Four new species of Chryseobacterium from the rhizosphere of coastal sand dune plants, Chryseobacterium elymi sp. nov., Chryseobacterium hagamense sp. nov., Chryseobacterium lathyri sp. nov. and Chryseobacterium rhizosphaerae sp. nov

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 herbae Isolated from the Rhizospheric Soil of Pyrola calliantha H. Andres in Segrila Mountain on the Tibetan Plateau

A non-motile, Gram-staining-negative, orange-pigmented bacterium called herbae pc1-10T was discovered in Tibet in the soil around Pyrola calliantha H. Andres' roots. The isolate thrived in the temperature range of 10-30 °C (optimal, 25 °C), pH range of 5.0-9.0 (optimum, pH = 6.0), and the NaCl concentration range of 0-1.8% (optimal, 0%). The DNA G+C content of the novel strain was 37.94 mol%. It showed the function of dissolving organophosphorus, acquiring iron from the environment by siderophore and producing indole acetic acid. Moreover, the genome of strain herbae pc1-10T harbors two antibiotic resistance genes (IND-4 and AdeF) encoding a β-lactamase, and the membrane fusion protein of the multidrug efflux complex AdeFGH; antibiotic-resistance-related proteins were detected using the Shotgun proteomics technology. The OrthoANIu values between strains Chryseobacterium herbae pc1-10T; Chryseobacterium oleae CT348T; Chryseobacterium kwangjuense KJ1R5T; and Chryseobacterium vrystaatense R-23566T were 90.94%, 82.96%, and 85.19%, respectively. The in silico DDH values between strains herbae pc1-10T; C. oleae CT348T; C. kwangjuense KJ1R5T; and C. vrystaatense R-23566T were 41.7%, 26.6%, and 29.7%, respectively. Chryseobacterium oleae, Chryseobacterium vrystaatense, and Chryseobacterium kwangjuense, which had 16S rRNA gene sequence similarity scores of 97.80%, 97.52%, and 96.75%, respectively, were its closest phylogenetic relatives. Chryseobacterium herbae sp. nov. is proposed as the designation for the strain herbae pc1-10T (=GDMCC 1.3255 = JCM 35711), which represented a type species based on genotypic and morphological characteristics. This study provides deep knowledge of a Chryseobacterium herbae characteristic description and urges the need for further genomic studies on microorganisms living in alpine ecosystems, especially around medicinal plants.

Ecotin: A versatile protease inhibitor of bacteria and eukaryotes

Serine protease inhibitors are a large family of proteins involved in important pathways and processes, such as inflammatory responses and blood clotting. Most are characterized by a precise mode of action, thereby targeting a narrow range of protease substrates. However, the serine-protease inhibitor ecotin is able to inhibit a broad range of serine proteases that display a wide range of specificities. This specificity is driven by special structural features which allow unique flexibility upon binding to targets. Although frequently observed in many human/animal-associated bacteria, ecotin homologs may also be found in plant-associated taxa and environmental species. The purpose of this review is to provide an update on the biological importance, role in host-microbe interactions, and evolutionary relationship between ecotin orthologs isolated from Eukaryotic and Prokaryotic species across the Tree of Life.

Changes of Endophytic Bacterial Community in Mature Leaves of Prunus laurocerasus L. during the Seasonal Transition from Winter Dormancy to Vegetative Growth

Diverse communities of bacterial endophytes inhabit plant tissues, and these bacteria play important roles for plant growth and health. Cherry laurel (Prunus laurocerasus L.) is a broadleaf evergreen shrub that is widely grown in temperate zones for its ornamental and medicinal properties, however virtually nothing is known about its associated bacterial community. In this study, we analysed the matured one-year-old leaves of this plant using Illumina-based 16S rRNA gene metabarcoding to reveal the community structure of endophytic bacteria and understand its shifts during the seasonal transition from winter dormancy to a spring vegetative state. The overall community was composed of four dominant phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes). Corynebacterium, Acinetobacter, and Chryseobacterium genera were the most prevalent bacteria, comprising 13.3%, 6.9%, and 6.8% of the amplicon sequence variants (ASVs), respectively. The ASV richness and diversity increased significantly in May as compared to other sampling months (February, March, and April). We observed high variation in the overall community structure of endophytic bacteria among collection dates. The variation was only reflected by a few core community members, suggesting that the changes of the endophytic community during winter/spring seasonal transition are mostly associated with the less abundant community members. We identified biomarker taxa for late winter, mid spring, and late spring collection dates. This study is the first one to report on the diversity and composition of bacterial endophytes in the leaves of cherry laurel and its shifts across the dormancy-to-vegetative seasonal transition.

Chryseobacterium endalhagicum sp. nov., isolated from seed of leguminous plant

A Gram-stain-negative, yellow-pigmented bacterium, designated as L7^T, was isolated from seeds of Alhagi sparsifolia Shap., a leguminous plant that grows in northwest PR China. Strain L7^T was found to be non-flagellated, non-spore forming rods which can grow at 10–37 °C, pH 6.0–8.5 and in 0–3 % (v/w) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain L7^T belongs to the genus Chryseobacterium with sequence similarities to Chryseobacterium vietnamense GIMN1.005^T (98.1%), C. bernardetii NCCTC13530^T (98.0%), C. vrystaatense LMG 22846^T (97.9%), C. nakagawai NCTC13529^T (97.7%), C. shigense DSM 17126^T (97.6%) and C. rhizosphaerae RSB3-1^T (97.5%). The average nucleotide identity of strain L7^T to 31 reference strains were 78.6–85.6 %, lower than the species delineation threshold of 95 %. MK-6 was the only respiratory quinone of L7^T and major fatty acids were iso-C_15 : 0, iso-C_17 : 0 3-OH, C_16 : 1 ω7c and/or C_16 : 1 ω6c, isoC_17 : 1 ω9c and/or C_16 : 0 10-methyl. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, two unidentified aminolipids, three unidentified glycolipids and two unidentified lipids. The G+C content of the genome was 38.58 mol%. On the basis of polyphasic taxonomy analyses in this study, strain L7^T is considered to represent a novel species in the genus Chryseobacterium, for which the name Chryseobacterium endalhagicum sp. nov. is proposed. The type strain is L7^T (=MCCC 1K05687^T=JCM 34506^T)

Microbiome Fingerprint as Biomarker for Geographical Origin and Heredity in Crocus sativus: A Feasibility Study

Host–microbiome interactions are specific and not random, making them defining entities for the host. The hypothesis proposed by various researchers earlier, that both plants and animals harbor specific inheritable core microbiome, is being augmented in the present study. Additionally, a case for using microbial fingerprint as a biomarker, not only for plant identification but also as a geographical indicator, has been investigated, taking Crocus sativus, saffron, as a study material. Crocus sativus, a monogenetic herb, on account of its male sterility and vegetative propagation, is reported to lack genome based molecular markers. Cormosphere microbiome (microbiome associated with corm) has been compared across three geographical locations, in two continents, to identify the core and unique microbiome, during the vegetative phase of its growth. Microbiome analysis done at phylum and genus level, using next generation sequencing technology, revealed that cormosphere at three locations harbored common phyla. At genus level, 24 genera were found common to all three geographical locations, indicating them to be part of the core microbiome of saffron. However, there were some bacterial genera unique to Kashmir, Kishtwar, and Morocco that can be used to develop microbial markers/geographical indicators for saffron grown in these regions. This is a preliminary study, indicating that the location specific bacterial community can be used to develop microbial barcodes but needs further augmentation with high coverage data from other saffron growing geographical regions.

Microbiomes of commercially-available pine nuts and sesame seeds

Metagenomic analysis of food is becoming more routine and can provide important information pertaining to the shelf life potential and the safety of these products. However, less information is available on the microbiomes associated with low water activity foods. Pine nuts and sesame seeds, and food products which contain these ingredients, have been associated with recalls due to contamination with bacterial foodborne pathogens. The objective of this study was to identify the microbial community of pine nuts and sesame seeds using targeted 16S rRNA sequencing technology. Ten different brands of each seed type were assessed, and core microbiomes were determined. A total of 21 and 16 unique taxa with proportional abundances >1% in at least one brand were identified in the pine nuts and sesame seeds, respectively. Members of the core pine nut microbiome included the genera Alishewanella, Aminivibrio, Mycoplasma, Streptococcus, and unassigned OTUs in the families of Desulfobacteraceae and Xanthomonadaceae. For sesame seeds, the core microbiome included Aminivibrio, Chryseolina, Okibacterium, and unassigned OTUs in the family Flavobacteriaceae. The microbiomes of these seeds revealed that these products are dominated by environmental bacterial genera commonly isolated from soil, water, and plants; bacterial genera containing species known as commensal organisms were also identified. Understanding these microbiomes can aid in the risk assessment of these products by identifying food spoilage potential and community members which may co-enrich with foodborne bacterial pathogens.

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

Strain CA7^T, a Gram-stain-negative, non-motile, non-spore-forming, aerobic and rod-shaped bacterial strain, was isolated from raw cow's milk collected from a farm affiliated with Chung-Ang University, Anseong, Korea, and characterized by a polyphasic approach. Optimal growth of strain CA7^T was observed on tryptic soy agar at 30 °C and pH 7.0 with 0 % NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CA7^T belonged to the genus Chryseobacterium. The most closely related strains (16S rRNA gene sequence similarity indicated in parentheses), based on the phylogenetic analysis, were Chryseobacterium rhizosphaerae KCTC 22548^T (98.08 %), Chryseobacterium nakagawai CCUG 60563^T (98.61 %), Chryseobacterium jejuense KACC 12501^T (97.85 %) and Chryseobacterium aurantiacum KCTC 62135^T (97.78 %). Whole genome sequencing indicated that the genome size was 5 125 723 bp and had a DNA G+C content of 37.4 mol%. Average nucleotide identity values for strain CA7^T with C. rhizosphaerae, C. nakagawai, C. jejuense, C. aurantiacum, and the type species of the genus Chryseobacterium, C. gleum, were 80.2, 79.8, 79.8, 79.6 and 80.4 %, respectively. The digital DNA-DNA hybridization values of CA7^T compared to C. rhizosphaerae, C. nakagawai, C. jejuense, C. aurantiacum and C. gleum were 24.1, 23.9, 23.9, 23.7 and 24.3 %, respectively. The major fatty acids were iso-C_15 : 0, summed feature 9 (iso-C_17 : 1 ω9c and/or C_16 : 0 10-methyl), iso-C_17 : 0 3-OH and summed feature 3 (iso-C_15 : 0 2-OH and/or C_16 : 1 ω7c). Menaquinone-6 was the only respiratory quinone. The major polar lipid was phosphatidylethanolamine. Based on this polyphasic taxonomic study, strain CA7^T represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium vaccae sp. nov. is proposed. The type strain is CA7^T (=KACC 21402^T=JCM 33749^T).

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.

Isolation of Chryseobacterium siluri sp. nov., from liver of diseased catfish (Silurus asotus)

Yellow-pigmented, circular bacteria (strain SNU WT7) were isolated from the liver of moribund eastern catfish (Silurus asotus). Our study focused on the taxonomic description of SNU WT7 using phylogenetic, phenotypic, and chemotaxonomic analyses. The 16S rRNA gene sequence of the SNU WT7 strain was highly similar to that of Chryseobacterium haifense H38^T (97.29% similarity), followed by Chryseobacterium hominis P2K6^T (97.22% similarity), while other species exhibited similarity values of less than 97.0%. The genome of strain SNU WT7 displayed average nucleotide identity and genome-to-genome distance values of 72.35% and 22.0%, respectively, which clearly indicated that the novel species was distant from the other Chryseobacterium species, with its closest relative being C. haifense H38^T. Furthermore, the phenotypic characteristics, including acid production from glucose, D-fructose, lactose, and maltose, of strain SNU WT 7 differed from those of C. haifense H38^T. The major polar lipid of the strain was phosphatidylethanolamine, and several unidentified aminolipids and lipids were also present. Similar to other Chryseobacterium species, the quinone system was composed mainly of MK-6. The genome of SNU WT7 is 2,690,367 bp with a G + C content of 43.6%. Taken together, our data indicate that the isolate SNU WT7 represents a novel species of the genus Chryseobacterium. Thus, we present the name Chryseobacterium siluri sp. nov. for the novel type strain SNU WT7^T (KCTC 72626, JCM 33707).

Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities

Rhizosphere bacterial communities are vital for plants, yet the composition of rhizobacterial communities and the complex interactions between roots and microbiota, or between microbiota, are largely unknown. In this study, we investigated the structure and composition of rhizobacterial communities in two soybean cultivars and their recombinant inbred lines contrasting in nodulation through 16S rRNA amplicon sequencing in two years of field trials. Our results demonstrate that soybean plants are able to select microbes from bulk soils at the taxonomic and functional level. Soybean genotype significantly influenced the structure of rhizobacterial communities and resulted in dramatically different co-occurrence networks of rhizobacterial communities between different genotypes of soybean plants. Furthermore, the introduction of exogenous rhizobia through inoculation altered soybean rhizobacterial communities in genotype-dependent manner. Rhizobium inoculation not only stimulated the proliferation of potential beneficial microbes but also increased connections in rhizobacterial networks and changed the hub microbes, all of which led to the association of distinctive bacterial communities. Taken together, we demonstrated that the assembly of soybean rhizobacterial communities was determined by both genotype and the introduction of exogenous rhizobia. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents.

Draft Genome Sequences of Seven Chryseobacterium Type Strains

In an honors course on “Omics Sciences,” draft genome sequences of Chryseobacterium elymi KCTC 22547^T, Chryseobacterium flavum KCTC 12877^T, Chryseobacterium hispanicum KCTC 22104^T, Chryseobacterium lathyri KCTC 22544^T, “Candidatus Chryseobacterium massiliae” CCUG 51329^T, Chryseobacterium piscium CCUG 51923^T, and Chryseobacterium rhizosphaerae KCTC 22548^T were generated to facilitate phylogenomic comparisons within the genus.

In an honors course on “Omics Sciences,” draft genome sequences of Chryseobacterium elymi KCTC 22547^T, Chryseobacterium flavum KCTC 12877^T, Chryseobacterium hispanicum KCTC 22104^T, Chryseobacterium lathyri KCTC 22544^T, “Candidatus Chryseobacterium massiliae” CCUG 51329^T, Chryseobacterium piscium CCUG 51923^T, and Chryseobacterium rhizosphaerae KCTC 22548^T were generated to facilitate phylogenomic comparisons within the genus.

Chryseobacterium chengduensis sp. nov. isolated from the air of captive giant panda enclosures in Chengdu, China

A Gram-negative, aerobic, non-motile, rod-shaped bacterial strain, designated 25-1(T), was isolated from the air inside giant panda enclosures at the Chengdu Research Base of Giant Panda Breeding, China. Strain 25-1(T) grew optimally at pH 7.0-8.0, at 28-30 °C and in the presence of NaCl concentrations from 0.0% to 0.5 %. 16S rRNA gene sequence analysis indicated that strain 25-1(T) belongs to the genus Chryseobacterium within the family Flavobacteriaceae and is related most closely to C. carnis G81(T) (96.4% similarity), C. lathyri RBA2-6(T) (95.8% similarity), and C. zeae JM1085(T) (95.8% similarity). Its genomic DNA G+C molar composition was 36.2%. The major cellular fatty acids were iso-C15:0 (44.0%), iso-C17:0 3OH (19.8%) and C16:1 ω7c/16:1 ω6c (12.7%). The only isoprenoid quinone was menaquinone 6 (MK-6). The major polar lipids were phosphatidylethanolamine, two unidentified amino lipids and two unidentified lipids. The DNA-DNA relatedness between strain 25-1(T) and C. lathyri RBA2-6(T) was 38%. Phenotypic, genotypic, and phylogenetic characteristics indicated that strain 25-1(T) is a novel member of the genus Chryseobacterium, for which the name C. chengduensis sp. nov. is proposed. The type strain is 25-1(T) (CCTCC AB2015133(T)=DSM 100396(T)).

Draft Genome Sequence of Chryseobacterium sp. JV274 Isolated from Maize Rhizosphere

We report the draft genome sequence of Chryseobacterium sp. JV274. This strain was isolated from the rhizosphere of maize during a greenhouse experiment. JV274 harbors genes involved in flexirubin production (darA and darB genes), bacterial competition (type VI secretion system), and gliding (bacterial motility; type IX secretion system).

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype

Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea (Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium, and unclassified Enterobacteriacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions.

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 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 hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium

A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated AG13(T), isolated from a rain water pond at a plant nursery in Spain and characterized as a plant-growth-promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best over a temperature range of 15-40 °C, at pH 5.0-8.0 and with 0-4 % (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 37.2 mol%. The strain had 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 and iso-C17 : 0 3-OH. The main polar lipids were phosphatidylethanolamine, aminolipids and several unidentified lipids. The 16S rRNA gene showed 92.0-97.2 % sequence similarity with those of the members of the genus Chryseobacterium. Based on chemotaxonomic and phenotypic traits, and DNA-DNA hybridizations with the type strains of the most closely related species, the isolate is proposed to represent a novel species, Chryseobacterium hispalense, type strain AG13(T) ( = DSM 25574(T) = CCUG 63019(T)). Emended descriptions of the species Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium are also provided.

Plant growth promoting bacteria from Crocus sativus rhizosphere

Present study deals with the isolation of rhizobacteria and selection of plant growth promoting bacteria from Crocus sativus (Saffron) rhizosphere during its flowering period (October-November). Bacterial load was compared between rhizosphere and bulk soil by counting CFU/gm of roots and soil respectively, and was found to be ~40 times more in rhizosphere. In total 100 bacterial isolates were selected randomly from rhizosphere and bulk soil (50 each) and screened for in-vitro and in vivo plant growth promoting properties. The randomly isolated bacteria were identified by microscopy, biochemical tests and sequence homology of V1-V3 region of 16S rRNA gene. Polyphasic identification categorized Saffron rhizobacteria and bulk soil bacteria into sixteen different bacterial species with Bacillus aryabhattai (WRF5-rhizosphere; WBF3, WBF4A and WBF4B-bulk soil) common to both rhizosphere as well as bulk soil. Pseudomonas sp. in rhizosphere and Bacillus and Brevibacterium sp. in the bulk soil were the predominant genera respectively. The isolated rhizobacteria were screened for plant growth promotion activity like phosphate solubilization, siderophore and indole acetic acid production. 50 % produced siderophore and 33 % were able to solubilize phosphate whereas all the rhizobacterial isolates produced indole acetic acid. The six potential PGPR showing in vitro activities were used in pot trial to check their efficacy in vivo. These bacteria consortia demonstrated in vivo PGP activity and can be used as PGPR in Saffron as biofertilizers.This is the first report on the isolation of rhizobacteria from the Saffron rhizosphere, screening for plant growth promoting bacteria and their effect on the growth of Saffron plant.

Identification and virulence of Chryseobacterium indologenes isolated from diseased yellow perch (Perca flavescens)

AIM

To identify pathogen of diseased yellow perch and determine their virulence.

METHODS AND RESULTS

Fifteen Gram-negative bacterial isolates were recovered from the skin lesions of diseased yellow perch (Perca flavescens). Based on API 20NE test, ten isolates were found to share 67.2-99.9% homologies with Chryseobactertium indologenes. Based on fatty acid methyl ester analysis, 13 isolates were found to share similarities with C. indologenes and other species of Chryseobacterium. Based on sequencing results of partial 16S rRNA gene, 13 isolates shared 99% identities (e value = 2e-50) with the 16S rRNA sequence of C. indologenes (GenBank HQ259684). Based on the 16S-23S rRNA intergenic spacer region (ISR) sequence, the 13 isolates shared 88% identity (e value = 1e-165) with the 16S-23S ISR sequence of C. indologenes (GenBank EU014570). T-coffee multiple sequence alignment revealed that the partial 16S rRNA or the 16S-23S ISR sequence of the 13 isolates shared 100% identity with each other. When healthy yellow perch were exposed to the 15 isolates by bath immersion (c. 6 × 10(7) CFU ml(-1) for 1 h), only C. indologenes isolates killed 10-20% of fish, whereas other isolates were avirulent. When yellow perch were exposed to C. indologenes by intraperitoneal injection, mortality was dose dependent, with LD(50) and LD(95) values of 1.5 × 10(8) and 3.2 × 10(8) CFU per fish, respectively.

CONCLUSIONS

Chryseobactertium indologenes could be pathogenic to yellow perch.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report on the isolation of C. indologenes from diseased yellow perch. Virulence studies suggested that C. indologenes could become pathogenic to yellow perch.

Chryseobacterium rigui sp. nov., isolated from an estuarine wetland

A bacterium, designated strain CJ16(T), was isolated from the estuarine wetland of the Han River. Cells of the isolate were yellow-pigmented, Gram-stain-negative, non-motile and rod-shaped. Growth of strain CJ16(T) was observed in TSB at 5-37 °C (optimum 30 °C), at pH 5.0-9.0 (optimum pH 6.0) and with 0-3 % (w/v) NaCl (optimum 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CJ16(T) was most closely related to Chryseobacterium hagamense KCTC 22545(T) (97.2 % 16S rRNA gene sequence similarity). Genomic relatedness based on DNA-DNA hybridization between strain CJ16(T) and C. hagamense KCTC 22545(T) was 23 % (strain CJ16(T) as probe) and 19 % (strain KCTC 22545(T) as probe). Chemotaxonomic analysis revealed that strain CJ16(T) possessed MK-6 as the major isoprenoid quinone and sym-homospermidine as the predominant polyamine. The predominant fatty acids were iso-C15 : 0 (26.9 %), iso-C17 : 0 3-OH (16.8 %) and summed feature 9 (comprising C16 : 0 10-methyl and/or iso-C17 : 1ω9c; 10.5 %). The DNA G+C content of strain CJ16(T) was 37.9 mol%. Based on phenotypic, genotypic and phylogenetic studies, strain CJ16(T) represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium rigui sp. nov. is proposed. The type strain is CJ16(T) ( = KACC 16560(T)  = JCM 18078(T)).

Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil

A Gram-reaction-negative, yellow-pigmented, gliding, rod-shaped, aerobic bacterium (RA5-111T) was isolated from foreshore soil. The taxonomic status of the novel isolate was determined using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain RA5-111T could be assigned to the genus Gramella, with sequence similarities of 97.7, 97.3 and 96.2 % to the type strains of Gramella echinicola, Gramella portivictoriae and Gramella marina, respectively. Chemotaxonomic and phenotypic characteristics also supported the affiliation of strain RA5-111T with the genus Gramella. The genomic DNA G+C content was 39.1 mol%. The isolate contained MK-6 as the predominant menaquinone, iso-C15 : 0, iso-C17 : 0 3-OH and a summed feature (iso-C15 : 0 2-OH and/or C16 : 1ω7c) as major fatty acids, and phosphatidylethanolamine and unknown phospholipids as the polar lipids. DNA–DNA relatedness, phenotypic, genotypic and chemotaxonomic data clearly indicate that the isolate represents a novel species of the genus Gramella, for which the name Gramella gaetbulicola sp. nov. is proposed. The type strain is RA5-111T ( = KCTC 23022T  = JCM 16528T  = NBRC 106272T).

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.