Partial Characterization of Three Bacteriophages Isolated from Aquaculture Hatchery Water and Their Potential in the Biocontrol of Vibrio spp.

Bacteriophages are currently considered one of the most promising alternatives to antibiotics under the 'One Health' approach due to their ability to effectively combat bacterial infections. This study aimed to characterize Vibrio species in hatchery water samples collected from an aquaculture farm and investigate the biocontrol potential of their bacteriophages. Vibrio spp. (n = 32) isolates confirmed by LNA probe-based qPCR were used as hosts. Three Vibrio phages were isolated. IKEM_vK exhibited a broad host range, infecting V. harveyi (n = 8), V. alginolyticus (n = 2), V. azureus (n = 1), and V. ordalii (n = 1). IKEM_v5 showed lytic activity against V. anguillarum (n = 4) and V. ordalii (n = 1), while IKEM_v14 was specific to V. scophtalmi (n = 4). The morphological appearance of phages and their lytic effects on the host were visualized using scanning electron microscopy (SEM). All three phages remained relatively stable within the pH range of 6-11 and up to 60 °C. The lytic activities and biofilm inhibition capabilities of these phages against planktonic Vibrio cells support their potential applications in controlling vibriosis in aquaculture systems.

Genomic Insights into the Symbiotic and Plant Growth-Promoting Traits of "Candidatus Phyllobacterium onerii" sp. nov. Isolated from Endemic Astragalus flavescens.

A novel strain of Gram-negative, rod-shaped aerobic bacteria, identified as IY22, was isolated from the root nodules of Astragalus flavescens. The analysis of the 16S rDNA and recA (recombinase A) gene sequences indicated that the strain belongs to the genus Phyllobacterium. During the phylogenetic analysis, it was found that strain IY22 is closely related to P. trifolii strain PETP02T and P. bourgognense strain STM 201T. The genome of IY22 was determined to be 6,010,116 base pairs long with a DNA G+C ratio of 56.37 mol%. The average nucleotide identity (ANI) values showed a range from 91.7% to 93.6% when compared to its close relatives. Moreover, IY22 and related strains had digital DNA-DNA hybridization (dDDH) values ranging from 16.9% to 54.70%. Multiple genes (including nodACDSNZ, nifH/frxC, nifUS, fixABCJ, and sufABCDES) associated with symbiotic nitrogen fixation have been detected in strain IY22. Furthermore, this strain features genes that contribute to improving plant growth in various demanding environments. This study reports the first evidence of an association between A. flavescens and a rhizobial species. Native high-altitude legumes are a potential source of new rhizobia, and we believe that they act as a form of insurance for biodiversity against the threats of desertification and drought.

The Effects of Paddy Cultivation and Microbiota Members on Arsenic Accumulation in Rice Grain.

Access to safe food is one of the most important issues. In this context, rice plays a prominent role. Because high levels of arsenic in rice grain are a potential concern for human health, in this study, we determined the amounts of arsenic in water and soil used in the rice development stage, changes in the arsC and mcrA genes using qRT-PCR, and the abundance and diversity (with metabarcoding) of the dominant microbiota. When the rice grain and husk samples were evaluated in terms of arsenic accumulation, the highest values (1.62 ppm) were obtained from areas where groundwater was used as irrigation water, whereas the lowest values (0.21 ppm) occurred in samples from the stream. It was observed that the abundance of the Comamonadaceae family and Limnohabitans genus members was at the highest level in groundwater during grain formation. As rice development progressed, arsenic accumulated in the roots, shoots, and rice grain. Although the highest arsC values were reached in the field where groundwater was used, methane production increased in areas where surface water sources were used. In order to provide arsenic-free rice consumption, the preferred soil, water source, microbiota members, rice type, and anthropogenic inputs for use on agricultural land should be evaluated rigorously.

Selection and Molecular Response of AHL-lactonase (aiiA) Producing Bacillus sp. Under Penicillin G-induced Conditions.

Quorum sensing (QS) is the process by which microorganisms employ chemicals called autoinducers (AIs) to communicate with their population. The QS mechanism generally controls the expression of the virulence related genes in bacteria. N-acyl homoserine lactones (AHLs) are the most widespread QS molecules. Due to their diverse AHL-lactonase activities, Bacillus species make particularly suitable candidates for procedures such as demolition of pathogenic bacterial QS signals and bioremediation of ß-lactam antibiotics from contaminated environments. In this study, seven Bacillus strains with Quorum quenching (QQ) activity were isolated using an enrichment medium supplemented with Penicillin G (PenG). The AHL-lactonase encoding gene (aiiA) was amplified by PCR and sequenced. Amino acid sequences underwent multiple sequence alignment. Docking studies were carried out with both C6HSL and PenG ligand using AutoDock tools. The aiiA amino acid sequences of the isolates were found to be well conserved. Furthermore, amino acid sequence alignment revealed that 74.9% of amino acid sequences were conserved in the genus Bacillus. Docking of the C6HSL to wild type (3DHA) and H97D variant reduced the docking score by only 0.1 kcal/mol for the mutated protein. When PenG docked with a higher (1.5 kcal/mol) score as a ligand to wild-type and mutant receptors, the docking score for the mutated protein likewise decreased by 0.1 kcal/mol. This research contributed to the diversification of organisms with QQ activity and beta-lactam antibiotic resistance. It also clarified the binding score of the PenG ligand to the Bacillus AHL lactonase molecule for the first time.

Biofilm Formation by Salmonella enterica Strains.

Biofilm formation by five different Salmonella enterica strains was assessed qualitatively and quantitatively under different incubation conditions. The strains exhibited different adherence abilities to test tubes. The isolates revealed Red Dry and Rough (RDAR) and Brown Dry and Rough (BDAR) morphotypes when cultured on Congo Red Agar (CRA). The pellicles formed by the tested strains ranged from strong to fragile when incubated in LB without NaCl at 27 °C. Smooth and White (SAW) morphotype on CRA and very weak pellicles were observed when the bacterial strains were incubated at 37 °C. The effect of temperature and media on biofilm formation by the tested strains was significant. Among the five Salmonella isolates, S. enteritidis TM 6 and S. enteritidis TM 68 formed strong biofilms when incubated in LB without NaCl at 27 °C for 24 h and consequently selected to be analysed under scanning electron microscope (SEM). Scanning electron micrographs revealed that S. enteritidis TM 6 formed more complex colonies when compared to those formed by S. enteritidis TM 68. As far as we know, this is the first study that provides quantitative and qualitative data for 5 Salmonella enterica isolates in different media mimicking four different nutritional conditions at two different temperatures after 24 and 48 h. The strains included two serovars S. bredeney and S. anatum, which are rarely accounted for. Additionally, the studies that described S. enteritidis biofilms under SEM are extremely limited, which makes it among the first comprehensive studies that screened for S. enteritidis biofilms.

New fructofuranoside in fruit of Pyrus amygdaliformis Vill.

The new compound 2-O-ß-D-fructofuranosylglycerol was isolated from the hexane residue. Also 2-O-methyl-α-fructofuranoside was isolated for the first time from the fruits of Pyrus amygdaliformis Vill. The chemical structure of isolated carbohydrates was identified using NMR, mass spectroscopic technique and literature data. The minimal inhibitory concentrations (MIC) of P. amygdaliformis Vill. hexane, dichloromethane and butanol extracts of fruits were used for testing microorganisms. Hexane extract showed antimicrobial activity against Escherichia coli, Klebsiella pneumoniae, Enterococcus faecalis and Salmonella typhimurium with MIC ranging between 25 and 0.39 mg/mL. The most sensitive strain was found to be K. pneumoniae with MIC value at 0.39 mg/mL in hexane extract.[Figure: see text].

Inhibition of Salmonella enteritidis biofilms by Salmonella invasion protein-targeting aptamer.

The current study aimed to assess the inhibitory effect of a DNA aptamer (Apt17) which targeted Salmonella invasion proteinA (SipA). The effect of Apt17, on biofilm formation by two Salmonella enteritidis strains, was tested either separately or in combination with ampicillin at different Sub MIC concentrations. Maximum inhibitory effect equivalent to 24.34% and 26.81% was recorded when Apt17 was co-incubated with S. enteritidis TM 6 and S. enteritidis TM 68 respectively for 13 h. The inhibitory effect of Apt17 was also confirmed with Triphenyl Tetrazolium Chloride. Under Scanning Electron Microscope, the presence of Apt17 resulted in altered three dimensional structure. While the treated cells of S. enteritidis TM 6 were arranged as monolayers, the sessile aggregates of S. enteritidis TM 68 appeared thinner and exhibited less surface coverage when compared to control. Moreover, the treated cells lost their exopolysaccharide matrix. The co-incubation of Apt17 with ampicillin MIC/10 for 24 h, inhibited the biofilms of S. enteritidis TM 6 and S. enteritidis TM 68 by 12.5 and 20.9% respectively. This study demonstrated quantitative and qualitative antibiofilm effect of Apt17 against the biofilms of two Salmonella enteritidis strains. According to our knowledge, this is the first study employing an aptamer that targets SipA protein to inhibit biofilm formation in Salmonella.

Single-stranded DNA (ssDNA) Aptamer targeting SipA protein inhibits Salmonella Enteritidis invasion of intestinal epithelial cells.

Salmonella Enteritidis is an important pathogen that can invade the intestinal cells of its host causing salmonellosis. SipA protein, an effector protein secreted by T3SS, maintains invasion of host cells more efficient. Thus, inhibitory aptamers against SipA protein were developed using magnetic bead-based Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method. The enriched sequences were obtained after 9 SELEX rounds. Among which, an aptamer namely Apt17 displayed Kd values equivalent to 114.9 and 63.4 nM at 27 °C and 37 °C, respectively. The effect of Apt17 on adhesion and invasion of Caco-2 cells by the tested strains was determined. While the adhesion and invasion of Salmonella Enteritidis TM 6 were inhibited by 70% and 37.7%, those of Salmonella Enteritidis TM 68 were inhibited by 45.71% and 39.5% respectively. These results represent a corner stone for future studies that could aim to develop putative inhibitors against Salmonellosis.

Streptomyces sp. TEM 33 possesses high lipolytic activity in solid-state fermentation in comparison with submerged fermentation.

Solid-state fermentation (SSF) is a bioprocess that doesn't need an excess of free water, and it offers potential benefits for microbial cultivation for bioprocesses and product development. In comparing the antibiotic production, few detailed reports could be found with lipolytic enzyme production by Streptomycetes in SSF. Taking this knowledge into consideration, we prefer to purify Actinomycetes species as a new source for lipase production. The lipase-producing strain Streptomyces sp. TEM 33 was isolated from soil and lipase production was managed by solid-state fermentation (SSF) in comparison with submerged fermentation (SmF). Bioprocess-affecting factors like initial moisture content, incubation time, and various carbon and nitrogen additives and the other enzymes secreted into the media were optimized. Lipase activity was measured as 1.74 ± 0.0005 U/g dry substrate (gds) by the p-nitrophenylpalmitate (pNPP) method on day 6 of fermentation with 71.43% final substrate moisture content. In order to understand the metabolic priority in SSF, cellulase and xylanase activity of Streptomyces sp. TEM33 was also measured. The microorganism degrades the wheat bran to its usable form by excreting cellulases and xylanases; then it secretes the lipase that is necessary for degrading the oil in the medium.

Assessment of antimicrobial activity of nanosized Ag doped TiO(2) colloids.

In the present research, the antimicrobial effects of nanosized silver (Ag) doped TiO(2) colloidal solutions prepared using a sol-gel technique were investigated. In order to determine the solution characteristics, the turbidity, viscosity and pH of the colloidal solutions were measured. Differential thermal analysis-thermogravimetry equipment was used to determine the chemical structures and reaction types of the films formed from these solutions. The morphology of Ag doped TiO(2) nanoparticles was evaluated by atomic force microscopy. The disc diffusion method was employed to explore antimicrobial activity, and the Broth Microdilution method was used to obtain MIC values of nanosized Ag doped TiO(2) colloidal solutions against the test microorganisms Escherichia coli, Staphylococcus aureus, Candida albicans, Bacillus subtilis, and Salmonella typhimurium. It was found that the silver doped TiO(2) nanoparticles inhibited the growth and multiplication of the test microorganisms, including the fungus C. albicans. Antimicrobial activity was observed against all tested microorganisms at a very low concentration of 1.125-2.81 µg/ml of nano silver in 1-25 % Ag-TiO(2) solutions.

Production of laccase from Trametes trogii TEM H2: a newly isolated white-rot fungus by air sampling.

This work represents the first report of isolation of potential laccase producers by air sampling using media supplemented with 2,2-azinobis (3-ethylbenzothiazoline-6-sulfonate) and guaiacol for laccase production and secretion indicators. Nine fungal isolates showed positive reactions with 2,2-azinobis (3-ethylbenzothiazoline-6-sulfonate) and guaiacol. The isolate named TEM H2 exhibited the largest and intensive oxidation zones with 2,2-azinobis (3-ethylbenzothiazoline-6-sulfonate) (85 mm) and guaiacol (66 mm) and therefore it was selected for detailed investigations. The strain was identified as Trametes trogii TEM H2 due to the morphological characteristics and the comparison of internal transcribed spacer ribosomal DNA gene sequences. The laccase production was screened in different liquid cultures. The best laccase production medium was determined as soluble starch yeast extract medium in which laccase production was reached to a maximum level (989.6 U l(-1) ) on the 8(th) day of cultivation. Effects of different initial pH values on laccase production were tested. Optimum pH value for laccase production in soluble starch yeast extract medium was determined as pH 3.0 with 15425.0 U l(-1) laccase production at 12(th) day of cultivation. In addition, effects of eight inducers (veratryl alcohol, ferulic acid, 1-Hydroxybenzotriazole, syringic acid, 2,2-azinobis (3-ethylbenzothiazoline-6-sulfonate), 1 mmol l(-1) CuSO(4) , 3% ethanol, guaiacol) were examined. Only cultures with 2,5-xylidine exhibited 1.9 fold increase in laccase activity reaching to 28890.0 U l(-1).

Voltammetric determination of epinephrine by White rot fungi (Phanerochaete chrysosporium ME446) cells based microbial biosensor.

The lyophilized biomass of White rot fungi (Phanerochaete chrysosporium ME446) was immobilized in gelatine using glutaraldehyde crosslinking agent on a Pt working electrode. The fungal cells retained their laccase activity under entrapped state. The immobilized cells were used as a source of laccase to develop amperometric epinephrine biosensor. The catalytic action of the laccase in the biosensor released an epinephrinequinone as a result of redox activity, thereby causing an increase in the current. The optimal working conditions of the biosensor were carried out at pH 4.5 (50 mM acetate buffer containing 100 mM K(3)Fe(CN)(6)), and 20°C. The sensor response was linear over a range of 5-100 µM epinephrine. The detection limit of the biosensor was found to be 1.04 µM. In the optimization and characterization studies of the microbial biosensor some parameters such as effect of fungi and gelatine amount, percentage of glutaraldehyde on the biosensor response and substrate specificity were carried out. In the application studies of the biosensor, sensitive determination of epinephrine in pharmaceutical ampules was investigated.

Modification of lysozyme with oleoyl chloride for broadening the antimicrobial specificity.

Lysozyme from egg white was modified by covalent attachment of an oleyl group to the free amino groups of lysozyme. The aim of the chemical modification was to develop an effective antimicrobial lysozyme derivative against both gram-negative and gram-positive bacteria. Lysozyme with various degrees of modification was obtained by changing oleoyl chloride/lysozyme mass ratio. Lysozyme derivatives evidently exhibited an antimicrobial effect against Escherichia coli (ATCC 29998). The modification slightly changed the antimicrobial effect of lysozyme derivative against Staphylococcus aureus (ATCC 121002). Since there was a positive correlation between the modification degree and the antimicrobial effect against E. coli, it was concluded that the change in antimicrobial behavior was due to an increase in hydrophobicity of the enzyme molecule enabling it to penetrate through the bacterial membrane of E. coli. It was also shown that oleoyl chloride with an MIC value of 10 mg/mL was effective against both E. coli and S. aureus.

Effects of biosorption parameter: kinetics, isotherm and thermodynamics for Ni(II) biosorption from aqueous solution by Circinella sp

Circinella sp. was employed as a biosorbent for removal of Ni(II) from aqueous solution. The biosorption kinetics and isotherms were investigated. The effect of several parameters, such as biosorbent dosage, contact time, initial concentration, pH and temperature, on biosorption process was evaluated. The kinetic studies indicated that the biosorption followed pseudo-second order kinetic model. Biosorption behaviour of Ni(II) on Circinella sp. was expressed by both Langmuir and Freundlich isotherms. The equilibrium data fit better to the Langmuir model compared to the Freundlich model in concentration range studied (1.0-3.0 mM). The thermodynamic parameters (AG°, AH° and AS°) were also determined, and it was found that the Ni(II) biosorption by Circinella sp. was spontaneous and endothermic in nature.

A novel glycoside from Acanthus hirsutus (Acanthaceae).

A novel glycoside, hirsutusoide (1), characterized as 2-(o-hydroxyphenyl)-2-hydroxyethenyl-O-beta-glucopyranoside, was isolated from the endemic Acanthus hirsutus Boiss. In addition to compound 1, three known glycosides, luteolin-7-O-beta-D-glucuronide (2), beta-sitosterol-3-O-beta-D-glucopyranoside (3) and (2R)-2-O-beta-D-glucopyranosyl-2H-1,4-benzoxazin-3(4H)-one (4), were also isolated. Compound 2 was the first report from this genus. Antimicrobial and antioxidant activity of the extracts and the novel compound were investigated by determining MIC (microg/mL) and IC50 (microg/mL) values, respectively.

Sensitive determination of L-lysine with a new amperometric microbial biosensor based on Saccharomyces cerevisiae yeast cells.

A new amperometric microbial biosensor based on Saccharomyces cerevisiae NRRL-12632 cells, which had been induced for lysine oxidase enzyme and immobilized in gelatin by a cross-linking agent was developed for the sensitive determination of L-lysine amino acid. To construct the microbial biosensor S. cerevisiae cells were activated and cultured in a suitable culture medium. By using gelatine (8.43 mg cm(-2)) and glutaraldehyde (0.25%), cells obtained in the logarithmic phase of the growth curve at the end of a 14 h period were immobilized and fixed on a pretreated oxygen sensitive Teflon membrane of a dissolved oxygen probe. The assay procedure of the microbial biosensor is based on the determination of the differences of the respiration activity of the cells on the oxygenmeter in the absence and the presence of L-lysine. According to the end point measurement technique used in the experiments it was determined that the microbial biosensor response depended linearly on L-lysine concentrations between 1.0 and 10.0 microM with a 1 min response time. In optimization studies of the microbial biosensor, the most suitable microorganism quantities were found to be 0.97x10(5)CFU cm(-2). In addition phosphate buffer (pH 7.5; 50 mM) and 30 degrees C were obtained as the optimum working conditions. In characterization studies of the microbial biosensor some parameters such as substrate specificity, interference effects of some substances on the microbial biosensor responses, reproducibility of the biosensor and operational and storage stability were investigated.

Flavonoid glycosides and methylinositol from Ebenus haussknechtii.

Two flavonoid glycosides (compounds 1 and 3) of which one is reported for the first time and a methylinositol (compound 2) were isolated from the aerial parts of Ebenus haussknechtii (Leguminosae). The structures were established as quercetin-7-O-[alpha-L-rhamnopyranosyl(1 --> 6)-beta-D-galactopyranoside] (1), morin-3-O-[4-[5-(4-hydroxyphenyl)pentanoyl]-alpha-L-rhamnopyranosyl(1 --> 6)-beta-D-galactopyranosyl]-7-4'-di-O-methyleter (3), and methylinositol (2) on the basis of chemical and spectroscopic means. The antimicrobial activities of the extracts have also been examined.

Whole cell immobilized amperometric biosensor based on Saccharomyces cerevisiae for selective determination of vitamin B1 (thiamine).

A new amperometric whole cell biosensor based on Saccharomyces cerevisiae immobilized in gelatin was developed for selective determination of vitamin B1 (thiamine). The biosensor was constructed by using gelatin and crosslinking agent glutaraldehyde to immobilize S. cerevisiae cells on the Teflon membrane of dissolved oxygen (DO) probe used as the basic electrode system combined with a digital oxygen meter. The cells were induced by vitamin B1 in the culture medium, and the cells used it as a carbon source in the absence of glucose. So, when the vitamin B1 solution is injected into the whole cell biosensor system, an increase in respiration activity of the cells results from the metabolic activity and causes a decrease in the DO concentration of interval surface of DO probe related to vitamin B1 concentration. The response time of the biosensor is 3 min, and the optimal working conditions of the biosensor were carried out as pH 7.0, 50mM Tris-HCl, and 30 degrees C. A linear relationship was obtained between the DO concentration decrease and vitamin B1 concentration between 5.0 x 10(-3) and 10(-1) microM. In the application studies of the biosensor, sensitive determination of vitamin B1 in the vitamin tablets was investigated.

Screening and simple purification of alanine dehydrogenase in Bacillus strains.

Alanine dehydrogenase (EC 1.4.1.1), in the presence of NAD+, catalyzes the reversible deamination of L-alanine. Screening of alanine dehydrogenase in bacillus strains was carried out to develop its utilization as an industrial and analytical catalyst. Eight bacillus strains were used, including Bacillus megaterium LA 199 which abundantly produces enzymes. Alanine dehydrogenase was purified simply from Bacillus megaterium LA 199 by heat treatment at pH 5.4, followed by DEAE-Sepharose CL-6B and Sepharose CL-2B chromotography. The enzyme consisted of six subunits with an identical molecular mass of 42.5 kDa. The Km were 1.17 x 10(-2) mM for NADH and 5.12 x 10(-2) mM for pyruvate.