Kocuria rhizophila

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Classification

Domain: Bacteria

Phylum: Actinomycetota

Class: Actinomycetia

Order: Micrococcales

Family: Micrococcaceae

Species

NCBI Taxonomy[5]: [1]

Kocuria rhizophila

Description and Significance

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].

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].

Genome Structure

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 and Metabolism

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]. K. rhizophila contains a multidrug efflux pump system which provides significant in providing tolerance to some organic toxins[1]. A protein in this pump is homologous to that of the plant pathogen Xanthomonas albilineans, suggesting a shared niche[1].

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]. It is a chemoorganoheterotroph adapted to utilize the compounds available in the rhizosphere[1].

Ecology and Pathogenesis

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, Typha angustifolia, and Glycine max[6,7,9,2,3]. K. rhizophila has been identified as a member of a marine biofilm on a ship hull[11]. The K. 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]. Raw chicken treated with oxalic acid was found to contain primarily K. rhizophila on its surface, suggesting some tolerance to oxalic acid in its habitat[15].

Symbiosis

K. rhizophila has been shown to have mutualistic interactions with maize, Glycine max, and Oxalis corniculata.[3,6,7] In maize and Oxalis corniculata, K. rhizophila strains have been shown to increase the salt tolerance of these plants.[6,7] When inoculated with K. rhizophila these host species were able to have greater biomass soil with low levels of salt compared to non-inoculated specimens as well as being able to survive more extreme levels of salt in soil.[6,7] K. rhizophila inoculated Glycine max, alongside application of citric acid, was able to improve the survivability and biomass of Glycine max in multi-metal contaminated soils as well as facilitating the uptake of Cd, Cr, Cu, and Ni into Glycine max.[3]

Pathogenesis

Kocuria rhizophila is an opportunistic pathogen. The first known clinical case of a patient with Kocuria rhizophila was in a six year-old boy that was infected with a contaminated Port-A-Cath.[12] The infection caused sepsis and acute pancreatitis.[12] These symptoms were repeated in a later K. rhizophila infection involving a three year-old girl.[13] The contamination was not detected because K. rhizophila is not considered a pathogenic bacteria.[12] K. rhizophila is frequently found in the skin microbiome and as such its presence does not indicate an infection of K. rhizophila causing disease like infections.[12] K. rhizophila has only been described as a pathogen in cases where the patient has a compromised immune system.[12,13]

References

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.

5 Schoch CL, et al. (2020). NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database Oxford. baaa062. PubMed: 32761142 PMC: PMC7408187

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.