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This study aimed to investigate the effects of different concentrations of fructooligosaccharide (FOS) instead of glucose (GLU) as the carbon source in the biofloc system. GLU was used as the carbon source in the control group, and 2.5%, 5.0%, 7.5%, and 10.0% FOS were used instead of GLU as the carbon source in experimental groups. Ammonium chloride was used the nitrogen source with a C/N ratio of 15. Bacillus subtilis was supplemented to promote biofloc formation. The results showed that the concentrations of ammonia nitrogen, nitrite nitrogen, nitrate nitrogen, and total nitrogen were reduced effectively in all groups. High-throughput 16S rRNA sequencing revealed that the abundance of Flavobacterium was significantly increased in the 2.5% FOS group (P < 0.05), while Acinetobacter was significantly increased in the 10.0% FOS group on the 14th day (P < 0.05), the abundance of Aeromonadaceae was significantly reduced in all experimental groups (P < 0.05). Compared with the control group, the abundance of Aeromonadaceae was significantly decreased in 2.5% FOS on the 28th day (P < 0.05). Correlation analysis between microbial community composition and environmental factors indicated Flavobacterium and norank_f__norank_o__Saccharimonadales were negatively associated with three forms of nitrogen. In summary, the substitution of GLU with 2.5% FOS as the carbon source in the biofloc system significantly increased the abundance of core bacteria (Flavobacterium and Acinetobacter) and significantly reduced harmful bacteria (Aeromonadaceae), thereby stabilizing bacterial communities within the aquatic environment. The positive effects exhibited by 10.0% FOS were similar to 2.5% FOS. Based on experimental results and cost, the recommended proportion of FOS as a substitute for GLU is 2.5%. This research provides a foundation for the application of FOS as a carbon source in biofloc system and serves as a reference for future studies in this field. [ABSTRACT FROM AUTHOR]

β-1,6-Glucan plays a crucial role in fungal cell walls by linking the outer layer of mannoproteins and the inner layer of β-1,3-glucan, contributing significantly to the maintenance of cell wall rigidity. Therefore, the hydrolysis of β-1,6-glucan by β-1,6-glucanase directly leads to the disintegration of the fungal cell wall. Here, a novel β-1,6-glucanase FlGlu30 was identified from the endophytic Flavobacterium sp. NAU1659 and heterologously expressed in Escherichia coli BL21 (DE3). The optimal reaction conditions of purified FlGlu30 were 50℃ and pH 6.0, resulting in a specific activity of 173.1 U/mg using pustulan as the substrate. The hydrolyzed products of FlGlu30 to pustulan were mainly gentianose within 1 h of reaction. With the extension of reaction time, gentianose was gradually hydrolyzed to glucose, indicating that FlGlu30 is an endo-β-1,6-glucanase. The germination of Magnaporthe oryzae Guy11 spores could not be inhibited by FlGlu30, but the appressorium formation of spores was completely inhibited under the concentration of 250.0 U/mL FlGlu30. The disruptions of cell wall and accumulation of intracellular reactive oxide species (ROS) were observed in FlGlu30-treated M. oryzae Guy11 cells, suggesting the significant importance of β-1,6-glucan as a potential antifungal target and the potential application of FlGlu30. Key points: • β-1,6-Glucan is a key component maintaining the rigid structure of fungal cell wall. • β-1,6-Glucanase is an antifungal protein with significant potential applications. • FlGlu30 is the first reported β-1, 6-glucanase derived from Flavobacterium. [ABSTRACT FROM AUTHOR]

Cariogenic biofilms have a matrix rich in exopolysaccharides (EPS), mutans and dextrans, that contribute to caries development. Although several physical and chemical treatments can be employed to remove oral biofilms, those are only partly efficient and use of biofilm-degrading enzymes represents an exciting opportunity to improve the performance of oral hygiene products. In the present study, a member of a glycosyl hydrolase family 66 from Flavobacterium johnsoniae (FjGH66) was heterologously expressed and biochemically characterized. The recombinant FjGH66 showed a hydrolytic activity against an early EPS-containing S. mutans biofilm, and, when associated with a α-(1,3)-glucosyl hydrolase (mutanase) from GH87 family, displayed outstanding performance, removing more than 80% of the plate-adhered biofilm. The mixture containing FjGH66 and Prevotella melaninogenica GH87 α-1,3-mutanase was added to a commercial mouthwash liquid to synergistically remove the biofilm. Dental floss and polyethylene disks coated with biofilm-degrading enzymes also degraded plate-adhered biofilm with a high efficiency. The results presented in this study might be valuable for future development of novel oral hygiene products. [ABSTRACT FROM AUTHOR]

Fusarium verticillioides is one of the most important fungal pathogens causing maize ear and stalk rots, thereby undermining global food security. Infected seeds are usually unhealthy for consumption due to contamination with fumonisin B1 (FB1) mycotoxin produced by the fungus as a virulence factor. Unveiling the molecular factors that determine fungal development and pathogenesis will help in the control and management of the diseases. Kex2 is a kexin-like Golgi-resident proprotein convertase that is involved in the activation of some important proproteins. Herein, we identified and functionally characterized FvKex2 in relation to F. verticillioides development and virulence by bioinformatics and functional genomics approaches. We found that FvKex2 is required for the fungal normal vegetative growth, because the growth of the ∆Fvkex2 mutant was significantly reduced on culture media compared to the wild-type and complemented strains. The mutant also produced very few conidia with morphologically abnormal shapes when compared with those from the wild type. However, the kexin-like protein was dispensable for the male role in sexual reproduction in F. verticillioides. In contrast, pathogenicity was nearly abolished on wounded maize stalks and sugarcane leaves in the absence of FvKEX2 gene, suggesting an essential role of Fvkex2 in the virulence of F. verticillioides. Furthermore, high-performance liquid chromatography analysis revealed that the ∆Fvkex2 mutant produced a significantly lower level of FB1 mycotoxin compared to the wild-type and complemented strains, consistent with the loss of virulence observed in the mutant. Taken together, our results indicate that FvKex2 is critical for vegetative growth, FB1 biosynthesis, and virulence, but dispensable for sexual reproduction in F. verticillioides. The study presents the kexin-like protein as a potential drug target for the management of the devastating maize ear and stalk rot diseases. Further studies should aim at uncovering the link between FvKex2 activity and FB1 biosynthesis genes. Key points: •The kexin-like protein FvKex2 contributes significantly to the vegetative growth of Fusarium verticillioides. •The conserved protein is required for fungal conidiation and conidial morphology, but dispensable for sexual reproduction. •Deletion of FvKEX2 greatly attenuates the virulence and mycotoxin production potential of F. verticillioides. [ABSTRACT FROM AUTHOR]

The glycoside hydrolase (GH) 87 α-1,3-glucanase (Agl-EK14) gene was cloned from the genomic DNA of the gram-negative bacterium Flavobacterium sp. EK14. The gene consisted of 2940 nucleotides and encoded 980 amino acid residues. The deduced amino acid sequence of Agl-EK14 included a signal peptide, a catalytic domain, a first immunoglobulin-like domain, a second immunoglobulin-like domain, a ricin B-like lectin domain, and a carboxyl-terminal domain (CTD) involved in extracellular secretion. Phylogenetic analysis of the catalytic domain of GH87 enzymes suggested that Agl-EK14 is distinct from known clusters, such as clusters composed of α-1,3-glucanases from bacilli and mycodextranases from actinomycetes. Agl-EK14 without the signal peptide and CTD hydrolyzed α-1,3-glucan, and the reaction residues from 1 and 2% substrates were almost negligible after 1440 min reaction. Agl-EK14 hydrolyzed the cell wall preparation of Aspergillus oryzae and released glucose, nigerose, and nigero-triose from the cell wall preparation. After treatment of A. oryzae live mycelia with Agl-EK14 (at least 0.5 nmol/ml), mycelia were no longer stained by red fluorescent protein-fused α-1,3-glucan binding domains of α-1,3-glucanase Agl-KA from Bacillus circulans KA-304. Results suggested that Agl-EK14 can be applied to a fungal cell wall lytic enzyme. [ABSTRACT FROM AUTHOR]

Aquatic pathogens contribute to the most severe economic loss in fishes. Nanoparticles are being developed as potent antimicrobial agents against various pathogens. The bacteria Aeromonas caviae is one of the most common aquatic pathogens that infects the majority of economically important fishes causing significant losses to the aquaculture industry. This study involved synthesizing and characterizing of a novel chitosan‐selenium nanoflower employing multiple spectroscopic and microscopic approaches. The UV‐vis spectra obtained at 265 nm indicated the formation of the Chitosan‐selenium nanoflower. The particle size analysis revealed the size of the nanoflowers to be 186.3 nm. The transmission electron micrographs revealed a unique nanoflower-like morphology. XRD spectrum revealed amorphous nature. The Raman spectrum showed a strong resonance peak at 254 cm−1 which is a characteristic absorption band for monoclinic Se and α‐Se. Cytotoxicity analysis of the synthesized nanoflowers against isolated fish pathogen Aeromonas caviae showed increasing toxicity in a dose‐dependent manner with maximum cytotoxicity of 75.06% at 1000 µg/mL. The DCFDA assay was conducted to estimate the increase in reactive oxygen species (ROS) production, and the highest percentage increase in ROS of 96.02% was observed at 1000 µg/mL. The lipid peroxidation assay was performed by quantification of the lipid oxidation product malondialdehyde (MDA). The highest percentage of lipid peroxidation was found to occur at a dose of 500 µg/mL. As a result, the synthesized chitosan‐selenium nanoflowers can be exploited as a promising antibacterial treatment against the fish pathogen Aeromonas caviae. [ABSTRACT FROM AUTHOR]

Background: Columnaris disease, instigated by Gram-negative Flavobacterium covae (F. covae), is a dreadful disease of many different genera of freshwater fish with alarmingly high mortality rates. Ictalurus punctatus (I. punctatus) is extremely prone to this disease. Despite the terrible implications of this disease, very little is known about how the host and the bacterium's virulence factor interact. Secreted extracellular proteins (SEPs) are key bacterial virulence agents that frequently provide immunogenicity. In a previous study, the major secreted extracellular proteins of F. covae were identified and their protective efficacy was verified in I. punctatus, and the results were published. In the current study, an endeavor has been made to examine the progressive shifts in I. punctatus immunity following immunization with F. covae SEPs in order to more thoroughly comprehend the host's intrinsic and acquired immune responses against F. covae infection. An enzyme-linked immunosorbent test (ELISA) is operated to analyze specific humoral immune responses against SEPs of F. covae. Moreover, the expressions of immune-associated genes that are related to inherent and acquired immunity were monitored in the anterior kidneys and spleens of the vaccinated I. punctatus. Results: Marked rise in immunoglobulin M (IgM) levels were detected in the serum of I. punctatus vaccinated with different SEP formulations, including crude SEPs, heat-deactivated SEPs, and SEPs combined with adjuvant, at 14 and 21 days post-vaccination. At the same time points, a marked increase in the expression levels of clusters of differentiation (CD4-1 and CD8-β) and major histocompatibility complex (MHC-II) genes was detected in the vaccinated fish's anterior kidneys and spleens, while the highest levels of interleukin-8 (IL-8) and tumor necrosis factor alpha (TNF-α) up-regulations were detected in the immunized fish's anterior kidneys 14 days following vaccination. Conclusions: This work revealed that SEPs are an effective basis for vaccination against F. covae infection, eliciting humoral and inherent immune responses of I. punctatus after SEPs immunization. Improvements are needed to further enhance the I. punctatus immunological responses to SEPs of F. covae since these antigens remain a prospective candidate for future optimization and clinical trials in aquaculture settings. [ABSTRACT FROM AUTHOR]

Strain KK2020170T, a Gram-stain negative, yellow colony-forming bacterium, was isolated from surface seawater sampled in Kojima Bay, Okayama, Japan. Phylogenetic analysis based on the 16S rRNA gene revealed that strain KK2020170T belongs to the genus Flavobacterium, with Flavobacterium haoranii LQY-7T (98.1% similarity) being its closest relative, followed by Flavobacterium sediminis MEBiC07310T (96.9%) and Flavobacterium urocaniciphilum YIT 12746T (96.0%). Whole-genome shotgun sequencing showed that strain KK2020170T, when paralleled with F. haoranii LQY-7 T, had 81.3% average nucleotide identity, and 24.6% in silico DNA–DNA hybridization values, respectively. The DNA G + C content of strain KK2020170T was 31.1 mol%. The most abundant fatty acids (> 10%) of strain KK2020170T were iso-C15: 0, iso-C17: 0 3-OH and iso-C15: 1 G. The dominant respiratory quinone of the strain was menaquinone MK-6. Based on the phylogenetic and phenotypic analysis results, we propose that strain KK2020170T represents a novel species, for which the name Flavobacterium okayamense sp. nov. has been proposed. The type strain is KK2020170T (= ATCC TSD-280 T = NBRC 115344 T). [ABSTRACT FROM AUTHOR]

Two novel bacterial strains CJ74T and CJ75T belonging to the genus Flavobacterium were isolated from freshwater of Han River and ginseng soil, South Korea, respectively. Strain CJ74T was Gram-stain-negative, aerobic, rod-shaped, non-motile, and non-flagellated, and did not produce flexirubin-type pigments. Strain CJ75T was Gram-stain-negative, aerobic, rod-shaped, motile by gliding, and non-flagellated, and produced flexirubin-type pigments. Both strains were shown to grow optimally at 30 °C in the absence of NaCl on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ74T and CJ75T belonged to the genus Flavobacterium and were most closely related to Flavobacterium niveum TAPW14T and Flavobacterium foetidum CJ42T with 96.17% and 97.29% 16S rRNA sequence similarities, respectively. Genomic analyses including the reconstruction of phylogenomic tree, average nucleotide identity, and digital DNA-DNA hybridization suggested that they were novel species of the genus Flavobacterium. Both strains contained menaquinone 6 (MK-6) as the primary respiratory quinone and phosphatidylethanolamine as a major polar lipid. The predominant fatty acids of both strains were iso-C15:0 and summed feature 3 (C16:1ω7c and/or C16:1ω6c). Based on the polyphasic taxonomic study, strains CJ74T and CJ75T represent novel species of the genus Flavobacterium, for which names Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov. are proposed, respectively. The type strains are CJ74T (=KACC 19819T =JCM 32889T) and CJ75T (=KACC 23149T =JCM 36132T). [ABSTRACT FROM AUTHOR]

Flavobacterium species have emerged as a significant pathogen in aquaculture worldwide. Therefore, there is a need to investigate the occurrences of Flavobacterium species and their pathogenicity in aquaculture. In this study, gram-negative, short rod-shaped isolates of Flavobacterium tructae, positive for the flexirubin pigment test (30% KOH) and exhibiting gliding movement, were recovered from the caudal peduncle of farmed infected rainbow trout, Oncorhynchusmykiss, in the Indian Himalayan Region. The isolates were characterized by biochemical, 16S rRNA, phylogenetic analysis, and designated as laboratory strain RTFCPB 279 and submitted to NCBI (MT896143.1). Experimental infection of rainbow trout fingerlings with F.tructae RTFCPB 279 at 108 CFU mL−1 demonstrated clinical signs of disease progression, leading to nearly 50% cumulative mortality. The survival of the bacterium in blood serum, hemolytic activity, and biofilm formation were indirectly correlated with its virulence characteristics. The serum-enzyme assay showed a significant increase in aspartate aminotransferase (AST) and alanine aminotransferase (ALT) activities in the liver of infected trout. The histopathological assessment of the gill, liver, kidney, spleen, and muscle tissues of rainbow trout collected from both natural and experimental infections showed several degenerative changes. The test bacterium was found to be sensitive to macrolides, phenicols, tetracycline, aminoglycosides, and folate pathway inhibitors, indicating the potential therapeutic use of these antibiotics. The lowest MICs of 4, 16, and 32 μg mL−1 were recorded against the FDA-approved erythromycin, oxytetracycline, and florfenicol, respectively. The study concludes that F.tructae RTFCPB 279 is an opportunistic pathogen and the correlation between environmental factors and infection dynamics of F.tructae may require further investigation to evaluate its actual risk in global aquaculture. The prudent use of erythromycin and oxytetracycline can help control the infection of F.tructae in rainbow trout culture. Highlights: • Flavobacterium tructae, an opportunistic pathogen in the flavobacteria group, was isolated from farmed rainbow trout in the Indian Himalayan Region. • In the experimental infections of rainbow trout fingerlings at a concentration of 108 CFU mL-1, the bacterium demonstrated moderate pathogenicity. Additionally, the bacterium exhibited in vitro biofilm formation and haemolytic activity. • Antimicrobial susceptibility assays demonstrated F. tructae's sensitivity to various antibiotic classes, including macrolides, phenicols, tetracycline, aminoglycosides, and folate pathway inhibitors. • Among the approved antibiotics for aquaculture, erythromycin, florfenicol, and oxytetracycline recorded the lowest minimum inhibitory concentrations (MICs) against the bacterium [ABSTRACT FROM AUTHOR]

The dynamics of a community of four planktonic bacterial strains isolated from river water was followed in R2 broth for 72 h in batch experiments. These strains were identified as Janthinobacterium sp., Brevundimonas sp., Flavobacterium sp. and Variovorax sp. 16S rRNA gene sequencing and flow cytometry analyses were combined to monitor the change in abundance of each individual strain in bi-cultures and quadri-culture. Two interaction networks were constructed that summarize the impact of the strains on each other's growth rate in exponential phase and carrying capacity in stationary phase. The networks agree on the absence of positive interactions but also show differences, implying that ecological interactions can be specific to particular growth phases. Janthinobacterium sp. was the fastest growing strain and dominated the co-cultures. However, its growth rate was negatively affected by the presence of other strains 10 to 100 times less abundant than Janthinobacterium sp. In general, we saw a positive correlation between growth rate and carrying capacity in this system. In addition, growth rate in monoculture was predictive of carrying capacity in co-culture. Taken together, our results highlight the necessity to take growth phases into account when measuring interactions within a microbial community. In addition, evidence that a minor strain can greatly influence the dynamics of a dominant one underlines the necessity to choose population models that do not assume a linear dependency of interaction strength to abundance of other species for accurate parameterization from such empirical data. [ABSTRACT FROM AUTHOR]

Many bacteria belonging to the phylum Bacteroidetes move on solid surfaces, called gliding motility. In our previous study with the Bacteroidetes gliding bacterium Flavobacterium johnsoniae, we proposed a helical loop track model, where adhesive SprB filaments are propelled along a helical loop on the cell surface. In this study, we observed the gliding cell rotating counterclockwise about its axis when viewed from the rear to the advancing direction of the cell and revealed that one labeled SprB focus sometimes overtook and passed another SprB focus that was moving in the same direction. Several electron microscopic analyses revealed the presence of a possible multi-rail structure underneath the outer membrane, which was associated with SprB filaments and contained GldJ protein. These results provide insights into the mechanism of Bacteroidetes gliding motility, in which the SprB filaments are propelled along tracks that may form a multi-rail system underneath the outer membrane. The insights may give clues as to how the SprB filaments get their driving force. Electron microscopic visualization and movement analysis of the gliding machinery in Bacteroidetes provide insights into the mechanism of gliding motility, or the ability of these microbes to move on solid surfaces. [ABSTRACT FROM AUTHOR]

Conventional microbiological methods reveal the diversity of culturable microorganisms and are used for the isolation of strains with various properties. On the Argentine Islands-Kyiv Peninsula region, a study of microorganisms of plant communities has been reported; however, they to the full extent did not elucidate the microbial diversity. Animal populations are shifting because of climate change, which, together with anthropogenic influence, causes the shaping of microbial communities. The study aimed to establish the diversity, enumeration of microorganisms of different groups, and relationships with the physical and chemical properties of the samples from the ecosystem of the Argentine Islands-Kyiv Peninsula region that were collected from the vegetation and soils of the nesting and feeding site of Larus dominicanus (a Kelp Gull). The microbial communities and relationships between the Antarctic Peninsula maritime ecosystems (Galindez Island and Booth Island) factors were studied with the application of conventional microbiological techniques, statistical analyses, and 16S rRNA-based taxonomy. The study of the content of trace elements and the enumeration of cultivated microorganisms of different groups in soil samples demonstrated the difference in the enumeration of microorganisms between soil layers and the relationship between microbial enumeration and the properties of the samples. The samples from Booth Island differed in microbial enumeration from samples from Galindez Island. The greatest diversity and abundance of microorganisms were found in the samples from the most polluted due to the activity of the diesel station area. Among over 200 isolates, several of them were found to be tolerant to high levels of trace elements. [ABSTRACT FROM AUTHOR]

The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid protein structures facilitate the study of distant evolutionary relationships. Here we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which infects Flavobacterium sp. (Bacteroidetes). We report ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy reveals similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses with a major capsid protein composed of two upright β-sandwiches. The minimalistic structure of ΦCjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both ΦCjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and a shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution. Structural biology investigation of conserved capsid proteins facilitates the study of virus evolution. Here, characterization of the lipid-containing ssDNA bacteriophage ΦCjT23 suggests that this phage may serve as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. [ABSTRACT FROM AUTHOR]

Latest solutions in biotechnologies and biosensing targeted cold-active extremozymes. Analysis of acetaldehyde as a relevant quality indicator of wine is one example of application that could benefit from using low-temperatures operating catalysts. In search of novel aldehyde dehydrogenases (ALDH) with high stability and activity at low temperatures, the recombinant S2-ALDH from the Antarctic Flavobacterium PL002 was obtained by cloning and expression in Escherichia coli BL21(DE3). Structural and phylogenetic analyses revealed strong protein similarities (95%) with psychrophilic homologs, conserved active residues and structural elements conferring enzyme flexibility. Arrhenius plot revealed a conformational shift at 30 °C, favoring catalysis (low activation energy) at lower temperatures. In addition to a broad substrate specificity with preference for acetaldehyde (Km = 1.88 mM), this enzyme showed a high tolerance for ethanol (15%) and several salts and chelators (an advantage for wine analysis), while being sensitive to mercury (I50 = 1.21 µM). The neutral optimal pH (7.5) and the stability up to 40 °C and after lyophilization represent major assets for developing S2-ALDH-based sensors. An enzymatic electrochemical assay was developed for acetaldehyde detection in wines with proven accuracy in comparison with the reference spectrophotometric method, thus evidencing the potential of S2-ALDH as effective biocatalyst for industry and biosensing. [ABSTRACT FROM AUTHOR]

In the present study, we studied ecology of three species of mollusc-parasitic nematodes: Phasmarhabditis bohemica, P. bonaquaense and P. apuliae. We demonstrate that these facultative parasitic nematodes can grow in polyxenic and monoxenic combinations with bacteria Acinetobacter sp., Flavobacterium sp. and Pseudomonas sp. but some combinations do not support nematode reproduction. Bacteria Pseudomonas sp. did not support the growth of P. bonaquaense while P. apuliae grows only in combination with Flavobacterium sp. Composition of the culturing media apparently influenced the development time. Animal tissue-based substrates enabled slightly faster development than others. Similarly, also monoxenization of nematodes shortens the time to emergence of new dauer juveniles. Yields of dauer juveniles were usually higher in animal tissues than in other substrates. Generally, the most productive species was P. bohemica and the highest quality of dauer juveniles, expressed by their body size and lipid content, was reached in association with Flavobacterium sp. Our results provide the basis for further studies of monoxenic large scale production in liquid media and potentially development of these nematodes as promising mollusc biocontrol agents. [ABSTRACT FROM AUTHOR]

Two novel bacterial strains, KSM-R2A25T and KSM-R2A30T, were isolated from intestines of Cyclina sinensis (corb shell) and Channa argus (northern snakehead), respectively. Both specimens were collected in Korea. The strains were Gramstain-negative, non-motile, and strictly aerobic. According to phylogenetic analyses based on 16S rRNA gene sequences, strains belonged to the genus Flavobacterium within the family Flavobacteriaceae. 16S rRNA gene sequences of strains KSM-R2A25T and KSM-R2A30T were closely related to Flavobacterium cucumis DSM 18830T and Flavobacterium aquaticum JC164T with sequence similarities of 97.77% and 98.54%, respectively. Further genomic analyses including reconstruction of the UBCG tree and overall genome-related indices suggested them as novel species of the genus Flavobacterium. Both strains contained menaquinone with six isoprene units (MK-6) as a major isoprenoid quinone and iso-C15:1 G, iso-C15:0 and iso-C16:0 as major cellular fatty acids. The major polar lipid in both strains was phosphatidylethanolamine. The genomic G + C contents of strains KSM-R2A25T and KSM-R2A30T were 31.7 and 31.9%, respectively. Based on the polyphasic taxonomic study presented here, strains KSM-R2A25T and KSM-R2A30T represent novel species of the genus Flavobacterium, for which the names Flavobacterium cyclinae sp. nov and Flavobacterium channae sp. nov are proposed. The type strains of F. cyclinae sp. nov and F. channae sp. nov are KSM-R2A25T (= KCTC 82978T = JCM 34997T) and KSM-R2A30T (= KCTC 82979T = JCM 34998T), respectively. [ABSTRACT FROM AUTHOR]

Surface modification of fabrics is a powerful strategy that can endow fabrics with desired effects while keeping the intrinsic properties. Herein, an ordinary strategy, dipping-drying based layer-by-layer self-assembly (LbL) coating, is reported to functionalize fabrics' surfaces. Firstly, the novel cation waterborne polyurethanes (QAHDPU) and anion waterborne polyurethanes (HDPU) are successfully designed and synthesized. By incorporating targeted molecule, hydantoin diol (HD) and quaternary ammonium salt with long alkyl chain (DOQA), the QAHDPU are antibacterial and hydrophobically functionalized. Taking advantage of strong adhesion, waterborne polyurethanes (WPUs) are physically bonded to surfaces of fabrics to generate durable antibacterial and hydrophobic fabrics. The QAHDPU with long alkyl chain combined with rough and porous fabric surface fabricates hydrophobic fabric surface, which can prevent bacteria from adhering to the fabrics. Furthermore, the coated fabrics present excellent antibacterial properties after chlorination, forming a second barrier against bacteria. The chlorinated coated fabrics, can inactivate 85.0–99.9% of Staphylococcus aureus and 85.0–97.7% of Escherichia coli with contact time of 60 min. The hydrophobic properties of coated fabrics are greatly improved with water contact angles of 122.0°–141.1°. In addition, the proposed method is applicable for a variety of fibers and expected to be used for industrial production. [ABSTRACT FROM AUTHOR]

Feeding and digestion are metabolically demanding causing a rise on metabolic rate called Specific Dynamic Action (SDA). Although SDA has been vastly reported in fish, its potential consequences on the oxidative-antioxidant balance has not been evaluated to date in fish, a model with a long alkaline tide associated with feeding as well. Using rainbow trout (Oncorhynchus mykiss) as a model species, the aims of the present study were to: (1) assess potential oxidative damages and changes in oxidative defences after feeding on a single meal, and (2) identify the timescale of such changes over a 96 h post-feeding period. Oxidative damage in proteins and lipids and the activities of four enzymatic antioxidant defences: superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione-S-transferase (GST) were measured in gill, stomach, intestine and liver. DNA damage was measured in red blood cells. Fish were sampled before and after 1.5, 6, 24, 48, 72 and 96 h of ingestion of a 3% body mass ration. Trends of post-prandial damage were present in all tissues, but only protein oxidation varied significatively during digestion in the stomach. The intestine and stomach presented the highest enzymatic activities, likely due to the high metabolic action that these tissues have during digestion, with peaks during post-feeding: at 24 h of SOD in stomach and at 48 h of CAT in intestine. Observed GPx peaks during post-feeding in gills are likely due to the exacerbated demands for ion fluxes and/or oxygen during feeding. The differential response of the antioxidant system observed in tissues of rainbow trout during digestion indicates a coordinated and tissue-specific antioxidant defence. [ABSTRACT FROM AUTHOR]

A Gram-negative bacterial strain, named Kb82, was isolated from agricultural soil and a polyphasic approach was used for characterisation and to determine its taxonomic position. Based on 16S rRNA gene sequence analysis, the highest similarity was found with Flavobacterium artemisiae SYP-B1015 (98.2%). The highest ANI (83.3%) and dDDH (26.5%) values were found with Flavobacterium ginsenosidimutans THG 01 and Flavobacterium fluviale HYN0086T, respectively. The isolate is aerobic with rod-shaped cells, positive for catalase and negative for oxidase tests. The DNA G+C content is 34.7 mol%. The only isoprenoid quinone is menaquinone 6 (MK-6). The major fatty acids are iso-C15:0, summed feature 3 (C16:1ω7c/C16:1ω6c) and iso-C17:0 3OH. The major polar lipid is phosphatidylethanolamine. On the bases of phenotypic characteristics and analysis of 16S rRNA gene sequences, it is concluded that strain Kb82T represents a novel species in the Flavobacterium genus, for which the name Flavobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb82T (= LMG 31576T = NCAIM B.02635T). [ABSTRACT FROM AUTHOR]

During 2018 summer season (April–May), several young (1–3-year-old) arecanut seedlings exhibited yellowing, drying, drooping and wilting symptoms in farmer's gardens located in Dakshina Kannada district of Karnataka, India. The longitudinal section of the infected seedlings showed extensive decaying of fibrous roots which extended up to the collar region and ultimately resulted in the death of young seedlings. A series of cultural, morphological, molecular characterization using multi-gene phylogeny and pathogenicity assays with Koch's postulates confirmed the association of Fusarium falciforme (FSSC 3 + 4) as the causal organism of arecanut root decay disease. To the best of our knowledge, the present study confirms the first report of root decay disease caused by F. falciforme in arecanut. [ABSTRACT FROM AUTHOR]

Columnaris is a common flavobacterial disease affecting tilapia aquaculture. Flavobacterium columnare has been identified as being responsible for the heavy mortalities of earthen-pond-cultured Nile tilapia (Oreochromis niloticus) at the Fayoum Governorate, Egypt. Mortalities have been closely associated with bad husbandry in the overstocked ponds. Diseased fish showed fin and tail rot with a thick yellowish turbid mucus covering the affected skin and gills. Scanning electron microscopy revealed the presence of numerous bacterial cells dispersed in the affected gill tissues. Most of the investigated specimens (60%) were infected with F. columnare. Forty-seven bacterial isolates were phenotypically identified based on cultural and biochemical characteristics. Molecular identification, virulence property assessment, and antibiotic-sensitivity testing were performed on 10 randomly selected isolates. The identities of the isolates were confirmed by gene sequence and phylogenetic analyses. These isolates yielded variable results regarding virulence genes (gtf, norB, and trx) and ability to adhere to fish gills. All isolates exhibited proteolytic and chondroitin lyase activities but had different antibiotic-sensitivity profiles. The pathogenicity of one highly pathogenic isolate was tested via intramuscular injection into juvenile O. niloticus. The challenged fish showed fin rot and skin ulceration with 80% cumulative mortalities. The study discussed critical points in the pathogenesis of columnaris disease affecting Nile tilapia that may help to find out effective control measures and refers to the need for prudent use of antimicrobials in aquaculture to protect aquatic animals and human health. [ABSTRACT FROM AUTHOR]

Global decline of freshwater mussels (Unionoida) is threatening biodiversity and the essential ecosystem services that mussels provide. As filter-feeding organisms, freshwater mussels remove phytoplankton and suspended particles from the water. By filtering bacteria, freshwater mussels also decrease pathogen loads in the water. The objective of this study was to evaluate whether the common freshwater bivalve Anodonta anatina (duck mussel) could remove the bacterial fish pathogen Flavobacterium columnare from the water. Mussels reduced bacteria in both of the two experiments performed, so that the bacterial concentration at the end of the 96-h monitoring in mussel treatments was only 0.3–0.5 times that of the controls. Surprisingly, mussels did not reduce algal cell concentration statistically significantly. Mussel behavior (shell openness, foot position, and movement) was not affected by the presence of bacteria or algae, except for biodeposition formation, which was greatest in algal-fed treatments, followed by bacterial-fed treatments and controls, respectively. The intestines of bacteria-incubated A. anatina harbored F. columnare, suggesting that mussels ingested the bacteria. Present results suggest that freshwater mussels may also have a potential to mitigate aquaculture pathogen problems, as well as play a role in water quality management. [ABSTRACT FROM AUTHOR]

During a study aiming at isolation and genomic characterization of non-pathogenic fish symbionts, strain F-328T was isolated from skin mucus of healthy-seeming rainbow trout (Oncorhynchus mykiss) and subjected to polyphasic characterization, including a comprehensive genome analysis. Strain F-328T was Gram stain negative, none-gliding, strictly aerobic, and rod shaped. The 16S rRNA gene sequence of strain F-328T exhibited the highest level of identity (98.9%) with F. turcicum F-339T. The major fatty acids were iso-C15:0, C15:1 ω6c, and summed feature 3 (C16:1 ω7c, C16:1 ω6c). The polar lipid profile consisted mainly of phosphatidylethanolamine and aminolipids, while the predominant menaquinone was MK-6. The DNA G + C content and genome size of the strain were 35.3% and 3.4 Mb, respectively. Strain F-328T shows 93.8% average nucleotide identity and 53% digital DNA–DNA hybridization identity with the closest type strain F. turcicum F-339T. In addition, strain F-328T was found to carry antimicrobial resistance genes, which confer resistance to several antimicrobials, including aminoglycoside, macrolides, and streptogramin. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain F-328T should be classified as a novel species of the genus Flavobacterium for which the name Flavobacterium erciyesense sp. nov. is proposed, with F-328T as the type strain (= JCM 34201T = KCTC 82261T). [ABSTRACT FROM AUTHOR]

Objective: Fusobacterium nucleatum is an important oral pathogen involved in endodontic infections. This study aimed to assess the frequency of Fusobacterium nucleatum in primary and secondary endodontic infections and its associations with the clinical features in a Brazilian population by using both culture and nested PCR methods. Methods: A total of 100 microbial samples from patients with primary (n=50) and secondary endodontic infections (n=50) were analyzed by using culture and nested PCR methods. Strict anaerobic techniques were used for culture and identification of F. nucleatum. The DNA extracted from the samples was analyzed for the presence of target species by using species-specific primers. Results: Culture and nested PCR methods detected F. nucleatum, respectively, in 11/100 and 82/100 root canals. F. nucleatum was isolated by culture from 10/50 (20%) root canals with primary infections and from 1/50 (2%) root canal with secondary/persistent infections. Nested PCR detected F. nucleatum in 42/50 (84%) root canals with primary infections and in 40/50 (80%) root canals with secondary/persistent endodontic infections. F. nucleatum was associated with spontaneous pain, tenderness to percussion, pain on palpation, swelling, tooth mobility, wet root canals, hemorrhagic exudate, tooth decay, inadequate restoration, and poor endodontic filling. Conclusion: F. nucleatum was found in more cases of primary endodontic infections than in cases of secondary/persistent ones. A higher prevalence of F. nucleatum was detected by using the nested PCR method than by using culture. The presence of F. nucleatum in the root canals was associated with several clinical features. Clinical relevance: The high prevalence of F. nucleatum in the root canals detected by molecular methods, and its association with several clinical features reveals the importance of these species in the development of apical pathologies and reinforces the need of an endodontic treatment directed to bacterial elimination. [ABSTRACT FROM AUTHOR]

Co-infections are common in host-parasite interactions, but studies about their impact on the virulence of parasites/diseases are still scarce. The present study compared mortality induced by a fatal bacterial pathogen, Flavobacterium columnare between brown trout infected with glochidia from the endangered freshwater pearl mussel, Margaritifera margaritifera, and uninfected control fish during the parasitic period and after the parasitic period (i.e. glochidia detached) in a laboratory experiment. We hypothesised that glochidial infection would increase host susceptibility to and/or pathogenicity of the bacterial infection. We found that the highly virulent strain of F. columnare caused an intense disease outbreak, with mortality reaching 100% within 29 h. Opposite to the study hypothesis, both fresh ongoing and past infection (14 months post-infection) with glochidia prolonged the fish host's survival statistically significantly by 1 h compared to the control fish (two-way ANOVA: fresh-infection, F1, 82 = 7.144, p = 0.009 and post-infection, F1, 51 = 4.227, p = 0.044). Furthermore, fish survival time increased with glochidia abundance (MLR: post-infection, t = 2.103, p = 0.045). The mechanism could be connected to an enhanced non-specific immunity or changed gill structure of the fish, as F. columnare enters the fish body mainly via the gills, which is also the glochidia's attachment site. The results increase current knowledge about the interactions between freshwater mussels and their (commercially important) fish hosts and fish pathogens and also emphasise the importance of (unknown) ecosystem services (e.g., protection against pathogens) potentially associated with imperilled freshwater mussels. [ABSTRACT FROM AUTHOR]

Bacterial biofilms are aggregates of surface-associated cells embedded in an extracellular polysaccharide (EPS) matrix, and are typically stationary. Studies of bacterial collective movement have largely focused on swarming motility mediated by flagella or pili, in the absence of a biofilm. Here, we describe a unique mode of collective movement by a self-propelled, surface-associated biofilm-like multicellular structure. Flavobacterium johnsoniae cells, which move by gliding motility, self-assemble into spherical microcolonies with EPS cores when observed by an under-oil open microfluidic system. Small microcolonies merge, creating larger ones. Microscopic analysis and computer simulation indicate that microcolonies move by cells at the base of the structure, attached to the surface by one pole of the cell. Biochemical and mutant analyses show that an active process drives microcolony self-assembly and motility, which depend on the bacterial gliding apparatus. We hypothesize that this mode of collective bacterial movement on solid surfaces may play potential roles in biofilm dynamics, bacterial cargo transport, or microbial adaptation. However, whether this collective motility occurs on plant roots or soil particles, the native environment for F. johnsoniae, is unknown. Bacterial biofilms are aggregates of surface-associated cells embedded in an extracellular polysaccharide (EPS) matrix. Here, the authors describe a unique mode of collective movement by self-propelled, surface-associated spherical microcolonies with EPS cores in the gliding bacterium Flavobacterium johnsoniae. [ABSTRACT FROM AUTHOR]

A bacterial strain designated KDG-16 T is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16 T are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20–25 °C, pH 6–7, and with 0% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set reveal that strain KDG-16 T is affiliated with species in the genus Flavobacterium. Analysis of 16S rRNA gene sequences shows that strain KDG-16 T shares the highest similarity with Flavobacterium terrigena DSM 17934 T (97.7%). The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between strain KDG-16 T and the closely related Flavobacterium species are below the cut-off values of 95–96, 90 and 70%, respectively, used for species demarcation. Strain KDG-16 T contains iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized phospholipid, two uncharacterized aminolipids and two uncharacterized lipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. Genomic DNA G + C content of strain KDG-16 T is 31.6%. Based on the polyphasic taxonomic data obtained, strain KDG-16 T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium difficile sp. nov. is proposed. The type strain is KDG-16 T (= BCRC 81194 T = LMG 31332 T). [ABSTRACT FROM AUTHOR]

A Gram-stain negative, rod shaped, motile by gliding, yellow-pigmented, aerobic bacterium, designated SE-1-eT, was isolated from a soil sample collected on Dokdo Island, South Korea. The isolate was characterized taxonomically using a polyphasic approach based on the phenotypic and genomic analyses. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SE-1-eT belonged to the genus Flavobacterium in the family Flavobacteriaceae and had the highest sequence similarity with Flavobacterium cheongpyeongense IMCC34759T (97.5%), Flavobacterium arsenitoxidans S2-3HT (97.4%), Flavobacterium resistens BD-b365T (97.4%), and Flavobacterium chungangense CJ7T (97.4%). The predominant respiratory quinone of the isolate was found to be MK-6; the main polar lipid was phosphatidylethanolamine; and the major fatty acids were identified as summed feature 3 (C16:1ω7c/C16:1ω6c), C15:0 iso, and C16:0. The draft genome of strain SE-1-eT had a length of 3,715,609 bp and a DNA G + C content of 34.8 mol%. The nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between the novel isolate and F. cheongpyeongense IMCC34759T, F. resistens BD-b365T, and Flavobacterium chungangense CJ7T ranged from 74.9 to 75.3% and from 20.2 to 20.9%, respectively. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain SE-1-eT represents a novel species in the genus Flavobacterium, for which the name Flavobacterium agrisoli sp. nov. is proposed. The type strain is SE-1-eT (= KCTC 82352 T = JCM 34302 T). [ABSTRACT FROM AUTHOR]

A Gram-stain-negative, rod-shaped, aerobic and non-motile bacterium, designated P2-65T, was isolated from Moonsan stream water in the Republic of Korea. The temperature, NaCl concentration and pH ranges for growth of strain P2-65T were 10–37 °C, 0.0–3.0% (w/v) and 6.5–8.5 with optimum growth at 25–30 °C, 0.0–1.0% and 7.0–7.5, respectively. Comparison of 16S rRNA gene sequence showed that strain P2-65T was closely related to Flavobacterium cauense (95.4%) and Flavobacterium cheniae (95.3%). The major fatty acids were iso-C15:0, iso C17:0 3-OH, summed feature 3 (C16:1ω7c and/or C16:1ω6c), summed feature 9 (iso-C17:1ω9c and/or 10-methyl C16:0) and iso-C15:0 3-OH. The predominant respiratory quinone was menaquinone-6 (MK-6). The major polar lipids detected in the strain were phosphatidylethanolamine, one aminophospholipid, one unidentified aminolipid and one unidentified polar lipid. The G + C content of the genomic DNA was 39.7%. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values for strain P2-65T with closely related Flavobacterium species were below 74.8% and 20%, respectively. Based on polyphasic features, strain P2-65T is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium inviolabile sp. nov. is proposed. The type strain is P2-65T (= KCTC 62055T = NBRC 112953T). [ABSTRACT FROM AUTHOR]

Flavobacterium columnare is a problematic pathogen for the aquaculture industry where isolates are classified by genomovars. Suspended growth in a low nutrient media, like tryptone yeast extract salts, is a common method used for laboratory study. The presence of calcium and magnesium is the factor contributing to growth, virulence, and biofilm formation for F. columnare. Exponential growth occurs within 24 h for F. columnare when grown in complete tryptone yeast extract salts medium at 30 ºC. Withholding CaCl2 and MgSO4 components from a complete TYES formulation reduced or completely inhibited growth of genomovar I isolates but not the growth of genomovar II, IIB, or III isolates. Only 3 of 20 genomovar I isolates, MS-FC-4, FC-CSF-53, and 023-08-3, could achieve O.D. 540 readings ≥ 0.3 but only after 48-h incubation in cation-restricted TYES. Independently adding CaCl2 or MgSO4 to tryptone and yeast extracts did not result in a genomovar-specific growth phenotype, but generally demonstrated increased clumping with individual isolates presenting abnormal growth. Clumping formed filamentous strings that migrated to the top of the culture tube when isolates were grown in TYE+CaCl2. Several of the F. columnare isolates from all the genomovars exhibited delayed growth when a single cation source was provided. This study demonstrates phenotypic differences between and within genomovars of a single bacterial species when grown under different TYES media conditions. [ABSTRACT FROM AUTHOR]

Outbreaks of bacterial cold-water disease (BCWD), caused by Flavobacterium psychrophilum, are widespread in Japan, especially among ayu Plecoglossus altivelis. There are few investigations of F. psychrophilum in river water, and its seasonal distribution has not been clarified. We aimed to identify the spatiotemporal dynamics of F. psychrophilum and ayu to provide information that is useful for establishing a countermeasure for BCWD. Quantitative analysis of environmental DNA (eDNA) was used to clarify the year-round dynamics of ayu and F. psychrophilum. We sampled river water from the Nagara and Ibi rivers in Japan, and conducted monthly water sampling and eDNA quantification. Changes in the eDNA concentration of ayu were consistent with the known life histories of the fish. There was a strong negative correlation between the eDNA concentration of F. psychrophilum and water temperature, suggesting a strong dependence of F. psychrophilum dynamics in the river on water temperature. Furthermore, relatively high eDNA concentrations were recorded for both organisms in early summer and fall, suggesting that ayu is infected with F. psychrophilum during these seasons when experiencing up- and downmigration, respectively. [ABSTRACT FROM AUTHOR]

In this study, using a metagenomic approach, we explore the bacterial diversity of compost sites categorized based on their ambient temperatures. The two sites were Reckong Peo in the lower Himalayas and Tambaram in the southern region of the country, namely, CPR and CT. Following assembly of the raw reads from shotgun metagenomics, similarity hits were generated using NCBI BLAST + and SILVA database. A total of 1463 and 1483 species were annotated from CPR and CT. A species-level annotation was performed using a python-based literature search pipeline revealing their growth characteristics. Thermophiles Thermomonospora curvata and Thermus scotoductus were among the prominent species in CT. CPR too was seen abundant with Acidothermus cellulolyticus and Moorella thermoacetica, constituting 10% of the population. Nearly 3% of the identified species in the site CPR were psychrophilic. Although found higher in CPR, psychrophilic species were identified in CT too. Flavobacterium and Psychrobacter spp. were present in both sites without any significant changes in their relative distribution contrary to the thermophilic species abundance (z = − 4.3). Akin to the sequenced samples, database-derived metagenomes also showed similar distribution of thermophiles and psychrophiles. Identifying such peculiar prevalence of extremophiles can be central to understanding extended growth temperatures. [ABSTRACT FROM AUTHOR]

Rainbow trout fry syndrome (RTFS) and bacterial coldwater disease (BCWD) is a globally distributed freshwater fish disease caused by Flavobacterium psychrophilum. In spite of its importance, an effective vaccine is not still available. Manipulation of the microbiome of skin, which is a primary infection gate for pathogens, could be a novel countermeasure. For example, increasing the abundance of specific antagonistic bacteria against pathogens in fish skin might be effective to prevent fish disease. Here, we combined cultivation with 16S rRNA gene amplicon sequencing to obtain insight into the skin microbiome of the rainbow trout (Oncorhynchus mykiss) and searched for skin bacteria antagonistic to F. psychrophilum. By using multiple culture media, we obtained 174 isolates spanning 18 genera. Among them, Bosea sp. OX14 and Flavobacterium sp. GL7 respectively inhibited the growth of F. psychrophilum KU190628-78 and NCIMB 1947T, and produced antagonistic compounds of < 3 kDa in size. Sequences related to our isolates comprised 4.95% of skin microbial communities, and those related to strains OX14 and GL7 respectively comprised 1.60% and 0.17% of the skin microbiome. Comparisons with previously published microbiome data detected sequences related to strains OX14 and GL7 in skin of other rainbow trout and Atlantic salmon. [ABSTRACT FROM AUTHOR]

Bacterial strain BBQ-18T, isolated from a freshwater lake in Taiwan, is characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicate that strain BBQ-18T forms a phylogenetic lineage in the genus Flavobacterium. Strain BBQ-18T is most closely related to Flavobacterium alvei HR-AYT with 98.5% 16S rRNA gene sequence similarity. Strain BBQ-18T shows 70.5–89.5% average nucleotide identity and 13.7–38.2% digital DNA–DNA hybridization identity with the type strains of other closely related Flavobacterium species. The strain is Gram-stain negative, strictly aerobic, motile by gliding, rod shaped and formed yellow colonies. Optimal growth occurs at 25 °C, pH 6, and in the absence of NaCl. Strain BBQ-18T contains iso-C15:0, summed feature 3 (C16:1ω6c and/or C16:1ω7c) and anteiso-C15:0 as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, four uncharacterized aminophospholipids and two uncharacterized phospholipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. The DNA G+C content of the genomic DNA is 33.8%. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain BBQ-18T should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium undicola sp. nov. is proposed. The type strain is BBQ-18T (= BCRC 81050T = LMG 30052T = KCTC 52810T). [ABSTRACT FROM AUTHOR]

Silver chloride nanoparticles (AgClNps) were biosynthesized extracellularly by Flavobacterium panacis (DCY106T), which was isolated from the rhizosphere of Panax ginseng in Gochang, Republic of Korea. The reduction of silver nitrate by DCY106T was initiated within 24 h at 37 °C. The complete reaction did not require supplemental reducing or stabilizing agents, further demonstrating the facile and simple synthesis of this methodology. The formation of nanoparticles was confirmed by UV–Vis spectroscopy, showing the maximum absorbance at ~ 402 nm. Field emission transmission electron microscopy revealed a spherical structure of the nanoparticles. Furthermore, the average size of AgClNps was around 20.66 nm as determined by X-ray diffraction. Fourier transform infrared spectroscopy analysis showed that functional biomolecules, such as proteins or enzymes from the cell-free supernatant of DCY106T, may provide nanoparticle stabilization against aggregations. In addition, the biosynthesized AgClNps served as competent antimicrobial agents against several pathogenic bacteria and fungi. Antioxidant results determined by 2, 2-diphenyl-1-picrylhydrzyl (DPPH) scavenging assay exhibited an efficient antioxidant activity of AgClNps. Moreover, AgClNps also revealed the anticancer potential against human lung cancer cells. Thus, this study proposes a facile extracellular synthesis of AgClNps by F. panacis (DCY106T) are applicable as the potential antimicrobial, antioxidant, and anticancer agents. [ABSTRACT FROM AUTHOR]

Background: Rare ginsenosides (F2, Rg3, Gyp-XVII, and C-K) are pharmaceutically active components of Panax ginseng, which are derived from the conversion of major ginsenosides through various transformation methods. To date, most studies have failed to identify a competent bacterial strain and recombinant enzyme for converting protopanaxadiol (PPD)- and protopanaxatriol (PPT)-type ginsenosides to target minor ginsenosides. Method: Our study identified and employed nine sets of clones from different glycoside hydrolase bacterial strains for major ginsenoside bioconversion. Among these nine clones, only BglFc was selected based on its strong biotransformation ability and capacity to generate complete minor ginsenosides. bglFc was cloned and expressed in Escherichia coli using the pGEX-4T-1 vector system, and the recombinant enzyme was used for efficiently producing minor ginsenosides Results: Recombinant BglFc is 2,394 bp and 798 amino acid residues long, with a predicted molecular mass of 78.8 kDa. BglFc belongs to the glycoside hydrolase family 3, and demonstrates a promising ability to convert major ginsenosides into minor ones. The Km and Vmax values of pNPG were 0.81 ± 0.06 and 4.0 ± 0.2 mM·min−1·mg−1 of protein, respectively. Under optimal conditions (37°C, pH 7.0), the ginsenoside transformation pathways for BglFc were as follows: Rb1→Rd→Rg3(S)→Rh2(S); GypXVII →GypLXXV→C-K; GypLXXV→C-K; F2→C-K; Rb2 →C-O→C-Y; Rb3→C-Mx1→C-Mx; Rc→C-Mcl→C-Mc; Re→Rg2(S); and Rgl→Rhl(S), respectively. Conclusion: These results suggest that recombinant BglFc demonstrates a strong transformation activity for both PPD- and PPT-type major ginsenosides. Therefore, we conclude that BglFc can be used for gram unit production of various minor ginsenosides. Significance and Impact of Study: Previously, researchers have used a combination of enzymes for the production of minor ginsenosides. However, in this study, we found a favorable enzyme that can be used alone for the production of a different type of minor ginsenoside using the proposed conversion pathway. [ABSTRACT FROM AUTHOR]

Aims: The root endophyte Phomopsis liquidambaris B3 effectively protected peanut against root rot caused by Fusarium oxysporum. We investigated (i) the effects of preinoculation (before F. oxysporum inoculation) and postinoculation (post F. oxysporum inoculation) with B3 on pathogenic infection and (ii) the potential mechanisms underlying the suppression of root rot by B3 colonization. Methods: Peanut seedlings preinoculated, postinoculated or noninoculated with B3 and challenged or not challenged with F. oxysporum were cultivated in pots with sterilized vermiculite. The root rot severity, plant growth, defense-related enzyme activity and signaling compounds in plant tissues were investigated. Chemical manipulation experiments were performed to verify the signals involved in the suppression of root rot by B3. Results: B3 preinoculation efficiently suppressed root rot, as evidenced by decreased cell death, pathogenic colonization and disease severity; however, these effects were absent in the B3 posttreated roots. B3 preinoculation locally and systemically enhanced resistance against pathogenic infection, which coincided with increased activities of pathogenesis-related proteins. These increased activities positively correlated with increased salicylic acid (SA) and hydrogen peroxide (H2O2) levels, in which SA played a dominant role. Conclusions: Preinoculation with B3 effectively suppressed F. oxysporum infection in peanut roots by activating the SA-dependent defense pathway. [ABSTRACT FROM AUTHOR]

Rapid expansion of salmon aquaculture has resulted in high-density populations that host diverse infectious agents, for which surveillance and monitoring are critical to disease management. Screening can reveal infection diversity from which disease arises, differential patterns of infection in live and dead fish that are difficult to collect in wild populations, and potential risks associated with agent transmission between wild and farmed hosts. We report results from a multi-year infectious-agent screening program of farmed salmon in British Columbia, Canada, using quantitative PCR to assess presence and load of 58 infective agents (viruses, bacteria, and eukaryotes) in 2931 Atlantic salmon (Salmo salar). Our analysis reveals temporal trends, agent correlations within hosts, and agent-associated mortality signatures. Multiple agents, most notably Tenacibaculum maritimum, were elevated in dead and dying salmon. We also report detections of agents only recently shown to infect farmed salmon in BC (Atlantic salmon calicivirus, Cutthroat trout virus-2), detection in freshwater hatcheries of two marine agents (Kudoa thyrsites and Tenacibaculum maritimum), and detection in the ocean of a freshwater agent (Flavobacterium psychrophilum). Our results provide information for farm managers, regulators, and conservationists, and enable further work to explore patterns of multi-agent infection and farm/wild transmission risk. [ABSTRACT FROM AUTHOR]

Colony spreading of Flavobacterium johnsoniae is shown to include gliding motility using the cell surface adhesin SprB, and is drastically affected by agar and glucose concentrations. Wild-type (WT) and ΔsprB mutant cells formed nonspreading colonies on soft agar, but spreading dendritic colonies on soft agar containing glucose. In the presence of glucose, an initial cell growth-dependent phase was followed by a secondary SprB-independent, gliding motility-dependent phase. The branching pattern of a ΔsprB colony was less complex than the pattern formed by the WT. Mesoscopic and microstructural information was obtained by atmospheric scanning electron microscopy (ASEM) and transmission EM, respectively. In the growth-dependent phase of WT colonies, dendritic tips spread rapidly by the movement of individual cells. In the following SprB-independent phase, leading tips were extended outwards by the movement of dynamic windmill-like rolling centers, and the lipoproteins were expressed more abundantly. Dark spots in WT cells during the growth-dependent spreading phase were not observed in the SprB-independent phase. Various mutations showed that the lipoproteins and the motility machinery were necessary for SprB-independent spreading. Overall, SprB-independent colony spreading is influenced by the lipoproteins, some of which are involved in the gliding machinery, and medium conditions, which together determine the nutrient-seeking behavior. [ABSTRACT FROM AUTHOR]

A novel bacterium designated SSM4.2T was isolated from seaweed of Gouqi Island, which is the center of the Zhoushan fishing ground in the East China Sea. Strain SSM4.2T was Gram-stain-negative, bright yellow-pigmented, short rod-shaped, non-flagellated, non-spore forming, aerobic and motile by gliding. Growth was observed at 4–37 °C (optimum 25–30 °C), pH 6.0–8.0 (optimum pH 7.0) and 0–2.0% (w/v) NaCl (optimum 0%) concentration. The strain was catalase- and oxidase-positive. Menaquinone-6 (MK-6) was found as the sole respiratory quinone and zeaxanthin as the main carotenoid pigment. The predominant fatty acids (≥ 10%) were iso-C15:0, iso-C15:1 G, iso-C17:0 3-OH and summed feature 3 (C16:1ω7c /C16:1ω6c). The major polar lipid was phosphatidylethanolamine (PE). The genome size was 5.7 Mbp. The DNA G + C content was 34.1 mol%. 16S rRNA gene sequence revealed that strain SSM4.2T belongs to the genus Flavobacterium and shares high-sequence similarity with F. limi KACC 18851T (98.1%), F. hydrophilum KACC 19591T (97.6%), F. defluvii KCTC 12612T (97.1%), F. cheongpyeongense KACC 19592T (97.0%) and F. fluviatile KCTC 52446T (96.9%). Strain SSM4.2T had 73.2–84.6% average nucleotide identity and 19.1–29.4% digital DNA-DNA hybridization values with its closest type strains. Based on its phenotypic, chemotaxonomic, phylogenetic and genomic features, strain SSM4.2T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium ajazii sp. nov. is proposed. The type strain is SSM4.2T (= KCTC 72807T = MCCC 1K04370T). [ABSTRACT FROM AUTHOR]

Chitin is one of the most abundant renewable organic materials found on earth. The chitin utilization locus in Flavobacterium johnsoniae, which encodes necessary proteins for complete enzymatic depolymerization of crystalline chitin, has recently been characterized but no detailed structural information on the enzymes was provided. Here we present protein structures of the F. johnsoniae chitobiase (FjGH20) and chitinase B (FjChiB). FjGH20 is a multi-domain enzyme with a helical domain not before observed in other chitobiases and a domain organization reminiscent of GH84 (β-N-acetylglucosaminidase) family members. The structure of FjChiB reveals that the protein lacks loops and regions associated with exo-acting activity in other chitinases and instead has a more solvent accessible substrate binding cleft, which is consistent with its endo-chitinase activity. Additionally, small angle X-ray scattering data were collected for the internal 70 kDa region that connects the N- and C-terminal chitinase domains of the unique 158 kDa multi-domain chitinase A (FjChiA). The resulting model of the molecular envelope supports bioinformatic predictions of the region comprising six domains, each with similarities to either Fn3-like or Ig-like domains. Taken together, the results provide insights into chitin utilization by F. johnsoniae and reveal structural diversity in bacterial chitin metabolism. [ABSTRACT FROM AUTHOR]

The fungicide carbendazim is an ecotoxic pollutant frequently found in water reservoirs. The ability of microorganisms to remove pollutants found in diverse environments, soil, water, or air is well documented. Although microbial communities have many advantages in bioremediation processes, in many cases, those with the desired capabilities may be slow-growing or have low pollutant degradation rates. In these cases, the manipulation of the microbial community through enrichment with specialized microbial strains showing high specific growth rates and high rates and efficiencies of pollutant degradation is desirable. In this work, bacteria of the genera Klebsiella, Flavobacterium, and Stenotrophomonas, isolated from the biofilm attached to the packed zones of a biofilm reactor, were able to grow individually in selective medium containing carbendazim. In the three bacteria studied, the mheI gene encoding the first enzyme involved in the degradation of the fungicide carbendazim was found. Studying the dynamics of growth and carbendazim degradation of the three bacteria, the effect of co-formulants was also evaluated. The pure compound and a commercial formulation of carbendazim were used as substrates. Finally, the study made it possible to define the biokinetic advantages of these strains for amendment of microbial communities. [ABSTRACT FROM AUTHOR]

Fusarium pseudograminearum is an important pathogen of Fusarium crown rot and Fusarium head blight, which is able to infect wheat and barley worldwide, causing great economic losses. Transcription factors (TFs) of the basic leucine zipper (bZIP) protein family control important processes in all eukaryotes. In this study, we identified a gene, designated FpAda1, encoding a bZIP TF in F. pseudograminearum. The homolog of FpAda1 is also known to affect hyphal growth in Neurospora crassa. Deletion of FpAda1 in F. pseudograminearum resulted in defects in hyphal growth, mycelial branching and conidia formation. Pathogenicity assays showed that virulence of the Δfpada1 mutant was dramatically decreased on wheat coleoptiles and barley leaves. However, wheat coleoptile inoculation assay showed that Δfpada1 could penetrate and proliferate in wheat cells. Moreover, the FpAda1 was required for abnormal nuclear morphology in conidia and transcription of FpCdc2 and FpCdc42. Taken together, these results indicate that FpAda1 is an important transcription factor involved in growth and development in F. pseudograminearum. [ABSTRACT FROM AUTHOR]

A Gram-negative, non-motile, rod-shaped bacterial strain, designated GS13T, was isolated from sediments in a branch of the Nackdong River in Sangju, Korea. Optimal growth occurred at pH 7.0, 20 °C, and 0% NaCl. Phylogenetic analyses using 16S rRNA showed that strain GS13T is a member of the genus Flavobacterium, with highest similarity to Flavobacterium soyangense IMCC26223T (97.0%). The DNA G+C content of strain GS13T was 36.2 mol%. The dominant fatty acids were summed feature 3 (C16:1ω7c and/or C16:1ω6c) and iso-C15:0. The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids, three unidentified lipids, and one unidentified aminophospholipid. The predominant respiratory quinone was MK-6. Our data demonstrate that strain GS13T can be distinguished from closely-related Flavobacterium species. Thus, strain GS13T is a novel Flavobacterium species, and we propose the name Flavobacterium nackdongense sp. nov. The type strain is GS13T (=KCTC 62569T = JCM 32765T). [ABSTRACT FROM AUTHOR]

Rab GTPases are responsible for a variety of membrane trafficking and vesicular transportation in fungi. But the role of Rab GTPases in Fusarium verticillioides, one of the key corn pathogens worldwide, remains elusive. These Small GTPases in fungi, particularly those homologous to Saccharomyces cerevisiae Sec4, are known to be associated with protein secretion, vesicular trafficking, secondary metabolism and pathogenicity. In this study, our aim was to investigate the molecular functions of FvSec4 in F. verticillioides associated with physiology and virulence. Interestingly, the FvSec4 null mutation did not impair the expression of key conidiation-related genes. Also, the mutant did not show any defect in sexual development, including perithecia production. Meanwhile, GFP-FvSec4 localized to growing hyphal tips and raised the possibility that FvSec4 is involved in protein trafficking and endocytosis. The mutant exhibited defect in corn stalk rot virulence and also significant alteration of fumonisin B1 production. The mutation led to higher sensitivity to oxidative and cell wall stress agents, and defects in carbon utilization. Gene complementation fully restored the defects in the mutant demonstrating that FvSec4 plays important roles in these functions. Taken together, our data indicate that FvSec4 is critical in F. verticillioides hyphal development, virulence, mycotoxin production and stress responses. [ABSTRACT FROM AUTHOR]

A biofilm is represented by a community of microorganisms capable of adhering to a surface and producing substances that envelop the cells, forming an extracellular matrix. The extracellular matrix is responsible for protecting microorganisms against environmental stress, hosts the immune system and confers resistance to antimicrobials. Fusarium keratoplasticum is a common species of FSSC (Fusarium solani species complex) associated with human infections, being the most prevalent species related to biofilm formation in hospital water systems and internal pipelines. With this in mind, this study aimed to characterise the biofilm formed by the fungus F. keratoplasticum and to evaluate the effects of farnesol, a fungal quorum sensing (QS) molecule, on the preformed biofilm and also during its formation at different times (adhesion and 24, 48 and 72 h). F. keratoplasticum is able to adhere to an abiotic surface and form a dense biofilm in 72 h, with increased total biomass and matrix modulation with the presence of extracellular DNA, RNA, polysaccharides and proteins. Farnesol exhibited important anti-biofilm activity, causing the destruction of hyphae and the extracellular matrix in preformed biofilm and preventing the adhesion of conidia, filamentation and the formation of biofilm. Few studies have characterised the formation of biofilm by filamentous fungi. Our findings suggest that farnesol acts efficiently on F. keratoplasticum biofilm since this molecule is capable of breaking the extracellular matrix, thereby disarranging the biofilm. [ABSTRACT FROM AUTHOR]

Peroxisomes are ubiquitous single-membrane-bound organelles that perform a variety of biochemical functions in eukaryotic cells. Proteins involved in peroxisomal biogenesis are collectively called peroxins. Currently, functions of most peroxins in phytopathogenic fungi are poorly understood. Here, we report identification of PEX1 and PEX10 in the phytopathogenic fungus, Fusarium graminearum, namely FgPEX1 and FgPEX10, the orthologs of yeast ScPEX1 and ScPEX10. To functionally characterize FgPEX1 and FgPEX10, we constructed deletion mutants of FgPEX1 and FgPEX10 (ΔPEX1 and ΔPEX10) by targeting gene-replacement strategies. Our data demonstrate that both mutants displayed reduced mycelial growth, conidiation, and production of perithecia. Deletion of FgPEX1 and FgPEX10 resulted in a shortage of acetyl-CoA, which is an important reason for the reduced deoxynivalenol production and inhibited virulence of F. graminearum. Moreover, ΔPEX1 and ΔPEX10 showed an increased accumulation of lipid droplets and endogenous reactive oxygen species. In addition, FgPEX1 and FgPEX10 were found to be involved in the maintenance of cell wall integrity and Woronin bodies. [ABSTRACT FROM AUTHOR]

Flavobacterium psychrophilum can be divided into three genotypes, G-C type (ayu type), A-C type (multi-fish type), and A-T type (salmon-trout type), by two single-nucleotide polymorphisms in the DNA gyrase subunit A (gyrA) gene. We isolated F. psychrophilum from various samples collected from the lower basin of a river flowing into Lake Biwa, as a model for bacterial survey, in Shiga Prefecture in June, September, and December from 2010 to 2013 and investigated their gyrA genotypes. All three types of F. psychrophilum were isolated in June when ayu went up the river from the lake. In September, ayu gathered in the lower river basin for spawning and became high in density, almost all of the isolates were of the G-C genotype and the A-T genotype was never isolated. In December, only the A-T type was isolated from the river samples, when Biwa trout Oncorhynchus masou rhodurus came to the river to spawn and were present in the sampling area. In accordance with the seasonal change of the host fish species in the river, the genotype of F. psychrophilum isolated from the environment seems to have changed as well. [ABSTRACT FROM AUTHOR]

A yellow-pigmented bacterial strain, GS03T, was isolated from sediment in a branch of the Nackdong River in Sangju, Korea. Cells were observed to be Gram-negative, aerobic and rod-shaped with gliding motility, and to be positive for catalase and oxidase. Growth was found to occur at 4–30 °C (optimum 25 °C), at pH 7.0–8.5 (optimum pH 7.5) and at NaCl 0% (optimum NaCl 0%, w/v). The major cellular fatty acids (> 10% of the total) were identified as iso C15:0, iso C15:1 G, C15:1ω6c, iso C15: 0 3-OH and iso C17: 0 3-OH. The major respiratory quinone was found to be menaquinone MK-6. The genome sequence of GS03T is 3.1 Mb with G+C content of 36.1 mol%. The major polar lipids of the isolate were identified as phosphatidylethanolamine, three unidentified aminolipids, two unidentified phospholipids, an unidentified lipid and an unidentified aminophospholipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GS03T clusters with Flavobacterium paronense KNUS1TT, with similarity of 96.8%. The phenotypic, phylogenetic, and chemotaxonomic characteristics indicate that strain GS03T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium sangjuense sp. nov. is proposed. The type strain is GS03T (= FBCC 502459T = KCTC 62568T = JCM 32764T). [ABSTRACT FROM AUTHOR]