Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance

Delftia tsuruhatensis has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete genome sequence of a clinical D. tsuruhatensis strain, TR1180, isolated from a sputum specimen of a female patient in China in 2019. Phylogenetic and average nucleotide identity analysis demonstrated that TR1180 is a member of D. tsuruhatensis. TR1180 exhibited resistance to β-lactam, aminoglycoside, tetracycline and sulphonamide antibiotics, but was susceptible to phenicols, fluoroquinolones and macrolides. Its genome is a single, circular chromosome measuring 6,711,018 bp in size. Whole-genome analysis identified 17 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, as well as 24 potential virulence factors and a number of metal resistance genes. Our data showed that Delftia possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of Delftia strains. Comparative genomics analysis of TR1180 with other publicly available genomes of Delftia showed diverse genomic features among these strains. D. tsuruhatensis TR1180 harbored a unique 38-kb genomic island flanked by a pair of 29-bp direct repeats with the insertion of a novel In4-like integron containing most of the specific antibiotic resistance genes within the genome. This study reports the findings of a fully sequenced genome from clinical D. tsuruhatensis, which provide researchers and clinicians with valuable insights into this uncommon species.

PELUANG LIMBAH KELAPA SAWIT UNTUK PRODUKSI POLIHIDROKSIALKANOAT SEBAGAI BIOPLASTIK / The Opportunities of Oil Palm Waste for Production of Polyhydroxyalkanoate as Bioplastic

<p align="center">ABSTRAK</p><p> Plastik konvensional merupakan plastik berbasis minyak bumi (petrokimia), yang memiliki permasalahan meliputi ketersediaan bahan baku semakin sedikit dan sampah plastik ini menyebabkan polusi lingkungan karena sulit mengalami degradasi secara alami. Oleh karena itu, plastik yang dibuat dari bahan baku yang <em>biodegradable</em> dan berkelanjutan perlu untuk terus dikembangkan. Bioplastik adalah plastik yang dibuat dari bahan alami dan salah satu bahan bakunya adalah polihidroksialkanoat (PHA), yang memiliki sifat <em>biodegradable</em>, fleksibel dan termoplastik. Polihidroksialkanoat dihasilkan oleh bakteri sebagai cadangan karbon dan energi intraseluler menggunakan substrat seperti gula dan asam lemak. Bioplastik berbahan PHA telah dibuat menjadi barang dagangan sebagai bahan kemasan. Peningkatan sifat fisik dari PHA sebagai bahan kemasan dilakukan melalui pencampuran dengan bahan polimer yang <em>biodegradable</em>, plastisiser, dan antimokroba. Kelemahan produksi PHA adalah biaya produksinya tinggi namun dapat diminimalisasi dengan menggunakan bahan baku yang tepat. Limbah cair dan padat dari industri kelapa sawit merupakan bahan yang berpotensi untuk produksi PHA karena dengan pemanfaatannya dapat meminimalkan limbah, meningkatkan nilai tambah dan mendukung industri kelapa sawit yang berkelanjutan. Jenis-jenis PHA yang dihasilkan dari limbah cair dan padat dari industri kelapa sawit sangat tergantung dari substrat dan bakteri yang digunakan. Strategi yang dapat dilakukan untuk mempercepat hilirisasi bioplastik berbasis PHA dari industri kelapa sawit meliputi: (1) penggunaan teknologi pengolahan limbah cair dan padat dari pabrik kelapa sawit secara terintegrasi, (2) penggunaan bakteri yang tepat untuk mengakumulasi PHA dari limbah cair (seperti <em>Rhodobacter sphaeroides, Delftia tsuruhatensis</em> Bet002, <em>Betaproteobacteria, Alphaproteobacteria, Gammaproteo-bacteria</em>), dan limbah padat (seperti <em>B. megaterium</em>, <em>Bacillus cereus suaeda</em> B-001), dan (3) pemanfaatan PHA pada produk yang memiliki nilai tambah tinggi seperti produk biomedis dan farmasi.</p><p> </p><p align="center"> ABSTRACT</p><p> Conventional plastic is petroleum-based plastic, which has problems including the availability of fewer raw materials, and this plastic waste causes environmental pollution because it is difficult to natural degradation. Therefore, plastics made from biodegradable and sustainable raw materials need to develop. Bioplastics are plastics made from natural materials and one of the raw materials is polyhydroxyalkanoate (PHA), which has biodegradable, flexible, and thermoplastic properties. Polyhydroxyalkanoate is produced by bacteria as carbon reserves and intracellular energy using substrates such as sugar and fatty acids. Bioplastics made from PHA have been commercialized as packaging materials. Improvement of the physical properties of PHA as a packaging material is conducted by mixing it with biodegradable polymerizers, plasticizers, and antimicrobials. The disadvantage of PHA production is that its production costs are high but can be minimized by using appropriate raw materials. Liquid and solid waste from the oil palm industry are materials that have the potential for the production of PHA because its utilization can minimize waste, increase added value, and support the sustainable oil palm industry. The types of PHA that are produced from liquid and solid wastes from the palm oil industry are highly dependent on the substrate and bacteria used. Strategies that can be taken to accelerate the downstream of PHA-based bioplastics from the oil palm industry include: (1) the use of liquid and solid waste from the oil palm industry with integrated processing technology, (2) the use of appropriate bacteria to accumulate PHA from liquid waste (such as Rhodobacter sphaeroides, Delftia tsuruhatensis Bet002, Betaproteobacteria, Alphaproteobacteria, Gammapro-teobacteria), and solid waste (for example B. megaterium, Bacillus cereus suaeda B-001), and (3) utilization of PHA on products that have a high added value such as biomedical and pharmaceuticals products.</p><p> </p>

Oligotrophic Nitrification and Denitrification Bacterial Communities in a Constructed Sewage Treatment Ecosystem and Nitrogen Removal of Delftia tsuruhatensis NF4

Oligotrophic nitrifiers and denitrifiers play important roles in the removal of nitrogen from wastewater. Here, we studied the dominant bacterial populations of the sewage treatment ecosystem (STE) water from different processes and those of culture on oligotrophic heterotrophic nitrification (OHN) medium and oligotrophic aerobic denitrification (OAD) medium, using co-analysis of Illumina HiSeq DNA sequencing and traditional culture methods. The results showed that the STE water had no dominant population of oligotrophic nitrifiers or oligotrophic denitrifiers. However, after culturing on OHN medium and OAD medium, the core genera Pseudomonas, Aeromonas, and Acinetobacter that have the nitrogen removal capacity in oligotrophic environments, dominated in the bacterial community. The principal component analysis (PCA) showed that the bacterial community in the constructed rapid infiltration (CRI) effluent water of STE had high similarity with those of cultures on OHN medium and OAD medium, which prompt the special purification role of nitrogen in the CRI system. The sodium alginate immobilized OAD bacteria strain Delftia tsuruhatensis NF4 was isolated from the CRI system, with total nitrogen (TN) removal efficiency of 43.3% in sterilized STE influent water, and 60.1% in OAD medium on day three. The immobilization significantly influenced the TN and nitrate removal efficiency in OAD medium (p < 0.05), but not in sterilized STE influent water (p > 0.05). This study would lay the foundation for resource discovery of oligotrophic heterotrophic nitrifiers and aerobic denitrifiers in STE and further functional application of them on the bioremediation of wastewater.

A fluorescence immunoassay based on CdTe : Zn/ZnS quantum dots for the rapid detection of bacteria, taking Delftia tsuruhatensis CM’13 as an example

A fluorescence immunoassay has been widely applied in different fields due to its high sensitivity, simple operations, and high accuracy.

Pseudomonas aeruginosa quorum sensing inhibition by clinical isolate Delftia tsuruhatensis 11304: involvement of N-octadecanoylhomoserine lactones

Pseudomonas aeruginosa is one of the most common opportunistic pathogens that use quorum sensing (QS) system to regulate virulence factors expression and biofilm development. Delftia sp. 11304 was selected among 663 Gram-negative clinical isolates based on its QS inhibitory activity against P. aeruginosa MMA83 clinical isolate. Whole genome sequencing identified this isolate as D. tsuruhatensis and revealed genetic armamentarium of virulence factors and antibiotic resistance determinants. Ethyl acetate extract of D. tsuruhatensis 11304 culture supernatant (QSI extract) prevented biofilm formation of P. aeruginosa MMA83, but was unable to cause biofilm decomposition. QSI extract showed a synergistic effect in combination with meropenem and gentamycin, against P. aeruginosa MMA83. A dose-dependent reduction of the virulence factors: elastase, rhamnolipid and pyocyanin production by P. aeruginosa MMA83 and significant downregulation of lasI, lasR, rhlI, rhlR, pqs and mvfR expression were observed. Matrix-assisted Laser Desorption Ionization (MALDI) mass spectrometry of D. tsuruhatensis 11304 QSI extract revealed the presence of N-acyl homoserine lactones (AHL) with chain lengths of C12 to C18. The main ion peak was identified as N-octadecanoylhomoserine lactone (C18-HSL). Commercial C18-HSL (20 µM) reduced pyocyanin production as well as mRNA level of the lasI gene. A novel AHL species, dihydroxy-N-octadecanoylhomoserine lactone, was also described.

Enhancing Chlorobenzene Biodegradation by Delftia tsuruhatensis Using a Water-Silicone Oil Biphasic System

In this study, a water–silicone oil biphasic system was developed to enhance the biodegradation of monochlorobenzene (CB) by Delftia tsuruhatensis LW26. Compared to the single phase, the biphasic system with a suitable silicone oil fraction (v/v) of 20% allowed a 2.5-fold increase in the maximum tolerated CB concentration. The CB inhibition on D. tsuruhatensis LW26 was reduced in the presence of silicone oil, and the electron transport system activity was maintained at high levels even under high CB stress. Adhesion of cells to the water–oil interface at the water side was observed using confocal laser scanning microscopy. Nearly 75% of cells accumulated on the interface, implying that another interfacial substrate uptake pathway prevailed besides that initiated by cells in the aqueous phase. The 8-fold increase in cell surface hydrophobicity upon the addition of 20% (v/v) silicone oil showed that silicone oil modified the surface characteristics of D. tsuruhatensis LW26. The protein/polysaccharide ratio of extracellular polymeric substances (EPS) from D. tsuruhatensis LW26 presented a 3-fold enhancement. These results suggested that silicone oil induced the increase in the protein content of EPS and rendered cells hydrophobic. The resulting hydrophobic cells could adhere on the water–oil interface, improving the mass transfer by direct CB uptake from silicone oil.