Sporosarcina pasteurii

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Sporosarcina pasteurii
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Sporosarcina pasteurii

Bergey 2004

Sporosarcina pasteurii formerly known as Bacillus pasteurii from older taxonomies, is a gram positive bacterium with the ability to precipitate calcite and solidify sand given a calcium source and urea; through the process of microbiologically induced calcite precipitation (MICP) or biological cementation. [1] S. pasteurii has been proposed to be used as an ecologically sound biological construction material. Researchers studied the bacteria in conjunction with plastic and hard mineral; forming a material stronger than bone. [2] It is a commonly used for MICP since it is non-pathogenic and is able to produce high amounts of the enzyme urease which hydrolyzes urea to carbonate and ammonia. [3]

Contents

Physiology

S. pasteurii is a gram positive bacterium that is rod-like shaped in nature. It has the ability to form endospores in the right environmental conditions to enhance its survival, which is a characteristic of its bacillus class. [4] It has dimensions of 0.5 to 1.2 microns in width and 1.3 to 4.0 microns in length. Because it is an alkaliphile, it thrives in basic environments of pH 9–10. It can survive relatively harsh conditions up to a pH of 11.2. [3]

Metabolism and growth

S. pasteurii are soil-borne facultative anaerobes that are heterotrophic and require urea and ammonium for growth. [5] The ammonium is utilized in order to allow substrates to cross the cell membrane into the cell. [5] The urea is used as the nitrogen and carbon source for the bacterium. S. pasteurii are able to induce the hydrolysis of urea and use it as a source of energy by producing and secreting the urease enzyme. The enzyme hydrolyzes the urea to form carbonate and ammonia. During this hydrolysis, a few more spontaneous reactions are performed. Carbamate is hydrolyzed to carbonic acid and ammonia and then further hydrolyzed to ammonium and bicarbonate. [3] This process causes the pH of the reaction to increase 1-2 pH, making the environment more basic which promotes the conditions that this specific bacterium thrives in. [6] Maintaining a medium with this pH can be expensive for large scale production of this bacterium for biocementation. A wide range of factors can affect the growth rate of S. pasteurii. This includes finding the optimal temperature, pH, urea concentration, bacterial density, oxygen levels, etc. [6] It has been found that the optimal growing temperature is 30 °C, but this is independent of the other environmental factors present. [4] Since S. pasteurii are halotolerant, they can grow in the presence of low concentrations of aqueous chloride ions that are low enough to not inhibit bacterial cell growth. [6] This shows promising applications for MICP use.

S. pasteurii DSM 33 is described to be auxotrophic for L-methionine, L-cystein, thiamine and nicotinic acid. [7]

Genomic properties

The whole genome of S. pasteurii NCTC4822 was sequenced and reported under NCBI Accession Number: NZ_UGYZ01000000. With a chromosome length of 3.3 Mb, it contains 3,036 protein coding genes and has GC content of 39.17% . [8] When the ratio of known functional genes to the unknown genes is calculated, the bacterium shows highest ratios for transport, metabolism, and transcription. The high proportion of these functions allows the conversion of urea to carbonate ions which is necessary for the bio-mineralization process. [8] The bacterium has seven identified genes that are directly related to urease activity and assembly as well, which can be further studied to give insight about maximizing urease production for optimizing use of S. pasteurii in industrial applications. [8]

Applications with MICP

S. pasteurii have the unique capability of hydrolyzing urea and through a series of reactions, produce carbonate ions. This is done by secreting copious amounts of urease through the cell membrane. [4] When the bacterium is placed in a calcite rich environment, the negatively charged carbonate ions react with the positive metal ions like calcium to precipitate calcium carbonate, or bio-cement. [3] The calcium carbonate can then be used as a precipitate or can be crystallized as calcite to cement sand particles together. Therefore, when put into a calcium chloride environment, S. pasteurii are able to survive since they are halotolerant and alkaliphiles. Since the bacteria remain intact during harsh mineralization conditions, are robust, and carry a negative surface charge, they serve as good nucleation sites for MICP. [8] The negatively charged cell wall of the bacterium provides a site of interaction for the positively charged cations to form minerals. The extent of this interaction depends on a variety of factors including the characteristics of the cell surface, amount of peptidoglycan, amidation level of free carboxyl, and availability of teichoic acids. [6] S. pasteurii show a highly negative surface charge which can be shown in its highly negative zeta potential of -67 mV compared to non-mineralizing bacteria E. coli, S. aureus and B. subtilis at -28, -26 and -40.8 mV, respectively. [8] Aside from all of these benefits towards using S. pasteurii for MICP, there are limitations like undeveloped engineering scale-up, undesired by-products, uncontrolled growth, or dependence on growth conditions like urea or oxygen concentrations. [8]

Current and potential applications

Desertification exemplified by sand dunes advancing on Nouakchott, the capital of Mauritania Nouakchott SandDunesEncroaching.jpg
Desertification exemplified by sand dunes advancing on Nouakchott, the capital of Mauritania

S. pasteurii have a purpose in improving construction material as in concrete or mortar. Concrete is one of the most used materials in the world but it is susceptible to forming cracks which can be costly to fix. One solution is to embed this bacterium in the cracks and once it is activated using MICP. Minerals will form and repair the gap in a permanent environmentally-friendly way. One disadvantage is that this technique is possible only for external surfaces that are reachable. [6]

Another application is to use S. pasteurii in bio self-healing of concrete which involves implementing the bacterium into the concrete matrix during the concrete preparation to heal micro cracks. This has a benefit of minimal human intervention and yields more durable concrete with higher compressive strength. [6]

One limitation of using this bacterium for bio-mineralization is that although it is a facultative anaerobe, in the absence of oxygen, the bacterium is unable to synthesize urease anaerobically. A lack of oxygen also prevents MICP since its initiation relies heavily on oxygen. Therefore, at sites distant from the injection location or at great depths, the likelihood of precipitation decreases. [8] One potential fix is to couple this bacterium in the biocement with oxygen releasing compounds (ORCs) that are typically used for bioremediation and removal of pollutants from soil. [6] With this combination, the lack of oxygen can be diminished and the MICP can be optimized with the bacterium.

Some specific examples of current applications include:

More potential applications include:

Considerations of using this bacterium in industrial applications is scale-up potential, economic feasibility, long-term viability of bacteria, adhesion behavior of calcium carbonate, and polymorphism. [6]

See also

Related Research Articles

<span class="mw-page-title-main">Carbonate</span> Salt of carbonic acid

A carbonate is a salt of carbonic acid (H2CO3), characterized by the presence of the carbonate ion, a polyatomic ion with the formula CO2−3. The word carbonate may also refer to a carbonate ester, an organic compound containing the carbonate groupO=C(−O−)2.

<span class="mw-page-title-main">Calcite</span> Calcium carbonate mineral

Calcite is a carbonate mineral and the most stable polymorph of calcium carbonate (CaCO3). It is a very common mineral, particularly as a component of limestone. Calcite defines hardness 3 on the Mohs scale of mineral hardness, based on scratch hardness comparison. Large calcite crystals are used in optical equipment, and limestone composed mostly of calcite has numerous uses.

<span class="mw-page-title-main">Urease</span> Multiprotein Nickel-containing complex which hydrolyses urea

Ureases, functionally, belong to the superfamily of amidohydrolases and phosphotriesterases. Ureases are found in numerous bacteria, fungi, algae, plants, and some invertebrates, as well as in soils, as a soil enzyme. They are nickel-containing metalloenzymes of high molecular weight.

<span class="mw-page-title-main">Speleothem</span> Structure formed in a cave by the deposition of minerals from water

A speleothem is a geological formation by mineral deposits that accumulate over time in natural caves. Speleothems most commonly form in calcareous caves due to carbonate dissolution reactions. They can take a variety of forms, depending on their depositional history and environment. Their chemical composition, gradual growth, and preservation in caves make them useful paleoclimatic proxies.

<span class="mw-page-title-main">Dolomite (rock)</span> Sedimentary carbonate rock that contains a high percentage of the mineral dolomite

Dolomite (also known as dolomite rock, dolostone or dolomitic rock) is a sedimentary carbonate rock that contains a high percentage of the mineral dolomite, CaMg(CO3)2. It occurs widely, often in association with limestone and evaporites, though it is less abundant than limestone and rare in Cenozoic rock beds (beds less than about 66 million years in age). The first geologist to distinguish dolomite from limestone was Déodat Gratet de Dolomieu; a French mineralogist and geologist whom it is named after. He recognized and described the distinct characteristics of dolomite in the late 18th century, differentiating it from limestone.

The pedosphere is the outermost layer of the Earth that is composed of soil and subject to soil formation processes. It exists at the interface of the lithosphere, atmosphere, hydrosphere and biosphere. The pedosphere is the skin of the Earth and only develops when there is a dynamic interaction between the atmosphere, biosphere, lithosphere and the hydrosphere. The pedosphere is the foundation of terrestrial life on Earth.

<span class="mw-page-title-main">Carbonate rock</span> Class of sedimentary rock

Carbonate rocks are a class of sedimentary rocks composed primarily of carbonate minerals. The two major types are limestone, which is composed of calcite or aragonite (different crystal forms of CaCO3), and dolomite rock (also known as dolostone), which is composed of mineral dolomite (CaMg(CO3)2). They are usually classified based on texture and grain size. Importantly, carbonate rocks can exist as metamorphic and igneous rocks, too. When recrystallized carbonate rocks are metamorphosed, marble is created. Rare igneous carbonate rocks even exist as intrusive carbonatites and, even rarer, there exists volcanic carbonate lava.

<span class="mw-page-title-main">Biomineralization</span> Process by which living organisms produce minerals

Biomineralization, also written biomineralisation, is the process by which living organisms produce minerals, often resulting in hardened or stiffened mineralized tissues. It is an extremely widespread phenomenon: all six taxonomic kingdoms contain members that are able to form minerals, and over 60 different minerals have been identified in organisms. Examples include silicates in algae and diatoms, carbonates in invertebrates, and calcium phosphates and carbonates in vertebrates. These minerals often form structural features such as sea shells and the bone in mammals and birds.

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

Calcium lactate is a white crystalline salt with formula C
6
H
10
CaO
6
, consisting of two lactate anions H
3
C
(CHOH)CO
2
for each calcium cation Ca2+
. It forms several hydrates, the most common being the pentahydrate C
6
H
10
CaO
6
·5H
2
O
.

<span class="mw-page-title-main">Cementation (geology)</span> Process of chemical precipitation bonding sedimentary grains

Cementation involves ions carried in groundwater chemically precipitating to form new crystalline material between sedimentary grains. The new pore-filling minerals forms "bridges" between original sediment grains, thereby binding them together. In this way, sand becomes sandstone, and gravel becomes conglomerate or breccia. Cementation occurs as part of the diagenesis or lithification of sediments. Cementation occurs primarily below the water table regardless of sedimentary grain sizes present. Large volumes of pore water must pass through sediment pores for new mineral cements to crystallize and so millions of years are generally required to complete the cementation process. Common mineral cements include calcite, quartz, and silica phases like cristobalite, iron oxides, and clay minerals; other mineral cements also occur.

Urea (46-0-0) accounts for more than fifty percent of the world's nitrogenous fertilizers. It is found in granular or prill form, which allows urea to be easily stored, transported and applied in agricultural settings. It is also the cheapest form of granular nitrogen fertilizer. Since urea is not an oxidizer at standard temperature and pressure, it is safer to handle and less of a security risk than other common nitrogen fertilizers, such as ammonium nitrate. However, if urea is applied to the soil surface, a meaningful fraction of applied fertilizer nitrogen may be lost to the atmosphere as ammonia gas; this only occurs under certain conditions.

<span class="mw-page-title-main">Concrete degradation</span> Damage to concrete affecting its mechanical strength and its durability

Concrete degradation may have many different causes. Concrete is mostly damaged by the corrosion of reinforcement bars due to the carbonatation of hardened cement paste or chloride attack under wet conditions. Chemical damages are caused by the formation of expansive products produced by various chemical reactions, by aggressive chemical species present in groundwater and seawater, or by microorganisms. Other damaging processes can also involve calcium leaching by water infiltration and different physical phenomena initiating cracks formation and propagation. All these detrimental processes and damaging agents adversely affects the concrete mechanical strength and its durability.

<span class="mw-page-title-main">Microbiologically induced calcite precipitation</span>

Microbiologically induced calcium carbonate precipitation (MICP) is a bio-geochemical process that induces calcium carbonate precipitation within the soil matrix. Biomineralization in the form of calcium carbonate precipitation can be traced back to the Precambrian period. Calcium carbonate can be precipitated in three polymorphic forms, which in the order of their usual stabilities are calcite, aragonite and vaterite. The main groups of microorganisms that can induce the carbonate precipitation are photosynthetic microorganisms such as cyanobacteria and microalgae; sulfate-reducing bacteria; and some species of microorganisms involved in nitrogen cycle. Several mechanisms have been identified by which bacteria can induce the calcium carbonate precipitation, including urea hydrolysis, denitrification, sulfate production, and iron reduction. Two different pathways, or autotrophic and heterotrophic pathways, through which calcium carbonate is produced have been identified. There are three autotrophic pathways, which all result in depletion of carbon dioxide and favouring calcium carbonate precipitation. In heterotrophic pathway, two metabolic cycles can be involved: the nitrogen cycle and the sulfur cycle. Several applications of this process have been proposed, such as remediation of cracks and corrosion prevention in concrete, biogrout, sequestration of radionuclides and heavy metals.

Sporosarcina ureae is a type of bacteria of the genus Sporosarcina, and is closely related to the genus Bacillus. S. ureae is an aerobic, motile, spore-forming, Gram-positive coccus, originally isolated in the early 20th century from soil. S. ureae is distinguished by its ability to grow in relatively high concentrations of urea through production of at least one exourease, an enzyme that converts urea to ammonia. S. ureae has also been found to sporulate when environmental conditions become unfavorable, and can remain viable for up to a year.

Sporosarcina is a genus of bacteria.

Sporosarcina aquimarina is a rod-shaped bacterium of the genus Sporosarcina.

<span class="mw-page-title-main">Ginger Krieg Dosier</span> American architect

Ginger Krieg Dosier is an American architect who, in 2010, developed a technique for using microbiologically induced calcite precipitation to manufacture bricks for construction.

<span class="mw-page-title-main">Marine biogenic calcification</span> Shell formation mechanism

Marine biogenic calcification is the process by which marine organisms such as oysters and clams form calcium carbonate. Seawater is full of dissolved compounds, ions and nutrients that organisms can use for energy and, in the case of calcification, to build shells and outer structures. Calcifying organisms in the ocean include molluscs, foraminifera, coccolithophores, crustaceans, echinoderms such as sea urchins, and corals. The shells and skeletons produced from calcification have important functions for the physiology and ecology of the organisms that create them.

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

Microbialite is a benthic sedimentary deposit made of carbonate mud that is formed with the mediation of microbes. The constituent carbonate mud is a type of automicrite ; therefore, it precipitates in situ instead of being transported and deposited. Being formed in situ, a microbialite can be seen as a type of boundstone where reef builders are microbes, and precipitation of carbonate is biotically induced instead of forming tests, shells or skeletons.

A living building material (LBM) is a material used in construction or industrial design that behaves in a way resembling a living organism. Examples include: self-mending biocement, self-replicating concrete replacement, and mycelium-based composites for construction and packaging. Artistic projects include building components and household items.

References

  1. Chou CW, Aydilek A, Seagren E, Maugel T (November 2008). "Bacterially-induced calcite precipitation via ureolysis". American Society for Microbiology.
  2. "Microbial makers help humans to build tough stuff". Nature. 591 (7849): 180. 2021-03-04. Bibcode:2021Natur.591R.180.. doi:10.1038/d41586-021-00565-3.
  3. 1 2 3 4 Henze J, Randall DG (August 2018). "Microbial induced calcium carbonate precipitation at elevated pH values (>11) using Sporosarcina pasteurii". Journal of Environmental Chemical Engineering. 6 (4): 5008–5013. doi:10.1016/j.jece.2018.07.046. S2CID   105388152.
  4. 1 2 3 Bhaduri S, Debnath N, Mitra S, Liu Y, Kumar A (April 2016). "Microbiologically Induced Calcite Precipitation Mediated by Sporosarcina pasteurii". Journal of Visualized Experiments (110). doi:10.3791/53253. PMC   4941918 . PMID   27167458.
  5. 1 2 3 "Optimizing the use of sporosarcina pasteurii bacteria for the stiffening of sand". www.envirobiotechjournals.com. Retrieved 2020-05-04.
  6. 1 2 3 4 5 6 7 8 Seifan M, Berenjian A (November 2018). "Application of microbially induced calcium carbonate precipitation in designing bio self-healing concrete". World Journal of Microbiology & Biotechnology. 34 (11): 168. doi:10.1007/s11274-018-2552-2. PMID   30387067. S2CID   53295171.
  7. Lapierre FM, Schmid S, Ederer B, Ihling N, Büchs J, Huber R (Dec 2020). "Revealing nutritional requirements of MICP-relevant Sporosarcina pasteurii DSM33 for growth improvement in chemically defined and complex media". Scientific Reports. 10 (22448): 22448. Bibcode:2020NatSR..1022448L. doi: 10.1038/s41598-020-79904-9 . PMC   7775470 . PMID   33384450.
  8. 1 2 3 4 5 6 7 Ma L, Pang AP, Luo Y, Lu X, Lin F (January 2020). "Beneficial factors for biomineralization by ureolytic bacterium Sporosarcina pasteurii". Microbial Cell Factories. 19 (1): 12. doi: 10.1186/s12934-020-1281-z . PMC   6979283 . PMID   31973723.
  9. Holcim Awards 2008 Africa Middle East "Next Generation" 1st prize: Dune anti-desertification architecture, Sokoto, Nigeria, Holcim awards. Retrieved 20 February 2010.
  10. Magnus Larsson: Dune architect, TED.com. Retrieved 20 February 2010.
  11. bioMason @Green Challenge
  12. Torres-Aravena, Álvaro Esteban; Duarte-Nass, Carla; Azócar, Laura; Mella-Herrera, Rodrigo; Rivas, Mariella; Jeison, David (November 2018). "Can Microbially Induced Calcite Precipitation (MICP) through a Ureolytic Pathway Be Successfully Applied for Removing Heavy Metals from Wastewaters?". Crystals. 8 (11): 438. doi: 10.3390/cryst8110438 .
  13. Patent WO2019141880A1 "Verhindern oder vermindern von pflanzenwachstum durch biozementierung"