Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Paraburkholderia”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

8 recordsLinked to original sources
PubMed2025

Effects of a novel Paraburkholderia phage IPK on the phenanthrene degradation efficiency of the PAH-degrading strain Paraburkholderia caledonica Bk.

Phages are a major cause of bacterial mortality, affecting bacterial diversity and ecosystem functioning. However, the impact of phage-host interactions in contaminated environments and their role in pollutant biodegradation have largely been overlooked. We isolated and characterized a novel phage that infects the PAH-degrading bacterium Paraburkholderia caledonica Bk from a polycyclic aromatic hydrocarbon (PAH)-contaminated soil and investigated the effect of different multiplicity of infection (MOI) ratios on the degradation efficiency of phenanthrene. The phage IPK is a temperate phage with a wide pH and temperature tolerance and a burst size of 80  PFU ml⁻1. The phage was classified as a member of the Caudoviricetes and is related to Pseudomonas and Burkholderia phages. However, its low intergenomic similarity indicates that it is a new species. Three auxiliary metabolic genes (AMGs) related to amino acid metabolism and to bacterial growth regulation were identified in the phage genome. The highest multiplicity of infection (MOI 10) showed a rapid recovery of the host density and greater phenanthrene degradation than MOIs ranging from 0.01 to 1. This work highlights the important role of phage-host interactions in modulating the efficiency of pollutant degradation, which could be a key for improving the establishment of inoculants in bioremediation processes.

Phenanthrenes↗
PubMed2025

A rhamnose-rich O-antigen of Paraburkholderia phymatum MP20 is required for symbiosis with Mimosa pudica.

Paraburkholderia phymatum, a β-proteobacterium, forms a nitrogen-fixing symbiosis with many species of the large legume genus Mimosa as well as with common bean (Phaseolus vulgaris L.). Paraburkholderia are considered to have evolved nodulation independently from the well-studied α-proteobacteria symbionts of legumes. However, the detailed mechanisms important for β-rhizobia-legume symbiosis have not yet been determined. In this manuscript, we have sequenced the genome of P. phymatum MP20, a strain isolated from Mimosa pudica nodules, and utilized transposon mutagenesis to identify a mutant that showed delayed and ineffective nodulation of M. pudica. Further analysis revealed that the mutant strain produced an altered lipopolysaccharide lacking rhamnose containing O-antigen. Complementation with the wild-type gene restored the symbiosis. Microscopic analysis of the ineffective nodules showed that the mutant strain did not infect the cortical cells but was restricted to the endodermis. The results suggest that the O-antigen of P. phymatum is important for the bacterial infection of cortical cells and for nodule maturation. Further research will unveil the specific involvement of the glycosyltransferase gene in LPS biosynthesis and its impact on successful nodule formation by P. phymatum.IMPORTANCEThe nitrogen-fixing symbiosis between legumes and rhizobia is important for agricultural and environmental sustainability. The mechanisms of the symbiotic interactions are extensively studied using α-rhizobia. In contrast, mechanisms of symbiotic interactions important for β-rhizobia and their Caesalpinioid (mimosoid) legume hosts are not well known. Here, we describe the genome sequence of P. phymatum MP20, a β-rhizobia isolated from the nodules of M. pudica, and isolation and characterization of a transposon mutant defective in symbiosis. We demonstrate that the O-antigen of the LPS is required for nodulation and symbiotic nitrogen fixation. This study broadens our knowledge of symbiotic interactions in β-rhizobia and will lead to a better understanding of the wider rhizobial-legume symbiosis apart from the α-rhizobia.

Symbiosis↗
PubMed2025

Versatile sugar and valerate metabolic pathways in Paraburkholderia xenovorans LB400 enable tailored poly(3-hydroxybutyrate-co-3-hydroxyvalerate) production.

Poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) polymers are accumulated by diverse prokaryotes. Their distinct monomer compositions enable their use as tailored bioplastics. The aims were to characterize the poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesis by Paraburkholderia xenovorans LB400 using different sugars and valerate, and to gain genome-oriented insights into polyhydroxyalkanoate production. d-Glucose, d-mannitol, d-gluconate, and d-xylose were evaluated as sole carbon sources or supplemented with valerate. Polyhydroxyalkanoates synthesized by strain LB400 were characterized through GC-MS, GC-FID, FTIR, and 1H and 13C-NMR. P. xenovorans LB400 reached 1.00-1.39 g L-1 of dry cell weight (DCW) with a P(3HB) content of 21-43% w w-1 when grown on different sugars. The addition of valerate to the sugar-grown LB400 cultures yielded a DCW of 1.79 to 2.29 g L-1 and a P(3HB-co-3HV) content of 50.0‒51.2% w w-1, with varying 3HV compositions (28‒43 mol%). The highest 3HV incorporation was observed with d-xylose and valerate. Genomic analyses of strain LB400 revealed key elements of sugar metabolism influencing growth, polymer accumulation, and monomer composition. LB400 genome encodes the PhaJ-like R-specific hydratase and FadJ epimerase, which are potentially useful for modulating copolymer composition. PHA production under bioreactor conditions was evaluated. In a bioreactor fed with d-glucose, LB400 achieved a P(3HB) concentration of 2.2 g L-1. These findings highlight the metabolic versatility of P. xenovorans LB400 in utilizing diverse sugars to produce either P(3HB) or tailor-made P(3HB-co-3HV), supporting the development of bioplastics for specific applications. KEY POINTS: • Strain LB400 produced P(3HB-co-3HV) from various sugars and valerate. • Sugar type drives LB400 PHA copolymer synthesis and composition. • Strain LB400 PHA production was scaled up to a bioreactor.

Polyesters↗
PubMed2025

Surfing in the storm: how Paraburkholderia xenovorans thrives under stress during biodegradation of toxic aromatic compounds and other stressors.

The adaptive mechanisms of Burkholderiales during the catabolism of aromatic compounds and abiotic stress are crucial for their fitness and performance. The aims of this report are to review the bacterial adaptation mechanisms to aromatic compounds, oxidative stress, and environmental stressful conditions, focusing on the model aromatic-degrading Paraburkholderia xenovorans LB400, other Burkholderiales, and relevant degrading bacteria. These mechanisms include (i) the stress response during aromatic degradation, (ii) the oxidative stress response to aromatic compounds, (iii) the metabolic adaptation to oxidative stress, (iv) the osmoadaptation to saline stress, (v) the synthesis of siderophore during iron limitation, (vi) the proteostasis network, which plays a crucial role in cellular function maintenance, and (vii) the modification of cellular membranes, morphology, and bacterial lifestyle. Remarkably, we include, for the first time, novel genomic analyses on proteostasis networks, carbon metabolism modulation, and the synthesis of stress-related molecules in P. xenovorans. We analyzed these metabolic features in silico to gain insights into the adaptive strategies of P. xenovorans to challenging environmental conditions. Understanding how to enhance bacterial stress responses can lead to the selection of more robust strains capable of thriving in polluted environments, which is critical for improving biodegradation and bioremediation strategies.

Biodegradation, Environmental↗
PubMed2026

Experimental and genomic evidence clarifies the mycorrhizal helper role of a widespread bacterium in Bishop pine forests.

Whether a widespread bacterial strain of Paraburkholderia can enhance the physiological responses of ectomycorrhizal fungi (EcMF) and host Bishop pine seedling growth remains unclear. We developed a 'top-down meets bottom-up' approach that harmonized data from molecular field surveys, experimental forest soil manipulations, statistical interaction models, metabolomics studies, bacterial isolations, controlled growth chamber experiments, and comparative genomics analyses to test the direction and strength of Paraburkholderia-EcMF interactions on host seedling physiology and identify potential mechanisms that support these tripartite interactions. Paraburkholderia sp. D1E increased host root colonization of Suillus pungens - a keystone EcMF taxon for seedling establishment. Paraburkholderia-Suillus co-inoculations also often drove additive seedling growth responses (e.g. biomass and foliar chemistry) and generated nonadditive, positive effects on seedling shoot height. Genomic comparisons identified low chitin and high arabinitol utilization potential as distinguishing features of Paraburkholderia-EcMF symbioses. Our analyses provide experimental evidence, genomic resources, and cross-data validation that highlight potential mechanisms involved in a widespread bacteria-EcMF-tree interaction. Given the diversity of bacteria and fungi in the rhizosphere, however, this approach should continue to be applied to other species combinations to generalize interaction mechanisms among bacterial, fungal, and plant partners.

Paraburkholderia↗
PubMed2025

Breaking the reproducibility barrier with standardized protocols for plant-microbiome research.

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Plants↗
PubMed2026

Functional screening and single-cell cultivation of marine CO2-fixing bacteria via flow-mode Raman-activated cell sorting.

Most marine CO2-fixing microorganisms remain uncultivated due to strong culture bias and low throughput of conventional approaches, which fail to link in situ function with isolated strains and render slow-growing or low-abundance taxa virtually inaccessible. This study presents an integrated single-cell workflow that incorporates 13C-NaHCO3 labeling, high-throughput flow-mode Raman-activated cell sorting (RACS) and microwell cultivation for the isolation of active CO2-fixing bacteria from the Yellow Sea. Function-guided sorting was achieved by monitoring the 13C-induced Raman shifts of carotenoids (ν1 band: ∼1507 to ∼ 1503.78 cm-1 at 24 h). Genomic and physiological analyses identified Paraburkholderia aromaticivorans FR-4 as a novel facultative chemoautotrophic nitrite-oxidizing bacterium (NOB). Its genome encodes complete nitrite oxidation and Calvin cycle pathways, together with key carbon acquisition genes (carbonic anhydrase, bicarbonate transporter). FR-4 grows autotrophically using NO2- as the electron donor and CO2/HCO3- as the carbon source, confirming its ability to couple nitrite oxidation with carbon fixation, while retaining metabolic flexibility for heterotrophic growth. By directly linking in situ carbon-fixing activity, genotype, and phenotype, this workflow provides a targeted strategy for exploring elusive marine CO2-fixing bacteria and overcomes critical limitations of conventional cultivation.

Carbon-fixing↗
PubMed2024

Metagenome-based diversity and functional analysis of culturable microbes in sugarcane.

UNLABELLED: Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields. IMPORTANCE: This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.

Saccharum↗