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Environmental Science and Pollution... Jan 2019Lignin is a byproduct in the pulp and paper industry and is considered as a promising alternative for the provision of energy and chemicals. Currently, the efficient...
Lignin is a byproduct in the pulp and paper industry and is considered as a promising alternative for the provision of energy and chemicals. Currently, the efficient valorization of lignin is a challenge owing to its polymeric structure complexity. Here, we present a platform for bio-converting Kraft lignin (KL), to polyhydroxyalkanoate (PHA) by Pandoraea sp. B-6 (hereafter B-6). Depolymerization of KL by B-6 was first confirmed, and > 40% KL was degraded by B-6 in the initial 4 days. Characterization of PHA showed that up to 24.7% of PHA accumulated in B-6 grown in 6-g/L KL mineral medium. The composition, structure, and thermal properties of the produced PHA were analyzed, revealing that 3-hydroxybutyrate was the only monomer and that PHA was comparable with the commercially available bioplastics. Moreover, the genomic analysis illustrated three core enzymatic systems for lignin depolymerization including laccases, peroxidases, and Fenton-reaction enzymes; five catabolic pathways for LDAC degradation and a gene cluster consisting of bktB, phaR, phaB, phaA, and phaC genes involved in PHA biosynthesis. Accordingly, a basic model for the process from lignin depolymerization to PHA production was constructed. Our findings provide a comprehensive perspective for lignin valorization and bio-material production from waste.
Topics: Burkholderiaceae; Laccase; Lignin; Peroxidases; Polyhydroxyalkanoates; Solid Waste
PubMed: 30484053
DOI: 10.1007/s11356-018-3785-1 -
Microbiology Resource Announcements Jan 2020strain TF-18 was isolated from the roots of rice seedlings on selective medium containing four classes of antibiotics for isolation of Using Pacific Biosciences...
strain TF-18 was isolated from the roots of rice seedlings on selective medium containing four classes of antibiotics for isolation of Using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology, we report here a complete genome of 5,499,432 bases, a GC content of 64.8%, and 4,849 coding sequences.
PubMed: 31896624
DOI: 10.1128/MRA.01008-19 -
Sensors (Basel, Switzerland) Oct 2013Proteobacteria are known to communicate via signaling molecules and this process is known as quorum sensing. The most commonly studied quorum sensing molecules are...
Proteobacteria are known to communicate via signaling molecules and this process is known as quorum sensing. The most commonly studied quorum sensing molecules are N-acylhomoserine lactones (AHLs) that consists of a homoserine lactone moiety and an N-acyl side chain with various chain lengths and degrees of saturation at the C-3 position. We have isolated a bacterium, RB-44, from a site which was formally a landfill dumping ground. Using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis, this isolate was identified as a Pandoraea sp.which was then screened for AHL production using biosensors which indicated its quorum sensing properties. To identify the AHL profile of Pandoraea sp. RB-44, we used high resolution tandem mass spectrometry confirming that this isolate produced N-octanoylhomoserine lactone (C8-HSL). To the best of our knowledge, this is the first report that showed quorum sensing activity exhibited by Pandoraea sp. Our data add Pandoraea sp. to the growing number of bacteria that possess QS systems.
Topics: 4-Butyrolactone; Proteobacteria; Quorum Sensing; Soil Microbiology; Species Specificity
PubMed: 24145919
DOI: 10.3390/s131014121 -
Antimicrobial Agents and Chemotherapy Apr 2006Pandoraea spp. are gram-negative, glucose nonfermenting rods detectable in blood cultures and sputa of cystic fibrosis patients. They are resistant to various antibiotic...
Pandoraea spp. are gram-negative, glucose nonfermenting rods detectable in blood cultures and sputa of cystic fibrosis patients. They are resistant to various antibiotic groups, with imipenem being the only active beta-lactam. We isolated an imipenem-resistant (MIC, 64 microg/ml) Pandoraea pnomenusa strain from a cystic fibrosis patient. Cloning and sequencing identified two beta-lactamases of Bush group 2d, namely, the known OXA-33, located on an integron, and the novel carbapenem-hydrolyzing oxacillinase OXA-62. OXA-62 is only distantly related to other oxacillinases (OXA-50 being closest with 43% amino acid identity). It hydrolyzes penicillins, oxacillin, imipenem, and meropenem but not expanded-spectrum cephalosporins. The blaOXA-62 gene is chromosome located. No transposable elements were found in its genetic neighborhood. With OXA-62-specific primers, blaOXA-62 could be identified in all P. pnomenusa strains and appears to be species specific. This additional mechanism of carbapenem resistance further complicates the treatment of infections caused by P. pnomenusa.
Topics: Amino Acid Sequence; Betaproteobacteria; Carbapenems; Drug Resistance, Bacterial; Hydrolysis; Microbial Sensitivity Tests; Molecular Sequence Data; beta-Lactamases
PubMed: 16569848
DOI: 10.1128/AAC.50.4.1330-1335.2006 -
FEMS Microbiology Letters Feb 2002The recently described genus Pandoraea consists of five named species and four unnamed genomospecies, several of which have been identified in clinical specimens...
The recently described genus Pandoraea consists of five named species and four unnamed genomospecies, several of which have been identified in clinical specimens including respiratory secretions from persons with cystic fibrosis. We investigated whether it is possible to distinguish species of the genus Pandoraea by means of restriction fragment length polymorphism (RFLP) analysis and direct sequencing of the gyrB gene. Sixty-seven Pandoraea isolates were included. Species-specific RFLP patterns were obtained following digestion of the PCR-amplified gyrB gene with MspI. Specificity of RFLP groupings was confirmed by direct sequencing of several representative isolates. Our results indicate that RFLP analysis and sequencing of the gyrB gene are useful for the identification of Pandoraea species. We also found that further taxonomic studies within the beta-Proteobacteria using the gyrB gene would benefit from the development of additional primers allowing more efficient amplification of the gyrB gene. Our data also indicate that the taxonomic status of Pandoraea genomospecies 2 should be reinvestigated.
Topics: Bacterial Typing Techniques; Betaproteobacteria; Cystic Fibrosis; DNA Gyrase; DNA, Bacterial; Gram-Negative Bacterial Infections; Humans; Molecular Sequence Data; Phylogeny; Polymorphism, Restriction Fragment Length; Sequence Analysis, DNA
PubMed: 11934487
DOI: 10.1111/j.1574-6968.2002.tb11053.x -
World Journal of Microbiology &... Aug 2021The prospection of new degrading enzymes of the plant cell wall has been the subject of many studies and is fundamental for industries, due to the great biotechnological...
The prospection of new degrading enzymes of the plant cell wall has been the subject of many studies and is fundamental for industries, due to the great biotechnological importance of achieving a more efficient depolymerization conversion from plant polysaccharides to fermentable sugars, which are useful not only for biofuel production but also for various bioproducts. Thus, we explored the shotgun metagenome data of a bacterial community (CB10) isolated from sugarcane bagasse and recovered three metagenome-assembled genomes (MAGs). The genomic distance analyses, along with phylogenetic analysis, revealed the presence of a putative novel Chitinophaga species, a Pandoraea nosoerga, and Labrys sp. isolate. The isolation process for each one of these bacterial lineages from the community was carried out in order to relate them with the MAGs. The recovered draft genomes have reasonable completeness (72.67-100%) and contamination (0.26-2.66%) considering the respective marker lineage for Chitinophaga (Bacteroidetes), Pandoraea (Burkholderiales), and Labrys (Rhizobiales). The in-vitro assay detected cellulolytic activity (endoglucanases) only for the isolate Chitinophaga, and its genome analysis revealed 319 CAZymes, of which 115 are classified as plant cell wall degrading enzymes, which can act in fractions of hemicellulose and pectin. Our study highlights the potential of this Chitinophaga isolate provides several plant-polysaccharide-degrading enzymes.
Topics: Alphaproteobacteria; Bacteroidetes; Biodegradation, Environmental; Biomass; Burkholderiaceae; Genome, Bacterial; Lignin; Metagenome; Phylogeny; Plants; Polysaccharides
PubMed: 34448059
DOI: 10.1007/s11274-021-03128-w -
British Journal of Biomedical Science 2002
Topics: Adolescent; Bacterial Typing Techniques; Betaproteobacteria; Cystic Fibrosis; DNA, Bacterial; Humans; Male; Opportunistic Infections
PubMed: 12371061
DOI: 10.1080/09674845.2002.11978036 -
Journal of Biotechnology Jan 2016Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of...
Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.
Topics: Base Sequence; Biodegradation, Environmental; Burkholderiaceae; DNA, Bacterial; Genome, Bacterial; Molecular Sequence Data; Oxidation-Reduction; Oxidoreductases; Rhizosphere; Sequence Analysis, DNA; Soil Microbiology; Thiosulfates
PubMed: 26603120
DOI: 10.1016/j.jbiotec.2015.11.009 -
Frontiers in Microbiology 2016To date, information on plasmid analysis in spp. is scarce. To address the gap of knowledge on this, the complete sequences of eight plasmids from spp. namely DSM...
To date, information on plasmid analysis in spp. is scarce. To address the gap of knowledge on this, the complete sequences of eight plasmids from spp. namely DSM 23572 (pPF72-1, pPF72-2), DSM 23570 (pPO70-1, pPO70-2, pPO70-3, pPO70-4), NS15 (pPV15) and DSM 16535 (pPA35) were studied for the first time in this study. The information on plasmid sequences in spp. is useful as the sequences did not match any known plasmid sequence deposited in public databases. Replication genes were not identified in some plasmids, a situation that has led to the possibility of host interaction involvement. Some plasmids were also void of genes and intriguingly, gene was also not discovered in these plasmids. This further leads to the hypothesis of host-plasmid interaction. Plasmid stabilization/stability protein-encoding genes were observed in some plasmids but were not established for participating in plasmid segregation. Toxin-antitoxin systems MazEF, VapBC, RelBE, YgiT-MqsR, HigBA, and ParDE were identified across the plasmids and their presence would improve plasmid maintenance. Conjugation genes were identified portraying the conjugation ability amongst plasmids. Additionally, we found a shared region amongst some of the plasmids that consists of conjugation genes. The identification of genes involved in replication, segregation, toxin-antitoxin systems and conjugation, would aid the design of drugs to prevent the survival or transmission of plasmids carrying pathogenic properties. Additionally, genes conferring virulence and antibiotic resistance were identified amongst the plasmids. The observed features in the plasmids shed light on the spp. as opportunistic pathogens.
PubMed: 27790203
DOI: 10.3389/fmicb.2016.01606 -
BMC Pulmonary Medicine Feb 2017Pandoraea species are considered emerging pathogens in the context of cystic fibrosis (CF) and are difficult to identify by conventional biochemical methods. These...
BACKGROUND
Pandoraea species are considered emerging pathogens in the context of cystic fibrosis (CF) and are difficult to identify by conventional biochemical methods. These multidrug resistant bacteria remain poorly understood particularly in terms of natural resistance, mechanisms of acquired resistance and impact on the prognosis of the disease and the lung function. Among them, Pandoraea sputorum has been previously described in few cases of CF patients from Spain, Australia, France and United States, underlining the need of more clinical data for a better knowledge of its pathogenicity. This is the first report relating to P. sputorum in a CF patient in Argentina.
CASE PRESENTATION
Pandoraea sputorum was identified in a nine-year-old cystic fibrosis patient from Argentina, after treatment failure during an exacerbation. The isolates were successfully identified by combining molecular techniques based on 16S rRNA sequencing and mass spectrometry (MS) methods, after reassessing previous misidentified isolates by conventional methods. After first isolation of P. sputorum, patient's clinical condition worsened but later improved after a change in the treatment. Although isolates showed susceptibility to trimethoprim-sulfamethoxazole and imipenem, in our case, the antibiotic treatment failed in the eradication of P. sputorum.
CONCLUSIONS
All combined data showed a chronic colonization with P. sputorum associated to a deterioration of lung function. We noted that the presence of P. sputorum can be underestimated in CF patients and MALDI-TOF MS appears to be a promising means of accurate identification of Pandoraea species.
Topics: Argentina; Burkholderiaceae; Child; Cystic Fibrosis; Humans; Male; RNA, Ribosomal, 16S; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Sputum
PubMed: 28173787
DOI: 10.1186/s12890-017-0373-y