Pseudomonas oryzihabitans

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1. Classification

Domain: Bacteria Phylum: Proteobacteria Class: Gammaproteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: Pseudomonas oryzihabitans

2. Introduction

Pseudomonas oryzihabitans is a rod-shaped, Gram-negative bacterium known to cause infections in humans, in both immunocompromised and non-immunocompromised individuals. Some infections that P. oryzihabitans can cause include nosocomial (hospital-acquired) sepsis, bacteremia, endophthalmitis, and peritonitis (1). In other unique cases, P. oryzihabitans has been documented to cause urinary tract infections and green nail syndrome (2, 3). P. oryzihabitans is commonly found in hospital settings, on respiratory equipment and unsterilized medical tools (1). In nature, P. oryzihabitans can be found in moist environments, like soil, rice paddies, running or standing water, and groundwater (4,5). In these environments, P. oryzihabitans has potential to promote root growth via suppressing parasitic nematode populations, making it easier to grow and maintain certain crops (6). Additionally, P. oryzihabitans has a positive growth effect on members of the cucurbit family affected by Bacterial Fruit Blotch disease (BFB) (7). P. oryzihabitans also negatively impacts the growth of Muskmelon by causing stem and leaf rot (8). Overall, in this paper we discuss how P. oryzihabitans is a multifaceted organism that plays various roles ecologically, agriculturally, and medically that has not been compiled previously.

3. Genome structure

The genome of two strains of Pseudomonas oryzihabitans, AXSa06 and AXSa07, have been sequenced (9). The genome of the P. oryzihabitans strain AXSa06 has 5,109,344 base pairs in total and the AXSa07 strain has 4,666,115 base pairs. The two strains share a similar % G+C content, both around 66% of the whole genome (9). In the AXSa07 strain genome, there are 4495 protein coding sequences. However, the AXSa07 strain has 15 rRNA genes, higher than the AXSa06 strain, which has 5 rRNA genes (9). A key difference between the AXSa06 strain and the AXSa07 strain lies in their ACC deaminase activity. ACC deaminase activity is often used by soil microorganisms to enhance plant growth by inhibiting the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC), which is a precursor to ethylene, a hormone that controls plant maturation. The P. oryzihabitans strain AXSa06 has genes coding for ACC deaminase activity, while AXSa07 strain does not (9). In the P. oryzihabitans strain AXSa06 genome, there are 4929 protein coding sequences (9). Besides AXSa06 and AXSa07 strains, the genome of GCMCC 6169, a soil strain of P. oryzihabitans, was shown to encode the protein POEP1 which aids cellulose breakdown. Although POEP1 does not break down cellulose directly, it synergistically enhances the activity of cellulase, a protein that directly hydrolyzes cellulose for energy (10).

4. Cell structure

Pseudomonas oryzihabitans is a rod-shaped, Gram-negative bacteria that forms yellow-color colonies with a rough or wrinkled appearance (9). Since P. oryzihabitans is a Gram-negative bacteria, this means that it has a thin peptidoglycan cell wall with porins that allow substance passage and lipopolysaccharides that may cause toxicity to an infected host. The yellow pigmentation is not dissolvable in water (11). In addition, P. oryzihabitans is non-endospore forming (11). P. oryzihabitans bacterium is motile via one or more polar flagella (11).

5. Metabolic processes

P. oryzihabitans optimal growth conditions are 37℃, 7.5 pH (11). P. oryzihabitans does not ferment and cannot break down glucose (6). This bacterium can also break down 2,4-DNT, a common soil contaminant, (11). When an oxidase test was performed on the bacterium, P. oryzihabitans tested oxidase positive (12). The top two carbon sources for P. oryzihabitans are listed respectively: Lactose and Succinate all at 0.2%. The top three nitrogen sources for the bacterium’s growth yeast, casein, and KNO3 (12). A particular strain of P. oryzihabitans,PGP01, can achieve optimal growth by utilizing carbon and nitrogen sources from agro-food waste. Since P. oryzihabitans can have a positive relationship with plant roots, plant and food waste were used as nutrient sources (13). Frozen potato peel and pulp medium (FPP), tryptone (10 g/L), sugar cane molasses (10 g/L), along with NaCl (5 g/L) and K2HPO4 (2.5 g/L) were combined for optimal growth of P. oryzihabitans. The study demonstrated the potential of P. oryzihabitans in re-purposing and diminishing food waste using its metabolic processes (13). Metabolic ability for chemical substances in P. oryzihabitans can differ from other members of the Pseudomonas genus and within separate strains of P. oryzihabitans species. Two strains (NT0-1 and NT0-6) of P. oryzihabitans in particular have different H2O2 metabolism abilities in seedlings (14). Compared to the Pseudomonas fluorescens strains NT0-2 and NT0-8, which did not produce a level of H2O2 above detection, both P. oryzihabitans strains produce measurable amounts of H2O2 and have a 3.6 time decrease in H2O2 after 1.5 hours of inoculation. However, H2O2 concentration generated by P. oryzihabitans NT0-1 was 3.2 times higher than that of the NT0-6 strain, and the decrease in H2O2 metabolic concentration followed an initial increase (14). Other strains of P. oryzihabitans, such as the GCMCC 6169 strain, have a genome that encodes for the protein POEP1. When incubated together, POEP1 and cellulase produced a maximum cellulose breakdown amount of 4.2mg, while cellulase alone only hydrolyzed 2.00mg of cellulose after a 48 hour period (10). Furthermore, L-Asparaginase, a protein that catalyzes the production of aspartic acid and ammonia from the amino acid asparagine, was found in an endophytic strain of P. oryzihabitans isolated from Hibiscus rosa-sinensis (Shoeblack plant)(15). The endosymbiont P. oryzihabitans strain exhibited high L-Asparaginase activity (4.3 U/mL) under optimized growth environments. L-Asparaginase has crucial therapeutic value and effectively treats acute lymphocytic leukemia (ALL)(15).

6. Ecology

Pseudomonas oryzihabitans prefer to reside in moist environments, such as rice paddies, soil, and surgical equipment like catheters (4). P. oryzihabitans has been documented to have a beneficial effect in the growth of some plant species and a harmful effect on others. P. oryzihabitans can enhance tomato plant growth by suppressing the reproduction rate of Meloidogyne javanica, a nematode species that feeds on tomato. However, the mechanism of how exactly P. oryzihabitans metabolites interacted with nematode reproduction is still unknown (6). In addition to promoting plant growth, P. oryzihabitans can also cause stem and leaf rot in Muskmelon (8). Most discoveries of P. oryzihabitans are in wet environments like hospital equipment, rice paddies, and soil. P. oryzihabitans have also been documented to adhere to the surfaces of silicon beads in groundwater and form biofilms on such particulate surfaces (4). In rare cases, P. oryzihabitans thrives in dry environments, such as the nail bed, but the exact reason still needs to be investigated (2).

7. Pathology

Human infections of Pseudomonas oryzihabitans occur most commonly in immunocompromised patients who are hospitalized. Some common types of infections that P. oryzihabitans can cause in humans are bacteremia and peritonitis (1). Patients with a P. oryzihabitans infection can experience sepsis, displaying strong fever, fast breathing rates, and organ failure (1). Infections caused by P. oryzihabitans are often treated with antibiotics. However, most Pseudomonas species including P. oryzihabitans are resistant to penicillin and other antibiotics that target bacterial cell walls (2). Though it is rare for humans to acquire a P. oryzihabitans infection, the bacterium can infect hospitalized patients who have an underlying disease or have just undergone surgery. P. oryzihabitans is considered a potential nosocomial pathogen, meaning that its origin and spreading tends to start within a hospital setting (3). In addition to infecting hospitalized patients, there have also been rare cases of P. oryzihabitans infection in healthy individuals. A case of Green Nail Syndrome was caused by P. oryzihabitans in a healthy female after the removal of nail polish. The bacterium infected the patient during the buffing of her nail bed, which caused breakage of nail tissue and allowed for infection (2). P. oryzihabitans also caused a rare case of urinary-tract infection in a non-hospitalized, healthy adult male (3).

8. Current Research

Current research on Pseudomonas oryzihabitans is focused on the bacteria’s role in agriculture, such as its ability to protect certain plant species from disease, or cause disease in other plants. Bacterial Fruit Blotch (BFB) is a disease that poses a particular threat to members of the cucurbit family, which include melons, cucumber, and pumpkin. Among these, melons and watermelons are especially susceptible. When P. oryzihabitans Antg-12 strain was sprayed onto watermelon leaf, BFB disease severity of the watermelon sample decreased by ~56% and the fruit yield increased ~41% (7). By contrast, P. oryzihabitans was identified to be the cause of Bacterial fruit black rot disease in prickly ash trees (16). This was the first report yet documenting the association between P. oryzihabitans and Bacterial fruit black rot disease. Another prominent case of P. oryzihabitans infecting plants was when rice fields in China appeared to produce discolored rice grains as well as blight within the panicles of some rice plants. After performing Gram stain tests to determine the genus of the bacterium to be Pseudomonas, RNA sequencing was performed to discover that the species was oryzihabitans (12). This was a major discovery as it was the first instance in which P. oryzihabitans showed pathogenicity towards rice plants. P. oryzihabitans were also found to cause stem and leaf rot in Muskmelon plants, a cash crop in China (8). After isolating affected areas of the plants, submerging them in ethanol, and performing Gram stain tests, the bacterium responsible for this disease was determined to be P. oryzihabitans.

9. References

[1] Lucas K. G., T. E. Kiehn, K. A. Sobeck, D. Armstrong and A. E. Brown . 1994. Sepsis caused by Flavimonas oryzihabitans. Medicine 73(4): 209-214.

[2] Keunyoung H. and S. Cho. 2020. Chloronychia caused by Pseudomonas oryzihabitans infection. JAAD Case Rep. 6:918-920.

[3] Bhatawadekar S. M.. 2013. Community Acquired urinary tract infection by Pseudomonas oryzihabitans. J. Glob Infect Dis. 5:82-84.

[4] Dussart L., J. P. Dupont, I. Zimmerlin, M. Lacroix, J. M. Saiter, G. A. Junter and T. Jouenne. 2002. Occurrence of sessile Pseudomonas oryzihabitans from a karstified chalk aquifer. Water Research 37(7):1593-1600.

[5] Udoekong N. S., B. N. Bassey, A. E. Asuquo, O. D. Akan, C. I. Ifeanyi. 2021. Prevalence and Antimicrobial Resistance of Gram-Negative Bacteria Isolates in Shellfish Samples from Two River Estuaries in South-South Africa. Advances in Microbiology 11:428-443.

[6] Leontopoulos S., V., S. R. Gowen, E. Topalidou, I. K Vagelas and F. T. Gravanis. 2011. Pseudomonas oryzihabitans Suppress Damage Caused by Root-Knot Nematode Meloidogyne javanica on Tomato. Journal of Agriculture Science and Technology 5:502-507.

[7] Horuz S. 2021. Pseudomonas oryzihabitans: a potential bacterial antagonist for the management of bacterial fruit blotch (Acidovorax citrulli) of cucurbits. Journal of Plant Pathology. 103:751-758.

[8] Li J., G. Zhou, T. Wang, T. Lin, Y. Wang, P. Zhu, L. Xu, G. Ma. 2021. First Report of Pseudomonas oryzihabitans Causing Stem and Leaf Rot on Muskmelon in China. APS Publications 104:11.

[9] Leontidou K., S. Genitsaris, A. Papadopoulou, N. Kamou, I. Bosmali, T. Matsi, P. Madesis, D. Vokou, K. Karamanoli and I. Mellidou. 2020. Plant growth promoting rhizobacteria isolated from halophytes and drought tolerant plants: genomic characterisation and exploraction of phyto-beneficial traits. Scientific Reports. 10:14857.

[10] Qin Y. M., T. Heng, Y. Y. Liu, Y. D. Wang, J. R. Zhang and A. X. Tang. 2013. A novel non-hydrolytic protein from Pseudomonas oryzihabitans enhances the enzymatic hydrolysis of cellulose. Journal of Biotechnology 168(1):24-31.

[11] Habahbeh H. Biodegradation of some 2,4-Dinitrotoluene (2,4-DNT) by some bacteria isolated from Maan Quarries, Southern Jordan. (Mu’ tah University, 2015)

[12] Public Health England. UK Standards For Microbiology Investigations- Abdominal organ transport fluid testing. (2019).

[13] Cantebella D., R. Dolcet-Sanjuan, C. Solsona, L. Vilanova, R. Torres, N. Teixidó. 2021. Optimization of a food industry-waste-based medium for the production of the plant growth promoting microorganism Pseudomonas oryzihabitans PGP01 based on agro-food industries by-products. Biotechnology Reports 32.

[14] Gerna D., T. Roach, B. Mitter, W. Stöggl, I. Kranner. 2020. Hydrogen Peroxide Metabolism in Interkingdom Interaction Between Bacteria and Wheat Seeds and Seedlings. Molecular Plant-Microbe Interactions 33:336-348.

[15] Bhagat J, A. Kaur and B. S. Chadha. 2016. Single step purification of asparaginase from endophytic bacteria Pseudomonas oryzihabitans exhibiting high potential to reduce acrylamide in processed potato chips. Food and Bioproducts Processing 99:222-230.

[16] Liu Z., Y. He, Z. Xiang, Y. Yang, F. Nie, X. Liu, Z. Li and Q. Zeng. 2021. First Report of Pseudomonas oryzihabitans causing fruit black rot in prickly ash in China. Journal of Plant Diseases and Protection 128:1363-1366.

Edited by [Zhengtong (Selena) Gao], student of Jennifer Talbot for BI 311 General Microbiology, 2016, Boston University.