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Journal of Hazardous Materials Feb 2021Since the ban on the use of asbestos due to its carcinogenic properties, the removal of asbestos cement, representing the major asbestos-containing waste, has proven to...
Since the ban on the use of asbestos due to its carcinogenic properties, the removal of asbestos cement, representing the major asbestos-containing waste, has proven to be a challenge in most industrial countries. Asbestos-containing products are mainly disposed of in landfills and have remained untreated. Bioremediation involving bacteria previously reported the ability of Pseudomonas aeruginosa to release iron from flocking asbestos waste through a siderophore-driven mechanism. We examined the involvement of siderophore-producing Pseudomonas in the biodeterioration of asbestos cement. Iron and magnesium solubilization were evaluated by specific siderophore-producing mutants. The absence of one of the two siderophores affected iron extraction, whereas equivalent dissolution as that of the control was observed in the absence of siderophore. Both pyoverdine and pyochelin biosynthesis was repressed in the presence of asbestos cement, suggesting iron bioavailability from the waste. We compared the efficiency of various pyoverdines to scavenge iron from asbestos cement waste that revealed the efficiency of all pyoverdines. Pyoverdines were efficient in iron removal extracted continuously, with no evident extraction limit, in long-term weathering experiments with these pyoverdines. The optimization of pyoverdine-asbestos weathering may allow the development of a bioremediation process to avoid the disposal of such waste in landfills.
Topics: Asbestos; Iron; Pseudomonas; Pseudomonas aeruginosa; Siderophores
PubMed: 32853889
DOI: 10.1016/j.jhazmat.2020.123699 -
International Journal of Systematic and... Jan 2021During a study investigating the microbiota of raw milk and its semi-finished products, strains WS 5106 and WS 5096 were isolated from cream and skimmed milk...
During a study investigating the microbiota of raw milk and its semi-finished products, strains WS 5106 and WS 5096 were isolated from cream and skimmed milk concentrate. They could be assigned to the genus by their 16S rRNA sequences, but not to any validly named species. In this work, a polyphasic approach was used to characterize the novel strains and to investigate their taxonomic status. Examinations based on the topology of core genome phylogenomy as well as average nucleotide identity (ANIm) comparisons suggested a novel species within the subgroup. With pairwise ANIm values of 90.1 and 89.8 %, WS 5106 was most closely related to CECT 9765 and CECT 9766. The G+C content of strain WS 5106 was 60.1 mol%. Morphologic analyses revealed Gram-stain-negative, aerobic, catalase and oxidase positive, rod-shaped and motile cells. Proteolysis on skimmed milk agar as well as lipolysis on tributyrin agar occurred at both 28 and 6 °C. Tolerated growth conditions were temperatures between 4 and 34 °C, pH values between 6.0 and 8.0, and salt concentrations of up to 5 %. Fatty acid profiles showed a pattern typical for , with C as the dominant component. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and the dominating quinone was Q-9. Based on these results, it is proposed to classify the strains as a novel species, sp. nov., with WS 5106 (=DSM 111143=LMG 31863) as type strain and WS 5096 (=DSM 111129=LMG 31864) as an additional strain.
Topics: Animals; Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Germany; Milk; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Proteolysis; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone
PubMed: 33289627
DOI: 10.1099/ijsem.0.004597 -
Applied Microbiology and Biotechnology Aug 2023The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic...
The biocatalysis of β-myrcene into value-added compounds, with enhanced organoleptic/therapeutic properties, may be performed by resorting to specialized enzymatic machinery of β-myrcene-biotransforming bacteria. Few β-myrcene-biotransforming bacteria have been studied, limiting the diversity of genetic modules/catabolic pathways available for biotechnological research. In our model Pseudomonas sp. strain M1, the β-myrcene catabolic core-code was identified in a 28-kb genomic island (GI). The lack of close homologs of this β-myrcene-associated genetic code prompted a bioprospection of cork oak and eucalyptus rhizospheres, from 4 geographic locations in Portugal, to evaluate the environmental diversity and dissemination of the β-myrcene-biotransforming genetic trait (Myr). Soil microbiomes were enriched in β-myrcene-supplemented cultures, from which β-myrcene-biotransforming bacteria were isolated, belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Sphingobacteriia classes. From a panel of representative Myr isolates that included 7 bacterial genera, the production of β-myrcene derivatives previously reported in strain M1 was detected in Pseudomonas spp., Cupriavidus sp., Sphingobacterium sp., and Variovorax sp. A comparative genomics analysis against the genome of strain M1 found the M1-GI code in 11 new Pseudomonas genomes. Full nucleotide conservation of the β-myrcene core-code was observed throughout a 76-kb locus in strain M1 and all 11 Pseudomonas spp., resembling the structure of an integrative and conjugative element (ICE), despite being isolated from different niches. Furthermore, the characterization of isolates not harboring the Myr-related 76-kb locus suggested that they may biotransform β-myrcene via alternative catabolic loci, being thereby a novel source of enzymes and biomolecule catalogue for biotechnological exploitation. KEY POINTS: • The isolation of 150 Myr bacteria hints the ubiquity of such trait in the rhizosphere. • The Myr trait is spread across different bacterial taxonomic classes. • The core-code for the Myr trait was detected in a novel ICE, only found in Pseudomonas spp.
Topics: Rhizosphere; Acyclic Monoterpenes; Bacteria; Pseudomonas
PubMed: 37405434
DOI: 10.1007/s00253-023-12650-w -
International Journal of Systematic and... Apr 2021A beige-pigmented, oxidase-positive bacterial isolate, Wesi-4, isolated from charcoal in 2012, was examined in detail by applying a polyphasic taxonomic approach. Cells...
A beige-pigmented, oxidase-positive bacterial isolate, Wesi-4, isolated from charcoal in 2012, was examined in detail by applying a polyphasic taxonomic approach. Cells of the isolates were rod shaped and Gram-stain negative. Examination of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strains of and (both 97.3 %). Phylogenetic analyses on the basis of the 16S rRNA gene sequences indicated a separate position of Wesi-4, which was confirmed by multilocus sequence analyses (MLSA) based on the three loci , and and a core genome-based phylogenetic tree. Genome sequence based comparison of Wesi-4 and the type strains of and yielded average nucleotide identity values <95 % and DNA-DNA hybridization values <70 %, respectively. The polyamine pattern contains the major amines putrescine, cadaverine and spermidine. The quinone system contains predominantly ubiquinone Q-9 and in the polar lipid profile diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine are the major lipids. The fatty acid contains predominantly C, summed feature 3 (Cω7 and/or Cω6) and summed feature 8 (Cω7 and/or C ω6). In addition, physiological and biochemical tests revealed a clear phenotypic difference from . These cumulative data indicate that the isolate represents a novel species of the genus for which the name sp. nov. is proposed with Wesi-4 (=DSM 110367=CIP 111764=CCM 9017) as the type strain.
Topics: Alabama; Bacterial Typing Techniques; Base Composition; Charcoal; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Multilocus Sequence Typing; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Ubiquinone
PubMed: 33835910
DOI: 10.1099/ijsem.0.004750 -
International Journal of Systematic and... Jul 2021Two phytopathogenic bacteria, MAFF 301380 and MAFF 301381, isolated from rot lesions of lettuce ( L. var. L.) in Japan, were characterized using a polyphasic approach....
Two phytopathogenic bacteria, MAFF 301380 and MAFF 301381, isolated from rot lesions of lettuce ( L. var. L.) in Japan, were characterized using a polyphasic approach. The cells were Gram-reaction-negative, aerobic, non-spore-forming, rod-shaped and motile with one to three polar flagella. Analysis of the 16S rRNA gene sequences showed that the strains belong to the genus and are closely related to subsp. CFML 96-198 (99.72 %), subsp. P515/12 (99.65 %), DSM 17152 (99.51 %), DSM 18928 (99.44 %), CIP 105460 (99.44 %) and DSM 29167 (99.44 %). The genomic DNA G+C content was 60.4 mol% and the major fatty acids consisted of summed feature 3 (C 7/C 6), C and summed feature 8 (C 7/C 6). Phylogenetic analysis using the gene sequences and phylogenomic analyses based on the whole genome sequences demonstrated that the strains are members of the subgroup but formed a monophyletic and robust clade separated from their closest relatives. The average nucleotide identity and digital DNA-DNA hybridization values between the strains and their closely related species were 88.65 % or less and 36.3 % or less, respectively. The strains could be distinguished from their closest relatives by phenotypic characteristics, pathogenicity towards lettuce and whole-cell MALDI-TOF MS profiles. The evidence presented in this study supports the classification of the strains as representing a novel species, for which we propose the name sp. nov., with the type strain MAFF 301380 (=ICMP 23838).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Fatty Acids; Genes, Bacterial; Japan; Lactuca; Nucleic Acid Hybridization; Phylogeny; Plant Diseases; Pseudomonas; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 34309505
DOI: 10.1099/ijsem.0.004917 -
Natural Product Reports Jan 2020Bacteria of the genus Pseudomonas are ubiquitous in nature. Pseudomonads display a fascinating metabolic diversity, which correlates with their ability to colonize an... (Review)
Review
Bacteria of the genus Pseudomonas are ubiquitous in nature. Pseudomonads display a fascinating metabolic diversity, which correlates with their ability to colonize an extremely wide range of ecological niches. As a result, these bacteria are a prolific source of natural products. Biosynthesis of the latter is often orchestrated by arrays of chemical signals arising from intraspecies communication or interspecies relationships with bacteria, fungi, amoebae, plants, and insects. Especially nonribosomal lipopeptides, which have diverse biological activities, play important roles in the lifestyle of pseudomonads. In this review, we will focus on the molecular structures, properties, biosynthetic pathways, and biological functions of pseudomonal lipopeptides. This review is not only addressed to bio/chemists rather it serves as a comprehensive guide for all researchers (micro/biologists, ecologists, and environmental scientists) working in this multidisciplinary field.
Topics: Host-Pathogen Interactions; Lipopeptides; Molecular Structure; Plants; Pseudomonadaceae; Pseudomonas; Rhizosphere; Ribosomes; Soil Microbiology
PubMed: 31436775
DOI: 10.1039/c9np00022d -
Journal of Biomolecular Structure &... Mar 2023Oxalate decarboxylase (OxDC) is a Mn-dependent hexameric enzyme that is highly important in management of calcium oxalate mediated nephrolithiasis. The present study...
Oxalate decarboxylase (OxDC) is a Mn-dependent hexameric enzyme that is highly important in management of calcium oxalate mediated nephrolithiasis. The present study reported the production and purification of OxDC from sp. OXDC12 up to 45.3-fold with an overall yield of 7%. The purified OxDC displayed a single band of approximately 40 kDa on SDS-PAGE and 240 kDa on Native-PAGE suggesting it to be a hexameric enzyme. The purified OxDC displayed an optimum activity at 26 °C and pH 4.5 in the presence of substrate sodium oxalate (30 mg/mL) with a and value of 43.9 mM and 8.9 µmol/min, respectively and an activation energy of 52.49 kJ/mol. The enzyme activity was significantly enhanced by adding -phenylenediamine to the reaction mixture. OxDC exhibited a very low 17 haemolytic activity which suggested a relatively safer therapeutic aspect of the tested OxDC. The structure prediction studies of the OxDC revealed a tertiary structure with α/β chains that formed the barrel structure, typical of all cupin domains. The Ramachandran plot produced by PROCHECK shows that 90.5% of the residues are in the most favoured region and hence the OxDC model produced was a good one. Docking studies revealed the binding of the metal ions and ligands to cluster of three histidine residues in the terminal domain that formed the active site pocket of the enzyme. It was suggested that the histidine coordinated Mn2+ ion was critical for substrate recognition and binding and was also directly involved in OxDC catalyses.highlightsOxalate decarboxylase (OxDC) was successfully purified from sp. OXDC12 up-to 45.3-fold.The and values of the purified OxDC were calculated as 43.9 mM and 8.9 µmol/min, respectively.Genre analysis and structure prediction studies revealed the presence of barrel structure typical of all cupin domains. The model exhibited a bi-cupin domain that forms the dimer of the homo-hexameric OxDC.Docking experiments revealed that the cluster of three HIS residues in the terminal domain of the tested enzyme formed the active site pocket for binding of Mn as well as the ligands.Communicated by Ramaswamy H. Sarma.
Topics: Pseudomonas; Histidine; Ligands; Carboxy-Lyases; Ions
PubMed: 35007451
DOI: 10.1080/07391102.2021.2024882 -
Current Microbiology May 2023Riverine ecosystems polluted by pharmaceutical and metal industries are potential incubators of bacteria with dual resistance to heavy metals and antibiotics. The...
Molecular Evidence for Occurrence of Heavy Metal and Antibiotic Resistance Genes Among Predominant Metal Tolerant Pseudomonas sp. and Serratia sp. Prevalent in the Teesta River.
Riverine ecosystems polluted by pharmaceutical and metal industries are potential incubators of bacteria with dual resistance to heavy metals and antibiotics. The processes of co-resistance and cross resistance that empower bacteria to negotiate these challenges, strongly endorse dangers of antibiotic resistance generated by metal stress. Therefore, investigation into the molecular evidence of heavy metal and antibiotic resistance genes was the prime focus of this study. The selected Pseudomonas and Serratia species isolates evinced by their minimum inhibitory concentration and multiple antibiotic resistance (MAR) index showed significant heavy metal tolerance and multi-antibiotic resistance capability, respectively. Consequently, isolates with higher tolerance for the most toxic metal cadmium evinced high MAR index value (0.53 for Pseudomonas sp., and 0.46 for Serratia sp.) in the present investigation. Metal tolerance genes belonging to P-type and resistance nodulation division family of proteins were evident in these isolates. The antibiotic resistance genes like mexB, mexF and mexY occurred in Pseudomonas isolates while sdeB genes were present in Serratia isolates. Phylogenetic incongruency and GC composition analysis of P-type genes suggested that some of these isolates had acquired resistance through horizontal gene transfer (HGT). Therefore, the Teesta River has become a reservoir for resistant gene exchange or movement via selective pressure exerted by metals and antibiotics. The resultant adaptive mechanisms and altered phenotypes are potential tools to track metal tolerant strains with clinically significant antibiotic resistance traits.
Topics: Anti-Bacterial Agents; Pseudomonas; Rivers; Ecosystem; Phylogeny; Metals, Heavy; Drug Resistance, Microbial; Bacteria
PubMed: 37227565
DOI: 10.1007/s00284-023-03334-9 -
Letters in Applied Microbiology Oct 2020Aeromonas and Pseudomonas are important bacterial species involved in spoilage of refrigerated freshwater fish. In this study, 10 Aeromonas and seven Pseudomonas...
Aeromonas and Pseudomonas are important bacterial species involved in spoilage of refrigerated freshwater fish. In this study, 10 Aeromonas and seven Pseudomonas bacterial strains were isolated from spoiled grass carp and identified. Twelve of seventeen bacterial strains showed high potential of biofilm formation and 14 of 17 can produce extracellular protease. In order to explore the spoilage capacity of dual-species, the sterile grass carp fillets were inoculated with mono- and dual-species of Aeromonas salmonicida and Pseudomonas azotoformans strains. The results revealed significantly higher levels of the total viable count and total volatile basic nitrogen in dual-species as compared to mono-species from day 6. The higher contents of histamine, cadaverine and serious degradation in muscles tissue were also observed in dual-species after 10 days of storage. Results of in vitro experiments showed that the co-culture of A. salmonicida and P. azotoformans significantly increased the bacterial maximum growth rate, promoted the biofilm formation and improved the spoilage capacity of bacterial strains. This study has revealed that the co-culture of Aeromonas and Pseudomonas bacterial strains accelerated spoilage process of grass carp and increased biofilm formation. It indicates that the mixed-cultures of spoilage micro-organisms pose a huge threat to food industry.
Topics: Aeromonas; Animals; Biofilms; Carps; Coculture Techniques; Food Contamination; Pseudomonas
PubMed: 32542738
DOI: 10.1111/lam.13341 -
Nucleic Acids Research Mar 2020Tight and coordinate regulation of virulence determinants is essential for bacterial biology and involves dynamic shaping of transcriptional regulatory networks during...
Tight and coordinate regulation of virulence determinants is essential for bacterial biology and involves dynamic shaping of transcriptional regulatory networks during evolution. The horizontally transferred two-partner secretion system ExlB-ExlA is instrumental in the virulence of different Pseudomonas species, ranging from soil- and plant-dwelling biocontrol agents to the major human pathogen Pseudomonas aeruginosa. Here, we identify a Cro/CI-like repressor, named ErfA, which together with Vfr, a CRP-like activator, controls exlBA expression in P. aeruginosa. The characterization of ErfA regulon across P. aeruginosa subfamilies revealed a second conserved target, the ergAB operon, with functions unrelated to virulence. To gain insights into this functional dichotomy, we defined the pan-regulon of ErfA in several Pseudomonas species and found ergAB as the sole conserved target of ErfA. The analysis of 446 exlBA promoter sequences from all exlBA+ genomes revealed a wide variety of regulatory sequences, as ErfA- and Vfr-binding sites were found to have evolved specifically in P. aeruginosa and nearly each species carries different regulatory sequences for this operon. We propose that the emergence of different regulatory cis-elements in the promoters of horizontally transferred genes is an example of plasticity of regulatory networks evolving to provide an adapted response in each individual niche.
Topics: A549 Cells; Bacterial Proteins; Bacterial Toxins; Base Sequence; Gene Expression Regulation, Bacterial; Humans; Operon; Promoter Regions, Genetic; Protein Binding; Pseudomonas; Repressor Proteins; Species Specificity; Transcription Factors; Virulence
PubMed: 31925438
DOI: 10.1093/nar/gkz1232