Kocuria rhizophila

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Classification

Domain: Bacteria

Phylum: Actinomycetota

Class: Actinomycetia

Order: Micrococcales

Family: Micrococcaceae

Species

NCBI: Taxonomy

Kocuria rhizophila

Description and Significance

Describe the appearance, habitat, etc. of the organism, and why you think it is important.

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Use in laboratory testing

The Kocuria rhizophila strain ATCC 9341 has been used in quality control for sterility testing, as a test for the effectiveness of antibiotics and fungicides, and for doxycycline, tetracycline, and chloramphenicol susceptibility testing since 1966 under the designation Micrococcus luteus[4]. This designation was corrected to the current name Kocuria rhizophila in 2003, and its use in these forms has continued since the designation change[4].

Use in multi-metal contaminated soils

Application of Kocuria rhizophila alongside citric acid has been shown to facilitate metal extraction from soil by plants[3]. The level of metal extraction is most fit for removing multi-metal contamination from soils, and it has been demonstrated to be effective in accumulating Cd, Cr, Cu, and Ni in Glycine max[3].

Ionizing radiation resistance

The Kocuria rhizophila strain PT10 has been shown to be resistant to ionizing radiation, isolated from roots of Panicum turgidum from the Tunisian Sahara[6]. Study of the PT10 strain has allowed for identification of mechanisms that generate ionizing radiation resistance[6].

Salt stress tolerance

The Kocuria rhizophila strains Y1 and 14ASP have been shown to enhance salt stress tolerance in maize and Oxalis corniculata respectively[7,9]. The strain Y1 is able to tolerate up to 10% environmental NaCl, and it transfers this tolerance to maize when inoculated[7]. Inoculation with strain Y1 in maize is associated with increased salt stress tolerance, changes in presence of plant hormones IAA and ABA, and increased gene expression of antioxidant and salt tolerance genes[7].

Appearance

Appearing to have a rigid cell wall, Kocuria rhizophila is a Gram-positive cocci[8]. Arrangements of K. rhizophila come in pairs, shorts chains, tetrads, cubical packets of eight, and irregular clusters[8]. K. Rhizophila usually form 2-3 millimeter whitish, round, convex colonies on initial isolation[8]. After prolonged incubation, K. Rhizophila might develop a yellowish pigmentation[8,12]. Under strict aerobic conditions the colonies progress to be dull and creamy with a yellow tinge[12].

Genome Structure

Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?

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Kocuria rhizophila has a single circular genome with 2,697,540 bp[1]. This is a relatively small genome compared to other species in the order Actinomycetales[1]. K. rhizophila strain DC2201's G+C content is 71.16%[1]. It is predicted it's genome contains 2,357 genes which code for proteins, 87.7% of which have the same function as proteins in other Actinobacteria[1]. It's genome contains over 200 genes related to membrane transport which have been theorized to help the bacterium use the chemicals around plant roots.1 Gene analysis shows some K. rhizophila genes have homology with dormancy genes of the closely related bacterium M. luteus which would provide tolerance to stresses in its environment[1].

Cell Structure, Metabolism and Life Cycle

Interesting features of cell structure; how it gains energy; what important molecules it produces.

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Cell structure

Kocuria rhizophila is a Gram-positive cocci morphology similar to Staphylococci[8]. It has cell structures which are potentially robust enough to be able to withstand some usually destructive organic compounds[10].

Metabolism

K. rhizophila has required strictly aerobic conditions to be successfully cultured[2]. However, gene analysis shows that it has the potential to grow under anaerobic conditions[1]. Analysis of K. rhizophila’s genome showed that it likely has catabolic pathways for several compounds produced during plant decomposition[1].

Ecology and Pathogenesis

Habitat; symbiosis; biogeochemical significance; contributions to environment.
If relevant, how does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.

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Habitat

Kocuria Rhizophila is adapted to live in is the rhizosphere, the soil surrounding plant roots[1]. K. rhizophila has been identified alongside and inside plant roots from a wide variety of environments including maize, Oxalis corniculata, Panicum turgidum, and Typha angustifolia[6,7,9,2]. K. rhizophila has been identified as a member of a marine biofilm on a ship hull[11]. TheK. rhizophila isolated from this biofilm produced EPS with a higher carbohydrate and protein content than the other bacteria isolated from the same biofilm[11]. It has also been identified in Domiati cheese, a type of soft white salty cheese, among other salt-tolerant bacteria[14].

Pathogenesis

Kocuria Rhizophila has also been found to be an opportunistic pathogen. The isolation along with the significance of this bacteria warrants great caution[12]. While it’s presence does warrant caution, K. Rhizophila’s residency does not confirm infection[12]. K. Rhizophila is as normal as a flora of skin and mucous membranes[12]. K. Rhizophila is ignored as a contaminant by laboratories because it is considered as a non pathogenic bacteria[12]. While it can be found in people and animals, it can be found to cause infection of pancreatitis and sepsis[12].

References

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1 Takarada, H., Sekine, M., Kosugi, H., Matsuo, Y., Fujisawa, T., Omata, S., Kishi, E., Shimizu, A., Tsukatani, N., Tanikawa, S., Fujita, N., & Harayama, S. (2008). Complete Genome Sequence of the Soil Actinomycete Kocuria rhizophila. Journal of Bacteriology, 190(12), 4139–4146.

2 Kovacs, G., J. Burghardt, S. Pradella, P. Schumann, E. Stackebrandt, and K. Marialigeti.1999. Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia). Int. J. Syst. Bacteriol.49:167-173.

3 Hussain, A., Amna, Kamran, M. A., Javed, M. T., Hayat, K., Farooq, M. A., Ali, N., Ali, M., Manghwar, H., Jan, F., & Chaudhary, H. J. (2019). Individual and combinatorial application of Kocuria rhizophila and citric acid on phytoextraction of multi-metal contaminated soils by Glycine max L. Environmental and Experimental Botany, 159, 23–33.

4 Tang, J. S., & Gillevet, P. M. (2003). Reclassification of ATCC 9341 from Micrococcus luteus to Kocuria rhizophila. International Journal of Systematic and Evolutionary Microbiology, 53(4), 995–997.

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6 Guesmi, S., Pujic, P., Nouioui, I., Dubost, A., Najjari, A., Ghedira, K., Igual, J. M., Miotello, G., Cherif, A., Armengaud, J., Klenk, H. P., Normand, P., & Sghaier, H. (2021). Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal. Genomics, 113(1), 317–330.

7 Li, X., Sun, P., Zhang, Y., Jin, C., & Guan, C. (2020). A novel PGPR strain Kocuria rhizophila Y1 enhances salt stress tolerance in maize by regulating phytohormone levels, nutrient acquisition, redox potential, ion homeostasis, photosynthetic capacity and stress-responsive genes expression. Environmental and Experimental Botany, 174, 104023.

8 Kandi, V., Palange, P., Vaish, R., Bhatti, A. B., Kale, V., Kandi, M. R., & Bhoomagiri, M. R. (2016). Emerging Bacterial Infection: Identification and Clinical Significance of Kocuria Species. Cureus.

9 Afridi, M. S., van Hamme, J. D., Bundschuh, J., Sumaira, Khan, M. N., Salam, A., Waqar, M., Munis, M. F. H., & Chaudhary, H. J. (2021). Biotechnological approaches in agriculture and environmental management - bacterium Kocuria rhizophila 14ASP as heavy metal and salt- tolerant plant growth- promoting strain. Biologia, 76(10), 3091–3105.

10 Fujita, K., Hagishita, T., Kurita, S., Kawakura, Y., Kobayashi, Y., Matsuyama, A., & Iwahashi, H. (2006). The cell structural properties of Kocuria rhizophila for aliphatic alcohol exposure. Enzyme and Microbial Technology, 39(3), 511–518.

11 S., K., Raghavan, V. (2018). Isolation and characterization of marine biofilm forming bacteria from a ship’s hull. Frontiers in Biology, 13(3), 208–214.

12 Becker, K., Rutsch, F., Uekötter, A., Kipp, F., König, J., Marquardt, T., Peters, G., & von Eiff, C. (2008). Kocuria rhizophila adds to the emerging spectrum of micrococcal species involved in human infections. Journal of clinical microbiology, 46(10), 3537–3539.

13 Moissenet, D., Becker, K., Mérens, A., Ferroni, A., Dubern, B., & Vu-Thien, H. (2012). Persistent Bloodstream Infection with Kocuria rhizophila Related to a Damaged Central Catheter. Journal of Clinical Microbiology, 50(4), 1495–1498.

14 El-Baradei, G., Delacroix-Buchet, A., & Ogier, J. C. (2007). Biodiversity of Bacterial Ecosystems in Traditional Egyptian Domiati Cheese. Applied and Environmental Microbiology, 73(4), 1248–1255.

15 ANANG, D. M., RUSUL, G., RADU, S., BAKAR, J., & BEUCHAT, L. R. (2006). Inhibitory Effect of Oxalic Acid on Bacterial Spoilage of Raw Chilled Chicken. Journal of Food Protection, 69(8), 1913–1919.

Author

Page authored by Timothy Biewer-Heisler, Joseph Bell, and Linnaea Awdey; students of Prof. Jay Lennon at IndianaUniversity.