Genus Chryseobacterium Research Articles

Chryseobacterium formosus sp. nov., a bacterium isolated from an ancient tree trunk.

A Gram-reaction-negative, non-motile and rod-shaped bacterium, designated as THG-DN3.6(T), was isolated from an ancient tree trunk from Republic of Korea. On the basis of 16S rRNA gene sequence analysis, strain THG-DN3.6(T) was shown to belong to the genus Chryseobacterium and the highest similarity to Chryseobacterium indoltheticum LMG 4025(T) (97.2%) and the closest phylogenetic relatives were Chryseobacterium scophthalmum (96.8%), Chryseobacterium piscium (96.7%) and Chryseobacterium balustinum KCTC 2903(T) (96.3%). The DNA G + C content of the isolate was 33.2 mol%. The predominant isoprenoid quinone was menaquinone-6. The major fatty acids were iso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω7t and/or iso-C15:0 2-OH), iso-C17:1 ω9c and iso-C17:0 3-OH. The major polar lipids of strain THG-DN3.6(T) were phosphatidylethanolamine. The mean DNA-DNA relatedness of strain THG-DN3.6(T) to C. indoltheticum LMG 4025(T) was 52 ± 0.5%. Based on the results of polyphasic characterization, strain THG-DN3.6(T) represented a novel species within the genus Chryseobacterium, for which the name Chryseobacterium formosus sp. nov. is proposed. The type strain is THG-DN3.6(T) (=KCTC 42606 = CCTCC AB 2015118). The NCBI GenBank accession number for the 16S rRNA gene sequence of strain THG-DN3.6(T) is KM035938.

Chryseobacterium solani sp. nov., isolated from field-grown eggplant rhizosphere soil.

Strain THG-EP9T, a Gram-stain-negative, aerobic, motile, rod-shaped bacterium was isolated from field-grown eggplant (Solanum melongena) rhizosphere soil collected in Pyeongtaek, Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-EP9T had closest similarity with Chryseobacterium ginsenosidimutans THG 15T (97.3 % 16S rRNA gene sequence similarity), Chryseobacterium soldanellicola PSD1-4T (97.2%), Chryseobacterium zeae JM-1085T (97.2%) and Chryseobacterium indoltheticum LMG 4025T (96.8%). DNA-DNA hybridization showed 5.7% and 9.1% DNA reassociation with Chryseobacterium ginsenosidimutans KACC 14527T and Chryseobacterium soldanellicola KCTC 12382T, respectively. Chemotaxonomic data revealed that strain THG-EP9T possesses menaquinone-6 as the only respiratory quinone and iso-C15 : 0 (29.0%), C16 : 0 (12.5%) and iso-C17 : 0 3-OH (11.9 %) as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified glycolipids, six unidentified aminolipids and two unidentified polar lipids. The DNA G+C content was 35.3 mol%. These data corroborated the affiliation of strain THG-EP9T to the genus Chryseobacterium. Thus, the isolate represents a novel species of this genus, for which the name Chryseobacterium solani sp. nov. is proposed, with THG-EP9T ( = KACC 17652T = JCM 19456T) as the type strain.

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 profundimaris sp. nov., a new member of the family Flavobacteriaceae isolated from deep-sea sediment.

A Gram-stain negative, strictly aerobic, rod-shaped, non-motile bacterium, designated strain DY46(T), was isolated from Atlantic Ocean sediment. The isolate was found to grow in medium containing 0-3.0% (w/v) NaCl (optimally at 0-1.0%), at 4-37°C and pH 5.0-8.0. Chemotaxonomic analysis detected MK-6 as the sole isoprenoid quinone. The major fatty acids were identified iso-C15:0, iso-C17:0 3-OH, iso-C17:1 ω9c and summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1 ω7c). The DNA G+C content was determined to be 40.7mol%. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain DY46(T) falls within the cluster comprising Chryseobacterium species. The levels of 16S rRNA gene sequence similarity between strain DY46(T) and the type strains of the Chryseobacterium species with validly published names ranged from 92.4 to 99.1%, the high values (>97%) being with Chryseobacterium takakiae A1-2(T) (99.1%), C. taiwanense BCRC 17412(T) (98.0%), C. taeanense PHA3-4(T) (97.3%), C. hispalense DSM 25574(T) (97.3%), C. camelliae THG C4-1(T) (97.2%), C. gregarium DSM 19109(T) (97.1%) and C. wanjuense R2A10-2(T) (97.0%). The DNA-DNA relatedness values between strain DY46(T) and the type strains of the above closely related species were 47, 57, 24, 34, 6, 40 and 21%, respectively. On the basis of phenotypic and genotypic characteristics, strain DY46(T) represents a novel member within the genus Chryseobacterium, for which the name Chryseobacterium profundimaris is proposed. The type strain is DY46(T) (=CGMCC 1.12663(T)=JCM 19801(T)).

Optimization of culture conditions for flexirubin production by Chryseobacterium artocarpi CECT 8497 using response surface methodology.

Flexirubins are the unique type of bacterial pigments produced by the bacteria from the genus Chryseobacterium, which are used in the treatment of chronic skin disease, eczema etc. and may serve as a chemotaxonomic marker. Chryseobacterium artocarpi CECT 8497, an yellowish-orange pigment producing strain was investigated for maximum production of pigment by optimizing medium composition employing response surface methodology (RSM). Culture conditions affecting pigment production were optimized statistically in shake flask experiments. Lactose, l-tryptophan and KH2PO4 were the most significant variables affecting pigment production. Box Behnken design (BBD) and RSM analysis were adopted to investigate the interactions between variables and determine the optimal values for maximum pigment production. Evaluation of the experimental results signified that the optimum conditions for maximum production of pigment (521.64 mg/L) in 50 L bioreactor were lactose 11.25 g/L, l-tryptophan 6 g/L and KH2PO4 650 ppm. Production under optimized conditions increased to 7.23 fold comparing to its production prior to optimization. Results of this study showed that statistical optimization of medium composition and their interaction effects enable short listing of the significant factors influencing maximum pigment production from Chryseobacterium artocarpi CECT 8497. In addition, this is the first report optimizing the process parameters for flexirubin type pigment production from Chryseobacterium artocarpi CECT 8497.

Chryseobacterium polytrichastri sp. nov., isolated from a moss (Polytrichastrum formosum), and emended description of the genus Chryseobacterium.

A Gram-stain negative, rod-shaped and non-endospore forming bacterium, designated strain YG4-6(T), was isolated from Polytrichastrum formosum collected from Gawalong glacier in Tibet, China and characterized by using a polyphasic taxonomic approach. The predominant fatty acids of strain YG4-6(T) were identified as iso-C15:0 (29.3 %), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c as defined by MIDI, 23.5 %) and iso-C17:0 3-OH (16.5 %). The major polar lipids were found to consist of five unidentified aminolipids and three unidentified lipids. Strain YG4-6(T) was found to contain MK-6 as the dominant menaquinone and the G+C content of its genomic DNA was determined to be 37.3 mol%. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain YG4-6(T) is affiliated to Chryseobacterium species, and its closest related species were Chryseobacterium aahli T68(T) (97.9 % sequence similarity), Chryseobacterium zeae JM-1085(T) (97.8 % sequence similarity), Chryseobacterium yeoncheonense DCY67(T) (97.6 % sequence similarity) and Chryseobacterium soldanellicola NBRC 100864(T) (97.2 % sequence similarity). However, the DNA-DNA relatedness values between these strains and strain YG4-6(T) were found to be clearly below 70 %. Based on the phylogenetic inference and phenotypic data, strain YG4-6(T) is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium polytrichastri sp. nov. is proposed. The type strain is YG4-6(T) (=CGMCC 1.12491(T) = DSM 26899(T)). An emended description of the genus Chryseobacterium is also proposed.

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 AG1-2(T), 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 AG1-2(T) 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 AG1-2(T) 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 AG1-2(T) was affiliated to species of the genus Chryseobacterium, and its closest related species were Chryseobacterium taiwanense Soil-3-27(T), Chryseobacterium hispalense AG13(T), Chryseobacterium camelliae THG C4-1(T) and Chryseobacterium taeanense PHA3-4(T) 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 AG1-2(T) were 29, 21, 21 and 45%, respectively. Based on phylogenetic inference and phenotypic data, strain AG1-2(T) 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 AG1-2(T) ( = CGMCC 1.12488(T) = DSM 26898(T)).

Diversity of bacteria carried by pinewood nematode in USA and phylogenetic comparison with isolates from other countries.

Pine wilt disease (PWD) is native to North America and has spread to Asia and Europe. Lately, mutualistic relationship has been suggested between the pinewood nematode (PWN), Bursaphelenchus xylophilus the causal nematode agent of PWD, and bacteria. In countries where PWN occurs, nematodes from diseased trees were reported to carry bacteria from several genera. However no data exists for the United States. The objective of this study was to evaluate the diversity of the bacterial community carried by B. xylophilus, isolated from different Pinus spp. with PWD in Nebraska, United States. The bacteria carried by PWN belonged to Gammaproteobacteria (79.9%), Betaproteobacteria (11.7%), Bacilli (5.0%), Alphaproteobacteria (1.7%) and Flavobacteriia (1.7%). Strains from the genera Chryseobacterium and Pigmentiphaga were found associated with the nematode for the first time. These results were compared to results from similar studies conducted from other countries of three continents in order to assess the diversity of bacteria with associated with PWN. The isolates from the United States, Portugal and China belonged to 25 different genera and only strains from the genus Pseudomonas were found in nematodes from all countries. The strains from China were closely related to P. fluorescens and the strains isolated from Portugal and USA were phylogenetically related to P. mohnii and P. lutea. Nematodes from the different countries are associated with bacteria of different species, not supporting a relationship between PWN with a particular bacterial species. Moreover, the diversity of the bacteria carried by the pinewood nematode seems to be related to the geographic area and the Pinus species. The roles these bacteria play within the pine trees or when associated with the nematodes, might be independent of the presence of the nematode in the tree and only related on the bacteria's relationship with the tree.

Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense

A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated CT348T, isolated from the ectorhizosphere of an organic olive tree in Spain and characterised as an efficient plant growth promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best in a temperature range of 5–35°C, at pH 5.0–8.0 and with 0–1% (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Chryseobacterium. The DNA G+C content of the novel strain was 38.2mol%. The strain contained a polyamine pattern with sym-homospermidine as the major compound and produced flexirubin-type pigments. MK-6 was the dominant menaquinone and the major cellular fatty acids were iso-C15:0, C17:1ω9c, iso-C17:0 3-OH and iso-C15:0 2-OH. The main polar lipids were phosphatidylethanolamine and several unidentified lipids and aminolipids. The 16S rRNA gene showed 92.2–97.8% sequence identity with the members of the genus Chyseobacterium. Based on the phenotypic traits and DNA–DNA hybridizations with the type strains of the most closely related species, the isolate is shown to represent a novel species, Chyseobacterium oleae, type strain CT348T (=DSM 25575 =CCUG 63020). Emended descriptions of the genus Chryseobacterium and C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense are also proposed.

Simultaneous heterotrophic nitrification and aerobic denitrification by Chryseobacterium sp. R31 isolated from abattoir wastewater.

A heterotrophic carbon utilizing microbe (R31) capable of simultaneous nitrification and denitrification (SND) was isolated from wastewater of an Indian slaughterhouse. From an initial COD value of 583.0 mg/L, 95.54% was removed whilst, from a starting NH4 +-N concentration of 55.7 mg/L, 95.87% was removed after 48 h contact. The concentrations of the intermediates hydroxylamine, nitrite, and nitrate were low, thus ensuring nitrogen removal. Aerobic denitrification occurring during ammonium removal by R31 was confirmed by utilization of both nitrate and nitrite as nitrogen substrates. Glucose and succinate were superior while acetate and citrate were poor substrates for nitrogen removal. Molecular phylogenetic identification, supported by chemotaxonomic and physiological properties, assigned R31 as a close relative of Chryseobacterium haifense. The NH4 +-N utilization rate and growth of strain R31 were found to be higher at C/N = 10 in comparison to those achieved with C/N ratios of 5 and 20. Monod kinetic coefficients, half saturation concentration (K s), maximum rate of substrate utilization (k), yield coefficient, (Y) and endogenous decay coefficient (K d) indicated potential application of R31 in large-scale SND process. This is the first report on concomitant carbon oxidation, nitrification, and denitrification in the genus Chryseobacterium and the associated kinetic coefficients.

Resistance to heavy metals and bioaccumulation of lead and zinc by Chryseobacterium solincola strain 1YB-R12T isolated from soil

A novel species of the genus Chryseobacterium which was isolated from soil, has been studied for resistance to heavy metals (lead, chromium, nickel, zinc, cadmium, copper and cobalt), antibiotic and its capacities for bioaccumulation of lead and zinc. It exhibited high minimal inhibitory concentration (MIC) values for metal ions tested ranging from 75 mg/l to 500 mg/l and antibiotic resistance to imipenem, cefuroxim, tetracyclin, nalidixic acid, fusidic acid, pipemidic acid, fosfomycin, cefalotin, dibekacin, furans and nitrofurantoin. The strain was able to accumulate more than 90% of lead and zinc during the active growth cycle. Study of pH effect on heavy metal removal indicated that the metal ion accumulation increased with increasing pH. Since Chryseobacterium solincolacouldgrow at the presence of significant concentrations of toxic metals and because of its high metal accumulation capacity in aerobic conditions, may be potentially applicable in situ bioremediation of heavy metals contaminating aqueou...

Molecular and functional characterization of bacteria isolated from straw and goat manure based vermicompost

A total of 193 vermicompost bacteria that exhibit antagonistic and biofertilizing potential were isolated from straw and goat manure based vermicompost produced by earthworm Eisenia foetida and taxonomically designated on the basis of their 16S rRNA sequence homology and subsequent molecular phylogeny analysis. Bacteria belonged to three major genera viz., Pseudomonas (15%), Bacillus (57%), Microbacterium (12%) and remaining bacteria comprised of genus Acinetobacter (5%), Chryseobacterium (3%), Arthrobacter, Pseudoxanthomonas, Stenotrophomonas, Paenibacillus, Rhodococcus, Enterobacter, Rheinheimera and Cellulomonas. Of 193 bacteria, 96 strains (49%) showed antagonistic potential against phytopathogenic fungus. Functional characterization of the bacteria was assessed by the production of protease, cellulase, lipase, xylanase, chitinase, amylase, gelatinase, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, indole-3-acetic acid (IAA), phosphate solubilization, nitrate reduction, and assimilation of different carbon sources. The bacterial strains showed a varying degree of carbon utilization profiles and majority of them were known to utilize citrate, malonate. A total of 86 strains produced protease (44%) and 99 strains (51%) produced cellulase. 51 strains (26%) produced IAA, 99 strains (51%) produced siderophores and 124 strains (64%) produced ACC deaminase. 52 strains (27%) showed phosphate solubilization while 24 strains (12%) produced HCN. 43 strains (22%) showed antibacterial activity against human pathogens under in vitro conditions. None of the strains tested positive for lipase and chitinase. A total of 31 strains (16%) produced DNase, 80 strains (41%) produced xylanase and 93 strains (48%) produced amylase. Among the vermicompost bacteria reported in the present study, Bacillus was found to be the predominant bacteria followed by Pseudomonas and Microbacterium. Present study, reports the molecular and functional characterization of vermicompost bacteria.

Chryseobacterium yeoncheonense sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field

A Gram-staining negative, aerobic, non-motile, non-flagellate, yellow-pigmented, rod-shaped bacterial strain, designated strain DCY67(T), was isolated from ginseng field in Republic of Korea. Strain DCY67(T) contained β-glucosidase activity which converts ginsenoside Rb1 to compound K. Optimum growth of DCY67(T) occurred at 30°C and pH 6.0-6.5. Analysis of the 16S rRNA gene sequences revealed that strain DCY67(T) belonged to the family Flavobacteriaceae and was most closely related to Chryseobacterium ginsenosidimutans THG 15(T) (97.5%). The genomic DNA G+C content was 36.1mol%. The predominant quinones were MK-6 (90.9%) and MK-7 (9.15%). The major fatty acids were iso-C15:0, summed feature 3 (containing C16:1 ω7c and/or C16:1 ω6c) and iso-C17:0 3-OH. On the basis of these phenotypic, genotypic and chemotaxonomic studies, strain DCY67(T) represents a novel species of the genus Chryseobacterium, for which, name Chryseobacterium yeoncheonense sp. nov. proposed the type strain is DCY67(T) (=KCTC 32090(T)=JCM 18516(T)).

Sequence Analysis of the Cas1 Gene in <i>Riemerella anatipestifer</i>

Objective: The aim was to analyze Riemerella anatipestifer (RA) Cas1 gene and acquire more useful information for guiding the further study of the gene. Methods: Using bioinformatics method, sequence analysis of RA Cas1 gene was carried out with some databases and software. Results: Composition analysis of RA Cas1 gene, and homology search, sequence alignment, phylogenetic tree analysis and physicochemical property analysis of RA Cas1 protein were performed. Homology search revealed that Cas1 protein sequence of R. anatipestifer showed high similarity to those of strains within the Genus Capnocytophaga and Chryseobacterium, in accordance with the result of multiple sequence alignment and phylogenetic tree analysis. The rare codon analysis showed that there was little rare codon string in RA Cas1 gene. Conclusion: Cas1 gene of R. anatipestifer was evolutionally closely related to those of the Genus Capnocytophaga and Chryseobacterium, and can be over-expressed in E.coli without considering the impact of rare codons on translation.

Xanthomonads and other yellow-pigmented Xanthomonas-like bacteria associated with tomato seeds in Tanzania

Tomato ( Solanum lycopersicum L.) seeds habour unique bacterial community that can be pathogenic or beneficial to their host. Xanthomonas causing bacterial leaf spot (BLSX) on tomato and other yellow-pigmented xanthomonads-like bacteria (XLB) that closely resemble BLSX were obtained from tomato seeds collected from Northern, Central and Southern highland regions of Tanzania. A total of 73 strains were isolated from 52 seed samples of 15 tomato cultivars. Results obtained with Biolog and sequence analysis of the 16S rRNA gene showed that samples originating from Central Tanzania harbored the most diverse populations of XLB and BLSX as compared to Northern and Southern Tanzania. The predominant bacterial genera in tomato seeds were Stenotrophomonas , Sphingomonas , Chryseobacterium , Xanthomonas , Pantoea and Flavobacterium . All strains identified by Biolog as Xanthomonas with exception of Xanthomonas campestris pv. malvacearum , were pathogenic on tomato and pepper plants. Strains identified by Biolog as Sphingomonas sanguinis and Sphingomonas terrae also incited black rot symptoms on pepper leaves. However, bacterial strains belonging to the genus Stenotrophomonas , Chryseobacterium , Pantoea and Flavobacterium were not pathogenic on tomato and pepper. Phylogenetic analysis showed that strains of the genus Xanthomonas are more closely related to Stenotrophomonas and Pantoea compared to the other bacterial genera found in tomato seeds. Key words: Xanthomonas , yellow-pigmented bacteria, seed, tomato, phylogeny.

Prokaryotic ultramicroforms in a Sphagnum peat bog of upper Volga catchment

The waters of small lakes located in swampy catchment areas of upper Volga contain considerable amounts of ultrasmall microbial cells that pass through 0.22-μm-pore-size filters. As shown in our previous study [1], most of these cells represent the bacterial genera Herbaspirillum, Herminiimonas, Curvibacter, and Burkholderia of the class Betaproteobacteria, as well as euryarchaea of the uncharacterized clade LDS. The aim of the present study was to investigate the possible effect of the waters draining swampy areas on the composition of the filterable microbial fraction in lakes fed by swampy catchments. To address this question molecular identification was performed of prokaryotic ultramicroforms in the peat of the ombrotrophic Sphagnum bog Obukhovskoe, located, like the lakes studied previously [1], in the Mologa-Sheksna catchment area. The number of filterable microorganisms in 1 g wet peat was 3.8 × 106 cells, or 0.5% of total microbial cell number in the peat. From the DNA of the filterable cell fraction, 100 clones of bacterial and 77 clones of archaeal 16S rRNA genes were obtained. The bacterial clone library contained 16S rRNA gene sequences representing the classes Beta- and Gammaproteobacteria (the genera Janthinobacterium and Pseudomonas, respectively) and the phylum Bacteroidetes (the genera Chryseobacterium and Epilithonimonas) and differed significantly from the clone library of bacterial ultramicroforms of lake water. By contrast, the pools of filterable archaea in bogs and lakes were essentially similar. They were represented by the euryarchaeal clade LDS and methanogens of the orders Methanobacteriales and Methanosarcinales. Additionally, the pool of filterable archaea of the bog included methanogens of the order Methanomicrobiales and representatives of the uncharacterized euryarchaeal clade RC-V (Rice Cluster V) and of the phylum Thaumarchaeota.

Chryseobacterium tructae sp. nov., isolated from rainbow trout (Oncorhynchus mykiss)

Three pale-orange bacteria (strains 1083-08, 1084-08T and 1095B-08) were isolated from diseased rainbow trout. The isolates were Gram-staining-negative, catalase- and oxidase-positive, rod-shaped cells. Analyses of their 16S rRNA gene sequences confirmed their adscription to the genus Chryseobacterium. The three isolates shared 100% 16S rRNA gene sequence similarity and 98.5% similarity with Chryseobacterium indologenes CCUG 14556T, being the closest phylogenetically related species. Genomic DNA–DNA hybridization similarity values between the three isolates were 94–100% and 2–39% between strain 1084-08T and the type strains of other related Chryseobacterium species, confirming that the isolates represent a novel species within the genus Chryseobacterium. The DNA G+C content of the species was 33.6–36.1mol%. The predominant respiratory quinone of strain 1084-08T was MK-6 and the major fatty acids were iso-C15:0, iso-C17:1ω9c, iso-C17:0 3-OH and C16:1ω6c. The isolates were distinguished from related Chryseobacterium species by a number of phenotypic properties. Based on the phenotypic, genotypic and phylogenetic findings, it is proposed that the new isolates from rainbow trout be classified as a new species of the genus Chryseobacterium, with the name of Chryseobacterium tructae sp. nov. The type strain is 1084-08T (=CECT 7798T=CCUG 60111T).

Chryseobacterium oncorhynchi sp. nov., isolated from rainbow trout ( Oncorhynchus mykiss)

Genotypic and phenotypic analyses were performed on five Gram-negative, catalase and oxidase-positive, rod-shaped bacteria isolated from the gill and liver of four rainbow trout. Studies based on comparative 16S rRNA gene sequence analysis showed that the five new isolates shared 99.8–100% sequence similarity and that they belong to the genus Chryseobacterium. The nearest phylogenetic neighbours of the strain 701B-08 T were Chryseobacterium ureilyticum F-Fue-04IIIaaaa T (99.1% 16S rRNA gene sequence similarity) and Chryseobacterium joosteii LMG 18212 T (98.6%). DNA–DNA hybridization values between the five isolates were 91–99% and ranged from 2 to 53% between strain 701B-08 T and the type strains of phylogenetically closely related species of Chryseobacterium. Strain 701B-08 T had a DNA G + C content of 36.3 mol%, the major fatty acids were iso-C 15:0, iso-C 17:1 ω9c, C 16:1 ω6c and iso-C 17:0 3-OH and the predominant respiratory quinone was MK-6. The novel isolates were distinguished from related Chryseobacterium species by physiological and biochemical tests. The genotypic and phenotypic properties of the isolates from rainbow trout suggest their classification as representatives of a novel species of the genus Chryseobacterium, for which the name Chryseobacterium oncorhynchi sp. nov. is proposed. The type strain is 701B-08 T (=CECT 7794 T = CCUG 60105 T).

Novel ultramicrobacteria, strains NF4 and NF5, of the genus Chryseobacterium: Facultative epibionts of Bacillus subtilis

Two strains, NF4 and NF5, of a yellow-colored gram-negative bacterium were isolated from sediments of Lake Baikal and from old oil sludge of the Nizhnekamsk oil-processing plant. The cells of the strains are ultrasmall coccoids or short rods, measuring 0.2–0.4 × 0.2–0.5 μm; the average cell volume ranges from 0.004 to 0.04 μm3. A considerable proportion (30–60%) of cells have nanometer dimensions (180–300 nm in diameter and 0.004–0.02 μm3 in volume). The new isolates are thus among the smallest representatives of presently known free-living ultramicrobacteria. The two studied isolates are gram-negative nonmotile cells possessing a pronounced outer membrane. The cells do not have flagella and are not capable of gliding motility. They divide by constriction, budding, and multiple septation. The multiplicity of reproduction mechanisms results in a high degree of cell polymorphism. The isolates are chemoorganotrophic, aerobic, psychrotolerant, oxidase- and catalase-positive. Their characteristic trait is the absence of extracellular hydrolytic enzymes, such as proteases, lipases, pectinases, and cellulases. Menaquinone MK-6 is the main respiratory quinone; the flexirubin pigment was not detected. The G + C contents of the DNA of strains NF4 and NF5 are 40.8 and 40.5 mol %, respectively. The DNA-DNA hybridization level of strains NF4 and NF5 was close to 100%. Analysis of the 16S rRNA gene sequences and the fatty acid compositions showed that the isolates are most closely related to certain representatives of the genus Chryseobacterium (C. solincola, C. antarcticum, and C. jeonii). However, the differences in the 16S rRNA gene sequences, as well as in the phenotypic properties, such as formation of ultrasmall cells, the absence of extracellular hydrolases, oligotrophy, and the capacity for epibiosis on bacterial cells, suggest that the studied strains belong to a new species of the genus Chryseobacterium. The capacity for epibiosis, i.e., the ability to exist in a tightly adhered state on the surfaces of host Bacillus subtilis cells, is a peculiar trait of the studied isolates. It is assumed that adhesion of the cells of strains NF4 and NF5 (members of the phylum Bacteroidetes) occurs via by the same unique mechanism as the mechanism that we previously described for representatives of Alphaproteobacteria (Kaistia sp., NF1, and NF3), which use polysaccharide chains equipped with sticky granules as trapping and constricting cords.

Degradation of N-Acylhomoserine Lactone Quorum Sensing Signaling Molecules by Potato Root Surface-Associated Chryseobacterium Strains

N-Acylhomoserine lactones (AHLs) are used as quorum-sensing signaling molecules by many Gram-negative bacteria. Here, 413 bacterial strains were obtained from the roots of potato plants and screened for AHL-degrading bacteria using Chromobacterium violaceum reporter strains. Sixty one isolates degraded N-hexanoyl-L-homoserine lactone (C6-HSL) within 24 h. Based on their 16S rRNA gene sequences, most of these isolates were assigned to the genus Chryseobacterium and divided into eight groups. Most of the strains degraded N-decanoyl-L-homoserine lactone (C10-HSL) and were active against 3-oxo-substituted AHLs. Groups V and VI were more effective at inactivating AHLs. One group V strain, StRB402, showed putative AHL-lactonase activity. This is the first report of AHL-degrading Chryseobacterium strains.