''Ideonella sakaiensis'' is a

bacterium Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

from the

genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of extant taxon, living and fossil organisms as well as Virus classification#ICTV classification, viruses. In the hierarchy of biological classification, genus com ...

'' Ideonella'' and family

Comamonadaceae The Comamonadaceae are a family of the Betaproteobacteria.Willems A., J. De Ley, M. Gillis, and K. Kersters. ''Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov.,comb. nov. for Alcali ...

capable of breaking down and consuming the plastic

polyethylene terephthalate Polyethylene terephthalate (or poly(ethylene terephthalate), PET, PETE, or the obsolete PETP or PET-P), is the most common thermoplastic polymer resin of the polyester family and is used in fibres for clothing, containers for liquids and foods ...

(PET) using it as both a carbon and energy source. The bacterium was originally isolated from a sediment sample taken outside of a

plastic bottle A plastic bottle is a bottle constructed from high-density or low density plastic. Plastic bottles are typically used to store liquids such as water, soft drinks, motor oil, cooking oil, medicine, shampoo, milk, and ink. The size ranges from v ...

recycling Recycling is the process of converting waste materials into new materials and objects. The recovery of energy from waste materials is often included in this concept. The recyclability of a material depends on its ability to reacquire the p ...

facility in Sakai City, Japan. *

Discovery

''Ideonella sakaiensis'' was first identified in 2016 by a team of researchers led by Kohei Oda of Kyoto Institute of Technology and Kenji Miyamoto of Keio University after collecting a sample of PET-contaminated sediment at a plastic bottle recycling facility in Sakai, Japan. The bacteria was first isolated from a consortium of microorganisms in the sediment sample, which included

protozoa Protozoa (singular: protozoan or protozoon; alternative plural: protozoans) are a group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic tissues and debris. Histo ...

and yeast-like cells. The entire microbial community was shown to mineralize 75% of the degraded PET into carbon dioxide once it had been initially degraded and assimilated by ''Ideonella sakaiensis''.

Characterization

Physical Attributes

''Ideonella sakaiensis'' is

gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...

aerobic Aerobic means "requiring air," in which "air" usually means oxygen. Aerobic may also refer to * Aerobic exercise, prolonged exercise of moderate intensity * Aerobics, a form of aerobic exercise * Aerobic respiration, the aerobic process of cellu ...

, and rod-shaped. Cells are motile and have a single

flagellum A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have f ...

. Colonies of ''I. sakaiensis'' are colorless, smooth, and circular. Its size varies from 0.6 to 0.8 μm in width and 1.2-1.5 μm in length.

Chemical Attributes

''I. sakaiensis'' also tests positive for

oxidase In biochemistry, an oxidase is an enzyme that catalyzes oxidation-reduction reactions, especially one involving dioxygen (O2) as the electron acceptor. In reactions involving donation of a hydrogen atom, oxygen is reduced to water (H2O) or hydro ...

and

catalase Catalase is a common enzyme found in nearly all living organisms exposed to oxygen (such as bacteria, plants, and animals) which catalyzes the decomposition of hydrogen peroxide to water and oxygen. It is a very important enzyme in protecting t ...

. The bacterium grows at a pH range of 5.5 to 9.0 (optimally at 7 to 7.5) and a temperature of 15–42°C (optimally at 30–37°C). Ideonella Sakaiensis Eating Plastics

Use of Characteristics

The gram negativity in bacteria makes it so they have resistant abilities and genes; this could include antibiotic resistance. The gram negativity as a characteristic also signifies this bacteria has a thin cell wall and has a high lipid content. The aerobic aspect of this bacteria makes it so that it can only grow and thrive in an environment that contains the presence of oxygen within their vicinity. Ideonella sakaiensis and other aerobic bacterium are therefore known to survive in oxygen-rich soil that is moist and aerated. The flagellum attached to this bacteria are used as motile organelles and are able to rotate and thrust the cell throughout its environment by creating motion. The bacterium was also shown to grow on Polyethylene terephthalate (PET) surface which is a type of plastic. The bacteria was able to adhere to the PET plastic with its thin flagellum. This is shown in the image to the right. These flagellum may also function to secrete PET-degrading enzymes onto the PET surface known as PETase. Through phylogenetic analysis, the species was shown to be a part of the genus '' Ideonella,'' but possessed a significantly different genome than other known species in the genus, including '' Ideonella dechloratans'' and '' Ideonella azotifigens,'' thus justifying its classification as a new species''.''

Degradation and assimilation of PET

''Ideonella sakaiensis'' adhere to PET surface and use a secreted PET

hydrolase Hydrolase is a class of enzyme that commonly perform as biochemical catalysts that use water to break a chemical bond, which typically results in dividing a larger molecule into smaller molecules. Some common examples of hydrolase enzymes are este ...

, or

PETase PETases are an esterase class of enzymes that catalyze the hydrolysis of polyethylene terephthalate (PET) plastic to monomeric mono-2-hydroxyethyl terephthalate (MHET). The idealized chemical reaction is (where n is the number of monomers in the ...

, to degrade the PET into mono(2-hydroxyethyl)terephthalic acid (MHET), a

heterodimer In biochemistry, a protein dimer is a macromolecular complex formed by two protein monomers, or single proteins, which are usually non-covalently bound. Many macromolecules, such as proteins or nucleic acids, form dimers. The word ''dimer'' has ...

composed of

terephthalic acid Terephthalic acid is an organic compound with formula C6H4(CO2H)2. This white solid is a commodity chemical, used principally as a precursor to the polyester PET, used to make clothing and plastic bottles. Several million tonnes are produced annua ...

(TPA) and

ethylene glycol Ethylene glycol (IUPAC name: ethane-1,2-diol) is an organic compound (a vicinal diol) with the formula . It is mainly used for two purposes, as a raw material in the manufacture of polyester fibers and for antifreeze formulations. It is an odo ...

. The PETase also degrades PET into another intermediate known as Bis-(2-hydroxyethyl) terephthalate (BHET), BHET can be converted into MHET after PET hydrolysis. The ''I. sakaiensis'' PETase functions by hydrolyzing the ester bonds present in PET with high specificity. The resulting MHET is then degraded into its two monomeric constituents by a lipid-anchored MHET hydrolase enzyme, or MHETase, on the cell's outer membrane. The overall mechanism of the PET plastic being broken down is exhibited in the image to the right. The monomeric constituents such as ethylene glycol is then taken up and used by ''I. sakaiensis'' and many other bacteria. The other constituent; terephthalic acid, a more recalcitrant compound, is imported into the ''I. sakaiensis'' cell via the terephthalic acid transporter protein. Once in the cell, the aromatic terephthalic acid molecule is oxidized by terephthalic acid-1,2-dioxygenase and 1,2-dihydroxy-3,5-cyclohexadiene-1,4-dicarboxylate dehydrogenase into a

catechol Catechol ( or ), also known as pyrocatechol or 1,2-dihydroxybenzene, is a toxic organic compound with the molecular formula . It is the ''ortho'' isomer of the three isomeric benzenediols. This colorless compound occurs naturally in trace amoun ...

intermediate. The catechol ring is then cleaved by PCA 3,4-dioxygenase before the compound is integrated into other metabolic pathways (e.g.

TCA cycle The citric acid cycle (CAC)—also known as the Krebs cycle or the TCA cycle (tricarboxylic acid cycle)—is a series of chemical reactions to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins ...

). As a result, both of the molecules derived from the PET are used by the cell to produce energy and to build necessary biomolecules. Eventually, the assimilated carbon may be mineralized to carbon dioxide and released into the atmosphere.

Impact and applications

The discovery of ''Ideonella sakaiensis'' has potential importance for the degradation of PET plastics. Prior to its discovery, the only known degraders of PET were a small number of bacteria and fungi, including ''

Fusarium solani ''Fusarium solani'' is a species complex of at least 26 closely related filamentous fungi in the division Ascomycota, family Nectriaceae. It is the anamorph of '' Nectria haematococca''. It is a common soil fungus and colonist of plant mater ...

'', and no organisms were definitively known to degrade PET as a primary carbon and energy source. The discovery of ''I. sakaiensis'' spurred discussion about PET biodegradation as a method of

and

bioremediation Bioremediation broadly refers to any process wherein a biological system (typically bacteria, microalgae, fungi, and plants), living or dead, is employed for removing environmental pollutants from air, water, soil, flue gasses, industrial effluent ...

. The

wild-type The wild type (WT) is the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard "normal" allele at a locus, in contrast to that produced by a non-standard, "m ...

bacterium is able to colonize and break down a thin (0.2 mm thickness) film of low-crystallinity (soft) PET in approximately 6 weeks, and the responsible PETase enzyme was shown to degrade high-crystallinity (hard) PET approximately 30-fold slower (180 weeks or more than 3 years) than low-crystallinity PET. A large amount of manufactured PET is highly crystalline (e.g. plastic bottles), so it is thought that any prospective applications of the ''I. sakaiensis'' PETase enzyme in recycling programs will need to be preceded by genetic optimization of the enzyme. The MHETase enzyme could also be optimized and used in recycling or bioremediation applications in combination with the PETase enzyme. It degrades the MHET produced by the PETase into ethylene glycol and terephthalic acid. Once formed, these two compounds can be further biodegraded into carbon dioxide by ''I. sakaiensis'' or other microbes, or they can be purified and used to manufacture new PET in an industrial recycling plant setting. ''Ideonella sakaiensis'' is being studied for this PET degrading capabilities as a means of water management issues of sewage fed fisheries. Various strains of this bacterium has been shown to not pose any threats to the growth and cultivation of fish. This species of bacteria are able to properly use PET as a source of carbon and thrive in wastewater and plastic polluted water ecosystems, showing its promise as a cost-effective anti-pollutant.

Genetic engineering Genetic engineering, also called genetic modification or genetic manipulation, is the modification and manipulation of an organism's genes using technology. It is a set of technologies used to change the genetic makeup of cells, including t ...

The PET plastic degrading enzyme of ''Ideonella sakaiensis'' known as;

, has been genetically modified and combined with MHETase to break down PET faster, which also degrades PEF (polyethylene furanoate) plastics. This along with other approaches may be useful in various efforts such as; recycling and upcycling of mixed plastics.

Coagulation Filtration System

In 2021, fifth graders Julia Stewart and Jacob Park created the concept of a Coagulation Filtration System for Toshiba's ExploraVision contest, which utilizes ''Ideonella sakaiensis'' in a process that filters, coagulates, flocculates, and sediments water in a more environmentally friendly and efficient way. This project won the 4-6 division of ExploraVision nationally.

References

External links

Type strain of ''Ideonella sakaiensis'' at Bac''Dive'' - the Bacterial Diversity Metadatabase
{{Taxonbar, from=Q23034816 Comamonadaceae Bacteria described in 2016 Organisms breaking down plastic