Whole-genome sequencing reveals growth-promoting traits of beneficial bacterium Priestia megaterium

Scientists have decoded the complete genome of a soil bacterium that can simultaneously boost plant growth, unlock locked-up nutrients in depleted fields, and even fend off a devastating fungal pathogen—capabilities that could help farmers cut back on chemical fertilizers. The strain, designated EL9 and identified as Priestia megaterium, was isolated from the rhizosphere—the thin layer of soil hugging plant roots—of tobacco grown under the pressure of long-term continuous cropping. A research team led by Zhenyu Zhang and Weichang Gao, with corresponding authors Jiayang Xu and Ying Jiang at Henan Agricultural University and the Guizhou Academy of Tobacco Science, reports in BMC Genomics that the bacterium carries a genetic arsenal for producing the plant hormone indole-3-acetic acid (IAA), dissolving insoluble phosphorus, and mobilizing potassium, three of the most sought-after functions in the search for effective biofertilizers.

The motivation behind the study lies in a stubborn agricultural problem. Continuous monoculture—planting the same crop season after season on the same land—degrades soil structure, depletes available nutrients, and encourages the buildup of soil-borne pathogens. Tobacco production, in particular, suffers from low fertilizer use efficiency and the chemical fixation of phosphorus and potassium, elements that are often abundant in soil minerals but locked in forms that plant roots cannot absorb. Phosphorus, for example, is frequently bound to calcium, iron, or aluminum in ways that render it inaccessible, while potassium can be trapped within the lattice of soil minerals. The conventional remedy has been to apply ever-larger doses of chemical fertilizer, an approach that inflates costs, pollutes waterways, and degrades soil biology over time. Plant growth-promoting rhizobacteria, or PGPR, offer an alternative: microbes that colonize the root zone and mobilize nutrients through their own metabolism.

To find a candidate strain worth sequencing, the team screened bacteria from tobacco rhizosphere soil and put EL9 through a battery of functional assays. In colorimetric tests, the strain produced IAA at a level equivalent to 55.47 milligrams per liter, a substantial output for a single isolate. IAA is the principal auxin hormone in plants; it stimulates cell elongation, root initiation, and overall vegetative development, so a root-dwelling bacterium that secretes IAA effectively hands its host plant a growth stimulus from the outside. In parallel assays, EL9 solubilized phosphate at 427.60 milligrams per liter and mobilized potassium at 172.29 milligrams per liter, confirming in the laboratory what the genome later explained in molecular detail: this organism is a triple-threat nutrient mobilizer.

The centerpiece of the study is the whole-genome sequence itself. EL9 carries a genome of approximately 5.10 megabases—a moderately sized bacterial genome typical of the Bacillaceae family, to which Priestia megaterium (formerly classified in the genus Bacillus) belongs. Within those five-plus million base pairs, the researchers identified a tryptophan biosynthesis gene cluster along with the amiE gene, genetic features that they link to the bacterium’s IAA-producing capacity. The connection is biochemically logical: the most common microbial route to IAA runs through tryptophan, an amino acid precursor that bacteria convert to auxin via several enzymatic pathways. A strain that can manufacture its own tryptophan and process it has an internal supply chain for hormone production. The amiE gene, encoding amidase activity, has been associated in prior literature with the conversion of indole-3-acetamide into active IAA, providing a plausible enzymatic step in that pathway.

Beyond auxin, the genome revealed genes involved in phosphorus transport, sulfate assimilation, and core carbon and nitrogen metabolism. Phosphorus-solubilizing bacteria typically accomplish their work by secreting organic acids that chelate the metal cations binding phosphate, or by releasing phosphatases that cleave phosphate from organic molecules; the transport genes allow the freed phosphate to be imported into the cell, creating a sink that keeps the dissolution reaction moving forward. Sulfate assimilation genes point to the bacterium’s ability to take up inorganic sulfur and convert it into the sulfur-containing amino acids and cofactors it needs—an indicator of metabolic self-sufficiency in the nutrient-poor rhizosphere. Together, these gene families sketch the picture of a generalist capable of thriving in marginal soils while actively reworking the nutrient chemistry around plant roots.

Genomic sequences alone, however convincing, do not prove that a strain will perform in a living field. The team therefore moved from in silico analysis to pot experiments, testing EL9 on three crop species: tobacco, Chinese cabbage, and wheat. Across all three, inoculation with EL9 significantly increased the levels of IAA, available phosphorus, and available potassium in the rhizosphere soil, and these chemical changes were mirrored by measurable improvements in plant growth and root development. Root architecture matters enormously in agriculture—deeper, denser root systems capture more water and nutrients and confer drought resilience—so the observation that EL9-treated plants developed enhanced roots is among the most practically significant findings of the study.

The researchers then scaled up to field trials with tobacco, the crop from which the strain originally came. The results confirmed improvements in agronomic traits and, critically, in the quality of cured leaves, the end product on which tobacco farmers’ income depends. Field performance is where many laboratory-promising biofertilizer candidates falter, because real soils present competition from resident microbiota, fluctuating moisture and temperature, and heterogeneous nutrient distributions. That EL9 maintained its effects under field conditions strengthens the case that its genome-encoded traits translate into genuine agronomic value rather than remaining a petri-dish curiosity.

Safety is a non-negotiable concern for any organism intended for large-scale environmental release, and the team addressed it directly with a genomic risk assessment. In silico analyses of the EL9 genome revealed no complete or obvious pathogenicity determinants—no integrated arsenal of toxin genes, virulence factors, or antibiotic resistance cassettes of the kind that would raise red flags for regulators. This matters because the genus historically placed in Bacillus includes Bacillus anthracis, the anthrax agent, and any agricultural relative must be shown to lack the genetic machinery for harming animals or humans. Additionally, plate assays suggested preliminary antagonistic activity against Fusarium oxysporum, a notorious soil-borne fungus that causes vascular wilt diseases in a wide range of crops. If EL9’s antifungal capacity holds up in further testing, the strain could offer disease suppression as a fourth benefit stacked on top of hormone production and phosphorus and potassium mobilization.

The significance of the work extends beyond one bacterium. Biofertilizer development has long suffered from a disconnect between genomic potential and field performance: strains are identified, their genes catalogued, and then the products underperform in real soils, or they work for one crop but not others. EL9’s combination of a well-characterized genetic repertoire, demonstrated efficacy across three botanically distinct crops—tobacco is a solanaceous broadleaf, Chinese cabbage a brassica, and wheat a cereal grass—and confirmed field results makes it an unusually well-documented candidate. The multi-crop success also hints that the strain’s benefits derive from general mechanisms of nutrient mobilization and hormone provision rather than from a narrow, host-specific interaction.

There are still hurdles between the current results and commercial deployment. The authors describe the antifungal activity as preliminary, based on plate assays, and field-scale disease suppression has not yet been demonstrated. Formulation science—how to deliver live bacteria to fields in a stable, shelf-stable product—remains a separate engineering challenge, as does registration under agricultural regulations, which vary by country. The researchers note that the article is being shared early as a citable, peer-reviewed accepted manuscript, with a final version of record to follow. Funding for the work came from the China National Tobacco Corporation’s Science and Technology Key Program and the Natural Science Foundation of Henan Province.

Nevertheless, the study offers a template for how modern genomics can accelerate the search for sustainable agricultural inputs. Rather than relying solely on trial and error, researchers can now sequence a promising isolate, read its functional genes like a parts list, verify safety computationally before any environmental exposure, and only then invest in greenhouse and field validation. In an era when agriculture must produce more with fewer chemical inputs and less environmental damage, a single microorganism that can feed plants, stimulate their roots, and potentially shield them from fungal attackers is exactly the kind of multifunctional tool the field has been looking for. EL9 may prove to be one of the clearer examples of a microbe whose genome tells the whole story—a story that ends in healthier soil and crops grown with a lighter chemical footprint.