Syntrophy
{{short description|Cooperation between microbial species to digest a substrate}}
In biology, syntrophy,{{Citation |last1=Gentry |first1=Terry J. |title=Chapter 19 - Microbial Diversity and Interactions in Natural Ecosystems |date=2015-01-01 |url=https://www.sciencedirect.com/science/article/pii/B9780123946263000193 |work=Environmental Microbiology (Third Edition) |pages=441–460 |editor-last=Pepper |editor-first=Ian L. |access-date=2023-12-27 |place=San Diego |publisher=Academic Press |doi=10.1016/b978-0-12-394626-3.00019-3 |isbn=978-0-12-394626-3 |last2=Pepper |first2=Ian L. |last3=Pierson |first3=Leland S. |editor2-last=Gerba |editor2-first=Charles P. |editor3-last=Gentry |editor3-first=Terry J.|url-access=subscription }}{{Citation |last=Marietou |first=Angeliki |title=Chapter Two - Sulfate reducing microorganisms in high temperature oil reservoirs |date=2021-01-01 |url=https://www.sciencedirect.com/science/article/pii/S006521642100006X |journal=Advances in Applied Microbiology |volume=116 |pages=99–131 |editor-last=Gadd |editor-first=Geoffrey Michael |access-date=2023-12-27 |publisher=Academic Press |doi=10.1016/bs.aambs.2021.03.004 |pmid=34353505 |editor2-last=Sariaslani |editor2-first=Sima|url-access=subscription }} syntrophism,{{Cite web |date=2022-09-30 |title=syntrophism {{!}} biology {{!}} Britannica |url=https://www.britannica.com/science/syntrophism |access-date=2023-12-27 |archive-url=https://web.archive.org/web/20220930004228/https://www.britannica.com/science/syntrophism |archive-date=2022-09-30 }}{{Cite web |date=2022-08-19 |title=Syntrophism Definition & Meaning {{!}} Merriam-Webster Medical |url=https://www.merriam-webster.com/medical/syntrophism |access-date=2023-12-27 |archive-url=https://web.archive.org/web/20220819204804/https://www.merriam-webster.com/medical/syntrophism |archive-date=2022-08-19 }} or cross-feeding ({{ety|el|syn|together||trophe|nourishment}}) is the cooperative interaction between at least two microbial species to degrade a single substrate.{{cite book | vauthors = Kamagata Y | chapter = Syntrophy in Anaerobic Digestion |date=2015-03-15 |chapter-url=https://www.worldscientific.com/doi/abs/10.1142/9781783267910_0002 | title = Anaerobic Biotechnology |pages=13–30 |publisher=Imperial College Press |doi=10.1142/9781783267910_0002 |isbn=978-1-78326-790-3 |access-date=2022-11-11}}{{cite journal | vauthors = Hao L, Michaelsen TY, Singleton CM, Dottorini G, Kirkegaard RH, Albertsen M, Nielsen PH, Dueholm MS | display-authors = 6 | title = Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics | journal = The ISME Journal | volume = 14 | issue = 4 | pages = 906–918 | date = April 2020 | pmid = 31896784 | pmc = 7082340 | doi = 10.1038/s41396-019-0571-0 | bibcode = 2020ISMEJ..14..906H }} This type of biological interaction typically involves the transfer of one or more metabolic intermediates between two or more metabolically diverse microbial species living in close proximity to each other.{{cite book | vauthors = Schink B, Stams AJ | chapter = Syntrophism Among Prokaryotes |date=2013 | title = The Prokaryotes: Prokaryotic Communities and Ecophysiology |pages=471–493 | veditors = Rosenberg E, DeLong EF, Lory S, Stackebrandt E |place=Berlin, Heidelberg |publisher=Springer |language=en |doi=10.1007/978-3-642-30123-0_59 |isbn=978-3-642-30123-0 | chapter-url = http://nbn-resolving.de/urn:nbn:de:bsz:352-276499 }} Thus, syntrophy can be considered an obligatory interdependency and a mutualistic metabolism between different microbial species, wherein the growth of one partner depends on the nutrients, growth factors, or substrates provided by the other(s).{{cite journal | vauthors = Dolfing J | title = Syntrophy in microbial fuel cells | journal = The ISME Journal | volume = 8 | issue = 1 | pages = 4–5 | date = January 2014 | pmid = 24173460 | pmc = 3869025 | doi = 10.1038/ismej.2013.198 | bibcode = 2014ISMEJ...8....4D }}{{cite journal | vauthors = Morris BE, Henneberger R, Huber H, Moissl-Eichinger C | title = Microbial syntrophy: interaction for the common good | journal = FEMS Microbiology Reviews | volume = 37 | issue = 3 | pages = 384–406 | date = May 2013 | pmid = 23480449 | doi = 10.1111/1574-6976.12019 | doi-access = free }}
Microbial syntrophy
Syntrophy is often used synonymously for mutualistic symbiosis especially between at least two different bacterial species. Syntrophy differs from symbiosis in a way that syntrophic relationship is primarily based on closely linked metabolic interactions to maintain thermodynamically favorable lifestyle in a given environment.{{cite journal | vauthors = Sieber JR, McInerney MJ, Gunsalus RP | title = Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation | journal = Annual Review of Microbiology | volume = 66 | pages = 429–452 | date = 2012 | pmid = 22803797 | doi = 10.1146/annurev-micro-090110-102844 }}{{cite journal | vauthors = McInerney MJ, Sieber JR, Gunsalus RP | title = Syntrophy in anaerobic global carbon cycles | journal = Current Opinion in Biotechnology | volume = 20 | issue = 6 | pages = 623–632 | date = December 2009 | pmid = 19897353 | pmc = 2790021 | doi = 10.1016/j.copbio.2009.10.001 }}{{cite journal | vauthors = McInerney MJ, Rohlin L, Mouttaki H, Kim U, Krupp RS, Rios-Hernandez L, Sieber J, Struchtemeyer CG, Bhattacharyya A, Campbell JW, Gunsalus RP | display-authors = 6 | title = The genome of Syntrophus aciditrophicus: life at the thermodynamic limit of microbial growth | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 18 | pages = 7600–7605 | date = May 2007 | pmid = 17442750 | pmc = 1863511 | doi = 10.1073/pnas.0610456104 | doi-access = free | bibcode = 2007PNAS..104.7600M }} Syntrophy plays an important role in a large number of microbial processes especially in oxygen limited environments, methanogenic environments and anaerobic systems.{{cite journal | vauthors = McInerney MJ, Sieber JR, Gunsalus RP | title = Syntrophy in anaerobic global carbon cycles | journal = Current Opinion in Biotechnology | volume = 20 | issue = 6 | pages = 623–632 | date = December 2009 | pmid = 19897353 | pmc = 2790021 | doi = 10.1016/j.copbio.2009.10.001 | series = Chemical biotechnology ● Pharmaceutical biotechnology }}{{Cite book | vauthors = Worm P, Müller N, Plugge CM, Stams AJ, Schink B | chapter = Syntrophy in methanogenic degradation. | title = (Endo)symbiotic Methanogenic Archaea | date = 2010 | pages = 143–173 | publisher = Springer | location = Berlin, Heidelberg |series=Microbiology Monographs |volume=19 |language=en |doi=10.1007/978-3-642-13615-3_9 |isbn=978-3-642-13614-6 }} In anoxic or methanogenic environments such as wetlands, swamps, paddy fields, landfills, digestive tract of ruminants, and anerobic digesters syntrophy is employed to overcome the energy constraints as the reactions in these environments proceed close to thermodynamic equilibrium.{{cite journal | vauthors = Jackson BE, McInerney MJ | title = Anaerobic microbial metabolism can proceed close to thermodynamic limits | journal = Nature | volume = 415 | issue = 6870 | pages = 454–456 | date = January 2002 | pmid = 11807560 | doi = 10.1038/415454a | s2cid = 9126984 | bibcode = 2002Natur.415..454J }}
= Mechanism of microbial syntrophy =
The main mechanism of syntrophy is removing the metabolic end products of one species so as to create an energetically favorable environment for another species. This obligate metabolic cooperation is required to facilitate the degradation of complex organic substrates under anaerobic conditions. Complex organic compounds such as ethanol, propionate, butyrate, and lactate cannot be directly used as substrates for methanogenesis by methanogens. On the other hand, fermentation of these organic compounds cannot occur in fermenting microorganisms unless the hydrogen concentration is reduced to a low level by the methanogens. The key mechanism that ensures the success of syntrophy is interspecies electron transfer.{{Cite journal |vauthors = Zhang M, Zang L |date=2019 |title=A review of interspecies electron transfer in anaerobic digestion |journal=IOP Conf. Ser: Earth Environ|volume=310 |issue=4 |page=042026 |doi=10.1088/1755-1315/310/4/042026 |bibcode=2019E&ES..310d2026Z |s2cid=202886264 |doi-access=free }} The interspecies electron transfer can be carried out via three ways: interspecies hydrogen transfer, interspecies formate transfer and interspecies direct electron transfer.{{cite journal | vauthors = Rotaru AE, Shrestha PM, Liu F, Ueki T, Nevin K, Summers ZM, Lovley DR | title = Interspecies electron transfer via hydrogen and formate rather than direct electrical connections in cocultures of Pelobacter carbinolicus and Geobacter sulfurreducens | journal = Applied and Environmental Microbiology | volume = 78 | issue = 21 | pages = 7645–7651 | date = November 2012 | pmid = 22923399 | pmc = 3485699 | doi = 10.1128/AEM.01946-12 | bibcode = 2012ApEnM..78.7645R }} Reverse electron transport is prominent in syntrophic metabolism.
The metabolic reactions and the energy involved for syntrophic degradation with H2 consumption:{{Cite journal | vauthors = Zhang Y, Li C, Yuan Z, Wang R, Angelidaki I, Zhu G |date=2023-01-15 |title=Syntrophy mechanism, microbial population, and process optimization for volatile fatty acids metabolism in anaerobic digestion |journal=Chemical Engineering Journal |language=en |volume=452 |pages=139137 |doi=10.1016/j.cej.2022.139137 |bibcode=2023ChEnJ.45239137Z |s2cid=252205776 |issn=1385-8947|url=https://backend.orbit.dtu.dk/ws/files/294418934/Manuscript_Yao_Zhang.pdf }}
A classical syntrophic relationship can be illustrated by the activity of Methanobacillus omelianskii. It was isolated several times from anaerobic sediments and sewage sludge and was regarded as a pure culture of an anaerobe converting ethanol to acetate and methane. In fact, however, the culture turned out to consist of a methanogenic archaeon "organism M.o.H" and a Gram-negative Bacterium "Organism S" which involves the oxidization of ethanol into acetate and methane mediated by interspecies hydrogen transfer. Individuals of organism S are observed as obligate anaerobic bacteria that use ethanol as an electron donor, whereas M.o.H are methanogens that oxidize hydrogen gas to produce methane.{{cite journal | vauthors = Wrede C, Dreier A, Kokoschka S, Hoppert M | title = Archaea in symbioses | journal = Archaea | volume = 2012 | pages = 596846 | date = 2012 | pmid = 23326206 | pmc = 3544247 | doi = 10.1155/2012/596846 | doi-access = free }}
Organism S: 2 Ethanol + 2 H2O → 2 Acetate− + 2 H+ + 4 H2 (ΔG°' = +9.6 kJ per reaction)
Strain M.o.H.: 4 H2 + CO2 → Methane + 2 H2O (ΔG°' = -131 kJ per reaction)
Co-culture:2 Ethanol + CO2 → 2 Acetate− + 2 H+ + Methane (ΔG°' = -113 kJ per reaction)
The oxidization of ethanol by organism S is made possible thanks to the methanogen M.o.H, which consumes the hydrogen produced by organism S, by turning the positive Gibbs free energy into negative Gibbs free energy. This situation favors growth of organism S and also provides energy for methanogens by consuming hydrogen. Down the line, acetate accumulation is also prevented by similar syntrophic relationship. Syntrophic degradation of substrates like butyrate and benzoate can also happen without hydrogen consumption.
An example of propionate and butyrate degradation with interspecies formate transfer carried out by the mutual system of Syntrophomonas wolfei and Methanobacterium formicicum:
: Propionate + 2H2O + 2CO2 → Acetate− + 3Formate− + 3H+ (ΔG°'=+65.3 kJ/mol)
:Butyrate + 2H2O + 2CO2 → 2Acetate- + 3Formate- + 3H+ (ΔG°'=+38.5 kJ/mol)
Direct interspecies electron transfer (DIET) which involves electron transfer without any electron carrier such as H2 or formate was reported in the co-culture system of Geobacter mettalireducens and Methanosaeto or Methanosarcina{{cite book | vauthors = Dubé CD, Guiot SR | chapter = Direct Interspecies Electron Transfer in Anaerobic Digestion: A Review | series = Advances in Biochemical Engineering/Biotechnology | title = Biogas Science and Technology | volume = 151 | pages = 101–15 | date = 2015 | pmid = 26337845 | doi = 10.1007/978-3-319-21993-6_4 | isbn = 978-3-319-21992-9 }}
Examples
= In ruminants =
The defining feature of ruminants, such as cows and goats, is a stomach called a rumen.{{Cite web |work = AnimalSmart.org |title=What's a Rumen |url=https://animalsmart.org/species/what%27s-a-rumen- |access-date=2022-11-21 |language=en}} The rumen contains billions of microbes, many of which are syntrophic.{{cite journal | vauthors = Ng F, Kittelmann S, Patchett ML, Attwood GT, Janssen PH, Rakonjac J, Gagic D | title = An adhesin from hydrogen-utilizing rumen methanogen Methanobrevibacter ruminantium M1 binds a broad range of hydrogen-producing microorganisms | journal = Environmental Microbiology | volume = 18 | issue = 9 | pages = 3010–3021 | date = September 2016 | pmid = 26643468 | doi = 10.1111/1462-2920.13155 | doi-access = free | bibcode = 2016EnvMi..18.3010N }} Some anaerobic fermenting microbes in the rumen (and other gastrointestinal tracts) are capable of degrading organic matter to short chain fatty acids, and hydrogen. The accumulating hydrogen inhibits the microbe's ability to continue degrading organic matter, but the presence of syntrophic hydrogen-consuming microbes allows continued growth by metabolizing the waste products. In addition, fermentative bacteria gain maximum energy yield when protons are used as electron acceptor with concurrent H2 production. Hydrogen-consuming organisms include methanogens, sulfate-reducers, acetogens, and others.{{Cite web | vauthors = Sapkota A |date=2022-07-12 |title=Syntrophism or Syntrophy Interaction- Definition, Examples |url=https://thebiologynotes.com/syntrophism-or-syntrophy/ |access-date=2022-11-21 |website=The Biology Notes |language=en-US}}
Some fermentation products, such as fatty acids longer than two carbon atoms, alcohols longer than one carbon atom, and branched chain and aromatic fatty acids, cannot directly be used in methanogenesis.{{Cite journal | vauthors = Kang D, Saha S, Kurade MB, Basak B, Ha G, Jeon B, Lee SS, Kim JR | display-authors = 6 |date= July 2021 |title=Dual-stage pulse-feed operation enhanced methanation of lipidic waste during co-digestion using acclimatized consortia |journal=Renewable and Sustainable Energy Reviews |language=en |volume=145 |pages=111096 |doi=10.1016/j.rser.2021.111096 | bibcode = 2021RSERv.14511096K |s2cid=234830362 |issn=1364-0321}} In acetogenesis processes, these products are oxidized to acetate and H2 by obligated proton reducing bacteria in syntrophic relationship with methanogenic archaea as low H2 partial pressure is essential for acetogenic reactions to be thermodynamically favorable (ΔG < 0).{{cite journal | vauthors = Stams AJ, de Bok FA, Plugge CM, van Eekert MH, Dolfing J, Schraa G | title = Exocellular electron transfer in anaerobic microbial communities | journal = Environmental Microbiology | volume = 8 | issue = 3 | pages = 371–382 | date = March 2006 | pmid = 16478444 | doi = 10.1111/j.1462-2920.2006.00989.x | bibcode = 2006EnvMi...8..371S }}
= Biodegradation of pollutants =
Syntrophic microbial food webs play an integral role in bioremediation especially in environments contaminated with crude oil and petrol. Environmental contamination with oil is of high ecological importance and can be effectively mediated through syntrophic degradation by complete mineralization of alkane, aliphatic and hydrocarbon chains.{{cite journal | vauthors = Ferry JG, Wolfe RS | title = Anaerobic degradation of benzoate to methane by a microbial consortium | journal = Archives of Microbiology | volume = 107 | issue = 1 | pages = 33–40 | date = February 1976 | pmid = 1252087 | doi = 10.1007/BF00427864 | bibcode = 1976ArMic.107...33F | s2cid = 31426072 }} The hydrocarbons of the oil are broken down after activation by fumarate, a chemical compound that is regenerated by other microorganisms.{{cite journal | vauthors = Callaghan AV, Morris BE, Pereira IA, McInerney MJ, Austin RN, Groves JT, Kukor JJ, Suflita JM, Young LY, Zylstra GJ, Wawrik B | display-authors = 6 | title = The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for anaerobic alkane oxidation | journal = Environmental Microbiology | volume = 14 | issue = 1 | pages = 101–113 | date = January 2012 | pmid = 21651686 | doi = 10.1111/j.1462-2920.2011.02516.x | bibcode = 2012EnvMi..14..101C }} Without regeneration, the microbes degrading the oil would eventually run out of fumarate and the process would cease. This breakdown is crucial in the processes of bioremediation and global carbon cycling.
Syntrophic microbial communities are key players in the breakdown of aromatic compounds, which are common pollutants. The degradation of aromatic benzoate to methane produces intermediate compounds such as formate, acetate, {{CO2|link=yes}} and H2. The buildup of these products makes benzoate degradation thermodynamically unfavorable. These intermediates can be metabolized syntrophically by methanogens and makes the degradation process thermodynamically favorable
= Degradation of amino acids =
Studies have shown that bacterial degradation of amino acids can be significantly enhanced through the process of syntrophy.{{Cite journal | vauthors = Zindel U, Freudenberg W, Rieth M, Andreesen JR, Schnell J, Widdel F |date= July 1988 |title=Eubacterium acidaminophilum sp. nov., a versatile amino acid-degrading anaerobe producing or utilizing H2 or formate |journal=Archives of Microbiology |language=en |volume=150 |issue=3 |pages=254–266 |doi=10.1007/BF00407789 |bibcode= 1988ArMic.150..254Z |issn=0302-8933 |s2cid=34824309}} Microbes growing poorly on amino acid substrates alanine, aspartate, serine, leucine, valine, and glycine can have their rate of growth dramatically increased by syntrophic H2 scavengers. These scavengers, like Methanospirillum and Acetobacterium, metabolize the H2 waste produced during amino acid breakdown, preventing a toxic build-up. Another way to improve amino acid breakdown is through interspecies electron transfer mediated by formate. Species like Desulfovibrio employ this method. Amino acid fermenting anaerobes such as Clostridium species, Peptostreptococcus asacchaarolyticus, Acidaminococcus fermentans were known to breakdown amino acids like glutamate with the help of hydrogen scavenging methanogenic partners without going through the usual Stickland fermentation pathway
= Anaerobic digestion =
Syntrophic theories of eukaryogenesis
Many symbiogenetic models of eukaryogenesis propose that the first eukaryotic cells were derived from endosymbiosis facilitated by microbial syntrophy between prokaryotic cells. Most of these models involve an archaeon and an alphaproteobacterium, where the dependence of the archaeon on the alphaproteobacterium leads the former to engulf the latter, the alphaproteobacterium then eventually becoming the mitochondria. While these models share the concept of syntrophic interaction as a key driver of endosymbiosis, they often differ on the exact nature of the metabolic interactions involved and the mechanisms by which eukaryogenesis occurred.
= Hydrogen hypothesis =
In 1998, William F. Martin and Miklós Müller introduced the hydrogen hypothesis, proposing that eukaryotes arose from syntrophic associations based on the transfer of H2.{{Cite journal |last1=Martin |first1=William |last2=Müller |first2=Miklós |date=March 1998 |title=The hydrogen hypothesis for the first eukaryote |url=https://www.nature.com/articles/32096 |journal=Nature |language=en |volume=392 |issue=6671 |pages=37–41 |doi=10.1038/32096 |pmid=9510246 |bibcode=1998Natur.392...37M |issn=1476-4687|url-access=subscription }} In this model, an syntrophic association arose where a anaerobic autotrophic methanogenic archaeon was dependent on the H2 made as a byproduct of anaerobic respiration by a facultatively anaerobic alphaproteobacterium. This syntrophy led the alphaproteobacterium to become an endosymbiont of the archaeon, serving as the precursor to the mitochondria.
= Dennis Searcy model =
Dennis Searcy proposed that the precursors to mitochondria were parasitic bacteria that developed a syntrophy with their hosts based upon the transfer of organic acids, H2 transfer, and the reciprocal exchange of sulfur compounds.{{Cite journal |last=Searcy |first=Dennis G. |date=August 2003 |title=Metabolic integration during the evolutionary origin of mitochondria |url=https://www.nature.com/articles/7290168 |journal=Cell Research |language=en |volume=13 |issue=4 |pages=229–238 |doi=10.1038/sj.cr.7290168 |pmid=12974613 |issn=1748-7838}}
= Reverse flow model =
The reverse flow model was created based on the metabolic analysis of Asgard archaea, which is thought to be the kingdom from which eukaryotes emerged.{{Cite journal |last1=Spang |first1=Anja |last2=Stairs |first2=Courtney W. |last3=Dombrowski |first3=Nina |last4=Eme |first4=Laura |last5=Lombard |first5=Jonathan |last6=Caceres |first6=Eva F. |last7=Greening |first7=Chris |last8=Baker |first8=Brett J. |last9=Ettema |first9=Thijs J. G. |date=July 2019 |title=Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism |url=https://www.nature.com/articles/s41564-019-0406-9 |journal=Nature Microbiology |language=en |volume=4 |issue=7 |pages=1138–1148 |doi=10.1038/s41564-019-0406-9 |pmid=30936488 |issn=2058-5276}}{{Cite journal |last1=Zaremba-Niedzwiedzka |first1=Katarzyna |last2=Caceres |first2=Eva F. |last3=Saw |first3=Jimmy H. |last4=Bäckström |first4=Disa |last5=Juzokaite |first5=Lina |last6=Vancaester |first6=Emmelien |last7=Seitz |first7=Kiley W. |last8=Anantharaman |first8=Karthik |last9=Starnawski |first9=Piotr |last10=Kjeldsen |first10=Kasper U. |last11=Stott |first11=Matthew B. |last12=Nunoura |first12=Takuro |last13=Banfield |first13=Jillian F. |last14=Schramm |first14=Andreas |last15=Baker |first15=Brett J. |date=January 2017 |title=Asgard archaea illuminate the origin of eukaryotic cellular complexity |url=https://www.nature.com/articles/nature21031 |journal=Nature |language=en |volume=541 |issue=7637 |pages=353–358 |doi=10.1038/nature21031 |pmid=28077874 |bibcode=2017Natur.541..353Z |osti=1580084 |issn=1476-4687}}{{Cite journal |last1=Spang |first1=Anja |last2=Saw |first2=Jimmy H. |last3=Jørgensen |first3=Steffen L. |last4=Zaremba-Niedzwiedzka |first4=Katarzyna |last5=Martijn |first5=Joran |last6=Lind |first6=Anders E. |last7=van Eijk |first7=Roel |last8=Schleper |first8=Christa |last9=Guy |first9=Lionel |last10=Ettema |first10=Thijs J. G. |date=May 2015 |title=Complex archaea that bridge the gap between prokaryotes and eukaryotes |journal=Nature |language=en |volume=521 |issue=7551 |pages=173–179 |doi=10.1038/nature14447 |pmid=25945739 |pmc=4444528 |bibcode=2015Natur.521..173S |issn=1476-4687}} This model proposes that a syntrophic association arose where anaerobic ancestral Asgard archaea generated and provided reducing equivalents that facultative anaerobic alphaproteobacteria used in the form of H2, small reduced compounds, or by direct electron transfer.
= Entangle-Engulf-Endogenize model =
The Entangle-Engulf-Endogenize (E3) model was created in 2020 based on the isolation of syntrophic archaea from deep sea marine sediment.{{Cite journal |last1=Imachi |first1=Hiroyuki |last2=Nobu |first2=Masaru K. |last3=Nakahara |first3=Nozomi |last4=Morono |first4=Yuki |last5=Ogawara |first5=Miyuki |last6=Takaki |first6=Yoshihiro |last7=Takano |first7=Yoshinori |last8=Uematsu |first8=Katsuyuki |last9=Ikuta |first9=Tetsuro |last10=Ito |first10=Motoo |last11=Matsui |first11=Yohei |last12=Miyazaki |first12=Masayuki |last13=Murata |first13=Kazuyoshi |last14=Saito |first14=Yumi |last15=Sakai |first15=Sanae |date=January 2020 |title=Isolation of an archaeon at the prokaryote–eukaryote interface |journal=Nature |language=en |volume=577 |issue=7791 |pages=519–525 |doi=10.1038/s41586-019-1916-6 |issn=1476-4687 |pmc=7015854 |pmid=31942073|bibcode=2020Natur.577..519I }} Unlike most other symbiogenetic models, the E3 model involves three separate types of microbes: a fermentative archaeon, a facultatively aerobic organotroph (which was acts as the precursor of the mitochondria), and sulfur-reducing bacteria (SRB). This model proposes that, originally, the fermentative archaeon may have degraded amino acids via syntrophic association with SRB and the facultatively aerobic organotroph. As oxygen levels began to rise, however, the interaction with the facultatively aerobic organotroph (which is though to have made the archaeon more aerotolerant) became stronger became stronger until it was engulfed (a process facilitated by syntrophic interaction with SRB). Additionally, the E3 model suggests that, instead of phagocytizing the facultatively aerobic organotroph, the archaeon used extracellular structures to enhance interactions and engulf the facultatively aerobic organotroph.
= Syntrophy hypothesis =
The syntrophy hypothesis was proposed in 2001 by researchers Purificación López-García and David Moreira before being refined in 2020 by the same researchers.{{Citation |last1=LóPez-García |first1=P. |title=The Syntrophy Hypothesis for the Origin of Eukaryotes |date=2002 |work=Symbiosis: Mechanisms and Model Systems |pages=131–146 |editor-last=Seckbach |editor-first=Joseph |url=https://link.springer.com/chapter/10.1007/0-306-48173-1_8 |access-date=2025-05-01 |place=Dordrecht |publisher=Springer Netherlands |language=en |doi=10.1007/0-306-48173-1_8 |isbn=978-0-306-48173-4 |last2=Moreira |first2=D.|url-access=subscription }}{{Cite journal |last1=López-García |first1=Purificación |last2=Moreira |first2=David |date=May 2020 |title=The Syntrophy hypothesis for the origin of eukaryotes revisited |url=https://www.nature.com/articles/s41564-020-0710-4 |journal=Nature Microbiology |language=en |volume=5 |issue=5 |pages=655–667 |doi=10.1038/s41564-020-0710-4 |pmid=32341569 |issn=2058-5276}} Similarly to the E3 model, the syntrophy hypothesis suggests that eukaryogenesis involved three different types of microbes: a complex sulfate-reducing deltaproteobacterium (the precursor to the cytoplasm), an H2-producing Asgard archaeon (the precursor to the nucleus), and a facultatively aerobic sulfide-oxidizing alphaproteobacterium (the precursor to mitochondria). In this model, the deltaproteobacteria forms syntrophic associations with both the Asgard archaeon (based on the transfer of H2) and the alphaproteobacterium (based on the redox of sulfur), leading both to become endosymbionts of the deltaproteobacteria. In this now obligatory symbiosis, organic compounds were degraded in the periplasmic space of the deltaproteobacteria before being moved to the archaeon for further degradation. This interaction drove the periplasm to develop and expand in close proximity with the archaeon to facilitate molecular exchange, resulting in an endomembrane system, transport channels, and the loss of the archaeal membrane. Ultimately, the archaeon became the nucleus while the periplasmic endomembrane system became the endoplasmic reticulum. Meanwhile, the consortium lost the metabolic capability for bacterial sulfate reduction and archaeal energy metabolism as it became more reliant on aerobic respiration performed by the alphaproteobacterium which, ultimately, became the mitochondrion.
Examples of syntrophic organisms
- Syntrophomonas wolfei is a gram-negative, anaerobic, fatty-acid oxidizing bacterium that forms syntrophic associations with H2-using bacteria.{{cite journal | vauthors = McInerney MJ, Bryant MP, Hespell RB, Costerton JW | title = Syntrophomonas wolfei gen. nov. sp. nov., an Anaerobic, Syntrophic, Fatty Acid-Oxidizing Bacterium | journal = Applied and Environmental Microbiology | volume = 41 | issue = 4 | pages = 1029–1039 | date = April 1981 | pmid = 16345745 | pmc = 243852 | doi = 10.1128/aem.41.4.1029-1039.1981 | bibcode = 1981ApEnM..41.1029M }}
- Syntrophobacter fumaroxidans is a gram-negative anaerobic bacterium that can oxidize propionate in pure cultures or in syntrophic association with Methanospirillum hungateii.{{Cite journal |last1=HARMSEN |first1=H. J. M. |last2=VAN KUIJK |first2=B. L. M. |last3=PLUGGE |first3=C. M. |last4=AKKERMANS |first4=A. D. L. |last5=DE VOS |first5=W. M. |last6=STAMS |first6=A. J. M. |date=1998-10-01 |title=Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium |url=https://doi.org/10.1099/00207713-48-4-1383 |journal=International Journal of Systematic Bacteriology |volume=48 |issue=4 |pages=1383–1387 |doi=10.1099/00207713-48-4-1383 |pmid=9828440 |issn=0020-7713}}
- Pelotomaculum thermopropionicum is a thermophilic, anaerobic, syntrophic propionate-oxidizing bacterium that, in co-culture with Methanothermobacter thermautotrophicus, can grow on propionate, ethanol, lactate, 1-butanol, 1-pentanol, 1,3-propanediol, 1-propanol, and ethylene glycol.{{Cite journal |last1=Imachi |first1=Hiroyuki |last2=Sekiguchi |first2=Yuji |last3=Kamagata |first3=Yoichi |last4=Hanada |first4=Satoshi |last5=Ohashi |first5=Akiyoshi |last6=Harada |first6=Hideki |date=2002-09-01 |title=Pelotomaculum thermopropionicum gen. nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium. |url=https://doi.org/10.1099/00207713-52-5-1729 |journal=International Journal of Systematic and Evolutionary Microbiology |volume=52 |issue=5 |pages=1729–1735 |doi=10.1099/00207713-52-5-1729 |pmid=12361280 |issn=1466-5026}}
- Syntrophus aciditrophicus is a gram-negative, obligately anaerobic, nonmotile, rod-shaped bacterium that, in syntrophic association with hydrogen/formate-using methanogens or sulfate reducers, degrades benzoate and fatty acids.{{Cite journal |last1=Jackson |first1=Bradley E. |last2=McInerney |first2=Michael J. |date=January 2002 |title=Anaerobic microbial metabolism can proceed close to thermodynamic limits |url=https://doi.org/10.1038/415454a |journal=Nature |volume=415 |issue=6870 |pages=454–456 |doi=10.1038/415454a |pmid=11807560 |bibcode=2002Natur.415..454J |issn=0028-0836|url-access=subscription }}{{Cite journal |last1=Jackson |first1=Bradley E. |last2=Bhupathiraju |first2=V. K. |last3=Tanner |first3=Ralph S. |last4=Woese |first4=Carl R. |last5=McInerney |first5=M. J. |date=1999-01-14 |title=Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms |url=https://doi.org/10.1007/s002030050685 |journal=Archives of Microbiology |volume=171 |issue=2 |pages=107–114 |doi=10.1007/s002030050685 |pmid=9914307 |bibcode=1999ArMic.171..107J |issn=0302-8933|url-access=subscription }}
- Syntrophus buswellii is a gram-negative, anaerobic, motile, rod-shaped bacterium that, in syntrophic association with H2-using bacteria, degrades benzoate.{{Cite journal |last1=Mountfort |first1=Douglas O. |last2=Bryant |first2=Marvin P. |date=1982 |title=Isolation and characterization of an anaerobic syntrophic benzoate-degrading bacterium from sewage sludge |url=https://doi.org/10.1007/bf00521285 |journal=Archives of Microbiology |volume=133 |issue=4 |pages=249–256 |doi=10.1007/bf00521285 |bibcode=1982ArMic.133..249M |issn=0302-8933|url-access=subscription }}
- Syntrophus gentianae is a obligately anaerobic bacterium that ferments benzoate in syntrophic association with H2-using bacteria.{{cite journal | vauthors = Schöcke L, Schink B | title = Membrane-bound proton-translocating pyrophosphatase of Syntrophus gentianae, a syntrophically benzoate-degrading fermenting bacterium | journal = European Journal of Biochemistry | volume = 256 | issue = 3 | pages = 589–594 | date = September 1998 | pmid = 9780235 | doi = 10.1046/j.1432-1327.1998.2560589.x | url = http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-59985 }}