Isolation, Genomic Characterization and Biotechnological Potential of Culturable Bacteria from Metal-Rich and Organic Soils of La Soledad Dam, Guanajuato, Mexico

Genomic Analysis and Characterization of Phenotypic Traits of Hydrocarbon-Degrading Actinobacterial Strains Isolated from a Sierozem Soil of Southern Kazakhstan

The self-purification capacity of oil-contaminated soils is largely determined by the metabolic activity of autochthonous oil-oxidizing microorganisms. This study examined three strains of actinobacteria, which are hydrocarbon degraders, isolated from oil-contaminated sierozem soil at the Daulet Asia landfill (Southern Kazakhstan). Functional gene analysis was conducted (genome completeness > 98%, and contamination < 3%), and the phenotypic properties of these bacterial strains were studied to assess their potential for bio- and phytoremediation technologies in the sharply continental arid climate of the Aral Sea region. The isolated strains Rhodococcus kroppenstedtii K18 and MF2 and Kocuria rosea K1 grow on oil (12–22% oil loss after 10 days of cultivation in liquid mineral salt medium) and diesel fuel and can utilize hexadecane and benzoate as the sole source of carbon and energy. Furthermore, Rhodococcus K18 and MF2 utilize dodecane and eicosane, while K. rosea K1 utilizes phenol and gentisate. A significant decrease in surface tension (to 31.4 mN/m) observed during cultivation of strains K18 and MF2 on minimal salt medium indicates the secretion of surfactants that increase the bioavailability of hydrophobic substrates. The studied strains possess a number of properties that promote plant growth: they produce auxins, solubilize calcium hydroxyapatite, and protect plants from infection by the phytopathogenic microorganisms Fusarium oxysporum and Pectobacterium wasabiae. Actinobacteria are compatible when co-cultivated, as no mutual growth inhibition was observed. This study expands our understanding of typical bacterial representatives of desert soil, and this may contribute to the development of bioremediation approaches for the restoration of disturbed biotopes under extreme environmental conditions.

Genomic insights into the bioremediation potential of Paenibacillus taichungensis strain 53b: a multi-resistant plant growth-promoting bacterium

Isolation, Molecular Characterization, and Screening for Hydrocarbon-degrading Potential of an Indigenous Enterobacter sp. from Petroleum-contaminated Soil for Bioremediation Applications

Petroleum hydrocarbon contamination creates ecological risks and motivates sustainable remediation strategies. This study isolated indigenous oil-degrading bacteria from petroleum-contaminated soils and screened their relative hydrocarbon-degrading potential. Four soil samples were collected from automobile-workshop sites in and around Bengaluru and Chikkaballapur, Karnataka, India. Samples were enriched in Bushnell–Haas minimal salt medium supplemented with 3% (v/v) used engine oil as the sole carbon source. Eight isolates were obtained and screened using an agar well diffusion clearance-zone assay. Morphological and biochemical characterisation was followed by 16S rRNA gene sequencing of the most active isolate. Isolate K2 produced the largest clearance zone (30 mm), followed by C2 (25 mm) and K3 (20 mm), whereas W1 and S1 produced 5 mm zones. BLASTn and phylogenetic analysis placed K2 within the Enterobacter cloacae complex, with 99.93% sequence identity to reference sequences in GenBank. The results indicate that indigenous bacteria from chronically hydrocarbon-contaminated soils can show differing relative activities under the screening conditions, with K2 displaying the strongest response among the isolates tested. Because the agar well diffusion assay does not directly quantify hydrocarbon removal, the observed clearance zones should be interpreted as a relative screening measure. Quantitative gravimetric or chromatographic analyses, together with soil-based validation, are required before the degradation efficiency and bioremediation applicability of K2 can be established.

Whole-genome sequencing and characterization of Pseudomonas stutzeri P1 endophyte isolated from potato unveils plant growth-promoting and other traits

Endophytic bacteria play an important role in plant growth promotion and stress tolerance, offering sustainable alternatives to chemical inputs in agriculture. In this study, an endophytic bacterial strain P1 was isolated and identified as Pseudomonas stutzeri , a plant-associated bacterium exhibiting multiple plant growth–promoting traits (PGPTs). Biochemical (qualitative and quantitative) and in vitro analyses demonstrated nitrogen fixation, phosphate solubilization, ammonia production, indole-3-acetic acid (IAA) production, biofilm formation, and tolerance to abiotic stresses, including salinity and drought. Furthermore, the P1 strain displayed strong biocontrol activity against the fungal pathogen Fusarium oxysporum f. sp. cumini, indicating its potential to mitigate biotic stress. Whole-genome sequencing generated a high-quality complete genome of 4,758,235 bp. Functional annotation showed enrichment of metabolic pathways associated with plant-microbe interactions and environmental adaptation. Further analyses using KEGG and PGPT-pred data confirmed the presence of genes associated with direct and indirect PGPT, such as nitrogen fixation, phosphate solubilization, biofilm formation, and stress tolerance. The genome also contained genes related to CAZymes, adhesion, and motility, highlighting a strong plant association, whereas the genome lacked major virulence factors and antimicrobial traits, supporting the non-pathogenic nature of the P1 strain. Overall, these findings demonstrate the potential of P1 as a promising bioinoculant candidate for sustainable agriculture in the potato sector.

Diversity and functional traits of indigenous microbiome in Hilla agricultural soils: implications for biocontrol and bioremediation

Genomic Characterization of Aerobically Culturable Gut-Associated Bacteria and Yeasts Isolated from Pooled Larval Midguts of the Lesser Mealworm Alphitobius diaperinus (Coleoptera: Tenebrionidae)

Simple Summary Advances in genome sequencing allow the identification of bacteria and yeasts with high taxonomic resolution, providing insights into microbial ecology, predicted metabolic potential, and functional roles beyond traditional morphology- or biochemistry-based methods. In this study, we investigated the culturable fraction of the gut microbiota derived from a single pooled sample of fifteen larvae of the lesser mealworm, Alphitobius diaperinus, a key pest in poultry production, under limited aerobic conditions. A total of twelve isolates were initially obtained (ten bacteria and two yeasts), but eight bacterial isolates were identical, so a single representative was selected. Using Illumina whole-genome sequencing, we identified three bacterial strains and two yeasts. Although this culturable fraction represents a minor proportion of the total gut community it offers a critical advantage over culture-independent approaches: these isolates can be maintained under laboratory conditions, enabling direct functional experiments, strain-level genomic resolution and biotechnological exploitation. No novel species were detected, yet our results reveal microorganisms with distinct functional profiles isolated in the larval gut. This work establishes a genome-resolved reference framework for the cultivable bacteria and yeasts isolates obtained from healthy A. diaperinus larvae in the present study and provides genomic resources for future ecological and functional investigations.