Genus Chryseobacterium Research Articles

Dynamic succession of the quantity and composition of epiphytic microorganisms at different growth stages on rice surface

The quality of silage is uneven, which is due to the difference of epiphytic microorganisms of raw materials. To improve the quality of fermentation, the quantity and composition of epiphytic microorganisms are usually analyzed to better prepare silage. In this research, plate coating method and 16S high-throughput sequencing were used to analyze the differences in the quantity and composition of rice epiphytic microorganisms during different growth stages. The Lactic acid bacteria (LAB) and aerobic bacteria were the highest at the flowering stage, the yeast was the highest at the milk ripening stage, and the mould was the highest at the full ripening stage. And the growth stage also had a great influence on the composition of epiphytic bacterial community, at the phylum level, it was mainly composed of Proteobacteria. And at the genus level, Pantoea, Acinetobacter, Pseudomonas and Chryseobacterium were dominanted at the flowering stage; Pantoea, Stenotrophomonas and Sphingobacterium were dominanted at the milk ripening stage; Acinetobacter, Pantoea, Chryseobacterium and Lactococcus were dominanted at the dough stage; Acinetobacter and Klebsiella were dominated at the full ripening stage. Overall, the growth stage significantly affected the quantity and composition of rice epiphytic microorganisms. Therefore, rice silage can be modulated reasonably according to the number and composition of epiphytic microorganisms in different growth stages.

The impact of benzoic acid and lactic acid on the treatment efficiency and microbial community in the sulfur autotrophic denitrification process.

Nitrate poses a potential threat to aquatic ecosystems. This study focuses on the sulfur autotrophic denitrification mechanism in the process of water culture wastewater treatment, which has been successfully applied to the degradation of nitrogen in water culture farm effluents. However, the coexistence of organic acids in the treatment process is a common environmental challenge, significantly affecting the activity of denitrifying bacteria. This paper aims to explore the effects of adding benzoic acid and lactic acid on denitrification performance, organic acid removal rate, and microbial population abundance in sulfur autotrophic denitrification systems under optimal operating conditions, sulfur deficiency, and high hydraulic load. In experiments with 50 mg·L-1 of benzoic acid or lactic acid alone, the results show that benzoic acid and lactic acid have a stimulating effect on denitrification activity, with the stimulating effect significantly greater than the inhibitory effect. Under optimal operating conditions, the average denitrification rate of the system remained above 99%; under S/N = 1.5 conditions, the average denitrification rate increased from 88.34% to 91.93% and 85.91%; under HRT = 6h conditions, the average denitrification rate increased from 75.25% to 97.79% and 96.58%. In addition, the addition of organic acids led to a decrease in microbial population abundance. At the phylum level, Proteobacteria has always been the dominant bacterial genus, and its relative abundance significantly increased after the addition of benzoic acid, from 40.2% to 61.5% and 62.4%. At the genus level, Thiobacillus, Sulfurimonas, Chryseobacterium, and Thermomonas maintained high population abundances under different conditions. PRACTITIONER POINTS: Employing autotrophic denitrification process for treating high-nitrate wastewater. Utilizing organic acids as external carbon sources. Denitrifying bacteria demonstrate high utilization efficiency towards organic acids. Organic acids promote denitrification more than they inhibit it. The promotion is manifested in the enhancement of activity and microbial abundance.

Chryseobacterium gotjawalense sp. nov. Isolated from Soil in the Volcanic Forest Gotjawal, Jeju Island.

Strain wdc7T, a rod-shaped bacterium, was isolated from soil in the Gotjawal Forest on Jeju Island, South Korea. Strain wdc7T was Gram stain-negative, facultatively anaerobic, catalase- and oxidase positive, yellow pigmented, and non-flagellated. It grew at 4-37 °C and pH 5.0-8.0 in 0-3% (w/v) NaCl. 16S rRNA gene sequencing analysis revealed that strain wdc7T belonged to the genus Chryseobacterium and was most closely related to Chryseobacterium salivictor NBC 122T, with a sequence similarity of 98.51%. Menaquinone 6 was the sole respiratory quinone, and C15:0 anteiso, C15:0 iso, and summed feature 9 were the major fatty acids. The genome length was 3.30 Mbp, with a 37% G + C content. Average amino acid identity, average nucleotide identity, and digital DNA-DNA relatedness between strain wdc7T and C. salivictor NBC 122T were 93.52%, 92.80%, and 49.7%, respectively. Digital genomic and polyphasic analyses showed that strain wdc7T likely represented a new species of the genus Chryseobacterium. We proposed the name Chryseobacterium gotjawalense sp. nov., with wdc7T (= KCTC 92440T = JCM 35602T) as the type strain.

Chryseobacterium metallicongregator, sp. nov., a bacterium possessing metallophore activity towards rare earth elements.

A polyphasic taxonomic study was carried out on strain ES2T, isolated from sediment of a wetland created to remediate acid drainage from a coal mine. The rod-shaped bacterium formed yellow/orange pigmented colonies and produced the pigment flexirubin. The 16S rRNA gene sequence results assigned the strain to Chryseobacterium, with 98.9 and 98.3 % similarity to Chryseobacterium vietnamense and Chryseobacterium cucumeris, respectively. Computation of the average nucleotide identity and digital DNA-DNA hybridization values with the closest phylogenetic neighbours of ES2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The dominant fatty acids of strain ES2T were iso-C15 : 0, iso-C17 : 1 ω9c, iso C17 : 0 3-OH, and iso-C15 : 0 2-OH. The DNA G+C content was 35.5 mol%. The major polar lipid was phosphatidylethanolamine while menaquinone-6 was the only menaquinone found. This bacterium has been previously shown to possess metallophore activity towards rare earth elements, and based on genome sequencing, possesses all required genes for siderophore production/activity, possibly identifying the source of this unique ability. On the basis of the results obtained here, this bacterium is assigned to the genus Chryseobacterium as representing a new species with the name Chryseobacterium metallicongregator sp. nov., type strain ES2T (=NRRL B-65679T=KCTC 102120T).

Description of Chryseobacterium fluminis sp. nov., a keratinolytic bacterium isolated from a freshwater river.

A Gram-stain-negative, aerobic, rod-shaped bacterial strain, designated MMS21-Ot14T, was isolated from a freshwater river, and shown to represent a novel species of the genus Chryseobacterium on the basis of the results from a polyphasic approach. The 16S rRNA gene sequence analysis revealed that MMS21-Ot14T represented a member of the genus Chryseobacterium of the family Weeksellaceae and was closely related to Chryseobacterium hagamense RHA2-9T (97.52 % sequence similarity), Chryseobacterium gwangjuense THG A18T (97.46 %) and Chryseobacterium gregarium P 461/12T (97.27 %). The optimal growth of MMS21-Ot14T occurred at 25-30 °C, pH 6.0-7.0 and in the absence of NaCl. MMS21-Ot14T was capable of hydrolysing casein, starch, DNA, Tween 20 and tyrosine. The strain also showed keratinolytic activity with keratin azure and decolourising activity with remazol brilliant blue R (RBBR), which indicated potential ability to degrade keratin and lignin. The main polar lipids of MMS21-Ot14T were phosphatidylethanolamine, unidentified aminophospholipids, unidentified aminolipids, an unidentified phospholipid and several unidentified lipids. The predominant fatty acids of MMS21-Ot14T were iso-C15 : 0 and iso-C17 : 0 3-OH, and the major isoprenoid quinone was menaquinone 6 (MK-6). The whole genome of MMS21-Ot14T was 5 062 016 bp in length with a DNA G+C content of 37.7 %. The average nucleotide identity and digital DNA-DNA hybridisation values between MMS21-Ot14T and phylogenetically related members of the genus Chryseobacterium were well below the threshold values for species delineation. It is evident from the results of this study that MMS21-Ot14T should be classified as representing a novel species of the genus Chryseobacterium, for which the name Chryseobacterium fluminis sp. nov. (type strain, MMS21-Ot14T = KCTC 92255T = LMG 32529T) is proposed.

Chryseobacterium pyrolae sp. nov., isolated from the rhizosphere soil of Pyrola calliantha H.

A novel Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated pc2-12T, was isolated from the rhizosphere soil of the herb Pyrola calliantha collected from arid areas of Tibet. The strain grew most vigorously with 1 % (w/v) NaCl, at pH 7.0 and at 25 °C. According to the results of 16S rRNA gene sequence analysis, pc2-12T was closely related to the members of the genus Chryseobacterium, with highest levels of sequence similarity to Chryseobacterium viscerum 687B-08T (98.42 %), Chryseobacterium oncorhynchi 701B-08T (98.11 %) and Chryseobacterium ureilyticum DSM 18017T (97.98 %). The average nucleotide identity values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 79.71, 79.49 and 79.26 %, respectively. The in silico DNA-DNA hybridisation values between pc2-12T and C. viscerum 687B-08T, C. oncorhynchi 701B-08T and C. ureilyticum DSM 18017T were 23.30, 23.00 and 22.90 %, respectively. The draft genome sequence of pc2-12T was 4.64 Mb long, with DNA G+C content of 37.0 mol%. The fatty acids contained in the cells of pc2-12T were mainly composed of iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The main polar lipid was phosphatidylethanolamine. MK-6 was the sole respiratory quinone. On the basis of the results of analysis of all the data described, pc2-12T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium pyrolae sp. nov., is proposed. The type strain is pc2-12T (=GDMCC 1.3256T= JCM 35712T).

Study on denitrification of hydroponic wastewater reverse osmosis concentrate using sulfur-autotrophic denitrification

Hydroponic agriculture is one of the sectors that generate the highest amounts of nitrogen-containing wastewater. Sulfur-autotrophic denitrification is considered a promising technology due to its stable and excellent denitrification performance, cost-effectiveness, and operational advantages. In order to investigate the denitrification performance and the contribution of the filter layer under high NO3--N concentration (600 mg·L−1), this experiment designed a denitrification system using Na2S2O3 as an electron donor. The results showed that the reactor achieved the highest denitrification efficiency with a hydraulic retention time of 12 h, pH of 7, and sulfur to nitrogen ratio of 2, maintaining a stable NO3--N removal efficiency of 99%. The majority of NO3--N was removed by the bottom filter layer (0–300 mm), accounting for 86% of the total denitrification. The microbial community in the lower part of the filter column was dominated by Proteobacteria, with relatively high abundances of the genera Chryseobacterium, Thiobacillus, and Sulfurimonas. Similarly, the microbial community structure in the upper filter layer was dominated by Proteobacteria, with an increased abundance of the genus Chryseobacterium and a significant reduction in the abundance of Sulfurimonas. The study indicates that SAD can achieve stable and efficient denitrification of wastewater from hydroponic reverse osmosis concentrate. Moreover, higher NO3--N concentrations can influence the bacterial community structure within the reactor.

Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities.

Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein-protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR-Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.

Chryseobacterium luquanense sp. nov., a casein-hydrolysing bacterium from the Jiaozi Mountain in Yunnan, PR China.

Strain KC 927T was isolated during an investigation of the soil bacteria diversity on Jiaozi Mountain, central Yunnan, Southwest China. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase-negative, catalase-positive and aerobic. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain KC 927T was a member of the genus Chryseobacterium and closely related to Chryseobacterium caseinilyticum GCR10T (98.4%), Chryseobacterium piscicola DSM 21068T (98.3 %) and 'Chryseobacterium formosus' CCTCC AB 2015118T (97.9 %). With a genome size of 4 348 708 bp, strain KC 927T had 33.5 mol% DNA G+C content and contained 4012 protein-coding genes and 77 RNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain KC 927T and C. caseinilyticum GCR10T, C. piscicola DSM 21068T and 'C. formosus' CCTCC AB 2015118T were 80.1, 79.6 and 90.7 %, and 25.5, 23.6 and 42.0 %, respectively. The main polar lipid of strain KC 927T was phosphatidylethanolamine and the respiratory quinone was MK-6. The major fatty acids (≥10 %) were iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain KC 927T represents a new species of the genus Chryseobacterium, for which the name Chryseobacterium luquanense sp. nov. is proposed. The type strain is KC 927T (=CGMCC 1.18760T=JCM 35707T).

Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease

BackgroundSoil metagenomics is a cultivation-independent molecular strategy for investigating and exploiting the diversity of soil microbial communities. Soil microbial diversity is essential because it is critical to sustaining soil health for agricultural productivity and protection against harmful organisms. This study aimed to perform a metagenomic analysis of the soybean endosphere (all microbial communities found in plant leaves) to reveal signatures of microbes for health and disease. ResultsThe dataset is based on the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) release “microbial diversity in soybean”. The quality control process rejected 21 of the evaluated sequences (0.03% of the total sequences). Dereplication determined that 68,994 sequences were artificial duplicate readings, and removed them from consideration. Ribosomal Ribonucleic acid (RNA) genes were present in 72,747 sequences that successfully passed quality control (QC). Finally, we found that hierarchical classification for taxonomic assignment was conducted using MG-RAST, and the considered dataset of the metagenome domain of bacteria (99.68%) dominated the other groups. In Eukaryotes (0.31%) and unclassified sequence 2 (0.00%) in the taxonomic classification of bacteria in the genus group, Streptomyces, Chryseobacterium, Ppaenibacillus, Bacillus, and Mitsuaria were found. We also found some biological pathways, such as CMP-KDO biosynthesis II (from D-arabinose 5-phosphate), tricarboxylic acid cycle (TCA) cycle (plant), citrate cycle (TCA cycle), fatty acid biosynthesis, and glyoxylate and dicarboxylate metabolism. Gene prediction uncovered 1,180 sequences, 15,172 of which included gene products, with the shortest sequence being 131 bases and maximum length 3829 base pairs. The gene list was additionally annotated using Integrated Microbial Genomes and Microbiomes. The annotation process yielded a total of 240 genes found in 177 bacterial strains. These gene products were found in the genome of strain 7598. Large volumes of data are generated using modern sequencing technology to sample all genes in all species present in a given complex sample. ConclusionsThese data revealed that it is a rich source of potential biomarkers for soybean plants. The results of this study will help us to understand the role of the endosphere microbiome in plant health and identify the microbial signatures of health and disease. The MG-RAST is a public resource for the automated phylogenetic and functional study of metagenomes. This is a powerful tool for investigating the diversity and function of microbial communities.

Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov., isolated from soil.

Two Gram-stain-negative, aerobic, yellow and rod-shaped bacteria, designated as strains PBS4-4T and GMJ5T, were isolated from soil samples collected in Goyang-si and Paju-si, Gyeonggi-do, Republic of Korea. Strains PBS4-4T and GMJ5T were both positive for catalase and oxidase. Strain PBS4-4T grew at 15-37 °C and pH 5.0-12.0. Strain GMJ5T grew at 15-37 °C and pH 5.0-11.0. Neither strain required NaCl for growth. 16S rRNA sequence analysis revealed that strains PBS4-4T and GMJ5T form a closely related cluster with the genus Chryseobacterium. The average nucleotide identity and digital DNA-DNA hybridization values between strain PBS4-4T and its closely related strains were 79.4-84.5% and 23.2-28.7 %, respectively. For GMJ5T, the values were 78.3-79.3% and 22.0-22.6 %, respectively. The major fatty acids shared by both novel strains were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). Strain GMJ5T had one other major fatty acid: iso-C17 : 0 3OH. Based on phenotypic, genomic and phylogenetic results, strains PBS4-4T and GMJ5T represent novel species within the genus Chryseobacterium, and the names Chryseobacterium edaphi sp. nov. and Chryseobacterium gilvum sp. nov. are proposed, respectively. The type strain of C. edaphi is PBS4-4T (=KACC 22882T=TBRC 17052T) and the type strain of C. gilvum is GMJ5T (=KACC 22883T=TBRC 17053T).

Chryseobacterium oryctis sp. nov., isolated from the gut of the beetle Oryctes rhinoceros, and Chryseobacterium kimseyorum sp. nov., isolated from a stick insect rearing cage.

Two strains of Chryseobacterium identified from different experiments are proposed to represent new species. Strain WLa1L2M3T was isolated from the digestive tract of an Oryctes rhinoceros beetle larva. Strain 09-1422T was isolated from a cage housing the stick insect Eurycantha calcarata. Sequence analysis of the 16S rRNA and rpoB genes found both strains to be similar but not identical to other Chryseobacterium species. Whole-genome sequencing suggested the isolates represent new species, with average nucleotide identity values ranging from 74.6 to 80.5 %. Genome-to-genome distance calculations produced values below 25.3 %, and digital DNA-DNA hybridization values were 13.7-29.9 %, all suggesting they are distinct species. The genomic DNA G+C content of WLa1L2M3T is approximately 32.53 %, and of 09-1422T is approximately 35.89 %. The predominant cellular fatty acids of strain WLa1L2M3T are C15 : 0 iso, summed feature 9 (C16 : 0 10OH or C17 : 1 iso ω6c), C17 : 0 iso 3OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C15 : 0 iso 3OH, C15 : 0 anteiso and C13 : 0 iso, and those of strain 09-1422T are C15 : 0 iso, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 0 iso 3OH, C15 : 0 anteiso, C15 : 0 iso 3OH, C16 : 1 ω7c, C17 : 0 2OH and C18 : 0. In addition, physiological and biochemical tests revealed phenotypic differences from related Chryseobacterium type strains. These cumulative data indicate that the two strains represent novel species of the genus Chryseobacterium for which the names Chryseobacterium oryctis sp. nov. and Chryseobacterium kimseyorum sp. nov. are proposed with WLa1L2M3T (=BCRC 81350T=JCM 35215T=CIP 112035T) and 09-1422T (=UCDFST 09-1422T=BCRC 81359T=CIP 112165T), as type strains, respectively.

Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated from the Aquatic Environment, South Korea

Two novel bacterial species CJ51T and CJ63T belonging to the genus Chryseobacterium were isolated from the Upo wetland and the Han River, South Korea, respectively. Cells of these strains were Gram-stain-negative, aerobic, non-motile, rod-shaped, and catalase- and oxidase-positive. Both strains were shown to grow optimally at 30°C and pH 7 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ51T and CJ63T belonged to the genus Chryseobacterium and were most closely related to Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT with 98.47% and 98.46% 16S rRNA sequence similarities, respectively. The average nucleotide identity values of strains CJ51T and CJ63T with its closely related type strains Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT were 81.9% and 82.1%, respectively. The major fatty acids of strains CJ51T and CJ63T were iso-C15:0, iso-C17:0 3-OH and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). Menaquinone 6 (MK-6) was identified as the primary respiratory quinone in both strains. The major polar lipids of strains CJ51T and CJ63T were phosphatidylethanolamine and several unidentified amino lipids and lipids. Based on polyphasic taxonomy data, strains CJ51T and CJ63T represent novel species of the genus Chryseobacterium, for which names Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. are proposed respectively. The type strains are CJ51T (= KACC 22749T = JCM 35632T) and CJ63T (= KACC 22750T = JCM 35633T).

Psychotropic endophytes of cereals as potential bioagents

Creating new biopesticides for protecting agricultural crops and developing their application methods, which are among the priority areas of the agro-industrial complex, are inextricably linked with continuous observation of soil microbiocenosis, growing plants, and changes in agro-climatic conditions in a specific region. Plant endophytes are potentially active bioagents for creating new microbiological preparations for protecting winter crops, as well as agricultural produce during its storage period. In connection with this, the morphophysiological characteristics of six isolates of endophytic bacteria, isolated at low temperatures from winter cereal plants, were studied. The species affiliation of the strains was determined - five isolates belonged to the genus Pseudomonas and one to the genus Chryseobacterium. An assessment of the antagonistic activity of endophytes in relation to phytopathogens causing rot of agricultural produce was conducted.

Three-Dimensional Biofilm Electrode Reactors with Polyurethane Sponge Carrier for Highly Efficient Treatment of Pharmaceuticals Wastewater Containing Tetrahydrofuran

Three-dimensional biofilm electrode reactors (3D-BERs) exhibit efficacy in the removal of refractory wastewater of pharmaceuticals due to the resistance of pharmaceutical wastewater to biodegradation. In this paper, a new 3D-BER with a polyurethane sponge carrier was applied to the treatment of pharmaceutical wastewater containing tetrahydrofuran (THF) with an objective of exploring the removal efficiency, degradation pathway and main functions of microorganisms of 3D-BERs for wastewater containing THF. The results indicate that when the voltage is 10 V, the highest CODCr removal efficiency is (95.9 ± 1.6)%. Compared to the control group, the removal rate was increased by 21.97 ± 4.69%. The main intermediates of THF, γ-butyrolactone and 4-hydroxybutyric acid, were detected, respectively, by Gas Chromatography–Mass Spectrometry (GC–MS), indicating that 3D-BERs contribute to the degradation of THF with electro-oxidation as well as microbial synergism. Microorganisms, such as Proteobacteria with extracellular electron transfer capacity, Bacteroidetes capable of degrading complex carbon sources and parthenogenic anaerobic bacteria Firmicutes, were found to be enriched by high-throughput sequencing analysis in 3D-BERs, which were conducive to the degradation of refractory pollutants. At the genus level, Chryseobacterium, Brevundimonas, Erysipelothrix, and Desulfovibrio were the main functional genera, whose degradation of THF intermediates was found by functional prediction, mainly through chemoheterotrophy, aerobic chemoheterotrophy, etc. It is to be hoped that this study will provide a solution to the practical treatment of pharmaceutical wastewater containing THF via this new 3D-BER system with a polyurethane sponge carrier.

Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey

Four strains, designated as C-2, C-17T, C-39T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089T while strains C-2, C-39T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17T, C-39T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17T and C-39T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid quinone and the presence of iso-C15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 – 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17T and C-39T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17T (=JCM 34190T = KCTC 82250T) and C-39T (=JCM 34191T = KCTC 822251T), respectively, are proposed.

Grape Pomace in Ewes Diet Affects Metagenomic Profile, Volatile Compounds and Biogenic Amines Contents of Ripened Cheese

The main objective of this research was to evaluate the development of volatile organic compounds (VOCs) and the accumulation of biogenic amines (BAs) in relation to the dynamic of microbial population composition in fresh and ripened cheese produced from raw milk of ewes fed a diet containing grape pomace (GP+) and fed a standard diet (Ctrl). Genomic DNA was extracted from the cheeses at 2 (T2), 60 (T60), 90 (T90) and 120 (T120) days of ripening and prepared for 16S rRNA-gene sequencing to characterize the cheese microbiota; furthermore, VOCs were determined via solid-phase microextraction combined with gas chromatography-mass spectrometry and biogenic amines by HPLC analyses. Diet did not affect the relative abundance of the main phyla identified, Proteobacteria characterized T2 samples, but the scenario changed during the ripening. At genus level, Pseudomonas, Chryseobacterium and Acinetobacter were the dominant taxa, however, a lower percentage of Pseudomonas was detected in GP+ cheeses. Enterococcus became dominant in ripened cheeses followed in Ctrl cheeses by Lactobacillus and in GP+ cheeses by Lactococcus. The diet affected the development of carboxylic acids and ketones but not of aldehydes. Low levels of esters were identified in all the samples. In total, four biogenic amines were determined in cheeses samples and their levels differed between the two groups and during ripening time. In 60, T90 and T120 GP+ cheeses, a lower amount of 2-phenylethylamine was found compared to Ctrl. Putrescine was detected only in GP+ samples and reached the highest level at 120 days. Conversely, the amount of cadaverine in GP+ samples was invariable during the ripening. The concentration of tyramine in GP+ samples was compared to Ctrl during the ripening. Overall, significant positive correlations between some families of bacteria and the formation of VOCs and BAs were found.

Insights into Evolutionary, Genomic, and Biogeographic Characterizations of Chryseobacterium nepalense Represented by a Polyvinyl Alcohol-Degrading Bacterium, AC3.

ABSTRACTChryseobacterium spp. are Gram-negative rods found ubiquitously in the environment, with certain species being reported as having unusual degrading properties. Polyvinyl alcohol (PVA) is used widely in industry but causes serious global environmental pollution. Here, we report the complete genome sequence of a novel bacterium, AC3, that efficiently degrades PVA. As the representative genome of Chryseobacterium nepalense, key genomic characteristics (e.g., mobile genetic elements, horizontal genes, genome-scale metabolic network, secondary metabolite biosynthesis gene clusters, and carbohydrate-active enzymes) were comprehensively investigated to reveal the potential genetic features of this species. Core genome phylogenetic analysis in combination with average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization values provided an accurate taxonomic position of C. nepalense in the genus Chryseobacterium. Comparative genomic analysis of AC3 with closely related species suggested evolutionary dynamics characterized by a species-specific genetic repertoire, dramatic rearrangements, and evolutionary constraints driven by selective pressure, which facilitated the speciation and adaptative evolution of C. nepalense. Biogeographic characterization indicated that this species is ubiquitously distributed not only in soil habitats but also in a variety of other source niches. Bioinformatic analysis revealed the potential genetic basis of PVA degradation in AC3, which included six putative genes associated with the synthesis of PVA dehydrogenase, cytochrome c, oxidized PVA hydrolase, and secondary alcohol dehydrogenase. Our study reports the first complete genome of C. nepalense with PVA-degrading properties, providing comprehensive insights into the genomic characteristics of this species and increasing our understanding of the microbial degradation of PVA.IMPORTANCE Although PVA is a biodegradable polymer, the widespread use of PVA in global industrialization has resulted in serious environmental problems. To date, knowledge of effective and applicable PVA-degrading bacteria is limited, and thus, the discovery of novel PVA biodegraders is pertinent. Here, we isolated a novel bacterial strain, AC3, which efficiently degraded PVA. The complete genome of AC3 was sequenced as the first genome sequence of the species C. nepalense. Comparative genomic analysis was performed to comprehensively investigate the phylogenetic relationships, genome-scale metabolic network, key genomic characteristics associated with genomic evolution, evolutionary dynamics between AC3 and its close relatives, and biogeographic characterization of C. nepalense, particularly regarding the potential genetic basis of PVA degradation. These findings could advance our understanding of the genomic characteristics of C. nepalense and PVA bioremediation.

Cadmium-resistant Chryseobacterium sp. DEMBc1 strain: characteristics and potential to assist phytoremediation and promote plant growth.

The effectiveness of phytoremediation is closely related to the various interactions between pollutants, soil particles, rhizosphere microorganisms, and plants. Therefore, the object of current study was a cadmium-tolerant bacterium isolated from the rye rhizosphere, with a high degree of genetic similarity to the genus Chryseobacterium. Chryseobacterium sp. DEMBc1 was able to grow with 36 different BiologGN2 carbon sources and show the adaptation to stress factors such as Cd (100 μg ml-1), low temperature (8 °C), and salinity (2% NaCl). Furthermore, it was shown that DEMBc1 had the characteristics of plant growth-promoting microorganisms: it was able to produce ammonia, indole acetic acid, 1-aminocyclopropane-1-carboxylic acid deaminase, and siderophores, as well as solubilize Ca3(PO4)3. After inoculation with DEMBc1, a significant decrease in the concentration of Cd was observed in the roots of Festuca ovina grown in Cd-polluted soil, compared to the non-inoculated Cd-polluted soil. It was also noticed that DEMBc1 produced a large amount of extracellular polymeric substances that were significantly higher than the cellular biomass. These polymers can form a barrier to reduce the translocation of Cd from the growth medium to the plant roots. According to the current study, DEMBc1 has a stabilizing potential and can decrease the mobility of Cd in the F. ovina rhizosphere, bioaccumulate metals in plant tissues, and effectively improve the bioavailability of nutrients, especially Fe, N, and P in a polluted environments.

Polar lipid characterization and description of Chryseobacterium capnotolerans sp. nov., isolated from high CO2-containing atmosphere and emended descriptions of the genus Chryseobacterium, and the species C. balustinum, C. daecheongense, C. formosense, C. gleum, C. indologenes, C. joostei, C. scophthalmum and C. ureilyticum.

Modified atmosphere (MA) packaging plays an important role in improving food quality and safety. By using different gas mixtures and packaging materials the shelf life of fresh produce can significantly be increased. A Gram-negative-staining, rod-shaped, orange-pigmented strain DH-B6T, has been isolated from MA packed raw pork sausage (20% CO2, 80% O2). The strain produced biofilms and showed growth at high CO2 levels of up to 40%. Complete 16S rRNA gene and whole-genome sequences revealed that strain DH-B6T belongs to the genus Chryseobacterium, being closely related to strain Chryseobacterium indologenes DSM 16777T (98.4%), followed by Chryseobacterium gleum NCTC11432T (98.3%) and Chryseobacterium lactis KC1864T (98.2%). Average nucleotide identity value between DH-B6T and C. indologenes DSM 16777T was 81.1% and digital DNA-DNA hybridisation was 24.9%, respectively. The DNA G+C content was 35.51 mol%. Chemotaxonomical analysis revealed the presence of the rare glycine lipid cytolipin, the serine-glycine lipid flavolipin and the sulfonolipid sulfobacin A, as well as phosphatidylethanolamine, monohexosyldiacylglycerol and ornithine lipid, including the hydroxylated forms. Major fatty acids were iC15 : 0 (50.7%) and iC17 : 1 cis 9 (28.7%), followed by iC15 : 0 2-OH (7.0%) and iC17 : 0 3-OH (6.2%). The isolated strain contained MK-6 as the only respiratory quinone and flexirubin-like pigments were detected as the major pigments. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, the strain DH-B6T (=DSM 110542T=LMG 31915T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium capnotolerans sp. nov. is proposed. Emended descriptions of the genus Chryseobacterium and eight species of this genus based on polar lipid characterisation are also proposed.