By reducing sulfate, many Desulfobacterota species substantially contribute to the sulfur cycle. [4]

Dissimilatory sulfate reduction Dissimilatory sulfate reduction.svg
Dissimilatory sulfate reduction

Microbial sulfur disproportionation (MSD) is a poorly known type of energy metabolism analogous to organic fermentation, where a single inorganic sulfur species of intermediate oxidation state is simultaneously oxidized and reduced, resulting in production of sulfide and sulfate. In Desulfobacterota, MSD is often present in species that also perform sulfate reduction. [6]

Sulfur oxidation is rare among Desulfobacterota. [16] However, several strains are known to perform this type of metabolism using diverse mechanisms. Strain MLMS-1 (Desulfobacterota incertae sedis ) couples oxidation of sulfide to reduction of arsenate. [17] Dissulfuribacter thermophilus (Dissulfuribacteria) oxidizes elemental sulfur with dissimilatory nitrate reduction to ammonium. [18] Desulfurivibrio alkaliphilus (Desulfobulbia) couples oxidation of sulfide to the dissimilatory reduction of nitrate and nitrite to ammonium. [16] Cable bacteria (Desulfobulbia), closely related to D. alkaliphilus, oxidize sulfide using a long-distance electron transport to oxygen or nitrate reduction — see below. [19] The genome of strain M19 (also Desulfobulbia) encodes the Sox system of sulfur oxidation. [20]

Fe(III) minerals can be microbially reduced by Fe-reducing bacteria (FeRB) using a wide range of organic compounds or H2 as electron donors. FeRB are widespread across Bacteria. Among Desulfobacterota, they are represented e.g. by the genus Geobacter (Desulfuromonadia). [21]

Certain species of the families Geobacteraceae and Desulfuromonadaceae (Desulfuromonadia) are able to use external surfaces as electron acceptors to complete respiration. [8] [22] [23] Species of the genus Geobacter use bacterial nanowires to transfer electrons to extracellular electron acceptors such as Fe(III) oxides. [10]

Alternative Electron Transport Chain to move electrons to outer membrane of Geobacter Sulfurreducens Geobacter Sulfurreducens Pathway.jpg
Alternative Electron Transport Chain to move electrons to outer membrane of Geobacter Sulfurreducens

Certain species of the class Syntrophia use simple organic molecules as electron donors and grow only in the presence of H2/formate-utilizing partners (methanogens or Desulfovibrio ) in syntrophic associations. [24]

The family Desulfobulbaceae contains two genera of cable bacteria: Ca.  Electronema and Ca.  Electrothrix. These filamentous bacteria conduct electricity across distances over 1 cm, which allows them to connect distant sources of electron donors and electron acceptors. [9]

Notable species

Microscopy

Phylogeny

The phylogeny is based on phylogenomic analysis:

120 marker proteins based GTDB 09-RS220 [33] [34] [35]

Waite et al. 2020 [2]

Thermodesulfo
‑bacteriota


16S rRNA based LTP_10_2024 [36] [37] [38]

Desulfobacterota G
Syntrophorhabdia

Syntrophorhabdales

"Desulfuromonadota"
"Desulfatiglandia"

Desulfatiglandales

Desulfobaccia

Desulfobaccales

Dissulfuribacteria

Dissulfuribacterales

"Binatota"
"Binatia"

"Binatales"

(Desulfobacterota B)
"Deferrisomatota"
(Desulfobacterota C)
"Deferrimicrobiota"
"Deferrimicrobiia"

"Deferrimicrobiales"

(Desulfobacterota E)
Thermodesulfo
‑bacteriota
Desulfobacterota G
Syntrophorhabdia

Syntrophorhabdales

"Dadaibacteriota"
"Dadabacteria"

"Nemesobacterales"

(Desulfobacterota D)
"Acidulodesulfobacteriota"
"Acidulodesulfobacteriia"

"Acidulidesulfobacterales"
(SZUA-79)

See also

Reference

  1. ↑ Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi: 10.1099/ijsem.0.005056 . PMID   34694987.
  2. 1 2 3 Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. (2020). "Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities". Int J Syst Evol Microbiol. 70 (11): 5972–6016. doi: 10.1099/ijsem.0.004213 . PMID   33151140.
  3. ↑ Gavriilidou, et al. (2023). "Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle". The ISME Journal. 17 (11): 1808–1818. Bibcode:2023ISMEJ..17.1808G. doi: 10.1038/s41396-023-01484-z . PMC   10579324 . PMID   37587369.
  4. 1 2 3 4 5 6 Waite, David W; Chuvochina, Maria; Pelikan, Claus; Parks, Donovan H; Yilmaz, Pelin; Wagner, Michael; Loy, Alexander; Naganuma, Takeshi; Nakai, Ryosuke; Whitman, William B; Hahn, Martin W; Kuever, Jan; Hugenholtz, Philip (2020-11-01). "Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5972–6016. doi: 10.1099/ijsem.0.004213 . ISSN   1466-5026. PMID   33151140.
  5. ↑ Müller, Albert Leopold; Kjeldsen, Kasper Urup; Rattei, Thomas; Pester, Michael; Loy, Alexander (2015-05-01). "Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases". The ISME Journal. 9 (5): 1152–1165. Bibcode:2015ISMEJ...9.1152M. doi:10.1038/ismej.2014.208. ISSN   1751-7362. PMC   4351914 . PMID   25343514.
  6. 1 2 Slobodkin, A. I.; Slobodkina, G. B. (2019). "Diversity of Sulfur-Disproportionating Microorganisms" . Microbiology. 88 (5): 509–522. doi:10.1134/S0026261719050138. ISSN   0026-2617.
  7. ↑ Slobodkina, G. B.; Reysenbach, A.-L.; Panteleeva, A. N.; Kostrikina, N. A.; Wagner, I. D.; Bonch-Osmolovskaya, E. A.; Slobodkin, A. I. (2012-10-01). "Deferrisoma camini gen. nov., sp. nov., a moderately thermophilic, dissimilatory iron(III)-reducing bacterium from a deep-sea hydrothermal vent that forms a distinct phylogenetic branch in the Deltaproteobacteria" . International Journal of Systematic and Evolutionary Microbiology. 62 (Pt_10): 2463–2468. doi:10.1099/ijs.0.038372-0. ISSN   1466-5026. PMID   22140176.
  8. 1 2 Bond, Daniel R.; Holmes, Dawn E.; Tender, Leonard M.; Lovley, Derek R. (2002-01-18). "Electrode-Reducing Microorganisms That Harvest Energy from Marine Sediments" . Science. 295 (5554): 483–485. Bibcode:2002Sci...295..483B. doi:10.1126/science.1066771. ISSN   0036-8075. PMID   11799240.
  9. 1 2 Pfeffer, Christian; Larsen, Steffen; Song, Jie; Dong, Mingdong; Besenbacher, Flemming; Meyer, Rikke Louise; Kjeldsen, Kasper Urup; Schreiber, Lars; Gorby, Yuri A.; El-Naggar, Mohamed Y.; Leung, Kar Man; Schramm, Andreas; Risgaard-Petersen, Nils; Nielsen, Lars Peter (2012). "Filamentous bacteria transport electrons over centimetre distances" . Nature. 491 (7423): 218–221. Bibcode:2012Natur.491..218P. doi:10.1038/nature11586. ISSN   0028-0836. PMID   23103872.
  10. 1 2 Reguera, Gemma; McCarthy, Kevin D.; Mehta, Teena; Nicoll, Julie S.; Tuominen, Mark T.; Lovley, Derek R. (2005). "Extracellular electron transfer via microbial nanowires" . Nature. 435 (7045): 1098–1101. Bibcode:2005Natur.435.1098R. doi:10.1038/nature03661. ISSN   0028-0836. PMID   15973408.
  11. 1 2 3 Krukenberg, Viola; Harding, Katie; Richter, Michael; Glöckner, Frank Oliver; Gruber-Vodicka, Harald R.; Adam, Birgit; Berg, Jasmine S.; Knittel, Katrin; Tegetmeyer, Halina E.; Boetius, Antje; Wegener, Gunter (2016). "Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane". Environmental Microbiology. 18 (9): 3073–3091. Bibcode:2016EnvMi..18.3073K. doi: 10.1111/1462-2920.13283 . ISSN   1462-2912. PMID   26971539.
  12. ↑ Martinez-Gutierrez, Carolina A; Aylward, Frank O (2021-12-09). Battistuzzi, Fabia Ursula (ed.). "Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea". Molecular Biology and Evolution. 38 (12): 5514–5527. doi:10.1093/molbev/msab254. ISSN   1537-1719. PMC   8662615 . PMID   34436605.
  13. ↑ Davín, Adrián A.; Woodcroft, Ben J.; Soo, Rochelle M.; Morel, Benoit; Murali, Ranjani; Schrempf, Dominik; Clark, James; Boussau, Bastien; Moody, Edmund R. R. (2023-08-11), An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event, doi: 10.1101/2023.08.08.552427 , retrieved 2025-03-27
  14. ↑ Knoblauch, Christian; Sahm, Kerstin; Jørgensen, Bo B. (1999-10-01). "Psychrophilic sulfate-reducing bacteria isolated from permanently cold Arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov. and Desulfotalea arctica sp. nov". International Journal of Systematic and Evolutionary Microbiology. 49 (4): 1631–1643. doi:10.1099/00207713-49-4-1631. ISSN   1466-5026. PMID   10555345.
  15. ↑ Isaksen, M. F.; Teske, Andreas (1996-09-13). "Desulforhopalus vacuolatus gen. nov., sp. nov., a new moderately psychrophilic sulfate-reducing bacterium with gas vacuoles isolated from a temperate estuary" . Archives of Microbiology. 166 (3): 160–168. Bibcode:1996ArMic.166..160I. doi:10.1007/s002030050371. ISSN   0302-8933.
  16. 1 2 Thorup, Casper; Schramm, Andreas; Findlay, Alyssa J.; Finster, Kai W.; Schreiber, Lars (2017-07-18). "Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium Desulfurivibrio alkaliphilus by Sulfide Oxidation with Nitrate". mBio. 8 (4): 10.1128/mbio.00671–17. doi:10.1128/mbio.00671-17. PMC   5516251 . PMID   28720728.
  17. ↑ Hoeft, Shelley E.; Kulp, Thomas R.; Stolz, John F.; Hollibaugh, James T.; Oremland, Ronald S. (2004). "Dissimilatory arsenate reduction with sulfide as electron donor: experiments with mono lake water and Isolation of strain MLMS-1, a chemoautotrophic arsenate respirer". Applied and Environmental Microbiology. 70 (5): 2741–2747. Bibcode:2004ApEnM..70.2741H. doi:10.1128/AEM.70.5.2741-2747.2004. ISSN   0099-2240. PMC   404439 . PMID   15128527.
  18. ↑ Slobodkina, Galina B.; Mardanov, Andrey V.; Ravin, Nikolai V.; Frolova, Anastasia A.; Chernyh, Nikolay A.; Bonch-Osmolovskaya, Elizaveta A.; Slobodkin, Alexander I. (2017). "Respiratory Ammonification of Nitrate Coupled to Anaerobic Oxidation of Elemental Sulfur in Deep-Sea Autotrophic Thermophilic Bacteria". Frontiers in Microbiology. 8: 87. doi: 10.3389/fmicb.2017.00087 . ISSN   1664-302X. PMC   5276818 . PMID   28194142.
  19. ↑ Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper T.; Bøggild, Andreas; Yang, Tingting; Kjeldsen, Kasper U.; Schramm, Andreas (2016). "A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema". Systematic and Applied Microbiology. 39 (5): 297–306. Bibcode:2016SyApM..39..297T. doi:10.1016/j.syapm.2016.05.006. ISSN   1618-0984. PMC   4958695 . PMID   27324572.
  20. ↑ Hemon, Marie; Novák, Lukáš; Allioux, Maxime; Ailliot, Léna; Vince, Erwann; Alain, Karine (2025-06-09). "Draft genome sequence of Desulfobacterota strain M19, a mesophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge". Microbiology Resource Announcements. 0 (0): e00295–25. doi:10.1128/mra.00295-25.
  21. ↑ Luef, Birgit; Fakra, Sirine C; Csencsits, Roseann; Wrighton, Kelly C; Williams, Kenneth H; Wilkins, Michael J; Downing, Kenneth H; Long, Philip E; Comolli, Luis R; Banfield, Jillian F (2013-02-01). "Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth". The ISME Journal. 7 (2): 338–350. Bibcode:2013ISMEJ...7..338L. doi:10.1038/ismej.2012.103. ISSN   1751-7362. PMC   3554402 . PMID   23038172.
  22. ↑ Holmes, Dawn E.; Nicoll, Julie S.; Bond, Daniel R.; Lovley, Derek R. (2004). "Potential Role of a Novel Psychrotolerant Member of the Family Geobacteraceae , Geopsychrobacter electrodiphilus gen. nov., sp. nov., in Electricity Production by a Marine Sediment Fuel Cell". Applied and Environmental Microbiology. 70 (10): 6023–6030. Bibcode:2004ApEnM..70.6023H. doi:10.1128/AEM.70.10.6023-6030.2004. ISSN   0099-2240. PMC   522133 . PMID   15466546.
  23. ↑ Reguera, Gemma; McCarthy, Kevin D.; Mehta, Teena; Nicoll, Julie S.; Tuominen, Mark T.; Lovley, Derek R. (2005). "Extracellular electron transfer via microbial nanowires" . Nature. 435 (7045): 1098–1101. Bibcode:2005Natur.435.1098R. doi:10.1038/nature03661. ISSN   0028-0836. PMID   15973408.
  24. ↑ Kuever, Jan (2014), Rosenberg, Eugene; DeLong, Edward F.; Lory, Stephen; Stackebrandt, Erko (eds.), "The Family Syntrophaceae" , The Prokaryotes, Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 281–288, doi:10.1007/978-3-642-39044-9_269, ISBN   978-3-642-39043-2 , retrieved 2025-03-27
  25. ↑ Gong, Yanming; Ebrahim, Ali; Feist, Adam M.; Embree, Mallory; Zhang, Tian; Lovley, Derek; Zengler, Karsten (2013-01-02). "Sulfide-Driven Microbial Electrosynthesis" . Environmental Science & Technology. 47 (1): 568–573. Bibcode:2013EnST...47..568G. doi:10.1021/es303837j. ISSN   0013-936X. PMID   23252645.
  26. ↑ McORIST, S.; Gebhart, C. J.; Boid, R.; Barns, S. M. (1995-10-01). "Characterization of Lawsonia intracellularis gen. nov., sp. nov., the Obligately Intracellular Bacterium of Porcine Proliferative Enteropathy". International Journal of Systematic Bacteriology. 45 (4): 820–825. doi:10.1099/00207713-45-4-820. ISSN   0020-7713. PMID   7547305.
  27. ↑ Gebhart, C. J.; Barns, S. M.; Mcorist, S.; Lin, G.-F.; Lawson, G. H. K. (1993-07-01). "Ileal Symbiont Intracellularis, an Obligate Intracellular Bacterium of Porcine Intestines Showing a Relationship to Desulfovibrio Species". International Journal of Systematic Bacteriology. 43 (3): 533–538. doi:10.1099/00207713-43-3-533. ISSN   0020-7713. PMID   8347512.
  28. ↑ Feio, M. J. (2004-09-01). "Desulfovibrio alaskensis sp. nov., a sulphate-reducing bacterium from a soured oil reservoir". International Journal of Systematic and Evolutionary Microbiology. 54 (5): 1747–1752. doi:10.1099/ijs.0.63118-0. hdl: 21.11116/0000-0001-D111-F . ISSN   1466-5026. PMID   15388739.
  29. ↑ Hauser, Loren J.; Land, Miriam L.; Brown, Steven D.; Larimer, Frank; Keller, Kimberly L.; Rapp-Giles, Barbara J.; Price, Morgan N.; Lin, Monica; Bruce, David C.; Detter, John C.; Tapia, Roxanne; Han, Cliff S.; Goodwin, Lynne A.; Cheng, Jan-Fang; Pitluck, Samuel (2011-08-15). "Complete Genome Sequence and Updated Annotation of Desulfovibrio alaskensis G20". Journal of Bacteriology. 193 (16): 4268–4269. doi:10.1128/JB.05400-11. ISSN   0021-9193. PMC   3147700 . PMID   21685289.
  30. ↑ Qiu, Yan-Ling; Hanada, Satoshi; Ohashi, Akiyoshi; Harada, Hideki; Kamagata, Yoichi; Sekiguchi, Yuji (2008). "Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the First Cultured Anaerobe Capable of Degrading Phenol to Acetate in Obligate Syntrophic Associations with a Hydrogenotrophic Methanogen". Applied and Environmental Microbiology. 74 (7): 2051–2058. Bibcode:2008ApEnM..74.2051Q. doi:10.1128/AEM.02378-07. ISSN   0099-2240. PMC   2292594 . PMID   18281436.
  31. ↑ Slobodkin, A. I.; Reysenbach, A.-L.; Slobodkina, G. B.; Kolganova, T. V.; Kostrikina, N. A.; Bonch-Osmolovskaya, E. A. (2013-06-01). "Dissulfuribacter thermophilus gen. nov., sp. nov., a thermophilic, autotrophic, sulfur-disproportionating, deeply branching deltaproteobacterium from a deep-sea hydrothermal vent" . International Journal of Systematic and Evolutionary Microbiology. 63 (Pt_6): 1967–1971. doi:10.1099/ijs.0.046938-0. ISSN   1466-5026. PMID   23024145.
  32. ↑ Fu, Tianda; Liu, Xiaomeng; Gao, Hongyan; Ward, Joy E.; Liu, Xiaorong; Yin, Bing; Wang, Zhongrui; Zhuo, Ye; Walker, David J. F.; Joshua Yang, J.; Chen, Jianhan; Lovley, Derek R.; Yao, Jun (2020-04-20). "Bioinspired bio-voltage memristors". Nature Communications. 11 (1): 1861. Bibcode:2020NatCo..11.1861F. doi:10.1038/s41467-020-15759-y. ISSN   2041-1723. PMC   7171104 . PMID   32313096.
  33. ↑ "GTDB release 09-RS220". Genome Taxonomy Database . Retrieved 10 May 2024.
  34. ↑ "bac120_r220.sp_labels". Genome Taxonomy Database . Retrieved 10 May 2024.
  35. ↑ "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2024.
  36. ↑ "The LTP" . Retrieved 10 December 2024.
  37. ↑ "LTP_all tree in newick format" . Retrieved 10 December 2024.
  38. ↑ "LTP_10_2024 Release Notes" (PDF). Retrieved 10 December 2024.
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