Rice Soil Bacterium Reveals Plant Growth Genes in Full Genome Scan

A bacterium pulled from the waterlogged soil around rice roots has had its entire genetic blueprint read, and the sequence reads like a catalogue of traits that plant scientists prize. Researchers in India isolated a strain of Acinetobacter lwoffii, designated DJPGP01, from rhizosphere soil collected in Raichur, Karnataka, and sequenced its genome end to end. The analysis, published in Current Genetics, uncovered genes tied to nitrogen assimilation, phosphate uptake, auxin production, biofilm formation and stress tolerance, the molecular toolkit that defines plant growth-promoting rhizobacteria, or PGPR. The team also confirmed one of those predicted traits directly in the laboratory, showing that the strain can dissolve insoluble phosphate on agar plates. The work positions a soil-dwelling member of a genus better known for hospital infections as a candidate for sustainable crop applications, while the authors themselves caution that genomic prediction is only the first step toward proving value in a real field.

The isolation began with a straightforward soil sample. One gram of rhizosphere soil was diluted in nine millilitres of water, shaken, serially diluted and streaked onto agar medium, yielding pure colonies that were one to two millimetres across, domed, mucoid and non-pigmented. Preliminary biochemical testing characterised the organism as aerobic, gram-negative, catalase-positive, oxidase-negative and nonmotile, a profile consistent with Acinetobacter. For sequencing, the team purified genomic DNA with a commercial kit, checked its integrity on an agarose gel, quantified it fluorometrically and prepared libraries with the Illumina DNA Prep kit. The library was run on an Illumina NextSeq 2000 instrument, generating 2 by 100 base pair reads. In total, 5.67 million paired-end reads, amounting to 572 megabases of sequence, were produced, with an average coverage of 150-fold across the genome. The raw reads were deposited in the NCBI Sequence Read Archive under bioproject PRJNA804363.

Assembly of that read pile required a comparison of competing algorithms. The researchers trimmed low-quality sequence with Fastp, leaving 5.64 million paired reads, and then assembled the cleaned data with three different programmes: SPAdes, Velvet and AByss. Quality statistics computed with QUAST 4.0 singled out the Velvet assembly, and after gap filling with GFinisher, using the genome of A. lwoffii strain H7 as a reference scaffold, the final draft measured 3,215,270 base pairs, or roughly 3.2 megabases, distributed across 35 scaffolds. The N50, a measure of contiguity, reached 260,745 base pairs, the largest scaffold spanned 434,866 base pairs, and the guanine-cytosine content settled at 43.06 percent. A quality assessment with CheckM, calibrated against 86 reference genomes from the Moraxellaceae family, rated the assembly 99.66 percent complete with 1.44 percent contamination, figures that indicate a near-single-chromosome reconstruction of high fidelity.

Annotation converted the assembled sequence into biological inventory. The Prokka pipeline identified 3,032 protein-coding genes, five ribosomal RNA genes, 70 transfer RNA genes, one tmRNA gene and 24 miscellaneous RNAs. Functional prediction covered 1,968 of the coding sequences, leaving 1,064 as hypothetical proteins of unknown role; 1,844 sequences were matched to UniProt entries, 1,564 to clusters of orthologous groups and 1,119 to enzyme commission numbers. A parallel annotation with RAST predicted 3,203 protein-encoding genes sorted into 275 subsystems, with amino acid metabolism and protein metabolism dominating the functional categories. Gene ontology enrichment highlighted translation, gene expression and nitrogen compound metabolism among biological processes, with catalytic activity and ion binding prominent among molecular functions, a pattern the authors read as evidence of dense enzymatic machinery for nutrient acquisition and stress adaptation.

Within that inventory sat the genes that give the strain its PGPR label. The genome carries gltD, involved in nitrogen assimilation, and the trpABCDE gene set, which underpins the synthesis of indole-3-acetic acid, the auxin that stimulates root elongation. The ilvIH genes point to acetoin production, a plant growth-promoting signalling molecule, while the pstABC transporter system handles phosphate uptake. Antioxidant genes including trxB, msrA, hmp, nhaX and nhaP suggest capacity to defuse oxidative stress, with hmp encoding a nitric-oxide-inducible flavohemoprotein that detoxifies free radicals. Biofilm-related genes such as mepB and fimA hint at the ability to colonise root surfaces and persist under environmental stress. The authors note that these assignments rest on sequence similarity, and that experimental validation of expression and activity remains necessary for most of them.

Pathway reconstruction sharpened the picture. Searching predicted proteins against the KEGG database assigned orthology identifiers to 1,602 genes and mapped 224 pathways. Metabolic pathways dominated, with 536 genes in global overview maps, followed by 218 genes in secondary metabolite biosynthesis and 162 in microbial metabolism in diverse environments. Environmental information processing revealed 52 genes in two-component signal transduction systems and 46 genes encoding ATP-binding cassette transporters, the membrane pumps that import nutrients and export toxins. Cellular process categories included 25 quorum sensing genes, the chemical communication system that coordinates biofilm formation and host colonisation, with named components including PhnA, PhnB, RpfB and the histidine sensor kinase QseC. The authors frame quorum sensing as central to how PGPR strains tolerate stress and establish themselves on host plants.

antiSMASH analysis added a chemical dimension, flagging five secondary metabolite gene clusters: three devoted to beta-lactone synthesis, one RiPP-like cluster and one aryl polyene cluster. The aryl polyene cluster contains 39 genes, including a core biosynthetic gene for 3-oxoacyl-acyl-carrier-protein synthase, a leucine-responsive regulatory protein, three transport genes and nine biosynthetic genes, and it shares more than 95 percent similarity with aryl polyene clusters from other A. lwoffii strains. Beta-lactone clusters are associated with antibacterial compounds that could help the bacterium outcompete soil pathogens, while aryl polyenes are polyunsaturated lipids implicated in biofilm formation, surface adhesion and environmental adaptation. Separately, IslandViewer 4 predicted 26 genomic islands, mostly populated by 186 genes of unknown function, regions the authors interpret as evidence of horizontal gene transfer and adaptation to varied environments.

Comparison with five clinical isolates of A. lwoffii revealed what makes the rice-soil strain distinctive. Across the six genomes, 5,840 genes were identified: 2,109 present in nearly all isolates and 3,731 with variable distribution. DJPGP01 carries 403 genes found in no other strain, including copA, a copper-exporting ATPase; yhbO, a universal stress protein; yqhD, an alcohol dehydrogenase; frmR, a regulator of formaldehyde detoxification; pks5, a polyketide synthase; nicP; and hcaB, a dioxygenase. Notably, epsL genes encoding components of a type II secretion system, linked to biofilm formation, are unique to DJPGP01 among the compared set. Conversely, 176 genes present in at least three clinical isolates are absent from DJPGP01, including arsenic resistance genes such as arsC and ArsH, a pattern the authors suggest may indicate diminished pathogenic potential, though they present this as a genomic observation rather than a safety determination.

Taxonomic placement anchored the strain firmly within A. lwoffii. The 16S ribosomal RNA sequence, 1,533 base pairs long, showed 99.66 percent similarity to A. lwoffii strain DSM 2403 and 99.45 percent to strain JCM 6840, above the accepted species threshold. Whole-genome comparison through the Type Strain Genome Server returned an average nucleotide identity of 95.96 percent against the reference strain H7, and digital DNA-DNA hybridisation values of 79.5 and 79.7 percent against A. lwoffii NCTC 5866, the closest type strain, placing the isolate within the species boundary. The one trait tested phenotypically, phosphate solubilisation, succeeded: spot-inoculated colonies on Pikovskaya’s agar produced clear halos over ten days of incubation, matching the genomic prediction of alkaline phosphatases, exopolyphosphatases and high-affinity phosphate transporters. The authors are explicit about limits: in silico predictions do not capture in-plant interactions, and controlled greenhouse experiments, field trials and studies of persistence in native soil communities are needed before any biofertilizer claim can be made.

Subject of Research: Whole-genome characterisation of the plant growth-promoting bacterium Acinetobacter lwoffii DJPGP01 isolated from rice rhizosphere soil

Article Title: Genome characterization of Acinetobacter species from the rice rhizosphere: a potential plant growth promoting rhizobacteria (PGPR)

Article References: Diwan, J. R., Mahadevaswamy, Patil, S., Bhanu, D., Devi, K. L., Hegde, S. N., Krishnaraj, P. U., Namitha, R., Pradhan, B. B., & Vashisht, D. (2025). Genome characterization of Acinetobacter species from the rice rhizosphere: a potential plant growth promoting rhizobacteria (PGPR). Current Genetics, 71(1), Article 27. https://doi.org/10.1007/s00294-025-01330-z

Image Credits: AI Generated

DOI: 10.1007/s00294-025-01330-z

Keywords: Acinetobacter lwoffii, rice rhizosphere, plant growth-promoting rhizobacteria, genome sequencing, phosphate solubilisation, indole-3-acetic acid, quorum sensing, secondary metabolite gene clusters, biofilm formation, comparative genomics, soil microbiology, sustainable agriculture