Synthetic microbial consortia

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a TEM picture of E. coli, chemoheterotrophic bacteria often used in synthetic microbial consortia. E. coli Bacteria (16578744517).jpg
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.

Contents

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

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

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

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

Related Research Articles

A xenobiotic is a chemical substance found within an organism that is not naturally produced or expected to be present within the organism. It can also cover substances that are present in much higher concentrations than are usual. Natural compounds can also become xenobiotics if they are taken up by another organism, such as the uptake of natural human hormones by fish found downstream of sewage treatment plant outfalls, or the chemical defenses produced by some organisms as protection against predators. The term "xenobiotic" is also used to refer to organs transplanted from one species to another.

<span class="mw-page-title-main">Bioremediation</span> Process used to treat contaminated media such as water and soil

Bioremediation broadly refers to any process wherein a biological system, living or dead, is employed for removing environmental pollutants from air, water, soil, flue gasses, industrial effluents etc., in natural or artificial settings. The natural ability of organisms to adsorb, accumulate, and degrade common and emerging pollutants has attracted the use of biological resources in treatment of contaminated environment. In comparison to conventional physicochemical treatment methods bioremediation may offer advantages as it aims to be sustainable, eco-friendly, cheap, and scalable.

<span class="mw-page-title-main">Polyhydroxybutyrate</span> Polymer

Polyhydroxybutyrate (PHB) is a polyhydroxyalkanoate (PHA), a polymer belonging to the polyesters class that are of interest as bio-derived and biodegradable plastics. The poly-3-hydroxybutyrate (P3HB) form of PHB is probably the most common type of polyhydroxyalkanoate, but other polymers of this class are produced by a variety of organisms: these include poly-4-hydroxybutyrate (P4HB), polyhydroxyvalerate (PHV), polyhydroxyhexanoate (PHH), polyhydroxyoctanoate (PHO) and their copolymers.

Biological augmentation is the addition of archaea or bacterial cultures required to speed up the rate of degradation of a contaminant. Organisms that originate from contaminated areas may already be able to break down waste, but perhaps inefficiently and slowly.

<span class="mw-page-title-main">Polyhydroxyalkanoates</span> Polyester family

Polyhydroxyalkanoates or PHAs are polyesters produced in nature by numerous microorganisms, including through bacterial fermentation of sugars or lipids. When produced by bacteria they serve as both a source of energy and as a carbon store. More than 150 different monomers can be combined within this family to give materials with extremely different properties. These plastics are biodegradable and are used in the production of bioplastics.

The word metagenics uses the prefix meta and the suffix gen. Literally, it means "the creation of something which creates". In the context of biotechnology, metagenics is the practice of engineering organisms to create a specific enzyme, protein, or other biochemicals from simpler starting materials. The genetic engineering of E. coli with the specific task of producing human insulin from starting amino acids is an example. E. coli has also been engineered to digest plant biomass and use it to produce hydrocarbons in order to synthesize biofuels. The applications of metagenics on E. coli also include higher alcohols, fatty-acid based chemicals and terpenes.

<span class="mw-page-title-main">Bioplastic</span> Plastics derived from renewable biomass sources

Bioplastics are plastic materials produced from renewable biomass sources, such as vegetable fats and oils, corn starch and rice starch, straw, woodchips, sawdust, recycled food waste, etc. Some bioplastics are obtained by processing directly from natural biopolymers including polysaccharides and proteins, while others are chemically synthesized from sugar derivatives and lipids from either plants or animals, or biologically generated by fermentation of sugars or lipids. In contrast, common plastics, such as fossil-fuel plastics are derived from petroleum or natural gas.

<span class="mw-page-title-main">Butanol fuel</span> Fuel for internal combustion engines

Butanol may be used as a fuel in an internal combustion engine. It is more similar to gasoline than it is to ethanol. A C4-hydrocarbon, butanol is a drop-in fuel and thus works in vehicles designed for use with gasoline without modification. Both n-butanol and isobutanol have been studied as possible fuels. Both can be produced from biomass (as "biobutanol" ) as well as from fossil fuels (as "petrobutanol"). The chemical properties depend on the isomer (n-butanol or isobutanol), not on the production method.

<span class="mw-page-title-main">Biodegradable plastic</span> Plastics that can be decomposed by the action of living organisms

Biodegradable plastics are plastics that can be decomposed by the action of living organisms, usually microbes, into water, carbon dioxide, and biomass. Biodegradable plastics are commonly produced with renewable raw materials, micro-organisms, petrochemicals, or combinations of all three.

The non-mevalonate pathway—also appearing as the mevalonate-independent pathway and the 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate (MEP/DOXP) pathway—is an alternative metabolic pathway for the biosynthesis of the isoprenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The currently preferred name for this pathway is the MEP pathway, since MEP is the first committed metabolite on the route to IPP.

Biosurfactant usually refers to surfactants of microbial origin. Most of the biosurfactants produced by microbes are synthesized extracellularly and many microbes are known to produce biosurfactants in large relative quantities. Some are of commercial interest. As a secondary metabolite of microorganisms, biosurfactants can be processed by the cultivation of biosurfactant producing microorganisms in the stationary phase on many sorts of low-priced substrates like biochar, plant oils, carbohydrates, wastes, etc. High-level production of biosurfactants can be controlled by regulation of environmental factors and growth circumstances.

Microbial biodegradation is the use of bioremediation and biotransformation methods to harness the naturally occurring ability of microbial xenobiotic metabolism to degrade, transform or accumulate environmental pollutants, including hydrocarbons, polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), heterocyclic compounds, pharmaceutical substances, radionuclides and metals.

Poly(3-hydroxybutyrate) depolymerase (EC 3.1.1.75, PHB depolymerase, systematic name poly[(R)-3-hydroxybutanoate] hydrolase) is an enzyme used in the degradation processes of a natural polyester poly(3-hydroxyburate). This enzyme has growing commercialization interests due to it implications in biodegradable plastic decomposition.

<span class="mw-page-title-main">Phototrophic biofilm</span> Microbial communities including microorganisms which use light as their energy source

Phototrophic biofilms are microbial communities generally comprising both phototrophic microorganisms, which use light as their energy source, and chemoheterotrophs. Thick laminated multilayered phototrophic biofilms are usually referred to as microbial mats or phototrophic mats. These organisms, which can be prokaryotic or eukaryotic organisms like bacteria, cyanobacteria, fungi, and microalgae, make up diverse microbial communities that are affixed in a mucous matrix, or film. These biofilms occur on contact surfaces in a range of terrestrial and aquatic environments. The formation of biofilms is a complex process and is dependent upon the availability of light as well as the relationships between the microorganisms. Biofilms serve a variety of roles in aquatic, terrestrial, and extreme environments; these roles include functions which are both beneficial and detrimental to the environment. In addition to these natural roles, phototrophic biofilms have also been adapted for applications such as crop production and protection, bioremediation, and wastewater treatment.

Synechocystis sp. PCC6803 is a strain of unicellular, freshwater cyanobacteria. Synechocystis sp. PCC6803 is capable of both phototrophic growth by oxygenic photosynthesis during light periods and heterotrophic growth by glycolysis and oxidative phosphorylation during dark periods. Gene expression is regulated by a circadian clock and the organism can effectively anticipate transitions between the light and dark phases.

A microbial consortium or microbial community, is two or more bacterial or microbial groups living symbiotically. Consortiums can be endosymbiotic or ectosymbiotic, or occasionally may be both. The protist Mixotricha paradoxa, itself an endosymbiont of the Mastotermes darwiniensis termite, is always found as a consortium of at least one endosymbiotic coccus, multiple ectosymbiotic species of flagellate or ciliate bacteria, and at least one species of helical Treponema bacteria that forms the basis of Mixotricha protists' locomotion.

<span class="mw-page-title-main">PHBV</span> Chemical compound

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate), commonly known as PHBV, is a polyhydroxyalkanoate-type polymer. It is biodegradable, nontoxic, biocompatible plastic produced naturally by bacteria and a good alternative for many non-biodegradable synthetic polymers. It is a thermoplastic linear aliphatic polyester. It is obtained by the copolymerization of 3-hydroxybutanoic acid and 3-hydroxypentanoic acid. PHBV is used in speciality packaging, orthopedic devices and in controlled release of drugs. PHBV undergoes bacterial degradation in the environment.

Biodegradable additives are additives that enhance the biodegradation of polymers by allowing microorganisms to utilize the carbon within the polymer chain as a source of energy. Biodegradable additives attract microorganisms to the polymer through quorum sensing after biofilm creation on the plastic product. Additives are generally in masterbatch formation that use carrier resins such as polyethylene (PE), polypropylene (PP), polystyrene (PS) or polyethylene terephthalate (PET).

Zobellella denitrificans is a Gram-negative, facultatively anaerobic, heterotrophic and denitrifying bacterium from the genus of Zobellella which has been isolated from sediments from a mangrove ecosystems from Miaoli County in Taiwan.

<span class="mw-page-title-main">Plastic degradation by marine bacteria</span> Ability of bacteria to break down plastic polymers

Plastic degradation in marine bacteria describes when certain pelagic bacteria break down polymers and use them as a primary source of carbon for energy. Polymers such as polyethylene (PE), polypropylene (PP), and polyethylene terephthalate (PET) are incredibly useful for their durability and relatively low cost of production, however it is their persistence and difficulty to be properly disposed of that is leading to pollution of the environment and disruption of natural processes. It is estimated that each year there are 9-14 million metric tons of plastic that are entering the ocean due to inefficient solutions for their disposal. The biochemical pathways that allow for certain microbes to break down these polymers into less harmful byproducts has been a topic of study to develop a suitable anti-pollutant.

References

  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. 1 2 3 4 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. 1 2 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. 1 2 3 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. 1 2 3 4 5 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. 1 2 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. 1 2 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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