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Bacterial communities are important factors governing changes in river ecology. We evaluated the diversity of bacterial communities in sediment and size-fractionated water samples collected from the Tama River, Tokyo, Japan, to verify their taxonomy and functional classes. Samples were collected from three river areas, namely up-, mid- and downstream, and analyzed using MiSeq shotgun metagenomic sequencing. Bacterial diversity in the river water was highest midstream for the free-living bacterial communities. Dominant bacterial classes upstream were Alphaproteobacteria and Betaproteobacteria, and there was a gradual shift to dominance by Actinobacteria mid- and downstream. Potential pathogenic genera, such as Flavobacterium, Mycobacterium and Bacteroides, also dominated mid- and downstream. Interestingly, Mycobacterium was most abundant midstream, whereas Pseudomonas was observed upstream. The gene possibly associated with sulfur metabolism, sigB, and those associated with purine metabolism, purF, purD, purN, purH, guaB and guaA, dominated in the bacterial communities found mid- and downstream and are thought to ensure survival and virulence in their environments. NO2-N, NH4-N and PO4-P were found to influence bacterial populations in water but not those residing in the sediment.

A bacterial strain designated KDG-16T is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16T are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20-25 oC, 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-16T is affiliated with species in the genus Flavobacterium. Analysis of 16S rRNA gene sequences shows that strain KDG-16T shares the highest similarity with Flavobacterium terrigena DSM 17934T (97.7%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain KDG-16T 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-16T 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-16T is 31.6%. Based on the polyphasic taxonomic data obtained, strain KDG-16T 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-16T (=BCRC 81194T =LMG 31332T).

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 (C16:1 ω7c/C16:1 ω6c), 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).

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-C17:1 ω9c 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).

Proteases secreted from bacteria into soil play a key role in the degradation of organic nitrogen, which is the first and, usually, the rate-limiting step of nitrogen cycling. However, the diversity of protease-producing bacteria and their excreted proteases in Antarctic soil have not yet been fully explored. Here we studied 20 soil samples from the South Shetland Islands, Antarctica and isolated 253 strains with protease activity. These protease-producing bacteria belonged to the phyla Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, and Deinococcus-Thermus. Thhe predominant genera were Arthrobacter (14.9%), Chryseobacterium (14.5%), Flavobacterium (14.5%), and Pseudomonas (14.5%). Most of these bacteria secreted serine proteases and metalloproteases. There was quite a large distribution in activity as quantified by protease and inhibition assays. Only a few strains secreted aspartic and/or cysteine proteases. Together these data provided novel insight into the diversity and mechanism of organic nitrogen degradation in Antarctic soils by various proteases, which may have potential in new biotechnological applications.

High-altitude cold habitats of the Karakoram are rarely explored for their bacterial community characterization and metabolite productions. In the present study, bacterial communities in ice, water, and sediments of Batura Glacier were investigated using culture-dependent and culture-independent methods. Twenty-seven cold-adapted bacterial strains (mostly psychrotrophic) were isolated using R2A, Tryptic Soy Agar (TSA), and Luria-Bertani (LB) media, at 4 °C and 15 °C. Most of the isolates exhibited growth at a wide range of temperature (4–35 °C), pH (5–12), and salinity (1–6%). Among the bacterial isolates, 52% were identified as Gram-positive and the remaining 48% represented as Gram-negative. The results of phylogenetic analysis indicated that all the culturable bacteria belonged to 3 major phylogenetic groups, i.e., Actinobacteria (48%), Bacteroidetes (26%), and Proteobacteria (22%), while Flavobacterium (26%), Arthrobacter (22%), and Pseudomonas (19%) were represented as the dominant genera. Similarly, Illumina amplicon sequencing of 16S rRNA genes after PCR amplification of DNA from the whole community revealed dominance of the same phylogenetic groups, Proteobacteria, Actinobacteria, and Bacteroidetes, while Arthrobacter, Mycoplana, Ochrobactrum, Kaistobacter, Janthinobacterium, and Flavobacterium were found as the dominant genera. Among the culturable isolates, 70% demonstrated activity for cellulases, 48% lipases, 41% proteases, 41% DNases, and only 7% for amylases. Most of the glacial isolates demonstrated antimicrobial activity against other microorganisms including the multiple-drug-resistant strains of Candida albicans, Klebsiella pneumoniae, Acinetobacter sp., and Bacillus sp. 67% of Gram-negative while 46% of Gram-positive glacial bacteria were resistant to trimethoprim/sulfamethoxazole. Resistance against methicillin and vancomycin among the Gram-positive isolates was 23% and 15%, respectively, while 11% of the Gram-negative isolates exhibited resistance against both colistin sulfate and nalidixic acid.

The long-known resistance to pathogens provided by host-associated microbiota fostered the notion that adding protective bacteria could prevent or attenuate infection. However, the identification of endogenous or exogenous bacteria conferring such protection is often hindered by the complexity of host microbial communities. Here, we used zebrafish and the fish pathogen Flavobacterium columnare as a model system to study the determinants of microbiota-associated colonization resistance. We compared infection susceptibility in germ-free, conventional and re-conventionalized larvae and showed that a consortium of 10 culturable bacterial species are sufficient to protect zebrafish. Whereas survival to F. columnare infection does not rely on host innate immunity, we used antibiotic dysbiosis to alter zebrafish microbiota composition, leading to the identification of two different protection strategies. We first identified that the bacterium Chryseobacterium massiliae individually protects both larvae and adult zebrafish. We also showed that an assembly of 9 endogenous zebrafish species that do not otherwise protect individually confer a community-level resistance to infection. Our study therefore provides a rational approach to identify key endogenous protecting bacteria and promising candidates to engineer resilient microbial communities. It also shows how direct experimental analysis of colonization resistance in low-complexity in vivo models can reveal unsuspected ecological strategies at play in microbiota-based protection against pathogens.

The intestinal microbiota is a crucial physiological system that offers multiple services to the host and contributes to the health of host. However, substantially less is known concerning the interrelation between amphibian gut microbiota and Cu exposure. R. chensinensis larvae were exposed to different concentrations of Cu (0, 0.1, 0.25, 0.75 μM) until reached Gosner stage 38. Histological and morphological data were measured by four Cu exposure conditions. Then, the diversity, structure, and composition of intestinal microbiota were analyzed via 16S rRNA gene sequencing. These results indicated that total body length, intestinal wet weight, and total body wet weight were reduced in 0.75 μM CuSO4 exposure group. Besides, obvious histopathologic alterations were observed in CuSO4 exposure groups. Alpha diversity significantly differentiated in 0.75 μM CuSO4 exposure group, and beta diversity showed 0.1 μM and 0.2 μM CuSO4 exposure groups separation with the control group. At the phylum level of intestinal microbial community, the relative abundances of Fusobacteria were significantly decreased, while Bacteroidetes was no significant difference in all CuSO4 exposure groups. Furthermore, at the genera level, Flavobacterium has a significant higher abundance in 0.75 μM CuSO4 exposure group, and high abundance of Rahnella was found in 0.1 μM CuSO4 exposure group. Also, Cu exposure affected the metabolism function of R. chensinensis tadpoles based on functional prediction analysis. This work provides new perspective to explore the effect of heavy metal on the intestinal health of amphibians.

Plant growth-promoting bacteria (PGPB) are indigenous to the plant rhizosphere and largely affect many events occurring during the plant life cycle, through either a direct or an indirect mechanism such as regulation of hormonal balance, facilitation of nutrients uptake and improvement of stress tolerance. Since drought stress, a representative abiotic stress, is one of the main reasons limiting plant growth, the identification of useful PGPB involved in drought stressresistance in plants and its application into the agricultural field could be utilized as a strategy to facilitate crop productivity. To obtain a useful PGPB that is involved in drought stress resistance, we checked the expression patterns of drought-inducible marker genes such as RD29A and RAB18 in Arabidopsis after application of 16 Flavobateria obtained from various environmental sources. After screening, a PGPB known as Flavobacterium crocinum HYN0056T, which contributes to more than twofold upregulation of drought-inducible marker genes, was finally selected for this study. Application of HYN0056T enhanced the tolerance against both drought stress, possibly via induction of stomatal closure, the highly related salt stress, in the presence of HYN0056T. Moreover, treatment of HYN0056T under drought and salt stresses resulted in enhanced upregulation of various drought- and salt-inducible genes in Arabidopsis. HYN0056T was responsible for the development of lateral roots under nonstress condition, implying that it may be involved in effective uptake of water/inorganic nutrients. Based on these results, we suggest that this bacterium could be used as a useful biocontrol agent to improve plant productivity, especially under drought/salt stress conditions.

Catfish is an important aquaculture species in the USA. Columnaris disease is distributed worldwide, affecting a wide variety of fish species including catfish . It leads to huge economic losses each year to the US catfish industry. Channel catfish in general is highly resistant to the disease, while blue catfish is highly susceptible. Genomic selection is an effective and accurate way to predict the breeding values and thus was expected to improve the prediction veracity of columnaris disease resistance in catfish effectively. In this study, two different methods, elastic net genomic best linear unbiased prediction (ENGBLUP) and genomic best linear unbiased prediction (GBLUP), were used to predict the columnaris disease resistance evaluated by binary survival status. Cross-validation showed that the prediction accuracy of ENGBLUP and GBLUP was 0.7347 and 0.4868, respectively, showing that ENGBLUP had a high prediction accuracy. It was shown that fitting QTL and polygenic effect with different distribution will improve genomic prediction accuracy for binary traits. In this study, an accurate and effective genomic selection method was proposed to predict the columnaris resistance in catfish, and its application should be beneficial to catfish breeding.

The antibiotic tiamulin (TIA) is common and widely used medication for dysentery eradication in swine productions. Tiamulin persists in livestock manure, and its residues have been found in various environment. This work obtained four tiamulin-degrading enriched bacterial consortia from a covered anaerobic lagoon system and a stabilized pond system of swine farms. Tiamulin was efficiently removed by the enriched cultures at the concentrations between 2.5 and 200 mg/L, with a removal of 60.1–99.9% during 16 h and a degradation half-life of 4.5–15.7 h. The stabilized pond system cultured with taimulin solely could eliminate tiamulin at the highest rates. The logistic substrate degradation model fit most of the experimental data. Next-generation amplicon sequencing was conducted, and it was found that the bacterial community was significantly impacted by the inoculum source, nutrient addition, and high tiamulin concentrations. Principal coordinate analysis (PCoA) indicated the similarity of bacterial communities in the original enriched samples and the 2.5 mg/L tiamulin-removed cultures. The 200 mg/L consortia were rather different and became similar to the other 200 mg/L consortia from different sources and cultures without nutrient supplementation. Shannon and Simpson indices suggested a reduction in bacterial diversity at high concentrations. The microbes that had high growth in the most efficient enriched culture, or which were abundant in all samples, or which increased with higher tiamulin concentrations were likely to be the major tiamulin-degrading bacteria. This is the first report suggested the possible roles of Achromobacter, Delftia, Flavobacterium, Pseudomonas, and Stenotrophomonas in tiamulin degradation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s40201-019-00426-2) contains supplementary material, which is available to authorized users.

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).

Tetrabromobisphenol A (TBBPA) is an emerging contaminant and exists widely in river and lake systems due to its widespread use. In natural water-sediment systems, hydrodynamic disturbances always exist. However, few studies have investigated the mechanism of TBBPA biodegradation under the influence of water disturbances. In this paper, using a specialized type of racetrack-style flumes, the TBBPA biodegradation in water-sediment systems was studied under the influence of three typical hydrodynamic disturbances. The results of 5-week experiments showed that strong hydrodynamic disturbances greatly accelerate the TBBPA biodegradation rate of the water-sediment systems. The half-lives (T1/2) under static condition (SC) were approximately 40.2 days, and the T1/2 was reduced to 16.0 days under strong hydrodynamic condition (SHC). Furthermore, the physicochemical properties and corresponding bacterial communities under these conditions were investigated to help explain the TBBPA biodegradation mechanism. The results showed that strong currents could promote dissolved oxygen (DO) levels, increase nutrient concentrations, and reduce the bacterial diversity in the sediment. Meanwhile, due to the increase in DO and nutrient concentrations, the aerobic bacterial genera conducting TBBPA biodegradation showed rapid growth with strong water disturbances, while the growth of anaerobic bacterial genera was inhibited. Citrobacter, which was the most dominant degrading bacterial genus (0.6%-14.9% in water and 3.5%-17.4% in sediment), was closely related to water disturbances and may be linked to enhanced TBBPA biodegradation. Other minor degrading bacterial genera, such as Bacillus, Sphingomonas, Anaeromyxobacter, Geobacter, Clostridium, and Flavobacterium, were also found in these water-sediment systems. The findings from this study showed the importance of considering hydrodynamic disturbance in understanding TBBPA biodegradation in aquatic environments.

Increasing evidence shows that static magnetic fields (SMFs) can affect microbial growth metabolism, but the specific mechanism is still unclear. In this study, we have investigated the effect of moderate-strength SMFs on growth and vitamin K2 biosynthesis of Flavobacterium sp. m1-14. First, we designed a series of different moderate-strength magnetic field intensities (0, 50, 100, 150, 190 mT) and exposure times (0, 24, 48, 72, 120 h). With the optimization of static magnetic field intensity and exposure time, biomass and vitamin K2 production significantly increased compared to control. The maximum vitamin K2 concentration and biomass were achieved when exposed to 100 mT SMF for 48 h; compared with the control group, they increased by 71.3% and 86.8%, respectively. Interestingly, it was found that both the cell viability and morphology changed significantly after SMF treatment. Second, the adenosine triphosphate (ATP) and glucose-6-phosphate dehydrogenase (G6PDH) metabolism is more vigorous after exposed to 100 mT SMF. This change affects the cell energy metabolism and fermentation behavior, and may partially explain the changes in bacterial biomass and vitamin K2 production. The results show that moderate-strength SMFs may be a promising method to promote bacterial growth and secondary metabolite synthesis.

The quality assessment of water, supplied to the end user, is an essential part to assess the physical, chemical, and biological status of water, which impacts on human health. For the quality assessment of drinking water treatment plants and distribution systems of Hyderabad City and Mehran University of Engineering and Technology, Jamshoro, Pakistan, 13 surface drinking water samples were collected from three treatment plants, two of Hyderabad City, including WASA treatment plant and its distribution system (n = 5), Hala Nakka treatment plant and its distribution system (n = 6), and Mehran University Employees Cooperative Housing Society (MUECHS) treatment plant and its distribution system (n = 2). Physicochemical parameters of all drinking water samples were in the range compared to EPA and WHO guidelines, except in L-12 sample. Notably, no free-chlorine was detected in all samples. In metagenomics analysis, targeting V3-V4 hypervariable region of 16S rRNA gene, in QIIME2 environment, high bacterial prevalence was observed in all samples. On average, 348 OTUs were observed per sample. Among all samples, treated water sample from the Hala Nakka Treatment Plant (HNTR) was the most diverse sample in bacterial composition (Shannon 7.51 and Simpsons reciprocal indices 0.98). Overall, Proteobacteria, Bacteroidetes, Cyanobacteria, Verrucomicrobia, and Actinobacteria were the five most abundant phyla (relative abundances of 43.6, 37.9, 8.5, 2.5, and 2.4 percent, respectively). Notably, Cyanobacteria are well-known toxin producers which effect the human, and animal health. At genus level, Flavobacterium (4.86%) and Aquirestis (3.77%) were the most abundant genera. Functional predictions, based on 16S rRNA gene by PICRUSt, predicted 6909 KEGG orthologies, relating to 245 KEGG pathways. Among the predicted pathways of KEGG orthologies, pathways to human infections were also found. In conclusion, this study gave a deep insight into bacterial contamination in drinking water samples of Hyderabad City and MUECHS treatment plants and water quality status in Hyderabad and Mehran University of Engineering and Technology.

Aeration strategy played an important role in reactor performance. In this study, when superficial upflow air velocity (SAV) decreased from 0.16 to 0.08 cm s−1, low dissolved oxygen concentration (DO) of 2.0 mg L−1 occurred in reactor. The required depth for anoxic microenvironment in biofilm decreased from 902.3 to 525.9 μm, which enhanced the growth of denitrifying bacteria and total nitrogen (TN) removal efficiency. However, decreasing aeration intensity resulted in insufficient hydraulic shear stress, which led to weak biofilm matrix structure. Mass biofilm detachment and reactor deterioration then occurred after 87 days of operation. An end gas recirculation aeration strategy was proposed to separately manipulate DO and aeration intensity. Low DO and high aeration intensity were simultaneously achieved, which enhanced the metabolism of denitrifying bacteria (such as Flavobacterium sp., Pseudorhodobacter sp., and Dok59 sp.) and EPS-producing bacteria (such as Zoogloea sp. and Rhodobacter sp.). Consequently, high TN removal performance (82.1 ± 2.7%) and stable biofilm structure were achieved.

Holistic approaches that simultaneously characterize responses of both microbial symbionts and their hosts to environmental shifts are imperative to understanding the role of microbiotas on host health. Using the northern leopard frog (Lithobates pipiens) as our model, we investigated the effects of a common trematode (family Echinostomatidae), a common agricultural antimicrobial (Sulfadimethoxine; SDM), and their interaction on amphibian skin microbiota and amphibian health (growth metrics and susceptibility to parasites). In the trematode-exposed individuals, we noted an increase in alpha diversity and a shift in microbial communities. In the SDM-treated individuals, we found a change in the composition of the skin microbiota similar to those induced by the trematode treatment. Groups treated with SDM, echinostomes, or a combination of SDM and echinostomes, had higher relative abundances of OTUs assigned to Flavobacterium and Acinetobacter. Both of these genera have been associated with infectious disease in amphibians and the production of anti-pathogen metabolites. Similar changes in microbial community composition between SDM and trematode exposed individuals may have resulted from stress-related disruption of host immunity. Despite changes in the microbiota, we found no effect of echinostomes and SDM on host health. Given the current disease- and pollution-related threats facing amphibians, our study highlights the need to continue to evaluate the influence of natural and anthropogenic stressors on host-associated microbial communities.

Increasing ocean temperatures associated with climate change have triggered the occurrence of diseases in marine resources such as macroalgae or seaweed. “Ice-ice” is one of the most devastating diseases affecting economically important seaweeds such as Gracilaria and Eucheuma. In this study, we investigate the bacterial composition of diseased and healthy Gracilaria verrucosa, a red seaweed cultured in brackish water ponds in Takalar, Indonesia. Morphologic and phenotypic characteristics showed that the isolates from diseased Gracilaria belong to various genera: Vibrio, Chromobacterium, Flavobacterium, Pseudomonas, and Achromobacter. Several bacteria were also isolated from healthy Gracilaria including Corynebacterium, Serratia, Shigella, Micrococcus, Proteus, and Flavobacterium. Using Koch’s postulates, bacterial pathogenicity was established by bath exposure of naive G. verrucosa to each of the bacteria isolated from diseased Gracilaria resulting in symptom characteristic of “ice-ice” disease. The antibacterial property of the green seaweed Caulerpa racemosa against the pathogenic bacteria was assessed using extracts that were prepared with solvents of various polarities such as hexane, chloroform, ethyl acetate, methanol, and methanol-water. The highest antibacterial activity was observed in methanol extracts Caulerpa while extracts using the other solvents showed moderate to low activities. These findings demonstrate the potential of Caulerpa to inactivate bacterial pathogens associated with “ice-ice” disease.

Strains YIM 102796T and YIM 102701-2T were isolated from the feces of Macaca mulatta and Hylobates hoolock, respectively, living in the Yunnan Wild Animal Park, Yunnan province of China. The two strains were Gram-stain-negative, non-gliding, produced flexirubin pigments, non-flagellated and aerobic bacteria. The 16S rRNA gene-based phylogenetic analysis indicate that both YIM 102796T and YIM 102701-2T are members of the genus Flavobacterium, closely related to F. ummariense DS-12T (95.9% similarity) and F. ceti 454-2T (93.8% similarity), respectively. The two strains shared 95.1 % 16S rRNA gene sequence similarity. The average nucleotide identity and digital DNA–DNA hybridization values between the two strains were 76.5% and 22.9%, respectively, indicating that they are separate species. DNA G+C contents of YIM 102796T and YIM 102701-2T were 32.3 mol% and 34.0 mol%, respectively. Strains are able to grow at 4–37 °C, at pH 7.0–8.0 and in 0–2% (w/v) NaCl. Predominant fatty acid constituents (>7 %) were iso-C15:0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 9 (iso-C17:1ω9c and/or 10-methylC16:0). Menaquinone 6 is major respiratory quinone. The predominant polar lipids were very similar to each other, comprising phosphatidylethanolamine, and multiple unknown aminolipids and unidentified polar lipids, and an unidentified aminophospholipid. On the basis of phenotypic and phylogenetic distinctiveness, it is suggested that the two strains represent two novel Flavobacterium species with strain YIM 102796T (=KCTC 52101T=CCTCC AB 2016015T) as the type strain of Flavobacterium viscosus sp. nov. and strain YIM 102701-2T (=KCTC 52100T=CCTCC AB 2016028T) as the type strain of Flavobacterium tangerina sp. nov.

Phosphorus (P) and potassium (K) are two important essential nutrient elements for plant growth and development but their availability is often limited in calcareous soils. The objective of this study was to determine the effects of applying microbial inoculants (MI, containing effective strains of Bacillus megaterium and Bacillus mucilaginous) on the availability of P and K, plant growth, and the bacterial community in calcareous soil. A greenhouse experiment was conducted to explore the effects of the addition of MI (control: without MI addition; treatment: with MI addition at the rate of 60 L ha−1) on the concentrations of P and K in soil and plant, soil bacterial community diversity and composition, and chili pepper (Capsicum annuum L.) growth. The results showed that MI inoculation significantly increased the fruit yields by 28.5% (p

Purpose Extracellular deoxyribonucleases (exDNases) from microbial origin contribute substantially to the restriction of extracellular DNA (exDNA) in the soil. Hence, it is imperative to understand the diversity of bacterial species capable of performing this important soil function and how crop species influence their dynamics in the soil. The present study investigates the occurrence of DNase-producing bacteria (DPB) in leachate samples obtained from soils in which the crop species of alfalfa (Medicago sativa L.), canola (Brassica napus L.), soybean (Glycine max [L.] Merr.) and wheat (Triticum aestivum L.) were raised in a growth room. Methods Selective media containing methyl green indicator was used to screen for DPB from leachate samples, whereas the 16S rRNA sequence analysis was employed to identify the isolates. Results The proportion of culturable DPB ranged between 5.72 and 40.01%; however, we did observe specific crop effects that shifted throughout the growing period. In general, higher proportions of exDNase producers were observed when the soils had lower nutrient levels. On using the 16S rRNA to classify the DPB isolates, most isolates were found to be members of the Bacillus genera, while other groups included Chryseobacterium, Fictibacillus, Flavobacterium, Microbacterium, Nubsella, Pseudomonas, Psychrobacillus, Rheinheimera, Serratia and Stenotrophomonas. Five candidate exDNase/nuclease-encoding proteins were also identified from Bacillus mycoides genomes using online databases. Conclusion Results from this study showed that crop species, growth stage and soil properties were important factors shaping the populations of DPB in leachate samples; however, soil properties seemed to have a greater influence on the trends observed on these bacterial populations. It may be possible to target soil indigenous bacteria that produce exDNases through management to decrease potential unintended effects of transgenes originating from genetically modified organisms (GMOs) or other introduced nucleic acid sequences in the environment.

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.

In the past, the potato plant microbiota and rhizosphere have been studied in detail to improve plant growth and fitness. However, less is known about the postharvest potato tuber microbiome and its role in storage stability. The storage stability of potatoes depends on genotype and storage conditions, but the soil in which tubers were grown could also play a role. To understand the ecology and functional role of the postharvest potato microbiota, we planted four potato varieties in five soil types and monitored them until the tubers started sprouting. During storage, the bacterial community of tubers was analysed by next-generation sequencing of the 16S rRNA gene amplicons. The potato tubers exhibited soil-dependent differences in sprouting behaviour. The statistical analysis revealed a strong shift of the tuber-associated bacterial community from harvest to dormancy break. By combining indicator species analysis and a correlation matrix, we predicted associations between members of the bacterial community and tuber sprouting behaviour. Based on this, we identified Flavobacterium sp. isolates, which were able to influence sprouting behaviour by inhibiting potato bud outgrowth.

In hospitals, Verona Integron-encoded Metallo-beta-lactamase (VIM)-positive Pseudomonas aeruginosa may colonize sink drains, and from there, be transmitted to patients. These hidden reservoirs are difficult to eradicate since P. aeruginosa forms biofilms that resist disinfection. However, little is known on the composition of these biofilms. Therefore, culturomics was used for the first time to investigate the viable microbiota in four hospital sink drain samples with longstanding VIM-positive P. aeruginosa drain reservoirs (inhabited by high-risk clone, sequence type ST111), and four drain samples where VIM-positive P. aeruginosa was not present. Microbial load and composition varied between samples, yielding between 471–18,904 distinct colonies and 8–20 genera. In two VIM-positive drain samples, P. aeruginosa was the most abundantly-isolated microorganism, and found in combination with other Gram-negative bacteria, Citrobacter, Enterobacter, or Stenotrophomonas. P. aeruginosa was in low abundance in the other two VIM-positive samples, and found with Gram-positive cocci (Enterococcus and Staphylococcus) or Sphingomonas. In VIM-negative drain samples, high abundances of Gram-negative non-fermenting bacteria, including Acinetobacter, non-aeruginosa Pseudomonas spp., Acidovorax, Chryseobacterium, Flavobacterium, and Sphingobium, as well as Candida, were cultured. Although additional experiments are needed to draw more firm conclusions on which microorganisms enable or inhibit VIM-positive P. aeruginosa persistence, our data provide unique insights into the microbial compositions of sink drain inlets.

The present paper aims to explore the rhizospheric bacterial communities associated with Saccharum arundinaceum grown on organometallic pollutants-rich hazardous distillery sludge. The sequence analysis of 16S rRNA V3–V4 hypervariable region with Illumina MiSeq platform showed 621,897 OTUs derived from rhizospheric and non-rhizospheric distillery sludge samples out of 1,191,014 and 901,757 sequences read, respectively. The major phyla detected in rhizospheric sludge sample were Proteobacteria (50%), Bacteriodetes (33%), Firmicutes (5%) Gemmatimonadetes (2%), Chloroflexi (2%), and Tenericutes (2%). The dominant three genera were detected as Rheinheimera (21%), Sphingobacterium (17%), and Idiomarina (8%). In addition, other minor genera such as uncultured Bacillus (4%), Acidothermus (4%), Bacillus (3%), Pseudomonas (2%), Flavobacterium (2%), uncultured bacterium (2%), Parapedobacter (2%), Alcanivorax (2%), Acholeplasma (2%), Hyphomonas (1%), and Aquamicrobium were also detected (1%) in rhizospheric sludge. Our results suggested that rhizospheric bacterial communities associated with S. arundinaceum were substantially different in richness, diversity, and relative abundance of taxa compared to non-rhizospheric sludge. Further, the comparative organic pollutant analysis from non-rhizospheric and rhizospheric sludge samples through GC–MS analysis revealed the disappearance of few compounds and generation of some compounds as new metabolic products by the activity of rhizospheric bacterial communities. The results of this study will be helpful in understanding the role of rhizospheric bacterial communities responsible for degradation and detoxification of complex organometallic waste and, thus, can help in designing appropriate phytoremediation studies for eco-restoration of polluted sites. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13205-020-02310-5) contains supplementary material, which is available to authorized users.

An aerobic, Gram-stain-negative, bright yellow-pigmented, oxidase and catalase-positive, non-motile, non-spore forming, rod-shaped strain designated DMN11T was isolated from the soil of crossroads of Jeju Island in South Korea. Colonies were circular, bright yellow-pigmented and smooth with regular edges and measured approximately 1–2 mm in diameter. Flexirubin-type pigments were absent. Phylogenetic tree analysis based on the 16SrRNA gene sequence revealed that the strain DMN11T formed a lineage within the family Flavobacteriaceae of the phylum Bacteroidetes, and it was the most closely related to Flavobacterium suzhouense XIN-1T and Flavobacterium hauense BX12T (98.6% and 98.2% similarity, respectively). The major isoprenoid quinone was MK-6. The major fatty acids were summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c), iso-C15:0 and iso-C15:0 3OH. The polar lipid profile of the strain DMN11T showed the presence of phosphatidylethanolamine (PE) as major lipid. The DNA G+C content was 35.3 mol%, as determined by the thermal denaturation method. The mean levels of DNA–DNA relatedness of the strain DMN11T with F. suzhouense XIN-1T and F. hauense BX12T were 20.5% and 29.2%, respectively. Thus, the data accumulated in this study support the suggestion that the strain DMN11T is considered to represent a novel species of the genus Flavobacterieum, for which the name Flavobacterium edaphi sp. nov. is proposed. The type strain is DMN11T (= KCTC 62114T = JCM 32372T).

Ubiquitous nature of prolamin proteins dubbed gluten from wheat and allied cereals imposes a major challenge in the treatment of celiac disease, an autoimmune disorder with no known treatment other than abstinence diet. Administration of hydrolytic glutenases as food supplement is an alternative to deliver the therapeutic agents directly to the small intestine, where sensitization of immune system and downstream reactions takes place. The aim of the present research was to evaluate the capacity of wheat grain to express and store hydrolytic enzymes capable of gluten detoxification. For this purpose, wheat scutellar calli were biolistically transformed to generate plants expressing a combination of glutenase genes for prolamin detoxification. Digestion of prolamins with barley endoprotease B2 (EP-HvB2) combined with Flavobacterium meningosepticum prolyl endopeptidase (PE-FmPep) or Pyrococcus furiosus prolyl endopeptidase (PE-PfuPep), significantly reduced (up to 67%) the amount of the indigestible gluten peptides of all prolamin families tested. Seven of the 168 generated lines showed inheritance of transgene to the T(2) generation. Reversed phase high performance liquid chromatography of gluten extracts under simulated gastrointestinal conditions allowed the identification of five T(2) lines that contained significantly reduced amounts of immunogenic, celiac disease-provoking gliadin peptides. These findings were complemented by the R5 ELISA test results where up to 72% reduction was observed in the content of immunogenic peptides. The developed wheat genotypes open new horizons for treating celiac disease by an intraluminal enzyme therapy without compromising their agronomical performance.

Carbohydrates are the product of carbon dioxide fixation by algae in the ocean. Their polysaccharides are depolymerized by marine bacteria, with a vast array of carbohydrate-active enzymes. These enzymes are important tools to establish biotechnological processes based on algal biomass. Green tides, which cover coastal areas with huge amounts of algae from the genus Ulva, represent a globally rising problem, but also an opportunity because their biomass could be used in biorefinery processes. One major component of their cell walls is the anionic polysaccharide ulvan for which the enzymatic depolymerization remains largely unknown. Ulvan lyases catalyze the initial depolymerization step of this polysaccharide, but only a few of these enzymes have been described. Here, we report the cloning, overexpression, purification, and detailed biochemical characterization of the endolytic ulvan lyase from Formosa agariphila KMM 3901T which is a member of the polysaccharide lyase family PL28. The identified biochemical parameters of the ulvan lyase reflect adaptation to the temperate ocean where the bacterium was isolated from a macroalgal surface. The NaCl concentration has a high influence on the turnover number of the enzyme and the affinity to ulvan. Divalent cations were shown to be essential for enzyme activity with Ca2+ likely being the native cofactor of the ulvan lyase. This study contributes to the understanding of ulvan lyases, which will be useful for future biorefinery applications of the abundant marine polysaccharide ulvan.

A novel bacterium designated S-42T was isolated from stream bank soil. Cells were found to be aerobic, Gram staining-negative, oxidase-positive, catalase-negative, non-motile, non-spore-forming, rod-shaped, and yellow-pigmented. The strain can grow at 15–35 °C, pH 6.0–10.0, and at 0.5% (w/v) NaCl concentration. Urea was hydrolysed. Flexirubin-type pigments were absent. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain S-42T formed a lineage within the family Flavobacteriaceae of the phylum Bacteroidetes that is distinct from various species of the genus Flavobacterium, including Flavobacterium maotaiense T9T (97.6% sequence similarity), Flavobacterium hibernum ATCC 51468T (97.4%), and Flavobacterium granuli Kw05T (97.1%). The 16S rRNA gene sequences identity between strain S-42T and other members of the genus Flavobacterium were < 97.0%. Strain S-42T contains MK-6 as sole respiratory quinone. The major polar lipids were identified as phosphatidylethanolamine and an unidentified aminolipid. The major cellular fatty acids were identified as iso-C15:0, summed feature 3 (C16:1ω7c and/or C16: 1ω6c), C16:0, anteiso-C15:0, iso-C17:0 3-OH, iso-C15:0 3-OH, and iso-C15:1 G. The DNA G + C content of the strain was 35.8 mol%. The polyphasic characterization indicated that strain S-42T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium ureilyticum sp. nov. is proposed. The type strain is S-42T (= KEMB 9005-537T = KACC 19115T = NBRC 112683T).

A novel, aerobic, Gram-stain-negative, non-motile, non-spore forming, rod-shaped bacterium, designated strain Dol 15-39T, was isolated from a seawater sample near Geoje Island in the South Sea, Republic of Korea. The strain was found to be oxidase-negative and catalase-positive. The isolate was observed to grow at temperatures from 4 to 37°C, at salinities of up to 7%, and at pH levels from 6 to 9; moreover, it was not able to degrade starch, DNA, esculin, or tyrosine. Phylogenetic analysis based on 16S rRNA gene sequences showed that Dol 15-39T was most closely related to Flavobacterium jumunjinense HME7102T with a sequence similarity of 97.3%. However, the levels of DNA-DNA relatedness between Dol 15-39T and the most closely related species were much lower than 70%, confirming that they represented distinct genomic species. The genomic DNA G + C content of Dol 15-39T was calculated to be 32.6 mol%. MK-6 was the predominant respiratory quinine, while iso-C15:0 (25.0%), iso-C15:1 G (17.0%), and iso-C17:0 3-OH (10.4%) were the major cellular fatty acids. Phosphatidylethanolamine was identified as a major polar lipid, while various unidentified aminolipids and polar lipids were also detected. Based on polyphasic taxonomic data, Dol 15-39T represents a novel species of the genus Flavobacterium, for which the name F. aquimarinum sp. nov. is proposed. The type strain is accessible under the culture collection numbers (KEMB 9005-617T = JCM 31930T).

In an effort to determine genus- or species-level taxonomic profiles and diversity of bacterial consortia in the Tama River around urban Tokyo, next-generation sequencing technology targeting a 16S ribosomal RNA (rRNA) gene amplicon was employed. Metagenomic analysis performed by an Ion Personal Genome Machine after sequentially filtering samples through 5-, 0.8- and 0.2-μm filters yielded 1.48 Gb of 16S sequences (average 2.38 M reads/sample). The results indicated that half of the bacterial sequences belonged to Proteobacteria, followed by Bacteroidetes, Actinobacteria and Cyanobacteria. Flavobacterium (Bacteroidetes), possibly including a potential fish pathogen, was the most numerous genera in the Tama River metagenome, and accounted for ~ 16% of assigned 16S reads, followed by Mycobacterium. Other dominant bacterial genera including Zoogloea, Sediminibacterium, Hyphomicrobium, Sphingopyxis, Thiothrix and Lysobacter, were thought to be associated with waste water and sludge. MiSeq metagenomic analysis revealed that environmental factors, particularly water temperature, influenced the bacterial composition throughout the year, with a strong negative correlation observed for Proteobacteria and a positive correlation for Bacteroidetes. In terms of bacterial genera, Flavobacterium was positively correlated with temperature, while Polaromonas, Pseudomonas and Bradyrhizobium were negatively correlated with this, suggesting dynamic change in the free-living bacterial population throughout the year and versatile adaptation strategies in relation to environmental factors.

Mangroves represent a special coastal vegetation along the coastlines of tropical and subtropical regions. Sulfonamide antibiotics (SAs) are the most commonly used antibiotics. The application of white-rot fungi extracellular enzyme-containing microcapsules (MC) for aerobic degradation of SAs in mangrove sediments was investigated in this study. Degradation of three SAs, sulfamethoxazole (SMX), sulfadimethoxine (SDM), and sulfamethazine (SMZ), was enhanced by adding MC to the sediments. The order of SA degradation in batch experiments was SMX > SDM > SMZ. Bioreactor experiments revealed that SA removal rates were higher with than without MC. The enhanced SA removal rates with MC persisted with three re-additions of SAs. Thirteen bacteria genera (Achromobacter, Acinetobacter, Alcaligenes, Aquamicrobium, Arthrobacter, Brevundimonas, Flavobacterium, Methylobacterium, Microbacterium, Oligotropha, Paracoccus, Pseudomonas, and Rhodococcus) were identified to be associated with SA degradation in mangrove sediments by combination of next-generation sequencing, bacterial strain isolation, and literature search results. Results of this study suggest that MC could be used for SA removal in mangrove sediments.

This research aimed to investigate the seasonal variations and antibacterial activities of essential oils (EOs) and their major components from bamboo leaves. The Phyllostachys heterocycla cv. Pubescens leaves have undergone steam distillation to prepare EOs; leaves collected in autumn had the highest amount of EOs (0.33%). Chemical characterization by gas chromatography/mass spectrometry (GC/MS) allowed the identification of 36 compounds. The major compounds (%) were ketones (52.25), alcohols (17.79), carboxylic acids (9.41) and alkane hydrocarbons (7.68), which included 6, 5, 7 and 9 distinct compounds, respectively. Antibacterial activities were registered against Gram-negative bacteria [Escherichia coli (minimum inhibitory concentration [MIC] = 2.25 mg/mL)], Gram-positive bacteria [Bacillus subtilis (MIC = 2.25 mg/mL)] and Saccharomyces cerevisiae. The antibacterial effect of the three major monomeric compounds (tricosane, cedrol and hexadecanoic acid) in bamboo leaf EOs and their mixtures was studied. We showed for the first time that tricosane had antimicrobial activity. We found that cedrol had the strongest antibacterial effect, followed by hexadecanoic acid. Cedrol at 5 mg/mL had the largest inhibition zones of up to 14.93 mm against Flavobacterium SHL45. The antimicrobial effect of the equal mixture ratio of the three monomers was higher than that when tricosane and hexadecanoic acid were tested alone, and was also higher than that of the combination of any two of them.

Ticks are among the most significant human-biting ectoparasites and they play a major role in transmission of many pathogenic agents to humans. In the present study, three species of Hyalomma ticks, Hyalomma aegyptium, H. marginatum and H. excavatum, were examined for the presence of zoonotic bacteria, both male and female ticks alike. Examination of microbial diversity with tag-encoded pyrosequencing indicates that H. marginatum and H. excavatum were more diversity rich than H. aegyptium. Although numerous pathogenic and non-pathogenic bacterial genera were detected, including Acidovorax, Bacillus, Bacteroides, Bdellovibrio, Clostridium, Curvibacter, Escherichia, Flavobacterium, Limnohabitans, Paenibacillus, Ralstonia, Sarcina, Sediminibacterium, Segetibacter Stenotrophomonas and Variovorax, the predominant zoonotic bacteria represented in these ticks were genera Borrelia, Francisella, and Rickettsia. To the authors' knowledge, this work represents the first detection of Yersinia enterocolitica in the tick H. excavatum, raising questions regarding the vector competency of this tick, as well as associations of different disease representations perhaps through previously unforeseen routes of pathogen introduction. Likewise, similar questions are related to the presence of Legionella pneumophila in one H. excavatum sample.

Gut microbiota are integral to the host, and have received increased attention in recent years. However, information regarding the intestinal microbiota of many aquaculture animals is insufficient; elucidating the dynamics of the intestinal microbiota can be beneficial for nutrition, immunity, and disease control. In this study, we used 16S rRNA sequencing to observe changes in the intestinal microbiota of gibel carp (Carassius auratus gibelio) associated with cyprinid herpesvirus 2 (CyHV-2) infection. Our results indicate that the diversity of the intestinal microbiota was strongly reduced, and the composition was dramatically altered following CyHV-2 infection. The most dominant species in healthy fish were Cetobacterium, Rhodobacter, and Crenothrix; meanwhile, Cetobacterium, Plesiomonas, Bacteroides, and Flavobacterium were the most abundant species in sick fish. Plesiomonas was highly abundant in infected samples, and could be used as a microbial biomarker for CyHV-2 infection. Chemical properties of the aquaculture water were significantly correlated with the microbial community structure; however, it is difficult to determine whether these changes are a cause or consequence of infection. However, it may be possible to use probiotics or prebiotics to restore the richness of the host intestinal microbiota in infected animals to maintain host health.

Drinking water disinfection plays a critical role in protecting humans from waterborne pathogens. Ferrate(VI) (FeVIO4 2−) has also been proposed as a disinfectant. This is the first study investigating the bacterial microbiomes of ferrate(VI)-treated water compared to chlorinated water. Tested water was collected after sand filtration and before disinfection from a drinking water treatment plant at Jiaxing, Zhejiang Province, China. A culture-independent method utilizing propidium monoazide was used with quantitative polymerase chain reaction and pyrosequencing of 16S rRNA genes to distinguish between the viable and nonviable bacterial populations. The operational taxonomic units and α-diversity indexes of the live bacterial phylotypes in the samples were determined. Viable bacteria remained in all samples following chlorination or ferrate treatment. However, the genera Vibrio, Salmonella, Shigella, Escherichia, Campylobacter, Yersinia, Plesiomonas, Legionella, and Helicobacter, which contain important human pathogens, were not present among the 25 dominant genera seen in these samples. The profiles of the bacteria remaining after treatment with either chlorine or ferrate differed. The ferrate-treated samples showed a reduced percent relative abundance of operational taxonomic units of the class Alphaproteobacteria within the total remaining viable bacteria. The genera Flavobacterium and Duganella were relatively resistant to treatment by either chlorine or ferrate(VI). At the highest doses of chlorine and ferrate(VI), the genus Sphingobium represented a greater percentage of live bacteria in the chlorinated sample than in the ferrate(VI)-treated sample. The results suggest that ferrate(VI) and chlorine could inactivate slightly different sets of bacteria and could have different mechanisms of bacterial inactivation.

Bacteria in the genus Polaribacter, belonging to the family Flavobacteriaceae, are typically isolated from marine environments. Polaribacter dokdonensis DSW-5, the type strain of the species, is a Gram-negative bacterium isolated from the East Sea of Korea. Whole genome shotgun sequencing was performed with the HiSeq 2000 platform and paired-end reads were generated at 188-fold coverage. The sequencing reads were assembled into two contigs with a total length of 3.08 Mb. The genome sequences of DSW-5 contain 2,776 proteincoding sequences and 41 RNA genes. Comparison of average nucleotide identities among six available Polaribacteria genomes including DSW-5 suggested that the DSW-5 genome is most similar to that of Polaribacter sp. MED152, which is a proteorhodopsin-containing marine bacterium. A phylogenomic analysis of the six Polaribacter strains and 245 Flavobacteriaceae bacteria confirmed a close relationship of the genus Polaribacter with Tenacibaculum and Kordia. DSW-5's genome has a gene encoding proteorhodopsin and genes encoding 85 enzymes belonging to carbohydrate-active enzyme families and involved in polysaccharide degradation, which may play important roles in energy metabolism of the bacterium in the marine ecosystem. With genes for 238 CAZymes and 203 peptidases, DSW-5 has a relatively high number of degrading enzymes for its genome size suggesting its characteristics as a free-living marine heterotroph.

Ultraviolet (UV) light irradiation has serious consequences for cell survival, including DNA damage by formation of cyclobutane pyrimidine dimers (CPD) and pyrimidine (6,4) pyrimidone photoproducts. In general, the Nucleotide Excision Repair pathway repairs these lesions; however, all living forms, except placental mammals and some marsupials, produce a flavoprotein known as photolyase that directly reverses these lesions. The aim of this work was the isolation and identification of Antarctic UVC-resistant bacteria, and the search for novel photolyases. Two Antarctic water samples were UVC-irradiated (254 nm; 50–200 J m− 2) and 12 UVC-resistant bacteria were isolated and identified by 16S rDNA amplification/analysis as members of the genera Pseudomonas, Janthinobacterium, Flavobacterium, Hymenobacter and Sphingomonas. The UVC 50% lethal dose and the photo-repair ability of isolates were analyzed. The occurrence of photolyase coding sequences in Pseudomonas, Hymenobacter and Sphingomonas isolates were searched by PCR or by searching in the draft DNA genome. Results suggest that Pseudomonas and Hymenobacter isolates produce CDP-photolyases, and Sphingomonas produces two CPD-photolyases and a 6,4-photolyase. Results suggest that the Antarctic environment is an important source of genetic material for the identification of novel photolyase genes with potential biotechnological applications.

The fungicide carbendazim is an ecotoxic agent affecting aquatic biota. Due to its suspected hormone-disrupting effects, it is considered a "priority hazard substance" by the Water Framework Directive of the European Commission, and its degradation is of major concern. In this work, a horizontal tubular biofilm reactor (HTBR) operating in plug-flow regime was used to study the kinetics of carbendazim removal by an acclimated microbial consortium. The reactor was operated in steady state continuous culture at eight different carbendazim loading rates. The concentrations of the fungicide were determined at several distances of the HTBR. At the loading rates tested, the highest instantaneous removal rates were observed in the first section of the tubular biofilm reactor. No evidence of inhibition of the catabolic activity of the microbial community was found. Strains of the genera Flectobacillus, Klebsiella, Stenotrophomonas, and Flavobacterium were identified in the biofilm; the last three degrade carbendazim in axenic culture.

This study presents taxonomic description of two novel diesel-degrading, psychrophilic strains: Kopri-42T and Kopri-43, isolated during screening of oil-degrading psychrotrophs from oil-contaminated Arctic soil. A preliminary 16S rRNA gene sequence and phylogenetic tree analysis indicated that these Arctic strains belonged to the genus Flavobacterium, with the nearest relative being Flavobacterium psychrolimnae LMG 22018T (98.9% sequence similarity). The pairwise 16S rRNA gene sequence identity between strains Kopri-42T and Kopri-43 was 99.7%. The DNA-DNA hybridization value between strain Kopri-42T and Kopri-43 was 88.6 ± 2.1% indicating that Kopri-42T and Kopri-43 represents two strains of the same genomospecies. The average nucleotide identity and in silico DNA-DNA hybridization values between strain Kopri-42T and nearest relative F. psychrolimnae LMG 22018T were 92.4% and 47.9%, respectively. These values support the authenticity of the novel species and confirmed the strain Kopri-42T belonged to the genus Flavobacterium as a new member. The morphological, physiological, biochemical and chemotaxonomic data also distinguished strain Kopri-42T from its closest phylogenetic neighbors. Based on the polyphasic data, strains Kopri-42T and Kopri-43 represents a single novel species of the genus Flavobacterium, for which the name Flavobacterium petrolei sp. nov. is proposed. The type strain is Kopri-42T (=KEMB 9005-710T = KACC 19625T = NBRC 113374T).

The genus Sappinia comprises free-living amoebae occurring worldwide in a variety of habitats such as soils, plant matter and freshwater ponds, but also animal faeces, and includes at present three species, S. pedata, S. diploidea and S. platani. The genus is potentially pathogenic, as indicated by the identification of S. pedata in a case of human amoebic encephalitis. Electron microscopy studies on some strains already revealed intracellular bacteria in Sappinia. In the current study, we performed 16S ribosomal RNA gene (rDNA) analysis of these bacterial endosymbionts. We first inferred relationships among Sappinia strains on the basis of 18S rDNA, demonstrating that S. pedata emerged as sister to a larger clade including S. diploidea, S. platani and a few 'S. diploidea-like' strains. Thus, bacterial 16S rDNA was searched for in representative strains of each Sappinia species/subgroup. We found that Sappinia strains were associated to distinct species of Flavobacterium or Pedobacter (phylum Bacteroidetes). These appear to be distributed following the amoebal host subgroups, and are not directly related to other Bacteroidetes species known as interacting with free-living amoebae. While all the endosymbionts' close relatives are known to grow on agar, bacteriological media inoculated with amoebal extracts remained negative. Overall, results indicate that the recovered bacteria are likely specific obligate endosymbionts of Sappinia species. Further studies, including additional amoebal strains and deep morphological and molecular analyses, will be necessary to confirm this hypothesis.

The oligochaete Grania sp. is a common inhabitant of Artigas Beach at Maxwell Bay (King George Island, South Shetland Islands, Maritime Antarctica) that proliferate during the summer season and feed on debris of red and brown algae. This investigation was undertaken to test the hypothesis that Grania sp. has an enzyme-producing microbiota that may facilitate the worm’s nutrient uptake by processing or metabolizing macroalgae compounds. A culture-based approach was used to investigate the occurrence of microorganisms able to degrade proteins, lipids and polysaccharides. Thirty-four hydrolytic enzyme-producing microorganisms associated with these worms, including bacteria and yeasts, were isolated and identified by sequencing a partial fragment of the 16S and 26S rDNA genes, respectively. These microorganisms have the ability to produce extracellular proteases, esterases, amylases, cellulases and agarases. The microbial genera found during this work (Flavobacterium, Pseudomonas, Salinibacterium, Psychrobacter, Cystobasidium and Rhodotorula) have been previously described in association with red and brown Antarctic algae. Our results suggest that this microbiome has a digestive capability that may assist Grania sp. in metabolizing nutrients from algae, leading us to consider the possibility of a mutualistic relationship between them. The association between the worm Grania sp. and a cold-active hydrolyzing microbiota may contribute to the macroalgae decomposition and nutrient recycling in the Antarctic ecosystem.

A novel bacterial strain, designated DCY106(T), was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY106(T) is Gram-negative, yellow-pigmented, non-flagellate, motile, non-spore-forming, rod-shaped, and strictly aerobic. The strain grows optimally at 25-30 °C and pH 6.5-7.5. Phylogenetically, strain DCY106(T) is closely related to Flavobacterium arsenitoxidans KCTC 22507(T) (98.41 %), followed by Flavobacterium cutihirudini LMG 26922(T) (97.67 %), Flavobacterium nitrogenifigens LMG 28694(T) (97.59 %), Flexibacter auranticus LMG 3987(T) (97.38 %), Flavobacterium defluvi KCTC 12612(T) (97.21 %) and Flavobacterium chilense LMG 26360(T) (97.05 %). The 16S rRNA gene sequence similarities to all other Flavobacterium species were below 97 %. The DNA G+C content of strain DCY106(T) is 34.2 mol% and the DNA-DNA relatedness between strain DCY106(T) and F. cutihirudini LMG 26922(T), F. auranticus LMG 3987(T), F. defluvi KCTC 12612(T) and F. chilense LMG 26360(T) were below 40.0 %. The menaquinone of the type MK-6 was found to be the predominant respiratory quinone. The major polar lipids were identified as phosphatidylethanolamine, phosphatidylserine, two unidentified aminolipids (APL1, APL6) and one unidentified lipid L2. C15:0, iso-C15:0 and summed feature 3 (iso-C15:0 2OH/C16:1 ω7c) were identified as the major fatty acids present in DCY106(T). The results of physiological and biochemical tests allowed strain DCY106(T) to be differentiated phenotypically from other recognized species belonging to the genus Flavobacterium. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Flavobacterium panacis sp. nov. is proposed with the type strain designated as DCY106(T) (= JCM 31468(T)= KCTC 42747(T)).

Environmentally transmitted opportunistic pathogens shuttle between two substantially different environments: outside-host and within-host habitats. These environments differ from each other especially with respect to nutrient availability. Consequently, the pathogens are required to regulate their behavior in response to environmental cues in order to survive, but how nutrients control the virulence in opportunistic pathogens is still poorly understood. In this study, we examined how nutrient level in the outside-host environment affects the gene expression of putative virulence factors of the opportunistic fish pathogen Flavobacterium columnare. The impact of environmental nutrient concentration on bacterial virulence was explored by cultivating the bacteria in various nutrient conditions, measuring the gene expression of putative virulence factors with RT-qPCR and, finally, experimentally challenging rainbow trout (Oncorhynchus mykiss) fry with these bacteria. Our results show that increased environmental nutrient concentration can increase the expression of putative virulence genes, chondroitinase (cslA) and collagenase, in the outside-host environment and may lead to more rapid fish mortality. These findings address that the environmental nutrients may act as significant triggers of virulence gene expression and therefore contribute to the interaction between an environmentally transmitted opportunistic pathogen and its host. peerReviewed

A novel bacterial strain, designated DCY70(T), was isolated from soil of a ginseng field in Republic of Korea and was characterized in order to determine its taxonomic position. The strain was Gram-reaction negative, yellow-pigmented, rod-shaped and catalase- and oxidase-positive. Based on the 16S rRNA gene sequence similarity, strain DCY70(T) was shown to belong to the genus Flavobacterium, most closely related to Flavobacterium oncorhynchi 631-08(T) (98.4 %), Flavobacterium plurextorum 1126-1H-08(T) (97.9 %), Flavobacterium chilense LM-09-Fp(T) (97.9 %) and Flavobacterium chungangense CJ(T) (97.7 %). The chemotaxonomic characteristics showed only menaquinone-6 (MK-6), iso-C15:0, iso-C15:0 3OH, iso-C17:0 3OH and summed feature 3 as major cellular fatty acids. Polar lipids were phosphatidylethanolamine (PE), two unidentified aminolipids, four unidentified polar lipids and one unidentified phospholipid. The DNA G+C content was 34.9 mol%. Based on the phylogenetic, phenotypic and genotypic data, a novel species, Flavobacterium panacisoli sp. nov., is proposed (=KCTC 32393(T) = JCM 19162(T)).

Background Environmentally growing pathogens present an increasing threat for human health, wildlife and food production. Treating the hosts with antibiotics or parasitic bacteriophages fail to eliminate diseases that grow also in the outside-host environment. However, bacteriophages could be utilized to suppress the pathogen population sizes in the outside-host environment in order to prevent disease outbreaks. Here, we introduce a novel epidemiological model to assess how the phage infections of the bacterial pathogens affect epidemiological dynamics of the environmentally growing pathogens. We assess whether the phage therapy in the outside-host environment could be utilized as a biological control method against these diseases. We also consider how phage-resistant competitors affect the outcome, a common problem in phage therapy. The models give predictions for the scenarios where the outside-host phage therapy will work and where it will fail to control the disease. Parameterization of the model is based on the fish columnaris disease that causes significant economic losses to aquaculture worldwide. However, the model is also suitable for other environmentally growing bacterial diseases. Results Transmission rates of the phage determine the success of infectious disease control, with high-transmission phage enabling the recovery of the host population that would in the absence of the phage go asymptotically extinct due to the disease. In the presence of outside-host bacterial competition between the pathogen and phage-resistant strain, the trade-off between the pathogen infectivity and the phage resistance determines phage therapy outcome from stable coexistence to local host extinction. Conclusions We propose that the success of phage therapy strongly depends on the underlying biology, such as the strength of trade-off between the pathogen infectivity and the phage-resistance, as well as on the rate that the phages infect the bacteria. Our results indicate that phage therapy can fail if there are phage-resistant bacteria and the trade-off between pathogen infectivity and phage resistance does not completely inhibit the pathogen infectivity. Also, the rate that the phages infect the bacteria should be sufficiently high for phage-therapy to succeed. Electronic supplementary material The online version of this article (10.1186/s12976-018-0079-8) contains supplementary material, which is available to authorized users.

Paracetamol, the most widely and globally used analgesic and antipyretic, is easily accumulated in aquatic environments. In the present study, the biodegradation of paracetamol in different media (one for general growth, one specific for sulfate reducing bacteria, a mineral salts medium and municipal wastewater) inoculated with two types of sludge (from anaerobic lagoon and from oxidation ditch) under different oxygenic conditions (anoxic; moderate oxygenation in open flasks and high oxygenation by aeration) was investigated. In addition, bacteria with relative abundances increasing simultaneously with paracetamol degradation, when this drug was the only carbon source, thus with a putative role in its degradation, were identified using 16S rRNA gene sequences. The results show that aerobic microorganisms had a major role in the degradation of paracetamol, with 50 mg/L totally removed from municipal wastewater after 2 days incubation with aeration, and that the metabolites 4-aminophenol and hydroquinone plus one compound not identified in this work were produced in the process. The identification of bacteria with a role in the degradation of paracetamol revealed a strain from genus Pseudomonas with the highest final relative abundance of 21.2%, confirming previous works reporting strains of this genus as paracetamol decomposers. Besides, genera Flavobacterium, Dokdonella and Methylophilus were also in evidence, with initial relative abundances of 1.66%, 1.48 and 0.00% (not detected) in the inoculum and 6.91%, 3.80 and 3.83% after incubation, respectively. Therefore, a putative role of these genera in paracetamol biodegradation is suggested for the first time. Erasmus Mundus Master in Chemical Innovation and Regulations (EMMC-ChIR) of Donaldben Mbagag NEBA by the Erasmus Mundus program of the European Commission info:eu-repo/semantics/publishedVersion

Gut microbiota plays a crucial importance in their host. Disturbance of the microbial structure and function is known to be associated with inflammatory intestinal disorders. Enteritis is a significant cause of high mortality in fish species, including grass carp (Ctenopharyngodon idellus). Study regarding the association between microbial alternations and enteritis in grass carp is still absent. In this study, changes in the gut microbiota of grass carp suffering from enteritis were investigated using NGS-based 16S rRNA sequencing. Six healthy and ten abnormal fish (showing reddening anus, red odiferous fluid accumulating in the abdominal capacity, and flatulence and haemorrhage in the intestine) were collected from a fish farm in Huanggang Fisheries Institute (Hubei, China). Our results revealed that the diversity, structure, and function of gut microbiota were significantly different between diseased and healthy fish (P

The succession of bacterial microbiota in tilapia fillets during cold storage at 4 °C was investigated employing PCR-DGGE method. Results showed that Pseudomonas was the most dominant genus during entire storage period. Shewanella and Psychrobacter were also always present, but became dominant only after 3 days of storage. Acinetobacter, Brevibacterium, Flavobacterium, Dietzia and Janthinobacterium were always the minor genera, among which Acinetobacter and Brevibacterium disappeared 6 days later, and Dietzia and Janthinobacterium only appeared at the end of storage. Further, the potential spoiler(s) of tilapia fillets at 4 °C were investigated in situ. The spoilage ability of a specific group of bacteria was evaluated as follows: Certain preservatives were selectively added to fillets to inhibit a specific group of bacteria, and then the changes in spoilage degree of fillets were determined. In this way the spoilage ability of the inhibited bacteria was evaluated. Our experiments showed that protamine strongly inhibited Pseudomonas but rarely inhibited Psychrobacter, Acinetobacter and Brevibacterium, but garlic juice, on the contrary, strongly inhibited the latter three but rarely inhibited the former. The mixed preservative, which consisted of protamine and garlic juice, didn't play better than protamine alone in preventing the spoilage of fillets. This indicated that Psychrobacter, Acinetobacter and Brevibacterium contribute little to the spoilage of tilapia fillets.

A bacterial strain, designated EC11(T) was isolated from brown alga Ecklonia cava collected from Jeju Island, Korea. EC11(T) was identified as a Gram-negative, rod-shaped and yellow-pigmented bacterial strain. The strain EC11(T) grew over a temperature range of 10 °C to 30 °C (optimally at 25 °C), and a pH range of 6.0-10.5 (optimally at pH 7.5). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EC11(T) belongs to the genus Flavobacterium. Strain EC11(T) shared close similarity with Flavobacterium jumunjinense HME7102(T) (96.4%), Flavobacterium dongtanense LW30(T) (95.8%), Flavobacterium haoranii LQY-7(T) (95.3%), and Flavobacterium urocaniciphilum (95.1%). The major fatty acids (> 5%) were iso-C17:0 3-OH (22.4%), iso-C15:0 3-OH (19.0%), C15:0 (12.4%), summed feature 3 (comprising C16:1 ω7c/ C16:1 ω6c; 9.78%), iso-C15:1 G (9.6%), and iso-C16:0 3-OH (9.0%). The DNA G+C content was 28.1 mol% and the strain contained MK-6 as the predominant menaquinone. The major polar lipids were phosphatidylethanolamine, two unknown aminolipids and three unknown polar lipids. Based on phenotypic, chemotaxonomic and phylogenetic analysis, strain EC11T represents a novel species of the Flavobacterium genus, for which the name Flavobacterium jejuensis sp. nov. is proposed. The type strain of F. jejuensis is EC11(T) (=KCTC 42149(T) = JCM 30735(T)).