Paenibacillus polymyxa: A Multifunctional Plant Growth-Promoter and Biocontrol Agent

Overview of the Microbe#

Paenibacillus polymyxa is a gram-positive, rod-shaped, spore-forming bacterium commonly found in soil and the rhizosphere of plants. It thrives in diverse environments – including plant tissues, animal guts, fermented foods, and even on the International Space Station[3]. Its resilient endospores withstand extreme conditions (heat, UV, pressure, biocides), allowing it to persist through pasteurization and harsh industrial processes[1]. P. polymyxa is renowned for synthesizing many bioactive compounds (e.g. lipopeptide antibiotics such as polymyxins and fusaricidins) with broad antimicrobial activity[1]. These traits underlie its multifaceted roles: it enhances soil fertility and plant growth while suppressing pathogens, making it valuable for sustainable agriculture and biotechnology[1].P. polymyxa was first described in 1880 as Clostridium polymyxa and later reclassified (1889 as Bacillus polymyxa, and in 1993 to the new genus Paenibacillus based on rRNA analysis)[1]. The genus Paenibacillus now includes over 150 species of spore-forming bacilli[2], with P. polymyxa as its type species and a key model organism. In nature, P. polymyxa is most often isolated from plant roots and soils[1][3]. Its cells are motile and form chains, and the bacteria metabolize a variety of substrates. P. polymyxa is considered non-pathogenic to humans and is even probiotic in some contexts, aligning with a One Health perspective on its use in plant, animal, and human health[1].

Nitrogen Fixation and Nutrient Solubilisation#

A hallmark of P. polymyxa is its ability to increase nutrient availability in soil. Several strains can fix atmospheric nitrogen by converting N₂ gas into ammonia, enriching soil nitrogen content for plant use[1]. This biological nitrogen fixation makes P. polymyxa a natural biofertilizer. In addition, P. polymyxa solubilizes mineral phosphates and micronutrients that are otherwise inaccessible to plants[1][3]. For example, the bacterium secretes organic acids that release phosphate from insoluble compounds, and it produces siderophore-like molecules to chelate iron (scavenging Fe³⁺ for plant uptake)[3][1]. Some strains also mobilize zinc and potassium from soil minerals. By making N, P, K, Zn, and Fe more available, P. polymyxa directly supports plant growth under nutrient-poor conditions[1][3].Beyond fixation and solubilization, P. polymyxa may influence soil chemistry via enzymes. It can produce phytases and phosphatases to release phosphorus, and it may alter pH or organic matter to benefit plant roots. These nutrient-enhancing activities are documented in laboratory and field studies[1][3]. Overall, P. polymyxa acts as a natural biofertilizer, reducing the need for synthetic fertilizers by improving soil nutrient cycling and availability.

Phytohormone Synthesis and Stress Alleviation#

P. polymyxa promotes plant growth not only via nutrition but also through hormones and stress mitigation. Many strains synthesize indole-3-acetic acid (IAA) – a key auxin (plant growth hormone) – and secrete it into the rhizosphere[1][2]. IAA stimulates root elongation and branching, helping seedlings establish robust root systems. Experiments with P. polymyxa ZYPP18, for example, confirmed that the strain produces an IAA-synthesis gene and boosts IAA levels[2]. The resulting enhanced root growth leads to better water and nutrient uptake. In addition to IAA, P. polymyxa may produce other phytohormones (such as gibberellins or cytokinins) and secrete enzymes that modulate ethylene levels. Many plant growth–promoting rhizobacteria (PGPR) contain the enzyme ACC deaminase, which lowers plant stress-ethylene; although direct evidence in P. polymyxa is still emerging, genome data suggest it harbors ACC deaminase genes[3].Under environmental stress (drought, salinity, heavy metals), P. polymyxa can help plants cope. Some strains produce exopolysaccharides (EPS) that bind salt ions and heavy metals, reducing toxicity. For instance, the salt-tolerant strain SC2 synthesizes EPS that sequester toxic ions and support osmoprotectant transport[1]. In practice, applying P. polymyxa to saline or polluted soils has been shown to alleviate stress effects on plants (e.g. increased antioxidant levels, better water retention, and reduced metal uptake)[1]. In summary, through hormone production and stress-protective metabolites, P. polymyxa enhances plant resilience to challenging environments and increases crop tolerance to salinity, drought, and contaminants.

Biocontrol of Phytopathogens#

P. polymyxa is widely exploited as a biocontrol agent against plant diseases. It produces a rich arsenal of antimicrobial compounds and enzymes that directly inhibit pathogens. Key antibiotics include polymyxins (cyclic lipopeptides targeting Gram-negative bacteria) and fusaricidins (polymyxin-related peptides with strong anti-fungal activity)[1][2]. Other metabolites reported include paenilan, tridecaptin, and various volatiles like 2,3-butanediol that can suppress or deter pathogens[1][2]. In vitro and greenhouse trials have shown P. polymyxa effectively inhibits many soil-borne fungi (e.g. Rhizoctonia, Fusarium, Sclerotinia) as well as bacterial pathogens (e.g. Pseudomonas spp.)[1]. One study found strain PKB1 produced antibiotics that significantly reduced Sclerotinia, Rhizoctonia, and Fusarium growth[1]. Another, strain ZYPP18, suppressed wheat sheath-blight disease by ~60% in field trials, while simultaneously promoting plant vigor[2].

P. polymyxa also induces plant defenses: treated plants often exhibit enhanced systemic resistance. Genome analyses suggest many strains can trigger host immune pathways[3]. For example, production of certain volatiles and cell-wall–degrading enzymes (chitinases, glucanases) by P. polymyxa elicits defense gene activation in plants. Table 2 (from [20]) highlights diverse biocontrol activities – from production of polymyxin B1 against Pseudomonas syringae to fusaricidin B against root-knot nematodes – that collectively protect crops[1]. By outcompeting pathogens (for nutrients and niche) and directly antagonizing them, P. polymyxa provides a natural, eco-friendly way to reduce chemical pesticide use in agriculture.

Industrial and Bioremediation Applications#

Beyond agriculture, P. polymyxa’s metabolic versatility has attracted industrial interest. The bacterium produces a variety of enzymes and biochemicals for industrial processes. Notably, it secretes proteases, cellulases, xylanases, lipases, and pectinases[1]. One of its enzymes, a glucomannanase from strain 3-3, has been characterized for breaking down Konjac glucomannan (a useful food/pharma polymer) into bioactive oligosaccharides[1]. P. polymyxa also carries ligninolytic enzymes (laccase, lignin peroxidases) enabling it to decompose lignin and agricultural waste[1]. This capacity could be harnessed to convert crop residues into animal feed or to improve paper processing.

A flagship industrial product from P. polymyxa is 2,3-butanediol (2,3-BDO), a renewable chemical feedstock. P. polymyxa can ferment sugars or glycerol to (2R,3R)-2,3-BDO – a precursor for biofuels and bioplastics. For example, strain PM3605 efficiently produced 2,3-BDO from crude glycerol with molasses supplementation[1]. Researchers have also engineered oxygen-limited fermentation and immobilized cell systems to boost yields[1]. These efforts mirror industrial goals to replace petroleum-derived chemicals with microbial processes. In principle, genome-reduced chassis (see Spotlight) may further improve 2,3-BDO and other metabolite production.On the bioremediation side, P. polymyxa contributes to pollutant cleanup. Its metabolic repertoire allows degradation of xenobiotics and adsorption of toxins. For example, P. polymyxa cultures have been used to break down lignin-rich waste[1] and to alter glass surfaces through microbial corrosion (suggesting enzyme-driven degradation of silicate materials)[1]. Importantly, the same EPS that aids salinity tolerance can bind heavy metals (lead, cadmium, etc.), immobilizing them and reducing their bioavailability[1]. As noted in a recent review, P. polymyxa is “being actively explored for bioremediation, particularly in the degradation of environmental pollutants,” thanks to its enzyme toolkit and antimicrobial compounds[1]. It also shows promise for bioadsorption (removing toxins) and surfactant production for oil spill cleanup. In summary, P. polymyxa is leveraged in industry for enzyme manufacture and fermentation products, and in environmental management to degrade waste and immobilize contaminants[1].

Challenges and Future Potential#

Despite its promise, deploying P. polymyxa at scale faces hurdles. Its performance can be inconsistent in field conditions: soil variability, climate, and native microbiota affect how well introduced strains colonize and persist[1]. Standardized formulations (e.g. spore carriers) and strain selection are still under development. Genetic tools for P. polymyxa have historically been limited, though recent advances (shuttle plasmids, CRISPR) are improving strain engineering[1][1]. Regulatory and ecological safety is another concern – releasing engineered or high-dose biocontrol strains into the environment requires thorough assessment to avoid unintended impacts[1]. Production costs and market acceptance also matter: bioproduct yields must exceed those of competing methods, and farmers must trust bioinoculants.Looking ahead, research is targeting these challenges. The complete genome of P. polymyxa DSM 365 was recently published, revealing new biosynthetic genes and enabling “genome-reduced” chassis engineering[4]. Future work may involve designing consortia (combining strains) or improving stress resilience through adaptive evolution. Scientists are also sequencing diverse P. polymyxa strains to map functional traits (e.g. nitrogen fixation vs. antibiotic production)[3]. Overall, P. polymyxa’s wide metabolic repertoire and compatibility with plants suggest strong future potential. As global agriculture shifts toward sustainability, P. polymyxa stands out as a bioresource that can meet crop production and environmental goals in an eco-friendly way[1].

Spotlight on Research: Paenibacillus polymyxa: From soil health to medical applications and molecular engineering.#

Brief Overview#

A recent notable study by Ravagnan et al. (2024) focused on developing P. polymyxa DSM 365 as a microbial chassis for biotechnology[4]. The researchers first obtained the complete closed genome sequence of strain DSM 365 (5.89 Mb) – an important foundation for genetic engineering. Genome analysis revealed a previously unknown non-ribosomal peptide synthase (NRPS) gene potentially involved in antibiotic (tridecaptin) production. Armed with the full genome, they then performed targeted top-down genome reduction: systematically knocking out non-essential regions and biosynthetic gene clusters. This approach aimed to create streamlined P. polymyxa “platform strains” with simplified metabolism.

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Key Insights#

From this work, the team derived two genome-reduced variants. In the first stage, they individually deleted 18 putative non-essential segments. Most mutants grew normally, indicating those deletions did not harm viability. The best mutants were combined to produce two final strains: GR1, lacking several secondary metabolite clusters, and GR2, with those and extra sequences (e.g. insertion sequences) removed[4]. Notably, both GR1 and GR2 retained growth rates and fermentation performance equal to the wild-type. Under bioreactor conditions, these engineered strains produced 2,3-butanediol and exopolysaccharide at the same titers as the parent strain[4]. In sum, the breakthroughs were (1) the first complete genome map of DSM 365, (2) discovery of a new NRPS gene, and (3) creation of chassis-like strains (GR1/GR2) that maintain productivity after substantial genome reduction.

Why This Matters#

This research matters because it advances P. polymyxa as a bioengineering platform. By removing unnecessary genetic “noise,” the engineered strains are now more predictable and stable for industrial use. The fact that GR1/GR2 preserved wild-type growth and product yields suggests P. polymyxa can be tuned as a chassis much like Bacillus subtilis or E. coli. These chassis strains can be further modified (e.g. with CRISPR) to overproduce desired chemicals or antibiotics. In the bigger picture, such efforts lower costs and improve safety: with fewer mobile genetic elements and toxins, the microbes can be more tightly controlled. Ultimately, this work paves the way for using P. polymyxa in sustainable biomanufacturing – from green solvents (2,3-BDO) to novel antimicrobials – fulfilling the promise of moving away from fossil-based processes

Summary Table: Spotlight Study#

Category	Details
Lead Researchers	Giulia Ravagnan et al.
Affiliations	Univ. of Münster; Forschungszentrum Jülich; Georg-August-Univ. Göttingen; NTNU Trondhei
Research Focus	Genome reduction in P. polymyxa; chassis development
Key Breakthroughs	• First complete genome of DSM 365 • Novel NRPS gene identified • Two genome-reduced strains (GR1, GR2) created
Collaborative Efforts	Multi-institution team across   Germany and Norway
Published Work	Front. Bioeng. Biotechnol. (2024) (Open Access)
Perspective	Platform strain engineering; synthetic biology
Publication Date	2024 Mar 28
Location	Germany / Norway
Key Findings	Streamlined P. polymyxa strains   (GR1, GR2) showed normal growth; 2,3-BDO and EPS production unchanged

Conclusion#

Paenibacillus polymyxa is a remarkable multifunctional microbe whose capabilities span agriculture, industry, and environmental management. It boosts plant growth by fixing nitrogen, solubilizing phosphates, and producing phytohormones[1], while simultaneously attacking pests with antibiotics and ISR induction. Industrially, it provides enzymes (for food, feed, and biofuels) and fermentative products like 2,3-butanediol[1]. Its metabolic versatility also enables bioremediation of waste and heavy metals[1]p. Challenges in consistency and regulation remain, but ongoing research – including complete genome mapping and chassis engineering – is overcoming these barriers[4][1]. As a result, P. polymyxa is poised to play an increasing role in sustainable agriculture and green biotechnology, offering an eco-friendly alternative to chemical fertilizers and pesticides, and contributing to biomanufacturing solutions for the future.

References#

1. Zalila-Kolsi I, Al-Barazie R (2025) Advancing sustainable practices with Paenibacillus polymyxa: From soil health to medical applications and molecular engineering. AIMS Microbiol 11(2):338–368. doi:10.3934/microbiol.2025016
   
2. Li X, Ma S, Meng Y, Wei W, Peng C, Ling C, Fan S, Liu Z (2023) Characterization of Antagonistic Bacteria Paenibacillus polymyxa ZYPP18 and the Effects on Plant Growth. Plants 12(13):2504. doi:10.3390/plants12132504
   
3. Wallner A, Antonielli L, Mesguida O, Rey P, Compant S, et al. (2024) Genomic diversity in Paenibacillus polymyxa: unveiling distinct species groups and functional variability. BMC Genomics 25:720. doi:10.1186/s12864-024-10610-w
   
4. Ravagnan G, Lesemann J, Müller MF, Poehlein A, Daniel R, Noack S, Kabisch J, Schmid J (2024) Genome reduction in Paenibacillus polymyxa DSM 365 for chassis development. Front. Bioeng. Biotechnol. 12:1378873. doi:10.3389/fbioe.2024.1378873