Niabella defluvii sp. nov., isolated from influent water of a wastewater treatment plant.

Strain I65T (=KACC 22647T=JCM 35315T), a novel Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped, and orange-pigmented bacterium was isolated from influent water of a wastewater treatment system after treatment with several antibiotics, such as meropenem, gentamicin, and macrolide. The newly identified bacterial strain I65T exhibits significant multi-drug and heavy metal resistance characteristics. Strain I65T was grown in Reasoner's 2A medium [0 %-2 % (w/v) NaCl (optimum, 0 %), pH 5.0-10.0 (optimum, pH 7.0), and 20-45°C (optimum, 30 °C)]. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain I65T was closely related to Niabella yanshanensis CCBAU 05354T (99.56 % sequence similarity), Niabella hibiscisoli THG-DN5.5T (97.51 %), and Niabella ginsengisoli GR10-1T (97.09 %). Further analysis of the whole-genome sequence confirmed that the digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain I65T and N. yanshanensis CCBAU 05354T were 23.4, 80.7, and 85.0 %, respectively, suggesting that strain I65T is distinct from N. yanshanensis. The genome size of strain I65T was 6.1 Mbp, as assessed using the Oxford Nanopore platform, and its genomic DNA G+C content was 43.0 mol%. The major fatty acids of strain I65T were iso-C15 : 0 and iso-C15 : 1 G, and the major respiratory quinone was MK-7. Moreover, the major polar lipid of strain I65T was phosphatidylethanolamine. Based on genotypic, chemotaxonomic, and phenotype data, strain I65T represents a novel species belonging to the genus Niabella, for which the name Niabella defluvii sp. nov. is proposed. The type strain is I65T (=KACC 22647T=JCM 35315T).

Antagonistic actions of Paucibacter aquatile B51 and its lasso peptide paucinodin toward cyanobacterial bloom-forming Microcystis aeruginosa PCC7806.

Superior antagonistic activity against axenic Microcystis aeruginosa PCC7806 was observed with Paucibacter sp. B51 isolated from cyanobacterial bloom samples among 43 tested freshwater bacterial species. Complete genome sequencing, analyzing average nucleotide identity and digital DNA-DNA hybridization, designated the B51 strain as Paucibacter aquatile. Electron and fluorescence microscopic image analyses revealed the presence of the B51 strain in the vicinity of M. aeruginosa cells, which might provoke direct inhibition of the photosynthetic activity of the PCC7806 cells, leading to perturbation of cellular metabolisms and consequent cell death. Our speculation was supported by the findings that growth failure of the PCC7806 cells led to low pH conditions with fewer chlorophylls and down-regulation of photosystem genes (e.g., psbD and psaB) during their 48-h co-culture condition. Interestingly, the concentrated ethyl acetate extracts obtained from B51-grown supernatant exhibited a growth-inhibitory effect on PCC7806. The physical separation of both strains by a filter system led to no inhibitory activity of the B51 cells, suggesting that contact-mediated anti-cyanobacterial compounds might also be responsible for hampering the growth of the PCC7806 cells. Bioinformatic tools identified 12 gene clusters that possibly produce secondary metabolites, including a class II lasso peptide in the B51 genome. Further chemical analysis demonstrated anti-cyanobacterial activity from fractionated samples having a rubrivinodin-like lasso peptide, named paucinodin. Taken together, both contact-mediated inhibition of photosynthesis and the lasso peptide secretion of the B51 strain are responsible for the anti-cyanobacterial activity of P. aquatile B51.

Chryseobacterium faecale sp. nov., isolated from camel feces.

Strain F4T (=KACC 22401T=JCM 34836T), a novel Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped bacterium, was isolated from camel (Camelus bactrianus) faeces. The newly identified bacterial strain F4T was grown in Reasoner's 2A medium [0-2 % (w/v) NaCl (optimum, 0 %), pH 7.0-8.0 (optimum, pH 7.0), and 18-40 °C (optimum, 30 °C)]. Phylogenetic analysis based on 16S rRNA gene sequencing confirmed that strain F4T belonged to the genus Chryseobacterium, with its closest neighbours being Chryseobacterium haifense DSM 19056T (98.0 %), Chryseobacterium anthropi CCUG 52764T (97.3 %), Chryseobacterium montana WG4T (95.7 %) and Chryseobacterium koreensis Chj70T (94.7 %). Complete genome sequence of strain F4T was obtained using a hybrid assembly pipeline integrating sequences obtained using both the Oxford Nanopore and Illumina platforms. Genomic comparisons of strain F4T with type species in the genus Chryseobacterium were conducted using digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity, resulting in values of ≤20.5, ≤77.9 and ≤80.8 %, respectively. The genomic DNA G+C content of type strain F4T was 39.7 mol%. The major fatty acids of the strain F4T were anteiso-C15 : 0 and iso-C18 : 3, and MK-6 was its major respiratory quinone. Moreover, the major polar lipid of strain F4T was phosphatidylethanolamine. The genome of strain F4T harbours only one antibiotic resistance gene (blaCME-1) encoding a ß-lactamase, which attributes ß-lactam antibiotic resistance. Based on the results of our chemotaxonomic, genotypic and phenotype analyses, strain F4T is identified as a novel species of the genus Chryseobacterium, for which the name Chryseobacterium faecale sp. nov. is proposed.

Improved biosynthesis of silver nanoparticles using keratinase from Stenotrophomonas maltophilia R13: reaction optimization, structural characterization, and biomedical activity.

In the present study, keratinase from Stenotrophomonas maltophilia R13 was used for the first time as a reducing agent for the eco-friendly synthesis of AgNPs. The keratinase produced by strain R13 was responsible for the reduction of silver ions and the subsequent formation of AgNPs. Maximum AgNP synthesis was achieved using 2 mM AgNO3 at pH 9 and 40 °C. Electron microscopy and dynamic light scattering analysis showed AgNPs were spherical and of average diameter ~ 8.4 nm. X-ray diffraction revealed that AgNPs were crystalline. FTIR indicated AgNPs were stabilized by proteins present in the crude enzyme solution of strain R13. AgNPs exhibited a broad antimicrobial spectrum against several pathogenic microorganisms, and the antimicrobial mechanism appeared to involve structural deformation of cells resulting in membrane leakage and subsequent lysis. AgNPs also displayed 1,1-diphenyl-2-picrylhydrazyl (IC50 = 0.0112 mg/ml), 2,2'-azinobis-3-ethylbenzothiazoline-6-sulfonate radical scavenging (IC50 = 0.0243 mg/ml), and anti-collagenase (IC50 = 23.5 mg/ml) activities.

Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress.

Both culture-independent and culture-dependent analyses using Nanopore-based 16S rRNA sequencing showed that short-term exposure of Antarctic soils to low temperature increased biomass with lower bacterial diversity and maintained high numbers of the phylum Proteobacteria, Firmicute, and Actinobacteria including Pseudarthrobacter species. The psychrophilic Pseudarthrobacter psychrotolerans YJ56 had superior growth at 13 °C, but could not grow at 30 °C, compared to other bacteria isolated from the same Antarctic soil. Unlike a single rod-shaped cell at 13 °C, strain YJ56 at 25 °C was morphologically shifted into a filamentous bacterium with several branches. Comparative genomics of strain YJ56 with other genera in the phylum Actinobacteria indicate remarkable copy numbers of rimJ genes that are possibly involved in dual functions, acetylation of ribosomal proteins, and stabilization of ribosomes by direct binding. Our proteomic data suggested that Actinobacteria cells experienced physiological stresses at 25 °C, showing the upregulation of chaperone proteins, GroEL and catalase, KatE. Level of proteins involved in the assembly of 50S ribosomal proteins and L29 in 50S ribosomal proteins increased at 13 °C, which suggested distinct roles of many ribosomal proteins under different conditions. Taken together, our data highlights the cellular filamentation and protein homeostasis of a psychrophilic YJ56 strain in coping with high-temperature stress.

AamA-mediated epigenetic control of genome-wide gene expression and phenotypic traits in Acinetobacter baumannii ATCC 17978.

Individual deletions of three genes encoding orphan DNA methyltransferases resulted in the occurrence of growth defect only in the aamA (encoding AcinetobacterAdenine Methylase A) mutant of A. baumannii strain ATCC 17978. Our single-molecule real-time sequencing-based methylome analysis revealed multiple AamA-mediated DNA methylation sites and proposed a potent census target motif (TTTRAATTYAAA). Loss of Dam led to modulation of genome-wide gene expression, and several Dam-target sites including the promoter region of the trmD operon (rpsP, rimM, trmD, and rplS) were identified through our methylome and transcriptome analyses. AamA methylation also appeared to control the expression of many genes linked to membrane functions (lolAB, lpxO), replication (dnaA) and protein synthesis (trmD operon) in the strain ATCC 17978. Interestingly, cellular resistance against several antibiotics and ethidium bromide through functions of efflux pumps diminished in the absence of the aamA gene, and the complementation of aamA gene restored the wild-type phenotypes. Other tested phenotypic traits such as outer-membrane vesicle production, biofilm formation and virulence were also affected in the aamA mutant. Collectively, our data indicated that epigenetic regulation through AamA-mediated DNA methylation of novel target sites mostly in the regulatory regions could contribute significantly to changes in multiple phenotypic traits in A. baumannii ATCC 17978.

Agricultural by-products and oyster shell as alternative nutrient sources for microbial sealing of early age cracks in mortar.

Bio-concrete using bacterially produced calcium carbonate can repair microcracks but is still relatively expensive due to the addition of bacteria, nutrients, and calcium sources. Agricultural by-products and oyster shells were used to produce economical bio-concrete. Sesame meal was the optimal agricultural by-product for low-cost spore production of the alkaliphilic Bacillus miscanthi strain AK13. Transcriptomic dataset was utilized to compare the gene expressions of AK13 strain under neutral and alkaline conditions, which suggested that NaCl and riboflavin could be chosen as growth-promoting factors at alkaline pH. The optimal levels of sesame meal, NaCl, and riboflavin were induced with the central composite design to create an economical medium, in which AK13 strain formed more spores with less price than in commercial sporulation medium. Calcium nitrate obtained from nitric acid treatment of oyster shell powder increased the initial compressive strength of cement mortar. Non-ureolytic calcium carbonate precipitation by AK13 using oyster shell-derived calcium ions was verified by energy-dispersive X-ray spectroscopy and X-ray diffraction analysis. Stereomicroscope and field emission scanning electron microscopy confirmed that oyster shell-derived calcium ions, along with soybean meal-solution, increased the bacterial survival and calcium carbonate precipitation inside mortar cracks. These data suggest the possibility of commercializing bacterial self-healing concrete with economical substitutes for culture medium, growth nutrient, and calcium sources.

Use of Methylcellulose-Based Pellet to Enhance the Bacterial Self-Healing of Cement Composite.

In this study, a new type of bacterial carrier using methylcellulose was presented, and its applicability to self-healing concrete has been explored. Methylcellulose, the main component of a 2 mm pellet-shaped carrier, can remain stable in alkaline environments and expand in neutral or acidic environments. These properties allow bacteria to survive in the high-alkaline and high-pressure environments of early age concrete, and the number of bacteria increases rapidly in the event of cracks, accelerating crack closure. The results show that the survival rate of bacterial spores inside the mortar was increased, and the pellet provides an enhanced biological anchor suitable for bacterial activity, bacterial growth, and mineral precipitation. Further, the results indicate an improved self-healing efficiency compared with mixing bacteria directly into the cement composite.

Biological synthesis and characterisation of silver nanoparticles using Pseudomonas geniculata H10 for pharmaceutical activity.

In the present study, silver nanoparticles (SNPs) were synthesised for the first time using Pseudomonas geniculata H10 as reducing and stabilising agents. The synthesis of SNPs was the maximum when the culture supernatant was treated with 2.5 mM AgNO3 at pH 7 and 40°C for 10 h. The SNPs were characterised by field emission scanning electron microscopy-energy-dispersive spectroscopy, transmission electron microscopy, dynamic light scattering, X-ray diffraction and UV-vis spectroscopy. Fourier transform infrared spectroscopy indicated the presence of proteins, suggesting they may have been responsible for the reduction and acted as capping agents. The SNPs displayed 1,1-diphenyl-2-picrylhydrazyl (IC50 = 28.301 µg/ml) and 2,2'-azinobis-3-ethylbenzothiazoline-6-sulphonate (IC50 = 27.076 µg/ml) radical scavenging activities. The SNPs exhibited a broad antimicrobial spectrum against several human pathogenic Gram-positive and Gram-negative bacteria and Candida albicans. The antimicrobial action of SNPs was due to cell deformation resulting in cytoplasmic leakage and subsequent lysis. The authors' results indicate P. geniculata H10 could be used to produce antimicrobial SNPs in a facile, non-toxic, cost-effective manner, and that these SNPs can be used as effective growth inhibitors in various microorganisms, making them applicable to various biomedical and environmental systems. As far as the authors are aware, this study is the first to describe the potential biomedical applications of SNPs synthesised using P. geniculata.