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International Journal of... 2024Heavy metal pollution threatens food security by accumulating in crops and soils, posing a significant challenge to modern agriculture due to its high toxicity. Urgent...
Heavy metal pollution threatens food security by accumulating in crops and soils, posing a significant challenge to modern agriculture due to its high toxicity. Urgent action is needed to restore affected agricultural fields. An efficient way to remove toxins is by bioremediation, which uses microorganisms. With the purpose of restoring soil in agriculture, this research attempts to assemble a consortium of microorganisms isolated from techno-genic soil. A number of promising strains, including , sp., , , and were chosen based on their capacity to eliminate heavy metals from tests. Heavy metal removal (Cd, Hg, As, Pb, and Ni) and phytohormone production have been shown to be effective using consortiums (, , and in a 1:1:2). In instances with mixed heavy-metal contamination, demonstrated efficacy because of its notable ability to absorb substantial quantities of heavy metals. The capacity of the cooperation to improve phytoremediation was investigated, with an emphasis on soil cleanup in agricultural areas. When combined with L., it was able to remove roughly 16% As, 14% Hg, 32% Ni, 26% Cd, and 33% Pb from the soil.
Topics: Biodegradation, Environmental; Metals, Heavy; Soil Pollutants; Soil Microbiology; Sorghum; Soil; Crops, Agricultural
PubMed: 38494751
DOI: 10.1080/15226514.2024.2327611 -
The Journal of Antimicrobial... May 2024To characterize VIM-type metallo-β-lactamase (MBL)-encoding genomic islands (GIs) in Pseudomonas aeruginosa and P. putida group isolates from Polish hospitals from...
OBJECTIVES
To characterize VIM-type metallo-β-lactamase (MBL)-encoding genomic islands (GIs) in Pseudomonas aeruginosa and P. putida group isolates from Polish hospitals from 2001-2015/16.
METHODS
Twelve P. aeruginosa and 20 P. putida group isolates producing VIM-like MBLs were selected from a large collection of these based on epidemiological and typing data. The organisms represented all major epidemic genotypes of these species spread in Poland with chromosomally located blaVIM gene-carrying integrons. The previously determined short-read sequences were complemented by long-read sequencing in this study. The comparative structural analysis of the GIs used a variety of bioinformatic tools.
RESULTS
Thirty different GIs with blaVIM integrons were identified in the 32 isolates, of which 24 GIs from 26 isolates were integrative and conjugative elements (ICEs) of the clc family. These in turn were dominated by 21 variants of the GI2/ICE6441 subfamily with a total of 19 VIM integrons, each inserted in the same position within the ICE's Tn21-like transposon Tn4380. The three other ICEs formed a novel ICE6705 subfamily, lacking Tn4380 and having different VIM integrons located in another site of the elements. The remaining six non-ICE GIs represented miscellaneous structures. The presence of various integrons in the same ICE sublineage, and of the same integron in different GIs, indicated circulation and recombination of the integron-carrying genetic platforms across Pseudomonas species/genotypes.
CONCLUSIONS
Despite the general diversity of the blaVIM-carrying GIs in Pseudomonas spp. in Poland, a clear predominance of broadly spread and rapidly evolving clc-type ICEs was documented, confirming their significant role in antimicrobial resistance epidemiology.
Topics: Genomic Islands; Poland; beta-Lactamases; Integrons; Humans; Pseudomonas Infections; Pseudomonas aeruginosa; Pseudomonas; Anti-Bacterial Agents; Genotype; Microbial Sensitivity Tests; DNA Transposable Elements
PubMed: 38488311
DOI: 10.1093/jac/dkae068 -
Cureus Feb 2024Nasal septum perforation (NSP) occurs secondary to many underlying etiologies, including facial trauma, drug use, malignancy, infection, or autoimmune disease. We...
A Case Report of Pseudomonas Infection in a Patient With Nasal Septum Perforation, Cocaine Use Disorder, and a Perinuclear Anti-neutrophil Cytoplasmic Antibody (p-ANCA)-Positive Assay.
Nasal septum perforation (NSP) occurs secondary to many underlying etiologies, including facial trauma, drug use, malignancy, infection, or autoimmune disease. We present the case of a 39-year-old female with a past medical history of cocaine use disorder who presented with symptoms concerning facial cellulitis unresponsive to antibiotic therapy. Physical exam and subsequent imaging revealed the presence of NSP. The patient underwent a full workup exploring potential etiologies of NSP in the setting of cocaine use disorder, with lab results indicating and cellulitis as well as a positive perinuclear anti-neutrophil cytoplasmic antibody (p-ANCA) assay. This case highlights the importance of maintaining a broad differential diagnosis for the etiology of NSP and avoiding anchoring bias.
PubMed: 38476784
DOI: 10.7759/cureus.54022 -
Journal of Agricultural and Food... Mar 2024Dipicolinic acid (DPA), a cyclic diacid, has garnered significant interest due to its potential applications in antimicrobial agents, antioxidants, chelating reagents,...
Dipicolinic acid (DPA), a cyclic diacid, has garnered significant interest due to its potential applications in antimicrobial agents, antioxidants, chelating reagents, and polymer precursors. However, its natural bioproduction is limited since DPA is only accumulated in Bacillus and Clostridium species during sporulation. Thus, heterologous production by engineered strains is of paramount importance for developing a sustainable biological route for DPA production. KT2440 has emerged as a promising host for the production of various chemicals thanks to its robustness, metabolic versatility, and genetic tractability. The dominant Entner-Doudoroff (ED) pathway for glucose metabolism in this strain offers an ideal route for DPA production due to the advantage of NADPH generation and the naturally balanced flux between glyceraldehyde-3-phosphate and pyruvate, which are both precursors for DPA synthesis. In this study, DPA production via the ED pathway was designed in KT2440. The systematically engineered strain produced dipicolinate with a titer of 11.72 g/L from glucose in a 5 L fermentor. This approach not only provides a sustainable green route for DPA production but also expands our understanding of the metabolic potential of the ED pathway in KT2440.
Topics: Pseudomonas putida; Carbohydrate Metabolism; Bioreactors; Antioxidants; Pyruvic Acid; Metabolic Engineering
PubMed: 38470347
DOI: 10.1021/acs.jafc.4c00003 -
BMC Genomics Mar 2024In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis...
In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.
Topics: Pseudomonas putida; Proteome; Multiomics; Biotechnology; Operon
PubMed: 38468234
DOI: 10.1186/s12864-024-10082-y -
Methods in Molecular Biology (Clifton,... 2024Simple and efficient DNA assembly methods have been widely used in synthetic biology. Here, we provide the protocol for the recently developed PEDA (phage...
Simple and efficient DNA assembly methods have been widely used in synthetic biology. Here, we provide the protocol for the recently developed PEDA (phage enzyme-assisted in vivo DNA assembly) method for direct in vivo assembly of individual DNA parts in multiple microorganisms, such as Escherichia coli, Ralstonia eutropha, Pseudomonas putida, Lactobacillus plantarum, and Yarrowia lipolytica. PEDA allows in vivo assembly of DNA fragments with homologous sequences as short as 5 bp, and the efficiency is comparable to the prevailing in vitro DNA assembly, which will broadly boost the rapid progress of synthetic biology.
Topics: Cloning, Molecular; DNA; Synthetic Biology; Pediocins
PubMed: 38468102
DOI: 10.1007/978-1-0716-3658-9_24 -
Methods in Molecular Biology (Clifton,... 2024Emerging microorganism Pseudomonas putida KT2440 is utilized for the synthesis of biobased chemicals from renewable feedstocks and for bioremediation. However, the...
Emerging microorganism Pseudomonas putida KT2440 is utilized for the synthesis of biobased chemicals from renewable feedstocks and for bioremediation. However, the methods for analyzing, engineering, and regulating the biosynthetic enzymes and protein complexes in this organism remain underdeveloped.Such attempts can be advanced by the genetic code expansion-enabled incorporation of noncanonical amino acids (ncAAs) into proteins, which also enables further controls over the strain's biological processes. Here, we give a step-by-step account of the incorporation of two ncAAs into any protein of interest (POI) in response to a UAG stop codon by two commonly used orthogonal archaeal tRNA synthetase and tRNA pairs. Using superfolder green fluorescent protein (sfGFP) as an example, this method lays down a solid foundation for future work to study and enhance the biological functions of KT2440.
Topics: Pseudomonas putida; Genetic Code; Amino Acids; RNA, Transfer; Amino Acyl-tRNA Synthetases
PubMed: 38468091
DOI: 10.1007/978-1-0716-3658-9_13 -
MicroLife 2024Bacteriophages play a crucial role in shaping bacterial communities, yet the mechanisms by which nonmotile bacteriophages interact with their hosts remain poorly...
Bacteriophages play a crucial role in shaping bacterial communities, yet the mechanisms by which nonmotile bacteriophages interact with their hosts remain poorly understood. This knowledge gap is especially pronounced in structured environments like soil, where spatial constraints and air-filled zones hinder aqueous diffusion. In soil, hyphae of filamentous microorganisms form a network of 'fungal highways' (FHs) that facilitate the dispersal of other microorganisms. We propose that FHs also promote bacteriophage dissemination. Viral particles can diffuse in liquid films surrounding hyphae or be transported by infectable (host) or uninfectable (nonhost) bacterial carriers coexisting on FH networks. To test this, two bacteriophages that infect DSM291 (host) but not KT2440 (nonhost) were used. In the absence of carriers, bacteriophages showed limited diffusion on 3D-printed abiotic networks, but diffusion was significantly improved in -formed FHs when the number of connecting hyphae exceeded 20. Transport by both host and nonhost carriers enhanced bacteriophage dissemination. Host carriers were five times more effective in transporting bacteriophages, particularly in FHs with over 30 connecting hyphae. This study enhances our understanding of bacteriophage dissemination in nonsaturated environments like soils, highlighting the importance of biotic networks and bacterial hosts in facilitating this process.
PubMed: 38463165
DOI: 10.1093/femsml/uqae004 -
Communications Biology Mar 2024Pseudomonas aeruginosa, a common nosocomial pathogen, relies on siderophores to acquire iron, crucial for its survival in various environments and during host...
Pseudomonas aeruginosa, a common nosocomial pathogen, relies on siderophores to acquire iron, crucial for its survival in various environments and during host infections. However, understanding the molecular mechanisms of siderophore regulation remains incomplete. In this study, we found that the BfmRS two-component system, previously associated with biofilm formation and quorum sensing, is essential for siderophore regulation under high osmolality stress. Activated BfmR directly bound to the promoter regions of pvd, fpv, and femARI gene clusters, thereby activating their transcription and promoting siderophore production. Subsequent proteomic and phenotypic analyses confirmed that deletion of BfmRS reduces siderophore-related proteins and impairs bacterial survival in iron-deficient conditions. Furthermore, phylogenetic analysis demonstrated the high conservation of the BfmRS system across Pseudomonas species, functional evidences also indicated that BfmR homologues from Pseudomonas putida KT2440 and Pseudomonas sp. MRSN12121 could bind to the promoter regions of key siderophore genes and osmolality-mediated increases in siderophore production were observed. This work illuminates a novel signaling pathway for siderophore regulation and enhances our understanding of siderophore-mediated bacterial interactions and community establishment.
Topics: Humans; Siderophores; Pseudomonas aeruginosa; Osmotic Pressure; Phylogeny; Proteomics; Iron; Pseudomonas; Pseudomonas Infections
PubMed: 38461208
DOI: 10.1038/s42003-024-05995-z -
Biofilm Jun 2024The ability of bacteria to adhere to and form biofilms on food contact surfaces poses serious challenges, as these may lead to the cross-contamination of food products....
The ability of bacteria to adhere to and form biofilms on food contact surfaces poses serious challenges, as these may lead to the cross-contamination of food products. Biomimetic topographic surface modifications have been explored to enhance the antifouling performance of materials. In this study, the topography of two plant leaves, var. (cauliflower, CF) and (white cabbage, WC), was replicated through wax moulding, and their antibiofilm potential was tested against single- and dual-species biofilms of and . Biomimetic surfaces exhibited higher roughness values ( = 4.0 ± 1.0 μm and = 3.3 ± 1.0 μm) than the flat control ( = 0.6 ± 0.2 μm), whilst the CF surface demonstrated a lower interfacial free energy () than the WC surface (-100.08 mJ m and -71.98 mJ m, respectively). The CF and WC surfaces had similar antibiofilm effects against single-species biofilms, achieving cell reductions of approximately 50% and 60% for and , respectively, compared to the control. Additionally, the biomimetic surfaces led to reductions of up to 60% in biovolume, 45% in thickness, and 60% in the surface coverage of single-species biofilms. For dual-species biofilms, only the strain growing on the WC surface exhibited a significant decrease in the cell count. However, confocal microscopy analysis revealed a 60% reduction in the total biovolume and surface coverage of mixed biofilms developed on both biomimetic surfaces. Furthermore, dual-species biofilms were mainly composed of , which reduced growth. Altogether, these results demonstrate that the surface properties of CF and WC biomimetic surfaces have the potential for reducing biofilm formation.
PubMed: 38444517
DOI: 10.1016/j.bioflm.2024.100185