Enterobacter cloacae: A Multifunctional Endophyte for Plant Growth Promotion and Bioremediation

Overview of the Microbe#

Enterobacter cloacae is a gram-negative, facultatively anaerobic, rod-shaped bacterium belonging to the family Enterobacteriaceae. Initially recognized for its opportunistic pathogenicity in humans, E. cloacae has emerged as a highly versatile species, demonstrating a broad ecological distribution and diverse metabolic capabilities [1]. It is ubiquitously found in soil, water, plants, and the gastrointestinal tracts of animals.

In the context of plant–microbe interactions, certain strains of E. cloacae have gained prominence as plant growth-promoting endophytes (PGPEs), colonizing the internal tissues of plants without causing harm. These beneficial strains contribute significantly to plant health by enhancing nutrient availability, producing phytohormones, alleviating abiotic stress, suppressing pathogens, and remediating environmental contaminants [2].The widespread adaptability, metabolic plasticity, and endophytic lifestyle of E. cloacae make it a prime candidate for integrated agricultural and environmental applications. Understanding the multifaceted roles of this microbe sheds light on its emerging biotechnological relevance.

Phosphate Solubilisation and Nutrient Mobilisation#

Phosphorus (P) is an essential macronutrient for plant development, but it often exists in insoluble forms in soil. E. cloacae has demonstrated robust phosphate-solubilizing abilities, thereby increasing the bioavailability of P for plant uptake. This is achieved via secretion of organic acids such as gluconic and citric acids, which chelate cations and lower the pH in the rhizosphere, leading to mineral dissolution [3].In addition to phosphate, E. cloacae aids in mobilizing other nutrients including potassium (K), iron (Fe), and zinc (Zn). It produces siderophores—iron-chelating compounds that scavenge Fe³⁺ from the environment—improving iron nutrition for plants while limiting pathogen access to this vital element [4] This nutrient mobilization enhances plant vigor, root biomass, and yields, especially under nutrient-deficient or degraded soil conditions.

Phytohormone Production and Stress Alleviation#

One of the key features of E. cloacae as a PGPE is its ability to biosynthesize phytohormones, particularly indole-3-acetic acid (IAA), cytokinins, and gibberellins. IAA, a form of auxin, plays a central role in root elongation, cell division, and differentiation, facilitating improved water and nutrient uptake [5]

Moreover, certain strains express the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which degrades ACC, the precursor of ethylene—a stress hormone that inhibits root growth under abiotic stress conditions such as drought, salinity, or heavy metal exposure [6]. By reducing ethylene levels, E. cloacae promote stress tolerance, seed germination, and root architecture remodeling.

In saline soils, inoculation with ACC deaminase-producing E. cloacae improves chlorophyll content, osmotic balance, and nutrient uptake. This functional repertoire positions the bacterium as a valuable bioinoculant for climate-resilient agriculture.

Biocontrol and Disease Suppression#

E. cloacae exhibits biocontrol activity against a range of phytopathogens through multiple mechanisms. These include:

• Antibiosis: Secretion of antimicrobial compounds such as phenazines, lipopeptides, and chitinases that inhibit fungal and bacterial pathogens.
• Competition: Rapid colonization of plant surfaces and endospheres prevents pathogen establishment.
• Induced Systemic Resistance (ISR): Activation of plant defense genes and systemic signaling pathways, enhancing resistance to diseases like bacterial wilt and root rot [7].

In practical applications, E. cloacae has shown effectiveness against pathogens including Fusarium oxysporum, Rhizoctonia solani, Pythium spp., and Xanthomonas campestris. It has been utilized in seed biopriming, root drenching, and foliar sprays for disease suppression in crops such as tomato, rice, cucumber, and sugarcane [8].

As antibiotic resistance becomes a global concern, biocontrol agents like E. cloacae offer eco-friendly alternatives to chemical pesticides, reducing environmental toxicity and preserving soil health.

Bioremediation of Organic Pollutants#

Beyond its agricultural functions, E. cloacae demonstrates potent bioremediation capabilities. Certain strains degrade toxic organic pollutants such as polycyclic aromatic hydrocarbons (PAHs), phenols, nitroaromatics, and pesticides. This is facilitated by their broad enzymatic machinery, including monooxygenases, dioxygenases, and reductases [9].

In petroleum-contaminated sites, E. cloacae has been isolated as a hydrocarbon degrader capable of metabolizing naphthalene and benzene derivatives. Similarly, in agricultural runoff systems, it contributes to the degradation of commonly used pesticides such as atrazine and chlorpyrifos [10].Coupled with its rhizospheric adaptability, E. cloacae has been proposed for phytoremediation-assisted strategies, where plants and microbes jointly detoxify polluted soils. Its ability to resist and transform heavy metals like cadmium (Cd), lead (Pb), and arsenic (As) also supports its role in restoring contaminated environments.

Challenges and Future Potential#

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Despite its promising profile, the deployment of E. cloacae in large-scale applications faces several challenges:

• Biosafety Concerns: As an opportunistic human pathogen, concerns about horizontal gene transfer and virulence potential must be rigorously addressed through strain selection and genomic screening.
• Strain Variability: Functional traits can vary significantly among strains; some may lack key genes for plant growth promotion or may possess undesirable traits.
• •Regulatory Hurdles: Biocontrol agents and biofertilizers must meet regulatory standards that include environmental safety, strain stability, and efficacy documentation.
• Field Performance: Laboratory successes often face reduced efficacy under field conditions due to competition with native microbiota, environmental fluctuations, and host specificity.

Nevertheless, the growing body of genomic and metabolomic data enables the rational design of microbial consortia, strain engineering, and precision agriculture approaches. Future research should focus on genome editing for safety and performance, understanding host–microbe signaling pathways, and optimizing formulations for field delivery.

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Spotlight on Research: Genomic Insights into the Plant Growth-Promoting Enterobacter cloacae UW4#

Brief Overview#

A seminal study titled “Genomic insights into the plant growth-promoting bacterium Enterobacter cloacae UW4” by Xu et al. [11], published in PLOS ONE, provides a comprehensive genomic perspective on the strain UW4, known for its robust plant growth-promoting abilities.

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Key Insights#

• The genome (4.7 Mb) encodes genes for IAA production, phosphate solubilization, siderophore biosynthesis, and ACC deaminase activity.
• Comparative genomics revealed unique operons related to heavy metal resistance and biodegradation pathways.
• The strain lacked key virulence genes associated with pathogenicity in clinical isolates, suggesting its biosafety for agricultural use.

Why This Matters#

This study provides the genetic blueprint that validates the multifunctionality of E. cloacae UW4 and offers targets for strain improvement and synthetic biology applications. It also exemplifies how genome sequencing can guide the development of bioinoculants by ensuring efficacy and safety.

Summary Table: Spotlight Study#

Category	Details
Lead Researchers	J. Xu, T. Zhang, B. Guo, D. Dong
Affiliations	Department of Biology, University of Waterloo, Canada
Research Focus	Genomics, plant-microbe interaction, microbial biotechnology
Key Breakthroughs	Full genome annotation, PGP gene identification, metal resistance operons
Collaborative Efforts	Supported by Agriculture and Agri-Food Canada and Genome Canada
Published Work	PLOS ONE, 2014, Volume 9, Issue 3
Perspective	Genomic-enabled functional insights
Publication Date	March 2014
Location	Ontario, Canada
Key Findings	PGP traits genetically confirmed; lacks virulence; suitable for biosafe agricultural use

Conclusion#

Enterobacter cloacae is no longer merely regarded as a clinical microbe but is increasingly appreciated for its multifaceted roles in agriculture and environmental restoration. From solubilizing nutrients and producing growth hormones to suppressing pathogens and detoxifying pollutants, it represents a model endophyte with real-world application potential.

However, responsible development demands rigorous biosafety screening, functional validation, and adaptive deployment strategies. With advances in genomics, synthetic biology, and systems microbiology, E. cloacae is poised to become a cornerstone of sustainable agriculture and ecological resilience in the face of mounting global challenges.

References#

1. Mezzatesta, M. L., Gona, F., & Stefani, S. (2012). Enterobacter cloacae complex: Clinical impact and emerging antibiotic resistance. Future Microbiology, 7(7), 887–902. https://doi.org/10.2217/fmb.12.61
2. Sessitsch, A., Hardoim, P., Döring, J., Weilharter, A., Krause, A., Woyke, T., … & Reinhold-Hurek, B. (2012). Functional characteristics of an Enterobacter isolate of the Enterobacter cloacae complex from the endorhiza of rice. Molecular Plant-Microbe Interactions, 25(6), 727–736. https://doi.org/10.1094/MPMI-09-11-0242
3. Rodríguez, H., & Fraga, R. (1999). Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnology Advances, 17(4–5), 319–339. https://doi.org/10.1016/S0734-9750(99)00014-2
4. Kloepper, J. W., Leong, J., Teintze, M., & Schroth, M. N. (1980). Enhanced plant growth by siderophores produced by plant growth-promoting rhizobacteria. Nature, 286(5776), 885–886. https://doi.org/10.1038/286885a0
5. Spaepen, S., Vanderleyden, J., & Remans, R. (2007). Indole-3-acetic acid in microbial and microorganism–plant signaling. FEMS Microbiology Reviews, 31(4), 425–448. https://doi.org/10.1111/j.1574-6976.2007.00072.x
6. Glick, B. R. (2012). Plant growth-promoting bacteria: Mechanisms and applications. Scientifica, 2012, 963401. https://doi.org/10.6064/2012/963401
7. Kumar, A., Maurya, B. R., & Raghuwanshi, R. (2012). Isolation and characterization of Enterobacter strains with plant growth promoting traits and their effect on Vigna radiata. Biocontrol Science and Technology, 22(6), 719–735. https://doi.org/10.1080/09583157.2012.683205
8. Nowak, J., Asiedu, S. K., & Lazarovits, G. (1997). Enhancement of disease resistance and plant growth by Enterobacter cloacae in greenhouse and field trials. Canadian Journal of Plant Pathology, 19(2), 145–153. https://doi.org/10.1080/07060669709500594
9.  Fatima, S., & Khan, M. S. (2017). Enterobacter cloacae strain PG01: A plant growth promoting and polycyclic aromatic hydrocarbon-degrading bacterium isolated from petroleum-contaminated soil. Environmental Science and Pollution Research, 24(21), 17214–17227. https://doi.org/10.1007/s11356-017-9365-2
10.   Sarkar, D., Acharya, A., Poddar, R., & Ghosh, S. (2017). Biodegradation of chlorpyrifos by Enterobacter cloacae strain SJRP17 isolated from paddy field soil. 3 Biotech, 7(5), 277. https://doi.org/10.1007/s13205-017-0926-7
11. Xu, J., Zhang, T., Guo, B., & Dong, D. (2014). Genomic insights into the plant growth-promoting bacterium Enterobacter cloacae UW4. PLOS ONE, 9(3), e96882. https://doi.org/10.1371/journal.pone.0096882