Deinococcus ficus

Deinococcus ficus
Scientific classification
Kingdom:	Bacteria
Phylum:	Deinococcus-Thermus
Class:	Deinococci
Order:	Deinococcales
Family:	Deinococcaceae
Genus:	Deinococcus
Species:	D. ficus
Binomial name
	Deinococcus ficus; Shashidhar and Bandekar 2005, emend. [1]

Last updated March 24, 2019

Deinococcus ficus strain CC-FR2-10^T is a recently discovered gram-positive bacteria which plays a role in the production of nitrogen fertilizer.^[1] It was originally isolated from a Ficus plant, hence its name.^[1]

Nitrogen Chemical element with atomic number 7

Nitrogen is a chemical element with symbol N and atomic number 7. It was first discovered and isolated by Scottish physician Daniel Rutherford in 1772. Although Carl Wilhelm Scheele and Henry Cavendish had independently done so at about the same time, Rutherford is generally accorded the credit because his work was published first. The name nitrogène was suggested by French chemist Jean-Antoine-Claude Chaptal in 1790, when it was found that nitrogen was present in nitric acid and nitrates. Antoine Lavoisier suggested instead the name azote, from the Greek ἀζωτικός "no life", as it is an asphyxiant gas; this name is instead used in many languages, such as French, Russian, Romanian and Turkish, and appears in the English names of some nitrogen compounds such as hydrazine, azides and azo compounds.

Fertilizer material of natural or synthetic origin that is applied to soils or leaves to supply plant nutrients for better growth

A fertilizer or fertiliser is any material of natural or synthetic origin that is applied to soils or to plant tissues to supply one or more plant nutrients essential to the growth of plants. Many sources of fertilizer exist, both natural and industrially produced.

Ficus is a genus of about 850 species of woody trees, shrubs, vines, epiphytes and hemiepiphytes in the family Moraceae. Collectively known as fig trees or figs, they are native throughout the tropics with a few species extending into the semi-warm temperate zone. The common fig (F. carica) is a temperate species native to southwest Asia and the Mediterranean region, which has been widely cultivated from ancient times for its fruit, also referred to as figs. The fruit of most other species are also edible though they are usually of only local economic importance or eaten as bushfood. However, they are extremely important food resources for wildlife. Figs are also of considerable cultural importance throughout the tropics, both as objects of worship and for their many practical uses.

Discovery

Deinococcus ficus was isolated in 2006 by Wei-An Lai, Peter Kämpfer, A. B. Arun, Fo-Ting Shen, Birgit Huber, P. D. Rekha1, and Chiu-Chung Young while the scientists were in the process of searching for certain rhizobacteria possessing the unique ability to aid in the vegetative growth of plants.^[1]D. ficus was given the species name ficus after it was isolated from the rhizosphere of the Ficus religiosa.^[1] After its discovery, various aspects such as its 16S rRNA gene sequence, respiratory quinones, structural polar lipids, and metabolic processes were tested through culturing on nutrient agar for two days at a temperature of 30 degrees Celsius.^[1] During this process, Deinococcus ficus was catalogued as strain CC-FR2-10^T.^[1] Although Deinococcus ficus has been proven useful in a variety of other functions, its role in the rhizosphere remains largely unknown.^[1]

Rhizobacteria are root-colonizing bacteria that form symbiotic relationships with many plants. The name comes from the Greek rhiza, meaning root. Though parasitic varieties of rhizobacteria exist, the term usually refers to bacteria that form a relationship beneficial for both parties (mutualism). They are an important group of microorganisms used in biofertilizer. Biofertilization accounts for about 65% of the nitrogen supply to crops worldwide. Rhizobacteria are often referred to as plant growth-promoting rhizobacteria, or PGPRs. The term PGPRs was first used by Joseph W. Kloepper in the late 1970s and has become commonly used in scientific literature. PGPRs have different relationships with different species of host plants. The two major classes of relationships are rhizospheric and endophytic. Rhizospheric relationships consist of the PGPRs that colonize the surface of the root, or superficial intercellular spaces of the host plant, often forming root nodules. The dominant species found in the rhizosphere is a microbe from the genus Azospirillum. Endophytic relationships involve the PGPRs residing and growing within the host plant in the apoplastic space.

A somatic cell or vegetal cell is any biological cell forming the body of an organism; that is, in a multicellular organism, any cell other than a gamete, germ cell, gametocyte or undifferentiated stem cell.

The rhizosphere is the narrow region of soil that is directly influenced by root secretions and associated soil microorganisms. The rhizosphere contains many bacteria and other microorganisms that feed on sloughed-off plant cells, termed rhizodeposition, and the proteins and sugars released by roots. This symbiosis leads to more complex interactions, influencing plant growth and competition for resources. Much of the nutrient cycling and disease suppression needed by plants occurs immediately adjacent to roots due to root exudants and communities of microorganisms. The rhizosphere also provides space to produce allelochemicals to control neighbors and relatives. The plant-soil feedback loop and other physical factors are important selective pressures for the communities and growth in the rhizosphere.

Phylogeny

The phylogenetic knowledge of Deinococcus ficus stems from its accidental discovery.^[1] After undergoing multiple rounds of phylogenetic analysis with 16S rRNA gene sequence, Deinococcus ficus CC-FR2-10^T was placed in the genus Deinococcus due to similarities in resistance of UV-light, gamma radiation, and desiccation.^[1]Deinococcus ficus has a number of close relatives including D. grandis with a 96.1% similar 16S rRNA gene sequence, D. radiodurans with a 94.3% similar 16S rRNA gene sequence, D. radiopugnans with a 93.2% similar 16S rRNA gene sequence, D. indicus with a 93.0% similar 16S rRNA gene sequence, D. proteolyticus with a 92.5% similar 16S rRNA gene sequence, D. murrayi with a 92.4% similar 16S rRNA gene sequence, and D. geothermal is with a 90.7% similar 16S rRNA gene sequence to that of D. ficus.^[1] As observed through high-performance liquid chromatography, D. ficus is further related to its fellow members of the genus Deinococcus through their mutual utilization of menaquinone (MK-8), a related compound of vitamin K2 found in fermented foods, as their major quinone.^[1]

Desiccation is the state of extreme dryness, or the process of extreme drying. A desiccant is a hygroscopic substance that induces or sustains such a state in its local vicinity in a moderately sealed container.

High-performance liquid chromatography method

High-performance liquid chromatography is a technique in analytical chemistry used to separate, identify, and quantify each component in a mixture. It relies on pumps to pass a pressurized liquid solvent containing the sample mixture through a column filled with a solid adsorbent material. Each component in the sample interacts slightly differently with the adsorbent material, causing different flow rates for the different components and leading to the separation of the components as they flow out of the column.

Vitamin K₂ or menaquinone has nine related compounds, generally subdivided into the short-chain menaquinones (with MK-4 as the most important member) and the long-chain menaquinones, of which MK-7, MK-8 and MK-9 are nutritionally the most recognized.

Characterization

D. ficus is a rod-shaped, non-motile, non-spore forming bacteria, proven after a three-day-long observation under a microscope in a semi-solid medium held at 30 degrees Celsius.^[1] After being flushed with 20% potassium hydroxide (KOH test), D. ficus was shown to exhibit pink pigmentation.^[1] Colonies of D. ficus were observed displaying translucent and shiny properties through testing on King's B agar, a fluorescence-detecting medium, for 48 hours.^[1]^[2] The specific pre-dominant polar lipid utilized by D. ficus is still unknown; however, through thin-layer chromatography, it is known to be a phosphoglycolipid, a Phosphate-containing fat molecule which plays a role in cell membrane structure.^[1]^[3]

A microscope is an instrument used to see objects that are too small to be seen by the naked eye. Microscopy is the science of investigating small objects and structures using such an instrument. Microscopic means invisible to the eye unless aided by a microscope.

Potassium hydroxide is an inorganic compound with the formula KOH, and is commonly called caustic potash.

The KOH Test for Candida albicans, also known as a potassium hydroxide preparation or KOH prep, is a quick, inexpensive fungal test to differentiate dermatophytes and Candida albicans symptoms from other skin disorders like psoriasis and eczema.

Physiology

D.ficus is known to grow in the rhizosphere of the F. religiosa plant, where it was discovered.^[1]D. ficus will grow on nutrient agar at 37 degrees Celsius, but it will not grow on nutrient agar in temperatures exceeding 42 degrees Celsius or falling below 5 degrees Celsius.^[1] Through the use of Degryse agar, a medium including 0.1 g of yeast extract per liter as well ammonium sulfate and filter sterilized carbon sources, it was discovered that D. ficus prefers growth under alkaline conditions but is able to tolerate a pH range of 5.5-10.^[1]^[4]

Ammonium sulfate (American English and international scientific usage; ammonium sulphate in British English); (NH₄)₂SO₄, is an inorganic salt with a number of commercial uses. The most common use is as a soil fertilizer. It contains 21% nitrogen and 24% sulfur.

Carbon Chemical element with atomic number 6

Carbon is a chemical element with symbol C and atomic number 6. It is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Three isotopes occur naturally, ¹²C and ¹³C being stable, while ¹⁴C is a radionuclide, decaying with a half-life of about 5,730 years. Carbon is one of the few elements known since antiquity.

In chemistry, pH is a scale used to specify how acidic or basic a water-based solution is. Acidic solutions have a lower pH, basic solutions have a higher pH. At room temperature, pure water is neither acidic nor basic and has a pH of 7.

Role in nitrogen fertilizer

Despite being a fairly newly discovered microorganism, various uses for D. ficus have already been identified. D. ficus can serve organic functions, such as being a valuable asset in the production of nitrogen fertilizer.^[5] Nitrogen fertilizer is advantageous due to the status of nitrogen as a crucial macronutrient, making it vital to proper plant growth due to its presence in chlorophyll as well as proteins and DNA.^[5] Therefore, photosynthesis cannot take place in the absence of nitrogen.^[5] In testing, exposure to ultraviolet light as well as translesion synthesis polymerase have resulted in certain mutations in D. ficus aided by the lexA-imuB-dnaE2 gene cassette, a cassette which codes for error-prone or lesion bypass polymerase activity.^[5] As shown by a detailed experiment involving liquid feather medium further explained on Zeng et al., these mutations increased the organism’s potential to perform keratinase processes.^[5] Poultry feathers are a harbor for beneficial proteins and nutrients; however, they contain a relatively high keratin concentration, making the process of their degradation fairly challenging due to the presence of a large number of disulfide bonds as well as cross linkages (bonds connecting chains of polymers together).^[5] Therefore, the keratinase-inducing properties of mainly UV-light but also translesion synthesis polymerase serve particularly useful functions through their induced mutations in D. ficus which allow it to enhance its ability to breakdown poultry feathers, leading to an increased availability of beneficial nutrients and proteins which can aid in this fertilizer production.^[5]

A microorganism, or microbe, is a microscopic organism, which may exist in its single-celled form or in a colony of cells.

Organic matter, organic material, or natural organic matter (NOM) refers to the large pool of carbon-based compounds found within natural and engineered, terrestrial and aquatic environments. It is matter composed of organic compounds that have come from the remains of organisms such as plants and animals and their waste products in the environment. Organic molecules can also be made by chemical reactions that don't involve life. Basic structures are created from cellulose, tannin, cutin, and lignin, along with other various proteins, lipids, and carbohydrates. Organic matter is very important in the movement of nutrients in the environment and plays a role in water retention on the surface of the planet.

Chlorophyll is any of several related green pigments found in cyanobacteria and the chloroplasts of algae and plants. Its name is derived from the Greek words χλωρός, chloros ("green") and φύλλον, phyllon ("leaf"). Chlorophyll is essential in photosynthesis, allowing plants to absorb energy from light.

Related Research Articles

Deinococcus–Thermus is a phylum of bacteria that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria. Cavalier-Smith calls this clade Hadobacteria.

A sigma factor is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it.

Thermus is a genus of thermophilic bacteria. It is one of several bacteria belonging to the Deinococcus–Thermus group. It includes the following species:

A growth medium or culture medium is a solid, liquid or semi-solid designed to support the growth of microorganisms or cells, or small plants like the moss Physcomitrella patens. Different types of media are used for growing different types of cells.

The rpoB gene encodes the β subunit of bacterial RNA polymerase. The rpoB gene also encodes for one of the subunits of the plastid-encoded plastid RNA polymerase (PEP) which is used by plants for the biogenesis of chloroplasts. An inhibitor of transcription in bacteria, tagetitoxin, also inhibits PEP, showing that the complex found in plants is very similar to the homologous enzyme in bacteria. It codes for 1342 amino acids, making it the second-largest polypeptide in the bacterial cell. It is the site of mutations that confer resistance to the rifamycin antibacterial agents, such as rifampin. Mutations in rpoB that confer resistance to rifamycins do so by altering residues of the rifamycin binding site on RNA polymerase, thereby reducing rifamycin binding affinity for rifamycins

In microbiology, streaking is a technique used to isolate a pure strain from a single species of microorganism, often bacteria. Samples can then be taken from the resulting colonies and a microbiological culture can be grown on a new plate so that the organism can be identified, studied, or tested.

Mycobacterium elephantis, a bacterium of the family Mycobacteriaceae, was discovered and isolated from a deceased elephant near India and may be linked to respiratory dysfunction. Organisms in the genus Mycobacterium are known to be aerobic and non-motile. Organisms within Mycobacterium belong to either the rapid growing group or the slow growing group. M. elephantis is classified as a rapid grower and relates most closely to Mycobacterium confluentis and Mycobacterium phlei.

fis is an E. coli gene encoding the Fis protein. The regulation of this gene is more complex than most other genes in the E. coli genome, as Fis is an important protein which regulates expression of other genes. It is supposed that fis is regulated by H-NS, IHF and CRP. It also regulates its own expression (autoregulation). Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions.

Bradyrhizobium is a genus of Gram-negative soil bacteria, many of which fix nitrogen. Nitrogen fixation is an important part of the nitrogen cycle. Plants cannot use atmospheric nitrogen (N₂); they must use nitrogen compounds such as nitrates.

16S ribosomal RNA is the component of the 30S small subunit of a prokaryotic ribosome that binds to the Shine-Dalgarno sequence. The genes coding for it are referred to as 16S rRNA gene and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. Carl Woese and George E. Fox were two of the people who pioneered the use of 16S rRNA in phylogenetics in 1977.

Deinococcus is one genus of three in the order Deinococcales of the bacterial phylum Deinococcus-Thermus highly resistant to environmental hazards. These bacteria have thick cell walls that give them Gram-positive stains, but they include a second membrane and so are closer in structure to Gram-negative bacteria. Deinococcus survive when their DNA is exposed to high doses of gamma and UV radiation. Whereas other bacteria change their structure in the presence of radiation, such as by forming endospores, Deinococcus tolerate it without changing their cellular form and do not retreat into a hardened structure. They are also characterized by the presence of the carotenoid pigment deinoxanthin that give them their pink color. They are usually isolated according to these two criteria.

A biofertilizer is a substance which contains living microorganisms which, when applied to seeds, plant surfaces, or soil, colonize the rhizosphere or the interior of the plant and promotes growth by increasing the supply or availability of primary nutrients to the host plant. Biofertilizers add nutrients through the natural processes of nitrogen fixation, solubilizing phosphorus, and stimulating plant growth through the synthesis of growth-promoting substances. Biofertilizers can be expected to reduce the use of synthetic fertilizers and pesticides. The microorganisms in biofertilizers restore the soil's natural nutrient cycle and build soil organic matter. Through the use of biofertilizers, healthy plants can be grown, while enhancing the sustainability and the health of the soil. Since they play several roles, a preferred scientific term for such beneficial bacteria is "plant-growth promoting rhizobacteria" (PGPR). Therefore, they are extremely advantageous in enriching soil fertility and fulfilling plant nutrient requirements by supplying the organic nutrients through microorganism and their byproducts. Hence, biofertilizers do not contain any chemicals which are harmful to the living soil.

LAR1 refers to a specific bacterial lineage in the order Rhizobiales that has most frequently been found directly in association with lichens.

CandidatusScalindua wagneri is a Gram-negative coccoid-shaped bacterium that was first isolated from a wastewater treatment plant. This bacterium is an obligate anaerobic chemolithotroph that undergoes anaerobic ammonium oxidation (anammox). It can be used in the wastewater treatment industry in nitrogen reactors to remove nitrogenous wastes from wastewater without contributing to fixed nitrogen loss and greenhouse gas emission.

Deinococcus frigens is a species of low temperature and drought-tolerating, UV-resistant bacteria from Antarctica. It is Gram-positive, non-motile and coccoid-shaped. Its type strain is AA-692. Individual Deinococcus frigens range in size from 0.9-2.0 μm and colonies appear orange or pink in color. Liquid-grown cells viewed using phase-contrast light microscopy and transmission electron microscopy on agar-coated slides show that isolated D. frigens appear to produce buds. Comparison of the genomes of Deiococcus radiodurans and D. frigens have predicted that no flagellar assembly exists in D. frigens.

Deinococcus marmoris is a Gram-positive bacterium isolated from Antarctica. As a species of the genus Deinococcus, the bacterium is UV-tolerant and able to withstand low temperatures.

Halostagnicola larsenii is a non-motile, aerobic, gram-negative, rod shaped archaeon. It is a halophilic, neutrophilic, chemo-organotroph and was isolated from samples taken from a saline lake in China. The etymology of the name comes from Halos Greek for salt, stagnum Latin for standing water, cola Latin for inhabitant or dweller, and Larsenii named after the Norwegian microbiologist, Helge Larsen, who was a pioneer in research regarding halophiles.

Deinococcus deserti is a Gram-negative, rod-shaped bacterium that belongs to the Deinococcaceae, a group of extremely radiotolerant bacteria. D. deserti and other Deinococcaceae exhibit an extraordinary ability to withstand ionizing radiation.

Xenophilus azovorans is a bacterium from the genus Xenophilus which has been isolated from soil in Switzerland.

References

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 Lai, W.-A., Peter Kämpfer, A.B. Arun, Fo-Ting Shen, Birgit Huber, P.D. Rekha, and Chiu-Chung Young. "Deinococcus Ficus Sp. Nov., Isolated from the Rhizosphere of Ficus Religiosa L." International Journal of Systematic and Evolutionary Microbiology 56.4 (2006): 787-91. Web.
↑ Johnsen, K. "Diversity of Pseudomonas Strains Isolated with King's B and Gould's S1 Agar Determined by Repetitive Extragenic Palindromic-polymerase Chain Reaction, 16S RDNA Sequencing and Fourier Transform Infrared Spectroscopy Characterisation." FEMS Microbiology Letters 173.1 (1999): 155-62. Web.
↑ OpenStax College, Biology. OpenStax College. 30 May 2013.<http://www.cnx.org/content/col11448/latest/>.
↑ Ferreira, A. C., M. F. Nobre, F. A. Rainey, M. T. Silva, R. Wait, J. Burghardt, A. P. Chung, and M. S. Da Costa. "Deinococcus Geothermalis Sp. Nov. and Deinococcus Murrayi Sp. Nov., Two Extremely Radiation-Resistant and Slightly Thermophilic Species from Hot Springs." International Journal of Systematic Bacteriology 47.4 (1997): 939-47. Web.
1 2 3 4 5 6 7 Zeng, You-Hong, Fo-Ting Shen, Chen-Chung Tan, Chieh-Chen Huang, and Chiu-Chung Young. "The Flexibility of UV-inducible Mutation in Deinococcus Ficus as Evidenced by the Existence of the ImuB–dnaE2 Gene Cassette and Generation of Superior Feather Degrading Bacteria." Microbiological Research 167.1 (2011): 40-47. Web.

External links

Type strain of Deinococcus ficus at BacDive - the Bacterial Diversity Metadatabase

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[RA-1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 Lai, W.-A., Peter Kämpfer, A.B. Arun, Fo-Ting Shen, Birgit Huber, P.D. Rekha, and Chiu-Chung Young. "Deinococcus Ficus Sp. Nov., Isolated from the Rhizosphere of Ficus Religiosa L." International Journal of Systematic and Evolutionary Microbiology 56.4 (2006): 787-91. Web.

[2] Johnsen, K. "Diversity of Pseudomonas Strains Isolated with King's B and Gould's S1 Agar Determined by Repetitive Extragenic Palindromic-polymerase Chain Reaction, 16S RDNA Sequencing and Fourier Transform Infrared Spectroscopy Characterisation." FEMS Microbiology Letters 173.1 (1999): 155-62. Web.

[3] OpenStax College, Biology. OpenStax College. 30 May 2013.<http://www.cnx.org/content/col11448/latest/>.

[4] Ferreira, A. C., M. F. Nobre, F. A. Rainey, M. T. Silva, R. Wait, J. Burghardt, A. P. Chung, and M. S. Da Costa. "Deinococcus Geothermalis Sp. Nov. and Deinococcus Murrayi Sp. Nov., Two Extremely Radiation-Resistant and Slightly Thermophilic Species from Hot Springs." International Journal of Systematic Bacteriology 47.4 (1997): 939-47. Web.

[ZE-5] 1 2 3 4 5 6 7 Zeng, You-Hong, Fo-Ting Shen, Chen-Chung Tan, Chieh-Chen Huang, and Chiu-Chung Young. "The Flexibility of UV-inducible Mutation in Deinococcus Ficus as Evidenced by the Existence of the ImuB–dnaE2 Gene Cassette and Generation of Superior Feather Degrading Bacteria." Microbiological Research 167.1 (2011): 40-47. Web.