Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan

Regulation of rhizospheric microbial network to enhance plant growth and resist pollutants: Unignorable weak electric field

The union of Plant Growth-Promoting Bacteria (PGPB) and rhizosphere confers a series of functions beneficial to plant. However, the lack of an opearable in situ method limits the further understanding on the mechanism. In this study, a weak electric field was designed to regulate rhizospheric microflora in a constructed root-splitting reactor. Compared with the control, the aboveground and underground biomass of rice seedling increased by 17 % and 18 % (p < 0.05) respectively under the exist of weak electric field of 0.14 V/cm. The joint action of rhizosphere and PGPB displayed the detoxification ability in the condition of soluble petroleum hydrocarbons, where the height, stem diameter, biomass and root vigor of the plant was increased by 58 %, 32 %, 43 % and 48 % respectively than the control. The selective reproduction of endophytes and ectophytes (denitrifying, auxin-producing, hydrocarbon-degrading and electroactive bacteria) was observed under applied weak electric field, which enhanced the nitrogen utilization, cellular metabolic activity and resistance to toxic organics of plant. This was further confirmed by the up-regulated OTUs related to the hydrocarbon degradation function, tryptophan metabolism and metabolism of nicotinate and nicotinamide. Moreover, the weak electric field also enhanced the transfer ability of partial endophytes grown in the root to improve plant stress resistance. The results in this work inspired an exercisable method for in situ enrichment of PGPB in the rhizosphere to cope with food crisis and provided a new way to deal with sudden environmental events.

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

Chryseobacterium 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.

Pathogenic Potential and Control of Chryseobacterium Species from Clinical, Fish, Food and Environmental Sources

Chryseobacterium species are isolated and taxonomically evaluated from a wide range of sources. While C. gleum and C. indologenes have been implicated in human disease, the potential pathogenicity of numerous other species have not been investigated. The aims were therefore to evaluate 37 Chryseobacterium species and Elizabethkingia meningoseptica from environmental, food, fish, water and clinical sources for production of haemolysis, growth at 37 °C, and production of virulence enzymes. The control of these strains were investigated by determination of antimicrobial and disinfectant resistance. All the species produced α- or β-haemolysis. In terms of growth at 37 °C and production of virulence enzymes, C. soldanellicola (environmental), C. oranimense (food) and C. koreense (natural mineral water) could be potential human pathogens. Chryseobacterium piscium might be pathogenic to fish. Trimethoprim could be the most effective antimicrobial for the treatment of a Chryseobacterium species infection, while the disinfectants that contain poly-dimethyl ammonium chloride or benzalkonium chloride could be regarded as the most effective for decontamination of surfaces contaminated with Chryseobacterium species.

Chryseobacterium schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea

Marseille-P9602T is a Chryseobacterium-like strain that we isolated from planarian Schmidtea mediterranea and characterized by taxono-genomic approach. We found that Marseille-P9602T strain exhibits a 16S rRNA gene sequence similarity of 98.76% with Chryseobacterium scophthalmum LMG 13028T strain, the closest phylogenetic neighbor. Marseille-P9602T strain was observed to be a yellowish-pigmented, Gram-negative, rod-shaped bacterium, growing in aerobic conditions and belonging to the Flavobacteriaceae family. The major fatty acids detected are 13-methyl-tetradecanoic acid (57%), 15-methylhexadecenoic acid (18%) and 12-methyl-tetradecanoic acid (8%). Marseille-P9602 strain size was found from genome assembly to be of 4,271,905 bp, with a 35.5% G + C content. The highest values obtained for Ortho-ANI and dDDH were 91.67% and 44.60%, respectively. Thus, hereby we unravel that Marseille-P9602 strain is sufficiently different from other closed related species and can be classified as a novel bacterial species, for which we propose the name of Chryseobacterium schmidteae sp. nov. Type strain is Marseille-P9602T (= CSUR P9602T = CECT 30295T).

Chryseobacterium lacus sp. nov. Isolated From the Surface Water of Two Lakes With Light-Induced Carotenoid Production

Two Gram-stain-negative, rod-shaped, gliding, catalase-positive, and facultative anaerobic strains, YLOS41^T and XH07, were isolated from surface water of Yilong Lake and West Lake of Dali in Yunnan Province, respectively. Both strains were yellow-colored under light conditions and white-colored under dark conditions. The results of physiological and chemotaxonomic characterization, sequencing and phylogenetic analysis, and draft genome sequence comparison demonstrated that the two strains represented a single novel species within the genus Chryseobacterium, for which the name Chryseobacterium lacus sp. nov. is proposed. The type strain is YLOS41^T (= KCTC 62352^T = MCCC 1H00300^T), and the second strain is XH07 (= KCTC 62993). During the cultivation process, we found that the colony color of the two strains changed from white to yellow with illumination. The study investigated the effects of light irradiation on the strain YLOS41^T. Results showed that light irradiation did not affect the growth of cells but significantly increased carotenoid synthesis, which caused the change of colony color. In-depth metabolic analysis was conducted by transcriptome. The predominant changes were found for genes involved in carotenoid synthesis as protection from light damage. Based on the genome and transcriptome, we proved that strain YLOS41^T possessed a complete synthetic pathway of carotenoid and speculated that the production was zeaxanthin. This was the first report of Chryseobacterium species with light-induced carotenoid synthesis. This study enhances our present knowledge on how Chryseobacterium species isolated from surface water responds to light damage.

A new microbial gluten-degrading prolyl endopeptidase: Potential application in celiac disease to reduce gluten immunogenic peptides

Gluten is a complex of proteins present in barley, wheat, rye and several varieties of oats that triggers celiac disease in genetically predisposed subjects. Gluten is notoriously difficult to digest by mammalian proteolytic enzymes and therefore, proline-rich digestion-resistant peptides contain multiple immunogenic epitopes. Prolyl endopeptidases (PEP) hydrolyse internal proline residues on the carboxyl side of peptides and have been proposed for food gluten detoxification and as oral enzyme supplementation for celiacs. The aim of this study was to identify new gluten-degrading microbial enzymes with the potential to reduce gluten immunogenicity by neutralizing its antigenic epitopes. Using a gluten-degrading colony screening approach, a bacterial isolate (2RA3) displaying the highest glutenase activity was selected, characterized and its genome completely sequenced. The identification through 16S rDNA gene sequencing showed a 99,1% similarity to Chryseobacterium taeanense. Hydrolysis of gluten immunogenic peptides (GIP) was further monitored, over a 48-hour period, by colony encapsulation in gliadin-containing microspheres, followed by detection with the G12 anti-GIP monoclonal antibody. Glutenase activity was detected in the extracellular medium of 2RA3 cultures, where gel electrophoresis and gliadin zymography revealed the presence of a ~50 kDa gluten-degrading enzyme. Nano-ESI-Q-TOF of the excised active band identified 7 peptides contained in the protein product predicted for an open reading frame (ORF) in the 2RA3 genome. Based on sequence similarity to the PEP family, the new enzyme was named PEP 2RA3. The PEP 2RA3 coding sequence was PCR-amplified from C. taeanense 2RA3, cloned and expressed in Escherichia coli as a C-terminally His-tagged recombinant protein and purified by Ni-NTA affinity chromatography. The recombinant protein, with predicted molecular mass and isoelectric point of 78.95 kDa and 6.8, respectively, shows PEP activity with standard chromogenic substrates, works optimally at pH 8.0 and 30°C and remains stable at pH 6.0 and 50°C, indicating a potential use in gluten-containing food process applications. The ability of the recombinant enzyme to degrade GIP in beer into smaller peptides was confirmed.

Description of Chryseobacterium timonianum sp. nov., isolated from a patient with pneumonia

Using a polyphasic taxonomic strategy, an aerobic, Gram-negative, non-motile, yellow pigmented rod isolated from a sputum sample of a patient with pneumonia was characterised. This bacterial strain, designated G972^T, could not be identified by our systematic MALDI-TOF screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 98.57% sequence identity with that of Chryseobacterium indologenes 16777^T, the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. The major cell fatty acids were identified as 13-methyl-tetradecanoic acid (61%), 3-hydroxy-heptadecanoic acid (16%) and 15-methyl-11-hexadecenoic acid (11%). D-glucose, D-mannose, aesculin, D-maltose, D-trehalose, and gentibiose are the main carbon source. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity values (ANI) of the strain G972^T against genomes of the type strains of related species ranged between 18.9 and 32.8% and between 71.46 and 83.61%, respectively, thus confirming again the new species status of the strain. Here, we describe the characteristics of this organism, complete genome sequence and annotation. The 5,390,132 bp size genome contains 4867 protein-coding genes, 89 RNAs (three genes are 5S rRNA, one gene is 16S rRNA, one gene is 23S rRNA and 84 tRNAs) with 35.51% GC content. Finally, on the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we conclude that strain strain G972^T (= DSM 103388^T = CSUR P2233^T) represents a novel species for which we propose the name Chryseobacterium timonianum. The 16S rRNA and genome sequences are available in GenBank database under accession numbers LT161886 and FJVD00000000.

Chryseobacterium lineare sp. nov., isolated from a limpid stream

A Gram-stain-negative, aerobic, non-motile, rod-shaped, yellow-pigmented bacterial strain, XC0022T, isolated from freshwater of a limpid stream in Zhejiang, China, was studied using a polyphasic approach. The phylogenetic analysis based on 16S rRNA gene sequences clearly showed an allocation to the genus Chryseobacterium with the highest sequence similarities of 98.0 % to Chryseobacterium taeanense PHA3-4T, 97.2 % to Chryseobacterium taihuense THMBM1T, 97.1 % to Chryseobacterium rigui CJ16T and 97.1 % to Chryseobacteriumprofundimaris DY46T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 97.0 % (92.3-96.8 %). DNA-DNA hybridization results showed that strain XC0022T was 55.3 %, 49.8 % and 31.1 % related to C. taeanense DSM 17071T, Chryseobacteriumtaichungense DSM 17453T and Chryseobacteriumgleum JCM 2410T, respectively. The quinone system was composed only of MK-6. Strain XC0022T possessed iso-C15 : 0, iso-C17 : 0 3-OH, C18 : 1ω9c and summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c) as the major fatty acids. The polar lipids profile consisted of one phosphatidylethanolamine, one unidentified glycolipid, four unidentified aminolipids and two unidentified lipids. The G+C content of the genomic DNA was 29.7 mol%. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain XC0022T (=KCTC 52364T=MCCC 1K02723T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium lineare sp. nov. is proposed.

Chryseobacterium montanum sp. nov. isolated from mountain soil

A Gram-staining-negative, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated WG4T, was isolated from soil of the Tianmen Mountain located in Hunan province, PR China. 16S rRNA gene sequence analysis showed that the strain belongs to the genus Chryseobacterium in the family Flavobacteriaceae, with 97.4 % and 97.1 % sequence identities to Chryseobacterium anthropi NF 1366T and Chryseobacterium haifense H38T, respectively. In comparison with the other strains representing the genus Chryseobacterium, the 16S rRNA gene sequence identities were less than 97.0 %. The DNA-DNA relatedness values were 63.3 % (±1) between C. anthropi NF 1366T and strain WG4T and 62.7 % (±2) between C. haifense DSM 19056T and strain WG4T. The DNA G+C content of strain WG4T was 37.7 mol%. The predominant fatty acids of strain WG4T were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, three unidentified lipids and two unidentified aminolipids. The major menaquinone of strain WG4T was menaquinone 6. Strain WG4T showed some unique physiological and biochemical characteristics, such as being negative for gelatin hydrolysis, and valine arylamidase and α-glucosidase activity, and positive for acid production from cellobiose. Based on the differentiating phylogenetic inference and biochemical data, strain WG4T represents a novel species, for which the name Chryseobacterium montanum sp. nov. is proposed, with the type strain WG4T (=KCTC 52204T=CCTCC AB 2016058T).

Chryseobacterium arachidiradicis sp. nov., isolated from the geocarposphere (soil around the peanut) of very immature peanuts (Arachis hypogaea)

A yellow-pigmented bacterial strain, 91A-612(T), isolated from the geocarposphere (soil around the peanut) of very immature peanuts (Arachis hypogaea) in Alabama, USA, was studied for its taxonomic position. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Chryseobacterium, showing the highest sequence similarities to the type strains of Chryseobacterium molle (98.4%), C. pallidum (98.3%) and C. hominis (97.8%). The 16S rRNA gene sequence similarities to the type strains of all other species of the genus Chryseobacterium were below 97.0%. The fatty acid profile of strain 91A-612(T) consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c) and iso-C17 : 0 3-OH. Major compounds in the polar lipid profile were phosphatidylethanolamine and several unidentified lipids, including two lipids that did not contain a sugar moiety, an amino group or a phosphate group (L3, L8), and an aminolipid (AL1). The quinone system was composed mainly of MK-6. The polyamine pattern contained sym-homospermidine as the major compound and moderate amounts of spermidine and spermine. DNA-DNA hybridizations between strain 91A-612(T) and the type strains of C. molle, C. pallidum and C. hominis resulted in relatedness values well below 70%. These data and the differentiating biochemical and chemotaxonomic properties showed that isolate 91A-612(T) represents a novel species of the genus Chryseobacterium, for which we propose the name Chryseobacterium arachidiradicis sp. nov. (type strain 91A-612(T) = LMG 27814(T)= CCM 8490(T) = CIP 110647(T)).

Chryseobacterium takakiae sp. nov., a member of the phylum Bacteroidetes isolated from Takakia lepidozioides

A Gram-stain-negative, rod-shaped and non-endospore-forming bacterium, designated strain AG1-2T, was isolated from Takakia lepidozioides collected from the Gawalong glacier in Tibet, China and characterized using a polyphasic taxonomic approach. The predominant fatty acids of strain AG1-2T were iso-C15 : 0 (36.0 %), iso-C17 : 0 3-OH (20.2 %), summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl, 16.4 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 11.1 %). The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Strain AG1-2T contained MK-6 as the dominant menaquinone, and the genomic DNA G+C content was 37.3 mol%. The phylogenetic analysis based on the 16S rRNA gene sequences showed that strain AG1-2T was affiliated to species of the genus Chryseobacterium , and its closest related species were Chryseobacterium taiwanense Soil-3-27T, Chryseobacterium hispalense AG13T, Chryseobacterium camelliae THG C4-1T and Chryseobacterium taeanense PHA3-4T with a sequence similarity of 98.0, 97.8, 97.3 and 97.1 %, respectively. However, the DNA–DNA relatedness values between these strains and strain AG1-2T were 29, 21, 21 and 45 %, respectively. Based on phylogenetic inference and phenotypic data, strain AG1-2T is considered to represent a novel species of the genus Chryseobacterium , for which the name Chryseobacterium takakiae sp. nov. is proposed. The type strain is AG1-2T ( = CGMCC 1.12488T = DSM 26898T).

Chryseobacterium gallinarum sp. nov., isolated from a chicken, and Chryseobacterium contaminans sp. nov., isolated as a contaminant from a rhizosphere sample

Two yellow-pigmented bacterial strains (100T and C26T), showing 98.4 % 16S rRNA gene sequence similarity to each other and isolated from a chicken in Germany and as a contaminant from an agar plate of a rhizosphere sample in Alabama, were studied by using a polyphasic taxonomic approach. Cells of both isolates were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequences of the two organisms with the sequences of the type strains of the most closely related species of the genus Chryseobacterium showed the highest sequence similarities of strains 100T and C26T to the type strains of Chryseobacterium joostei (respectively 97.5 and 98.2 %), C. viscerum (96.6, 97.8 %), C. gleum (97.1, 97.7 %), C. arthrosphaerae (97.3%, 97.7 %), C. indologenes (97.2, 97.7 %), C. tructae (96.6, 97.6 %), C. jejuense (97.0, 97.6 %) and C. oncorhynchi (96.3, 97.5 %); 16S rRNA gene sequence similarities to members of all other species of the genus Chryseobacterium were below 97.5 %. The fatty acid profiles of both strains consisted of the major fatty acids iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C17 : 1ω9c and iso-C17 : 0 3-OH, but also showed slight differences (absence or presence of C16 : 0 3-OH and iso-C15 : 1 F). DNA–DNA hybridizations between the two strains and between the novel strains and the type strains of C. joostei , C. indologenes , C. jejuense , C. tructae and C. viscerum resulted in relatedness values clearly below 70 %. These DNA–DNA hybridization results and the differentiating biochemical and chemotaxonomic properties showed that both strains 100T and C26T represent novel species, for which the names Chryseobacterium gallinarum sp. nov. (type strain 100T = LMG 27808T = CCM 8493T) and Chryseobacterium contaminans sp. nov. (type strain C26T = LMG 27810T = CCM 8492T) are proposed.

Chryseobacterium camelliae sp. nov., isolated from green tea

A Gram-staining-negative, strictly aerobic, non-motile, rod-shaped and flexirubin-type-pigmented strain, THG C4-1T, was isolated from green tea leaves in Jangheung-gun, Republic of Korea. Strain THG C4-1T grew well at 20–30 °C, at pH 7.0–7.5 and in the absence of NaCl on nutrient agar. Based on 16S rRNA gene sequence comparisons, strain THG C4-1T was most closely related to Chryseobacterium taiwanense Soil-3-27T (97.7 %), C. hagamense RHA2-9T (97.2 %), C. gregarium P 461/12T (97.2 %), C. ginsenosidimutans THG 15T (97.1 %), C. taeanense PHA3-4T (97.0 %) and C. daeguense K105T (97.0 %), but DNA–DNA relatedness between strain THG C4-1T and its closest phylogenetic neighbours was below 21 %. The DNA G+C content was 41.7 mol%. The only isoprenoid quinone detected in strain THG C4-1T was menaquinone 6 (MK-6). The major component of the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylethanolamine and unidentified aminolipids. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. These data supported the affiliation of strain THG C4-1T to the genus Chryseobacterium . The results of physiological and biochemical tests enabled strain THG C4-1T to be differentiated genotypically and phenotypically from recognized species of the genus Chryseobacterium . Therefore, the novel isolate represents a novel species, for which the name Chryseobacterium camelliae sp. nov. is proposed, with THG C4-1T ( = KACC 16985T = JCM 18745T) as the type strain.

Chryseobacterium gwangjuense sp. nov., isolated from soil

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacterial strain, THG-A18T, was isolated from soil of Gwangju province in South Korea. Strain THG-A18T grew optimally at 25–30 °C, at pH 7.0–8.0 and in the absence of NaCl. Strain THG-A18T displayed β-glucosidase activity, which enabled it to convert ginsenoside Rb1 to Rd. According to 16S rRNA gene sequence analysis, strain THG-A18T was shown to belong to the genus Chryseobacterium . The closest phylogenetic neighbours were Chryseobacterium ginsenosidimutans THG 15T (97.9 % 16S rRNA gene sequence similariity), C. defluvii B2T (97.7 %), C. daeguense K105T (97.6 %), C. taiwanense BCRC 17412T (97.5 %), C. indoltheticum LMG 4025T (97.4 %), C. gregarium P 461/12T (97.4 %) and C. lathyri RBA2-6T (97.3 %), but DNA–DNA relatedness values between these strains and strain THG-A18T were below 41.9 %. The G+C content of the genomic DNA was 36.4 mol%. The major respiratory quinone (MK-6) and fatty acids [iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0)] supported the affiliation of strain THG-A18T with the genus Chryseobacterium . The polar lipids of strain THG-A18T were phosphatidylethanolamine, four unidentified aminolipids and seven unidentified lipids. A number of physiological and biochemical tests allowed phenotypic differentiation of strain THG-A18T from recognized species of the genus Chryseobacterium . The name Chryseobacterium gwangjuense sp. nov. is proposed, with THG-A18T ( = KACC 16227T = LMG 26579T) as the type strain.

Chryseobacterium taihuense sp. nov., isolated from a eutrophic lake, and emended descriptions of the genus Chryseobacterium, Chryseobacterium taiwanense, Chryseobacterium jejuense and Chryseobacterium indoltheticum

Bacterial strain THMBM1(T) was isolated from decomposing algal scum that was collected during an algal bloom in Lake Taihu, Wuxi City, Jiangsu Province, China. Cells of strain THMBM1(T) were Gram-negative, facultatively anaerobic, non-motile rods. Colonies on tryptic soy agar were translucent and shiny with entire edges; yellow flexirubin-type pigments were produced. Growth was observed at 15-45 °C (optimum 30-37 °C), at pH 5.0-9.0 (optimum pH 8.0) and in the presence of 0-4.0 % (w/v) NaCl (optimum 0-1.0 %). Strain THMBM1(T) contained MK-6 as the sole respiratory quinone and sym-homospermidine as the predominant polyamine. The predominant cellular fatty acids were iso-C15 : 0 (53.2 %), iso-C17 : 0 3-OH (15.6 %) and iso-C17 : 1ω9c (11.9 %). The polar lipid profile consisted of phosphatidylethanolamine and five unidentified lipids. The DNA G+C content was 36.8 mol% (Tm). Strain THMBM1(T) was closely related to members of the genus Chryseobacterium, with 16S rRNA gene sequence similarities ranging from 92.9 to 97.2 %, the highest sequence similarities being with Chryseobacterium taiwanense BCRC 17412(T) (97.2 %) and C. gambrini 5-1St1a(T) (97.1 %). DNA-DNA relatedness between strain THMBM1(T) and C. taiwanense JCM 21767(T) and C. gambrini DSM 18014(T) was 34.1  and 23.0 %, respectively. Based on these results, it is concluded that strain THMBM1(T) represents a novel species, for which the name Chryseobacterium taihuense sp. nov. is proposed. The type strain is THMBM1(T) ( = CGMCC 1.10941(T)  = NBRC 108747(T)). Emended descriptions of the genus Chryseobacterium and C. taiwanense, C. jejuense and C. indoltheticum are also proposed.

Microbial and environmental effects on avian egg viability: do tropical mechanisms act in a temperate environment?

The viability of freshly laid avian eggs declines after several days of exposure to ambient temperatures above physiological zero, and declines occur faster in tropical than temperate ecosystems. Microbial infection during preincubation exposure has recently been shown as a second cause of egg viability decline in the tropics, but whether microbial processes influence the viability of wild bird eggs in temperate ecosystems is unknown. We determined the microbial load on eggshells, the incidence of microbial penetration of egg contents, and changes in the viability of wild bird eggs (Sialia mexicana, Tachycineta bicolor, Tachycineta thalassina) experimentally exposed to temperate-zone ambient conditions in situ in a mediterranean climate in northern California. Initial microbial loads on eggshells were generally low, although they were significantly higher on eggs laid in old boxes than in new boxes. Eggshell microbial loads did not increase with exposure to ambient conditions, were not reduced by twice-daily disinfection with alcohol, and were unaffected by parental incubation. The rate of microbial penetration into egg contents was low and unaffected by the duration of exposure. Nevertheless, egg viability declined very gradually and significantly with exposure duration, and the rate of decline differed among species. In contrast to studies performed in the tropics, we found little evidence that temperature or microbial mechanisms of egg viability decline were important at our temperate-zone site; neither temperatures above physiological zero nor alcohol disinfection was significantly related to hatching success. Delaying the onset of incubation until the penultimate or last egg of a clutch at our study site may maintain hatching synchrony without a large trade-off in egg viability. These results provide insight into the environmental mechanisms that may be responsible for large-scale latitudinal patterns in avian clutch size and hatching asynchrony.

Chryseobacterium chaponense sp. nov., isolated from farmed Atlantic salmon (Salmo salar)

Two bacterial strains, designated Sa 1147-06T and Sa 1143-06, were isolated from Atlantic salmon (Salmo salar) farmed in Lake Chapo, Chile, and were studied using a polyphasic approach. Both isolates were very similar; cells were rod-shaped, formed yellow-pigmented colonies and were Gram-reaction-negative. Based on 16S rRNA gene sequence analysis, strains Sa 1147-06T and Sa 1143-06 shared 100 % sequence similarity and showed 98.9 and 97.5 % sequence similarity to Chryseobacterium jeonii AT1047T and Chryseobacterium antarcticum AT1013T, respectively. Sequence similarities to all other members of the genus Chryseobacterium were below 97.3 %. The major fatty acids of strain Sa 1147-06T were iso-C13 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 1 ω9c, with iso-C15 : 0 3-OH, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH constituting the major hydroxylated fatty acids. DNA–DNA hybridizations with C. jeonii JMSNU 14049T and C. antarcticum JMNSU 14040T gave relatedness values of 20.7 % (reciprocal 15.1 %) and 15.7 % (reciprocal 25.7 %), respectively. Together, the DNA–DNA hybridization results and differentiating biochemical properties showed that strains Sa 1147-06T and Sa 1143-06 represent a novel species, for which the name Chryseobacterium chaponense sp. nov. is proposed. The type strain is Sa 1147-06T (=DSM 23145T =CCM 7737T).

Pseudomonas taiwanensis sp. nov., isolated from soil

A novel Gram-negative, rod-shaped, motile, non-spore-forming bacterial strain, CMST, isolated from soil was characterized using phenotypic and molecular taxonomic methods. 16S rRNA gene sequence analysis revealed that the organism belongs phylogenetically to the genus Pseudomonas. Pseudomonas monteilii, P. plecoglossicida and P. mosselii were the most closely related species, with 16S rRNA gene sequence similarities to the respective type strains of 99.79, 99.73 and 99.59 %. Relatively low gyrB gene sequence similarities (<90 %) and DNA–DNA reassociation values (<51 %) were obtained between the strain and its phylogenetically closest neighbours. The G+C content of strain CMST was 62.7 mol%. The major cellular fatty acids were C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C10 : 0 3-OH. Based on the phenotypic and genetic evidence, the strain is suggested to represent a novel species, for which the name Pseudomonas taiwanensis sp. nov. is proposed. The type strain is CMST (=BCRC 17751T =DSM 21245T).

Chryseobacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems

A bacterial strain (CC-VM-7T), isolated from the faeces of the pill millipede Arthrosphaera magna Attems collected in India, was studied to determine its taxonomic allocation. Cells stained Gram-negative and were rod-shaped. Comparative analyses of the 16S rRNA gene sequence of the strain with those of the most closely related species clearly suggested allocation to the genus Chryseobacterium, with the highest sequence similarities of 99.2 % to Chryseobacterium gleum CCUG 14555T, 98.6 % to Chryseobacterium indologenes CCUG 14556T and 98.4 % to Chryseobacterium aquifrigidense KCTC 12894T. 16S rRNA gene sequence similarities to all other species of the genus Chryseobacterium were below 98 %. The major whole-cell fatty acids were iso-C15 : 0 and iso-C17 : 1 ω9c. DNA–DNA hybridization resulted in relatedness values of only 29.6 % (reciprocal 31.3 %) to Chryseobacterium gleum CCUG 14555T, 41.2 % (reciprocal 38.8 %) to C. indologenes CCUG 14556T and 35.4 % (reciprocal 38.5 %) to C. aquifrigidense KCTC 12894T. DNA–DNA relatedness, biochemical and chemotaxonomic properties clearly show that strain CC-VM-7T represents a novel species, for which the name Chryseobacterium arthrosphaerae sp. nov. is proposed. The type strain is CC-VM-7T (=CCUG 57618T =CCM 7645T).

Chryseobacterium culicis sp. nov., isolated from the midgut of the mosquito Culex quinquefasciatus

A yellow-pigmented bacterial strain, R4-1A(T), isolated from the midgut of the mosquito Culex quinquefasciatus (a vector of lymphatic filariasis), was studied using a polyphasic approach. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of this organism with sequences of type strains of the most closely related species clearly showed an allocation to the genus Chryseobacterium, with the highest sequence similarities (all 97.9 %) to Chryseobacterium jejuense JS17-8(T), C. indologenes ATCC 29897(T), C. arthrosphaerae CC-VM-7(T) and C. aquifrigidense CW9(T). 16S rRNA gene sequence similarities to type strains of other Chryseobacterium species were below 97.5 %. The fatty acid profile of strain R4-1A(T) included the major fatty acids iso-15 : 0, summed feature 4 (comprising iso-15 : 0 2-OH and/or 16 : 1ω7c), iso-17 : 1ω9c and iso-17 : 0 3-OH. DNA-DNA hybridizations with C. jejuense KACC 12501(T), C. indologenes CCUG 14556(T), C. arthrosphaerae CC-VM-7(T) and C. aquifrigidense KCTC 12894(T) resulted in relatedness values of 38.3 % (reciprocal 30.5 %), 29.4 % (32.1 %), 23.2 % (37.2 %) and 29.5 % (47.1 %), respectively. These results and the differentiating biochemical and chemotaxonomic properties show that strain R4-1A(T) represents a novel species, for which the name Chryseobacterium culicis sp. nov. is proposed. The type strain is R4-1A(T) (=LMG 25442(T) =CCM 7716(T)).

Transfer of Sejongia antarctica, Sejongia jeonii and Sejongia marina to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov., Chryseobacterium jeonii comb. nov. and Chryseobacterium marinum comb. nov

The genus Sejongia was described in 2005, with the two species Sejongia antarctica and Sejongia jeonii, mainly on the basis of 16S rRNA gene sequence analysis. At that time, these organisms formed a quite separate branch in a 16S rRNA gene sequence-based tree, but, in subsequent studies, it became obvious that the species S. antarctica and S. jeonii and a third species, Sejongia marina, were most closely related (>95.0% similarity) to some Chryseobacterium species (e.g. Chryseobacterium hominis, C. formosense and C. haifense). In addition, there is no evidence for clear phenotypic (i.e. chemotaxonomic) differences between these organisms that justifies their assignment to different genera. For these reasons, a proposal is made to transfer these species to the genus Chryseobacterium as Chryseobacterium antarcticum comb. nov. (type strain AT1013T=JCM 12381T=IMSNU 14040T=KCTC 12225T), Chryseobacterium jeonii comb. nov. (type strain AT1047T=JCM 12382T=IMSNU 14049T=KCTC 12226T) and Chryseobacterium marinum comb. nov. (type strain IMCC3228T=KCCM 42689T=NBRC 103143T) on the basis of 16S rRNA gene sequence data and published phenotypic data.

Microbial fouling of a reverse osmosis municipal water treatment system

Microbial fouling of a municipal water treatment system using reverse osmosis was investigated. From a combination of growth and molecular assays, it was discovered that the prefilter unit concentrated and facilitated microbial growth, and such growth led to microbial fouling of the reverse osmosis unit. Few cells were observed in the prefilter influent, but substantial microbial contamination was observed in the prefilter effluent, and this correlated with increasing headloss across the prefilter. The effluent caused microbial fouling of the leading elements of the reverse osmosis unit, as determined by reduced permeate flow, analysis of the elements, and assays of the membrane foulant. Both the introduction of microorganisms to the reverse osmosis unit from the prefilter unit and headloss across the prefilter could be effectively controlled through cleansing of the prefilter housing unit with sulfuric acid. Such treatments must be performed at appropriate intervals to prevent subsequent microbial growth in the prefilter unit.

Chryseobacterium bovis sp. nov., isolated from raw cow's milk

Three Gram-negative, rod-shaped, oxidase-positive, aerobic, non-motile bacterial strains, designated H9T, H10 and H15, were isolated during a study on the diversity of culturable psychrotolerant bacteria in raw cow's milk. Comparisons of 16S rRNA gene sequences showed that the three strains were very closely related to each other (sequence similarities of 99.6-99.8 %). A polyphasic taxonomic study of the isolates resulted in their identification as members of the genus Chryseobacterium (family Flavobacteriaceae, phylum Bacteroidetes). The three strains showed < or =96.9 % sequence similarity with respect to the type strains of described Chryseobacterium species, indicating that H9T, H10 and H15 represent a novel species of the genus Chryseobacterium. The three strains grew at 7-37 degrees C (strain H10 grew at up to 41 degrees C), with 0-2.5 % NaCl and at pH 5.0-9.8. The dominant cellular fatty acids of strain H9T were 15 : 0 iso (38.9 %), 15 : 0 anteiso (15.6 %) and 17 : 0 iso 3-OH (12.7 %). Strain H10 also possessed 17 : 1 iso omega 9c (14.8 %) as a major fatty acid. On the basis of phenotypic properties and phylogenetic distinctiveness, the three milk isolates represent a novel species in the genus Chryseobacterium, for which the name Chryseobacterium bovis sp. nov. is proposed. The type strain is H9T (=LMG 24227T =DSM 19482T).

Chryseobacterium hominis sp. nov., to accommodate clinical isolates biochemically similar to CDC groups II-h and II-c

A collection of eight clinical strains from Belgian hospitals and three clinical strains of the CCUG collection were characterized biochemically as being similar to CDC groups II-h and II-c; the latter differs from group II-h only by positivity for sucrose acidification. These 11 strains were found to cluster according to 16S rRNA gene sequence similarity at a level of ≥99.5 %, and on the basis of their tDNA-PCR profile. Based on 16S rRNA gene sequence analysis, this collection of strains was related most closely to Chryseobacterium hispanicum (97.2 %), but they differed from the type strain of this species by the following phenotypic characteristics: growth at 37 °C, negativity for xylose acidification, positivity for acetate assimilation–alkalinization on Simmons’ agar base and absence of flexirubin pigments, and by their tDNA-PCR profile. Strain NF802T showed only 57.8 % DNA–DNA relatedness to the type strain of C. hispanicum. Fatty acid composition did not enable differentiation from C. hispanicum. The DNA G+C content of strain NF802T is 36.5 mol%. The name Chryseobacterium hominis sp. nov. is proposed for this taxon, with type strain NF802T (=CCUG 52711T=CIP 109415T).

Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the Bacillus subtilis group

The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA-DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid sequence similarities among the eight type strains were 75.4-95.0 % and 88.5-99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1-99.8 %. Results showed that gyrB gene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved by gyrB sequence analysis was in agreement with results obtained with DNA-DNA hybridization. It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group.

Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk

Strain H38T was isolated during a study on the diversity of culturable psychrotolerant bacteria in raw milk. Comparative 16S rRNA gene sequence analysis showed that strain H38T belongs to the genus Chryseobacterium (family Flavobacteriaceae, phylum Bacteroidetes), with the highest similarity (96.7 %) to Chryseobacterium hispanicum VP48T. Strain H38T grows aerobically, at 4–41 °C, with 0–2.5 % NaCl and at pH 6.5–10.5. Light induces the formation of yellow carotenoid pigments. The dominant cellular fatty acids are 15 : 0 iso (41.6 %), 15 : 0 anteiso (16.6 %) and 17 : 0 iso 3-OH (10.3 %). The G+C content of the DNA is 37.8 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain H38T (=LMG 24029T =DSM 19056T) is classified in the genus Chryseobacterium as the type strain of a novel species, for which the name Chryseobacterium haifense sp. nov. is proposed.

Paenibacillus taiwanensis sp. nov., isolated from soil in Taiwan

Among a large collection of Taiwanese soil isolates, a novel Gram-variable, rod-shaped, motile and endospore-forming bacterial strain, designated G-soil-2-3(T), was isolated from farmland soil in Wu-Feng, Taiwan. The isolate was subjected to a polyphasic study including 16S rRNA gene sequence analysis, DNA-DNA hybridization experiments, fatty acid analysis and comparative phenotypic characterization. 16S rRNA gene sequence analysis indicated that the organism belongs within the genus Paenibacillus. It contained menaquinone MK-7 as the predominant isoprenoid quinone and anteiso-C(15 : 0) (40.5 %), iso-C(15 : 0) (13.1 %), iso-C(16 : 0) (10.8 %) and anteiso-C(17 : 0) (7.3 %) as the major fatty acids. Phylogenetically, the closest relatives of strain G-soil-2-3(T) were the type strains of Paenibacillus assamensis, Paenibacillus alvei and Paenibacillus apiarius, with 16S rRNA gene sequence similarity of 95.7, 95 and 95.2 %, respectively. DNA-DNA hybridization experiments showed levels of relatedness of 2.8-9.0 % of strain G-soil-2-3(T) with these strains. The G+C content of the DNA was 44.6 mol%. Strain G-soil-2-3(T) was clearly distinguishable from P. assamensis, P. alvei and P. apiarius and thus represents a novel species of the genus Paenibacillus, for which the name Paenibacillus taiwanensis sp. nov. is proposed. The type strain is G-soil-2-3(T) (=BCRC 17411(T)=IAM 15414(T)=LMG 23799(T)=DSM 18679(T)).

Chryseobacterium luteum sp. nov., associated with the phyllosphere of grasses

Three isolates obtained from grass samples were investigated by means of a polyphasic taxonomic study and were shown to represent a novel species within the genus Chryseobacterium. Comparison of 16S rRNA gene sequences and phenotypic features indicated that the three isolates belonged to a single species. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours were Chryseobacterium shigense and Chryseobacterium vrystaatense, which formed a stable cluster with the isolates; this phylogeny was supported by a high bootstrap value and was obtained using different treeing methods. A DNA–DNA hybridization study with the closest neighbour, C. shigense DSM 17126T (98.3 % 16S rRNA gene sequence similarity), clearly demonstrated a separate species status for the grass isolate strain P 456/04T. Comparisons involving physiological properties and whole-cell fatty acid profiles confirmed this result at the phenotypic level. On the basis of these results, strain P 456/04T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium luteum sp. nov. is proposed. The type strain is P 456/04T (=DSM 18605T =LMG 23785T).

Chryseobacterium daeguense sp. nov., isolated from wastewater of a textile dye works

A Gram-negative, rod-shaped bacterial strain, K105T, was isolated from wastewater of a textile dye works in Korea and subjected to a polyphasic taxonomic study. Strain K105T grew optimally at pH 6.5–7.5 and 30–37 °C. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 1 ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C content was 36.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain K105T belonged to the genus Chryseobacterium. Strain K105T exhibited 16S rRNA gene sequence similarity values of less than 96.9 % to the type strains of recognized Chryseobacterium species. Strain K105T differed from phylogenetically related Chryseobacterium species in several phenotypic properties. On the basis of phenotypic and phylogenetic data, strain K105T (=KCTC 12841T=JCM 14362T) is placed in the genus Chryseobacterium as the type strain of a novel species, for which the name Chryseobacterium daeguense sp. nov. is proposed.