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Synthetic microbial consortia

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a TEM picture of E. coli, chemoheterotrophic bacteria often used in synthetic microbial consortia.

Synthetic microbial consortia or Synthetic microbial communities (commonly called SynComs) are multi-population systems that can contain a diverse range of microbial species, and are adjustable to serve a variety of industrial, ecological,[1] and tautological[clarification needed] interests. For synthetic biology, consortia take the ability to engineer novel cell behaviors to a population level.

Consortia are more common than not in nature, and generally prove to be more robust than monocultures.[2] Just over 7,000 species of bacteria have been cultured and identified to date. Many of the estimated 1.2 million bacteria species that remain have yet to be cultured and identified, in part due to inabilities to be cultured axenically.[3] Evidence for symbiosis between microbes strongly suggests it to have been a necessary precursor of the evolution of land plants and for their transition from algal communities in the sea to land.[4] When designing synthetic consortia, or editing naturally occurring consortia, synthetic biologists keep track of pH, temperature, initial metabolic profiles, incubation times, growth rate, and other pertinent variables.[2]

Biofuel

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One of the more salient applications of engineering behaviors and interactions between microbes in a community is the ability to combine or even switch metabolisms. The combination of autotrophic and heterotrophic microbes allows the unique possibility of a self-sufficient community that may produce desired biofuels to be collected.[2] Co-culture dyads of autotrophic Synechococcus elongatus and heterotrophic Escherichia coli were found to be able to grow synchronously when the strain of S. elongatus was transformed to include a gene for sucrose export.[5] The commensal combination of the sucrose-producing cyanobacteria with the modified E. coli metabolism may allow for a diverse array of metabolic products such as various butanol biofuels, terpenoids, and fatty-acid derived fuels.[6]

Including a heterotroph also provides a solution to the issues of contamination when producing carbohydrates, as competition may limit contaminant species viability.[2] In isolated systems this can be a restriction to the feasibility of large-scale biofuel operations, like algae ponds, where contamination can significantly reduce the desired output.[7]

Through interactions between Geobacter spp. and methanogens from the soil in a rice paddy field, it was discovered that the use of interspecies electron transfer stimulated the production of methane.[8] Considering the abundance of conductive metals in soils and the use of methane (natural gas) as a fuel, this may lead to a bioenergy-producing process.[8]

Bioremediation

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Use of the extensive range of microbial metabolism offers opportunities to those interested in bioremediation. Through consortia, synthetic biologists have been able to design an enhanced efficiency in bacteria that can excrete bio-surfactants as well as degrade hydrocarbons for the interests of cleaning oil contamination in Assam, India.[9] Their experiment took combinations of five native naturally occurring hydrocarbon-degrading bacteria, and analyzed the different cocktails to see which degraded poly-aromatic hydrocarbons the best.[9] The combination of Bacillus pumilis KS2 and Bacillus cereus R2 was found to be the most effective, degrading 84.15% of the TPH after 5 weeks.[9]

Further remediation efforts have turned to the issue of agricultural pesticide run-off. Pesticides vary in class and function, and in high concentration often lead to highly toxic environmental risks.[10] Of the over-500 types of pesticides in current use, two serious issues are their general lack of biodegradability and unpredictability.[11] In Kyrgyzstan, researchers assessed soil around a pesticide dump and discovered not only that the soil had poor microflora diversity, but that some of the species that were present used metabolic pathways to digest the pesticides.[10] The two most-efficient species found were Pseudomonas fluorescens and Bacillus polymyxa, with B. polymyxa degrading 48.2% of the pesticide Aldrin after 12 days.[10] However, when the strains were combined with each other as well as some other less-efficient yet native bacteria, pesticide degradation increased to 54.0% in the same conditions.[10] Doolatkeldieva et al. discussed their findings, saying

"It is consequently possible that the degrading capacity of the bacteria could be increased only through co-cultivation, which shows that these bacteria naturally coexist and are dependent on each other for the utilization of environmental substances. In the oxidation and hydrolysis pathways of pesticide degradation, each bacterium can produce metabolites that will be utilized by the enzyme system of the next bacterium".[10]

Bioplastic

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As an answer to the increase in use of non-biodegradable, oil-based plastics and its subsequent accumulation as waste, scientists have developed biodegradable and compostable alternatives often called bioplastics.[12] However, not all biologically created plastics are necessarily biodegradable, and this can be a source of confusion.[13][unreliable source?] Therefore it is important to distinguish between the types of bioplastics, biodegradable bioplastics which can be degraded by some microflora and simply bio-based plastics which are a renewable source of plastic but require more effort to dispose of.[13]

One of the bioplastics of interest is Polyhydroxybutyrate, abbreviated to PHB. PHB is a biodegradable bioplastic that has applications for food packaging due to being non-toxic.[14] Repurposed E. coli, as well as Halomonas boliviensis, have been shown to produce PHB.[15][16] PHB production starting from carbon dioxide in a co-culture between S. elongatus and H. boliviensis has proven to be a stable continually-productive pair for 5 months without the aid of antibiotics.[15]

See also

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References

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  1. ^ Martins, Samuel J.; Pasche, Josephine; Silva, Hiago Antonio O.; Selten, Gijs; Savastano, Noah; Abreu, Lucas Magalhães; Bais, Harsh P.; Garrett, Karen A.; Kraisitudomsook, Nattapol; Pieterse, Corné M. J.; Cernava, Tomislav (2023). "The Use of Synthetic Microbial Communities to Improve Plant Health". Phytopathology. 113 (8): 1369–1379. doi:10.1094/PHYTO-01-23-0016-IA. PMID 36858028.
  2. ^ a b c d Hays, Stephanie G.; Ducat, Daniel C. (14 February 2014). "Engineering cyanobacteria as photosynthetic feedstock factories". Photosynthesis Research. 123 (3): 285–295. doi:10.1007/s11120-014-9980-0. PMC 5851442. PMID 24526260.
  3. ^ Stewart, Eric J. (15 August 2012). "Growing Unculturable Bacteria". Journal of Bacteriology. 194 (16): 4151–4160. doi:10.1128/JB.00345-12. PMC 3416243. PMID 22661685.
  4. ^ Delaux, Pierre-Marc; Radhakrishnan, Guru V.; Jayaraman, Dhileepkumar; Cheema, Jitender; Malbreil, Mathilde; Volkening, Jeremy D.; Sekimoto, Hiroyuki; Nishiyama, Tomoaki; Melkonian, Michael (27 October 2015). "Algal ancestor of land plants was preadapted for symbiosis". Proceedings of the National Academy of Sciences of the United States of America. 112 (43): 13390–13395. Bibcode:2015PNAS..11213390D. doi:10.1073/pnas.1515426112. PMC 4629359. PMID 26438870.
  5. ^ Hays, Stephanie G.; Yan, Leo L. W.; Silver, Pamela A.; Ducat, Daniel C. (23 January 2017). "Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction". Journal of Biological Engineering. 11 (1): 4. doi:10.1186/s13036-017-0048-5. PMC 5259876. PMID 28127397.
  6. ^ Kang, Aram; Lee, Taek Soon (27 October 2015). "Converting Sugars to Biofuels: Ethanol and Beyond". Bioengineering. 2 (4): 184–203. doi:10.3390/bioengineering2040184. PMC 5597089. PMID 28952477.
  7. ^ McBride, Robert C.; Lopez, Salvador; Meenach, Chris; Burnett, Mike; Lee, Philip A.; Nohilly, Fiona; Behnke, Craig (June 2014). "Contamination Management in Low Cost Open Algae Ponds for Biofuels Production". Industrial Biotechnology. 10 (3): 221–7. doi:10.1089/ind.2013.0036.
  8. ^ a b Kato, Souichiro; Hashimoto, Kazuhito; Watanabe, Kazuya (July 2012). "Methanogenesis facilitated by electric syntrophy via (semi)conductive iron-oxide minerals". Environmental Microbiology. 14 (7): 1646–54. Bibcode:2012EnvMi..14.1646K. doi:10.1111/j.1462-2920.2011.02611.x. PMID 22004041.
  9. ^ a b c Patowary, Kaustuvmani; Patowary, Rupshikha; Kalita, Mohan C.; Deka, Suresh (14 July 2016). "Development of an Efficient Bacterial Consortium for the Potential Remediation of Hydrocarbons from Contaminated Sites". Frontiers in Microbiology. 7: 1092. doi:10.3389/fmicb.2016.01092. PMC 4943938. PMID 27471499.
  10. ^ a b c d e Doolotkeldieva, Tinatin; Konurbaeva, Maxabat; Bobusheva, Saykal (1 November 2018). "Microbial communities in pesticide-contaminated soils in Kyrgyzstan and bioremediation possibilities". Environmental Science and Pollution Research. 25 (32): 31848–31862. Bibcode:2018ESPR...2531848D. doi:10.1007/s11356-017-0048-5. PMC 6208721. PMID 28884389.
  11. ^ van der Werf, Hayo M.G. (December 1996). "Assessing the impact of pesticides on the environment". Agriculture, Ecosystems & Environment. 60 (2–3): 81–96. Bibcode:1996AgEE...60...81V. doi:10.1016/S0167-8809(96)01096-1.
  12. ^ Song, J. H.; Murphy, R. J.; Narayan, R.; Davies, G. B. H. (27 July 2009). "Biodegradable and compostable alternatives to conventional plastics". Philosophical Transactions of the Royal Society B: Biological Sciences. 364 (1526): 2127–2139. doi:10.1098/rstb.2008.0289. PMC 2873018. PMID 19528060.
  13. ^ a b Kunststoffe (August 2008). "What are Bioplastics?". Bio-plastics.org.
  14. ^ Hankermeyer, CR; Tjeerdema, RS (1999). "Polyhydroxybutyrate: Plastic Made and Degraded by Microorganisms". Reviews of Environmental Contamination and Toxicology. Vol. 159. pp. 1–24. doi:10.1007/978-1-4612-1496-0_1. ISBN 978-1-4612-7167-3. PMID 9921137.
  15. ^ a b Weiss, Taylor L.; Young, Eric J.; Ducat, Daniel C. (November 2017). "A synthetic, light-driven consortium of cyanobacteria and heterotrophic bacteria enables stable polyhydroxybutyrate production". Metabolic Engineering. 44: 236–245. doi:10.1016/j.ymben.2017.10.009. PMID 29061492.
  16. ^ Rahman, Asif; Linton, Elisabeth; Hatch, Alex D; Sims, Ronald C; Miller, Charles D (2013). "Secretion of polyhydroxybutyrate in Escherichia coli using a synthetic biological engineering approach". Journal of Biological Engineering. 7 (1): 24. doi:10.1186/1754-1611-7-24. PMC 4015293. PMID 24139229.

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