Identification of putative producers of rhamnolipids/glycolipids and their transporters using genome mining

In silico analysis of zosurabalpin-LptB2FG binding in Acinetobacter spp., Klebsiella pneumoniae, and Shigella flexneri: mechanisms underlying its differential efficacy

Zosurabalpin, a novel tethered macrocyclic peptide antibiotic, exhibits potent activity against Acinetobacter spp., particularly carbapenem-resistant Acinetobacter baumannii (CRAB). Zosurabalpin inhibits lipopolysaccharide (LPS) transport by targeting the LptB2FG protein complex, resulting in toxic LPS accumulation and bacterialdeath. This study investigates zosurabalpin's molecular specificity against Acinetobacter spp., its ineffectiveness against Klebsiella pneumoniae, and its potential efficacy against Shigella flexneri. Comparative analysis of LptB2FG sequences and structures, revealed significant differences in LptB2FG protein conformations, pocket geometry and electrostatic surface surrounding the binding pocket among the three species, which may influence zosurabalpin binding. Docking results for zosurabalpin showed lower binding affinities for K. pneumoniae and S. flexneri compared to Acinetobacter baylyi. Additionally, other zosurabalpin derivatives were tested showing improved binding affinities for K. pneumoniae but not for S. flexneri. These findings underscore the need for tailored zosurabalpin derivatives to enhance efficacy against a broader spectrum of Gram-negative bacteria.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-025-00343-3.

Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms

Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. Although it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp. RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia kirstenboschensis str. F3, led to the discovery of rhlM, whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ to navigate, grow, and outcompete other soil community members in postfire environments.

In Silico Identification of Natural Food Compounds as Potential Quorum-Sensing Inhibitors Targeting the LasR Receptor of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a major cause of nosocomial infections and is often associated with biofilm-mediated antibiotic resistance. The LasR protein is a key component of the quorum system in P. aeruginosa, allowing it to regulate its biofilm-induced pathogenicity. When the bacterial population reaches a sufficient density, the accumulation of N-(3-oxododecanoyl) acyl homoserine lactone (3O-C12-HSL) leads to the activation of the LasR receptor, which then acts as a transcriptional activator of target genes involved in biofilm formation and virulence, thereby increasing the bacteria's antibiotic resistance and enhancing its virulence. In this study, we performed a structure-based virtual screening of a natural food database of 10 997 compounds against the crystal structure of the ligand-binding domain of the LasR receptor (PDB ID: 3IX4). This allowed us to identify four molecules, namely ZINC000001580795, ZINC000014819517, ZINC000014708292, and ZINC000004098719, that exhibited a favorable binding mode and docking scores greater than -13 kcal/mol. Furthermore, the molecular dynamics simulation showed that these four molecules formed stable complexes with LasR during the 150-ns molecular dynamics (MD) simulation, indicating their potential for use as inhibitors of the LasR receptor in P. aeruginosa. However, further experimental validation is needed to confirm their activity.

Valorization of oily sludge waste using biosurfactant-producing bacteria

Oily sludge generated by the petroleum industry is not only an environmental hazard, but since it contains crude oil too, it is a valuable resource as well. This study demonstrates a methodology for the valorization of the oily sludge that allows the recovery of oil fractions by the action of microbes producing surface-active metabolites. Two bacterial isolates were used in the study that were producing different biosurfactants, identified via FTIR analysis as well as through genomic mapping of the biosurfactant pathways using RAST, ANTISMASH 7.0, STRING databases. Serratia spp. AKBS12, produced a mono-rhamnolipid, while Acinetobacter spp. AKBS16, produced emulsan. Although recovery efficiency of both biosurfactants was similar, the recovery profile with respect to the class of hydrocarbons differed. The rhamnolipid produced by Serratia spp. AKBS12 extracted mono-chained paraffins and linear alkanes, while emulsan, produced by Acinetobacter spp. AKBS16 could extract heavier paraffins. The extraction procedure is simple and involves mixing the biosurfactant with oily sludge at a temperature of 30 °C with an incubation of 9 days. Sulphuric acid precipitation releases the oil trapped in the oily sludge. The study is the first step in developing user-friendly, innovative technologies that can be linked to the concept of a circular economy.

Surface-active antibiotic production is a multifunctional adaptation for postfire microbes

Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microbes. While it is thought that fire-adapted microbes lie at the forefront of postfire ecosystem recovery, the specific strategies that these microbes use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp . RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia caledonica str. F3, led to the discovery of rhlM , whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ in order to navigate, grow, and outcompete other soil community members in postfire environments.

Significance Statement

Wildfires are increasing in frequency and intensity at a global scale. Microbes are the first colonizers of soil after fire events, but the adaptations that help these organisms survive in postfire environments are poorly understood. In this work, we show that a bacterium isolated from burned soil produces an unusual rhamnolipid biosurfactant that exhibits antimicrobial activity, enhances motility, and solubilizes potential nutrients derived from pyrolyzed organic matter. Collectively, our findings demonstrate that bacteria leverage specialized metabolites with multiple functions to meet the demands of life in postfire environments. Furthermore, this work reveals the potential of probing perturbed environments for the discovery of unique compounds and enzymes.

Improving Rhamnolipids Biosynthesis in Pseudomonas sp. L01 through Atmospheric and Room-Temperature Plasma (ARTP) Mutagenesis

Biosurfactants have significant applications in various industries, including microbial-enhanced oil recovery (MEOR). While the state-of-the-art genetic approaches can generate high-yield strains for biosurfactant production in fermenters, there remains a critical challenge in enhancing biosurfactant-producing strains for use in natural environments with minimal ecological risks. The objectives of this work are enhancing the strain's capacity for rhamnolipids production and exploring the genetic mechanisms for its improvement. In this study, we employed atmospheric and room-temperature plasma (ARTP) mutagenesis to enhance the biosynthesis of rhamnolipids in Pseudomonas sp. L01, a biosurfactant-producing strain isolated from petroleum-contaminated soil. Following ARTP treatment, we identified 13 high-yield mutants, with the highest yield of 3.45 ± 0.09 g/L, representing a 2.7-fold increase compared to the parent strain. To determine the genetic mechanisms behind the enhanced rhamnolipids biosynthesis, we sequenced the genomes of the strain L01 and five high-yield mutants. A comparative genomic analysis suggested that mutations in genes related to the synthesis of lipopolysaccharides (LPS) and the transport of rhamnolipids may contribute to the improved biosynthesis. To the best of our knowledge, this is the first instance of utilizing the ARTP approach to improve rhamnolipid production in Pseudomonas strains. Our study provides valuable insights into the enhancement of biosurfactant-producing strains and the regulatory mechanisms of rhamnolipids biosynthesis.

Rhamnolipids as Green Stabilizers of nZVI and Application in the Removal of Nitrate From Simulated Groundwater

Environmental contamination caused by inorganic compounds is a major problem affecting soils and surface water. Most remediation techniques are costly and generally lead to incomplete removal and production of secondary waste. Nanotechnology, in this scenario with the zero-valent iron nanoparticle, represents a new generation of environmental remediation technologies. It is non-toxic, abundant, cheap, easy to produce, and its production process is simple. However, in order to decrease the aggregation tendency, the zero-iron nanoparticle is frequently coated with chemical surfactants synthesized from petrochemical sources, which are persistent or partially biodegradable. Biosurfactants (rhamnolipids), extracellular compounds produced by microorganisms from hydrophilic and hydrophobic substrates can replace synthetic surfactants. This study investigated the efficiency of a rhamnolipid biosurfactant on the aggregation of nanoscale zer-valent iron (nZVI) and its efficiency in reducing nitrate in simulated groundwater at pH 4.0. Two methods were tested: 1) adding the rhamnolipid during chemical synthesis and 2) adding the rhamnolipid after chemical synthesis of nZVI. Scanning electron microscopy field emission, X-ray diffractometry, Fourier transform infrared spectroscopy, thermogravimetric analysis, Dynamic Light Scattering, and zeta potential measurements were used to characterize bare nZVI and rhamnolipid-coated nZVI. The effects of the type of nZVI and initial NO3 concentration were examined. Nanoscale zer-valent iron with the addition of the rhamnolipid after synthesis achieved the best removal rate of nitrate (about 78%), with an initial nitrate concentration of 25 mg L−1. The results suggest that nZVI functionalized with rhamnolipids is a promising strategy for the in situ remediations of groundwater contaminated by NO3, heavy metal, and inorganic carbon.