Pseudoxanthomonas composti sp. nov., isolated from compost.

A Gram-staining negative bacterium, designated as GSS15T, was isolated from compost in Guangzhou, China. Cells of strain GSS15T were rod-shaped and non-motile. The isolate was able to grow at 15-42 °C (optimum 30 °C) and pH 6.0-11.0 (optimum pH 8.0), and tolerate up to 6.0% NaCl (w/v). When the 16S rRNA gene sequence of the isolate was compared with those of other bacteria, the highest similarity was observed with Pseudoxanthomonas helianthi roo10T (96.9%). Furthermore, strain GSS15T showed low ANI (75.7-79.5%) and DDH (24.2-18.3%) values to the closely related species. Q-8 was the predominant respiratory quinone. The major cellular fatty acids ( > 5%) were iso-C15:0 (18.7%), C16:1ω7c (18.6%), anteiso-C15:0 (13.2%), C16:0 (9.8%), and iso-C16:0 (8.8%). The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Based on its phenotypic, chemotaxonomic and genotypic data, strain GSS15T (= KCTC 52974T = MCCC 1K03334T) is designated as the type strain of a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas composti sp. nov. is proposed.

Taxonomy and physiology of Pseudoxanthomonas arseniciresistens sp. nov., an arsenate and nitrate-reducing novel gammaproteobacterium from arsenic contaminated groundwater, India.

Reductive transformation of toxic arsenic (As) species by As reducing bacteria (AsRB) is a key process in As-biogeochemical-cycling within the subsurface aquifer environment. In this study, we have characterized a Gram-stain-negative, non-spore-forming, rod-shaped As reducing bacterium designated KAs 5-3T, isolated from highly As-contaminated groundwater of India. Strain KAs 5-3T displayed high 16S rRNA gene sequence similarity to the members of the genus Pseudoxanthomonas, with P. mexicana AMX 26BT (99.25% similarity), P. japonensis 12-3T (98.9 0%), P. putridarboris WD-12T (98.02%), and P. indica P15T (97.27%) as closest phylogenetic neighbours. DNA-DNA hybridization study unambiguously indicated that strain KAs 5-3T represented a novel species that was separate from reference strains of P. mexicana AMX 26BT (35.7%), P. japonensis 12-3T (35.5%), P. suwonensis 4M1T (35.5%), P. wuyuanensis XC21-2T (35.0%), P. indica P15T (32.5%), P. daejeonensis TR6-08T (32.0%), and P. putridarboris WD12T (22.1%). The DNA G+C content of strain KAs 5-3T was 64.9 mol %. The predominant fatty acids were C15:0 (37.4%), C16:0 iso (12.6%), C17:1 iso ω9c (10.5%), C15:0 anteiso (9.5%), C11:0 iso 3-OH (8.5%), and C16:1 ω7c/ C16:1 ω6c (7.5%). The major polar lipids were diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, and two unknown phospholipids (PL1, PL2). Ubiquinone 8 (Q8) was the predominant respiratory quinone and spermidine was the major polyamine of the strain KAs 5-3T. Cells of strain KAs 5-3T showed the ability to use O2, As5+, NO3-, NO2-, and Fe3+ as terminal electron acceptors as well as to reduce As5+ through the cytosolic process under aerobic incubations. Genes encoding arsenate reductase (arsC) for As-detoxification, nitrate- and nitrite reductase (narG and nirS) for denitrification were detected in the strain KAs 5-3T. Based on taxonomic and physiological data, strain KAs 5-3T is described as a new representative member of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas arseniciresistens sp. nov. is proposed. The type strain is KAs 5-3T (= LMG 29169T = MTCC 12116T = MCC 3121T).

Genomic analysis of Luteimonas abyssi XH031(T): insights into its adaption to the subseafloor environment of South Pacific Gyre and ecological role in biogeochemical cycle.

BACKGROUND: Luteimonas abyssi XH031(T), which was previously isolated from subseafloor environment of the South Pacific Gyre (SPG), was an aerobic, gram-negative bacterium, and was identified to be a novel species of the genus Luteimonas in the family of Xanthomonadaceae. The nutrients utilization and metabolic mechanisms of XH031(T) indicate its plasticity. In view of the above characteristics, its genome was sequenced, and an in-depth analysis of the XH031(T) genome was performed to elucidate its adaption to extreme ecological environment. RESULTS: Various macromolecules including polysaccharide, protein, lipid and DNA could be degraded at low temperature by XH031(T) under laboratory conditions, and its degradation abilities to starch, gelatin and casein were considerably strong. Genome sequence analysis indicated that XH031(T) possesses extensive enzyme-encoding genes compared with four other Luteimonas strains. In addition, intricate systems (such as two-component regulatory systems, secretion systems, etc.), which are often used by bacteria to modulate the interactions of bacteria with their environments, were predicted in the genome of XH031(T). Genes encoding a choline-glycine betaine transporter and 99 extracellular peptidases featured with halophilicity were predicted in the genome, which might help the bacterium to adapt to the salty marine environment. Moreover, there were many gene clusters in the genome encoding ATP-binding cassette superfamily transporters, major facilitator superfamily transporters and cytochrome P450s that might function in the process of various substrate transportation and metabolisms. Furthermore, drug resistance genes harbored in the genome might signify that XH031(T) has evolved hereditary adaptation to toxic environment. Finally, the annotation of metabolic pathways of the elements (such as carbon, nitrogen, sulfur, phosphor and iron) in the genome elucidated the degradation of organic matter in the deep sediment of the SPG. CONCLUSIONS: The genome analysis showed that XH031(T) had genetic advantages to adapt to subseafloor environment. The material metabolism manifests that the strain may play an important ecological role in the biogeochemical cycle of the SPG, and various cold-adapted extracelluar enzymes produced by the strain may have significant value in application.

Dyella jejuensis sp. nov., isolated from soil of Hallasan Mountain in Jeju Island.

A novel bacterium, designated JP1(T), was isolated from soil of Hallasan Mountain in Jeju Island. The isolate was a Gramnegative, aerobic, motile and rod-shaped (0.2-0.4 × 1.2-2.0 µm) bacterium. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain JP1(T) was closely related to Dyella koreensis with 97.6% similarity. Growth of strain JP1(T) occurred at 10-37°C, pH 5-7 and 0-1% (w/v) NaCl. The genomic DNA G+C content of strain JP1(T) was 62.1 mol%. The major fatty acids were iso-C16:0, iso-C17:1 ω9c, and iso-C15:0. The predominant quinone was ubiquinone-8. The major polar lipids of strain JP1(T) were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unidentified aminolipids and unidentified aminophospholipids. The DNA-DNA relatedness values between strain JP1(T) and previously reported Dyella species were <10%. Based on phenotypic, genotypic, and phylogenetic distinctness, strain JP1(T) represents a novel species in the genus Dyella, for which the name Dyella jejuensis sp. nov. is proposed. The type strain is JP1(T) (=KACC 17701(T) =JCM 19615(T)).

Pseudoxanthomonas gei sp. nov., a novel endophytic bacterium isolated from the stem of Geum aleppicum.

A Gram stain-negative, strictly aerobic, rod-shaped, non-motile and deep-yellow-coloured bacterial strain, designated ZFJR-3(T), was isolated from the stem of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China, and characterized by using a polyphasic approach. The novel isolate grew optimally at 25-28 °C and in the absence of NaCl. Flexirubin-type pigments were produced. The predominant respiratory quinone was ubiquinone-8 (Q-8) and the major cellular fatty acids were iso-C15:0 (29.2 %), iso-C16:0 (18.5 %), summed feature 9 (comprising iso-C17:1 ω9c and/or C16:0 10-methyl; 8.8 %), C16:1 ω7c alcohol (8.8 %), iso-C11:0 3-OH (6.9 %) and iso-C11:0 (6.8 %). The DNA G+C content was 66.1 mol %. The only polyamine was spermidine and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFJR-3(T) belongs to the genus Pseudoxanthomonas and was most closely related to Pseudoxanthomonas yeongjuensis KCTC 22757(T) (16S rRNA gene sequence similarity, 99.0 %) and Pseudoxanthomonas sacheonensis KCTC 22080(T) (98.0 %). The levels of 16S rRNA gene sequence similarity with respect to other Pseudoxanthomonas species with validly published names were less than 96.5 %. DNA-DNA relatedness values for strain ZFJR-3(T) with respect to its closely related neighbours P. yeongjuensis KCTC 22757(T) and P. sacheonensis KCTC 22080(T) were 48.7 and 36.3 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain ZFJR-3(T) is considered to represent a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas gei sp. nov. is proposed. The type strain is ZFJR-3(T) (=CCTCC AB 2013020(T) =KCTC 32298(T)).

Vulcaniibacterium tengchongense gen. nov., sp. nov. isolated from a geothermally heated soil sample, and reclassification of Lysobacter thermophilus Wei et al. 2012 as Vulcaniibacterium thermophilum comb. nov.

A thermotolerant Gram-staining negative and aerobic bacterium, designated strain YIM 77520(T), was isolated from a geothermally heated soil sample collected at Rehai National Park, Tengchong, Yunnan Province, South-West China. Cells of the strain were found to be rod-shaped and colonies were light beige and circular. The strain was found to grow in the presence of 0-2 % (w/v) total salts (optimum, 0 %), at pH 6.0-8.0 (optimum, pH 7.0) and 25-55 °C (optimum, 45 °C). The only quinone detected was Q-8 and the genomic DNA G+C content was determined to be 66.9 mol%. The major fatty acids (>10 %) were identified as iso-C16:0 and iso-C15:0. The phospholipids were found to consist of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, five unknown phospholipids and three aminophospholipids. Based on the 16S rRNA gene sequence analysis, strain YIM 77520(T) was found to form a cluster with Lysobacter thermophilus YIM 77875(T) and showed the highest 16S rRNA gene sequence similarity to L. thermophilus YIM 77875(T) (96.0 %). These two strains formed a distinct lineage of the family 'Xanthomonadaceae'. On the basis of the morphological and chemotaxonomic characteristics, as well as genotypic data, a new genus, Vulcaniibacterium gen. nov. is proposed with Vulcaniibacterium tengchongense sp. nov. as the type species. The type strain of V. tengchongense sp. nov. is strain YIM 77520(T) (=DSM 25623(T) = CCTCC AB 2011152(T)). Furthermore we propose that L. thermophilus Wei et al. 2012 is reclassified in the new genus as Vulcaniibacterium thermophilum comb. nov. (type strain YIM 77875(T) = CCTCC AB 2012064(T) = KCTC 32020(T)) based on polyphasic data.

Luteibacter rhizovicinus MIMR1 promotes root development in barley (Hordeum vulgare L.) under laboratory conditions.

In order to preserve environmental quality, alternative strategies to chemical-intensive agriculture are strongly needed. In this study, we characterized in vitro the potential plant growth promoting (PGP) properties of a gamma-proteobacterium, named MIMR1, originally isolated from apple shoots in micropropagation. The analysis of the 16S rRNA gene sequence allowed the taxonomic identification of MIMR1 as Luteibacter rhizovicinus. The PGP properties of MIMR1 were compared to Pseudomonas chlororaphis subsp. aurantiaca DSM 19603(T), which was selected as a reference PGP bacterium. By means of in vitro experiments, we showed that L. rhizovicinus MIMR1 and P. chlororaphis DSM 19603(T) have the ability to produce molecules able to chelate ferric ions and solubilize monocalcium phosphate. On the contrary, both strains were apparently unable to solubilize tricalcium phosphate. Furthermore, the ability to produce 3-indol acetic acid by MIMR1 was approximately three times higher than that of DSM 19603(T). By using fluorescent recombinants of strains MIMR1 and DSM 19603(T), we also demonstrated that both bacteria are able to abundantly proliferate and colonize the barley rhizosphere, preferentially localizing on root tips and in the rhizoplane. Finally, we observed a negative effect of DSM 19603(T) on barley seed germination and plant growth, whereas MIMR1, compared to the control, determined a significant increase of the weight of aerial part (+22 %), and the weight and length of roots (+53 and +32 %, respectively). The results obtained in this work make L. rhizovicinus MIMR1 a good candidate for possible use in the formulation of bio-fertilizers.

Arenimonas daejeonensis sp. nov., isolated from compost.

A Gram-negative, aerobic, motile and rod-shaped bacterium, designated strain T7-07(T), was isolated from compost in Daejeon, Korea. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain T7-07(T) had 99.0% gene sequence similarity with Arenimonas malthae KACC 14618(T) and 94.7-95.9% with other recognized species of the genus Arenimonas. Cells formed creamy white to yellowish colonies on R2A agar and contained Q-8 as the predominant ubiquinone, C(15:0) iso, C(16:0) iso, C(17:1) iso ω9c and C(11:0) iso 3-OH as the major fatty acids, and diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine and an unknown aminolipid as the major polar lipids. The DNA G+C content of strain T7-07(T) was 68.3 mol%. DNA-DNA reassociation experiments between T7-07(T) and Arenimonas malthae KACC 14618(T) resulted in a mean relatedness value of 22.2%. Combined genotypic and phenotypic data supported the conclusion that the strain T7-07(T) represents a novel species, for which the name Arenimonas daejeonensis sp. nov. is proposed. The type strain is T7-07(T) (=KCTC 12667(T)=DSM 18060(T)).

Adhesion mechanisms of plant-pathogenic Xanthomonadaceae.

The family Xanthomonadaceae is a wide-spread family of bacteria belonging to the gamma subdivision of the Gram-negative proteobacteria, including the two plant-pathogenic genera Xanthomonas and Xylella, and the related genus Stenotrophomonas. Adhesion is a widely conserved virulence mechanism among Gram-negative bacteria, no matter whether they are human, animal or plant pathogens, since attachment to the host tissue is one of the key early steps of the bacterial infection process. Bacterial attachment to surfaces is mediated by surface structures that are anchored in the bacterial outer membrane and cover a broad group of fimbrial and non-fimbrial structures, commonly known as adhesins. In this chapter, we discuss recent findings on candidate adhesins of plant-pathogenic Xanthomonadaceae, including polysaccharidic (lipopolysaccharides, exopolysaccharides) and proteineous structures (chaperone/usher pili, type IV pili, autotransporters, two-partner-secreted and other outer membrane adhesins), their involvement in the formation of biofilms and their mode of regulation via quorum sensing. We then compare the arsenals of adhesins among different Xanthomonas strains and evaluate their mode of selection. Finally, we summarize the sparse knowledge on specific adhesin receptors in plants and the possible role of RGD motifs in binding to integrin-like plant molecules.

The development of a liquid formulation of Pseudoxanthomonas sp. RN402 and its application in the treatment of pyrene-contaminated soil.

AIM: To develop a liquid formulation of Pseudoxanthomonas sp. RN402 for prolonged storage and maintaining high survival rates and pyrene biodegradability. METHODS AND RESULTS: Liquid formulations of RN402, designated as L-RN402, were prepared by suspending bacterial cells (109 CFU ml⁻¹) in various buffers. Analysis found that phosphate buffer containing glycerol maintained high survival rate (94%) as well as pyrene biodegradability of bacteria after a 30-day storage. This L-RN402 could be stored at 30°C for at least 6 months. Bioaugmentation treatment with stored L-RN402 resulted in the complete degradation of pyrene (300 mg kg⁻¹) in soil microcosms within 4 weeks. RN402 could be detected by denaturing gradient gel electrophoresis throughout the period; moreover, real-time PCR indicated the presence of high number of nidA-containing bacteria. CONCLUSIONS: A liquid formulation of RN402, an effective pyrene degrader, was developed by suspending RN402 in phosphate buffer containing 1% glycerol. This formulation could be stored at 30°C for at least 6 months and maintain high efficacy in the treatment of pyrene-contaminated soil. SIGNIFICANCE AND IMPACT OF THE STUDY: This work is the first description of a liquid formulation of pyrene-degrading bacteria for prolonged storage that retains biological activity for the treatment of environmental pollutants.

First case of fulminant sepsis due to Wohlfahrtiimonas chitiniclastica.

We report the first case of fulminant sepsis due to Wohlfahrtiimonas chitiniclastica. This case is also the first one reported in South America. We emphasize the importance of recognizing bacteria that live in the larvae of a parasitic fly as the causative agent of severe infections in homeless patients.

Rhodanobacter xiangquanii sp. nov., a novel anilofos-degrading bacterium isolated from a wastewater treating system.

A Gram-staining-negative, oxidase-positive, catalase-positive, non-motile, non-spore-forming, and rod-shaped bacterium, designated BJQ-6(T), was isolated from activated sludge of a waste-water treatment plant in Jiangsu Province, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BJQ-6(T) belonged to the genus Rhodanobacter, and shared 98.7% similarity with Rhodanobacter lindaniclasticus LMG 18385(T) and <97% similarities with other Rhodanobacter species. The major fatty acids were iso-C15:0 (17.6%), iso-C16:0 (19.3%), and Summed feature 9 (isoC17:1 ω9c and/or C16:0 10-methyl) (25.8%). The DNA G+C content of strain BJQ-6(T) was 64.8 mol%. Based on the phenotypic and phylogenetic considerations, strain BJQ-6(T) represents a novel species of the genus Rhodanobacter, for which the name Rhodanobacter xiangquanii sp. nov. is proposed. The type strain is BJQ-6(T) (=CCTCC AB 2010106(T) =KCTC 23100(T)).

Ignatzschineria indica sp. nov. and Ignatzschineria ureiclastica sp. nov., isolated from adult flesh flies (Diptera: Sarcophagidae).

Two Gram-negative-staining, aerobic, non-motile, rod-shaped bacteria, designated strains FFA1(T) and FFA3(T), and belonging to the class Gammaproteobacteria were isolated from the gastrointestinal tract of adult flesh flies (Diptera: Sarcophagidae). Phylogenetic analysis of 16S rRNA gene sequence data placed these two strains within the genus Ignatzschineria with similarities of 98.6 % (FFA1(T)) and 99.35 % (FFA3(T)) to Ignatzschineria larvae L1/68(T). The level of gene sequence similarity between strains FFA1(T) and FFA3(T) was 99 %, 97.15 % and 78.1 % based on the 16S rRNA, 23S rRNA and gyrB gene sequences, respectively. Strains FFA1(T) and FFA3(T) shared 24 % DNA-DNA relatedness. DNA-DNA hybridization revealed a very low level of relatedness between the novel strains (22 % for strain FFA1(T) and 44 % for strain FFA3(T)) and I. larvae L1/68(T) genomic DNA. The respiratory quinone was Q-8 in both novel strains. The DNA G+C contents were 41.1 mol% and 40.1 mol% for strains FFA1(T) and FFA3(T), respectively. The cell membrane of both strains consisted of phosphatidylglycerol, phosphatidylethanolamine, phospholipids and aminophospholipid. The major fatty acids for both strains were C(16 : 0), summed feature 8 (C(18 : 1)ω7c and/or C(18 : 1)ω6c), CyC(19 : 0)ω8c and C(14 : 0). The results of DNA-DNA hybridization between the two new strains and I. larvae L1/68(T), in combination with phylogenetic, chemotaxonomic, biochemical and electron microscopic data, demonstrated that strains FFA1(T) and FFA3(T) represented two novel species of the genus Ignatzschineria for which the names Ignatzschineria indica sp. nov. (type strain FFA1(T) = DSM 22309(T) = KCTC 22643(T) = NCIM 5325(T)) and Ignatzschineria ureiclastica sp. nov. (type strain FFA3(T) = DSM 22310(T) = KCTC 22644(T) = NCIM 5326(T)) are proposed.

Pseudoxanthomonas icgebensis sp. nov., isolated from the midgut of Anopheles stephensi field-collected larvae.

A Gram-negative, aerobic, golden yellow, rod-shaped bacterium, a strain designated ICGEB-L15(T), was isolated from the larval midgut of Anopheles stephensi captured in District Jhajjar, Haryana, India. The strain ICGEB-L15(T) grows at 30-50°C (optimum 30-37°C), pH 6.5-8.5 (optimum 7.0-8.0) and in the presence of 2% NaCl. The major fatty acids were iso-C(15:0) (22.5% of total fatty acid), anteiso-C(15:0) (16.5%), iso-C(17:1) 9c (10.3%), iso-C(16:0) (7.3%), C(16:0) (6.1%), and iso-C(11:0) (5.3%). The strain showed the highest 16S rRNA gene sequence similarities with the type strains Pseudoxanthomonas daejeonensis KCTC 12207(T) (97.4%), Pseudoxanthomonas kaohsiungensis J36(T) (97.17%), and Pseudoxanthomonas mexicana AMX 26B(T) (97.11%). The DNA relatedness between ICGEB-L15(T) and Pseudoxanthomonas daejeonensis KCTC 12207(T), Pseudoxanthomonas kaohsiungensis J36(T) and Pseudoxanthomonas mexicana AMX 26B(T) was 24.5%, 28.2%, and 33.6%, respectively. The G+C content of genomic DNA was 69.9 mol%. The major isoprenoid quinone of strain ICGEB-L15(T) was Q-8. The strain ICGEB-L15(T) represents a novel species of the genus Pseudoxanthomonas based on physiological, biochemical and phylogenetic properties; therefore, the name Pseudoxanthomonas icgebensis sp. nov. is proposed. The type strain is ICGEB-L15(T) (=KACC 14090(T) =DSM 22536(T)).

Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field.

A taxonomic study was carried out on Gsoil 142(T), a bacterial strain isolated from the soil collected in a ginseng field in Pocheon province, South Korea. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this bacterium to the Gammaproteobacteria, and it was most closely related to Hydrocarboniphaga effusa ATCC BAA 332(T) (94.4%, 16S rRNA gene sequence similarity), Nevskia ramosa DSM 11499(T) (94.1%) and Alkanibacter difficilis MN154.3(T) (92.0%). Strain Gsoil 142(T) was a gram-negative, strictly aerobic, motile, and rod-shaped bacterium. The G+C content of the genomic DNA was 69.9% and predominant ubiquinone was Q-8. Major fatty acids were summed feature 8 (C(18:1) omega7c and/or omega6c, 36.3%), summed feature 3 (iso-C(15:0) 2-OH and/or C(16:1) omega7c, 20.6%) and C(16:0) (17.4%). The major polar lipids detected in strain Gsoil 142(T) were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown glycolipid. On the basis of polyphasic evidence, it is proposed that strain Gsoil 142(T) should be placed in a novel genus and species, for which the name Panacagrimonas perspica gen. nov., sp. nov. is proposed. The type strain is Gsoil 142(T) (= KCTC 12982(T) = LMG 23239(T)).

Dokdonella ginsengisoli sp. nov., isolated from soil from a ginseng field, and emended description of the genus Dokdonella.

A Gram-negative, aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 191T, was isolated from a soil sample from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 191T belongs to the family Xanthomonadaceae and is related to Dokdonella fugitiva LMG 23001T (97.8% sequence similarity) and Dokdonella koreensis KCTC 12396T (96.9%). The G+C content of the genomic DNA was 68.7 mol%. The major respiratory quinone was Q-8 and the major fatty acids were iso-C17:1omega9c (30.6%), iso-C17:0 (21.6%) and iso-C15:0 (13.0%), supporting the affiliation of strain Gsoil 191T to the genus Dokdonella. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain Gsoil 191T and its closest phylogenetic neighbours were below 40%. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Gsoil 191T from recognized species of the genus Dokdonella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 191T represents a novel species of the genus Dokdonella, for which the name Dokdonella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 191T (=KCTC 12564T=DSM 17954T=CCUG 52462T).

Rudaea cellulosilytica gen. nov., sp. nov., isolated from soil.

A yellow-pigmented, Gram-negative, aerobic, rod-shaped bacterium, strain KIS3-4T, was isolated from soil collected on Daechung Island in the West Sea of Korea. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KIS3-4T in a distinct lineage in the family Xanthomonadaceae. Strain KIS3-4T shared 87.3-93.7% sequence similarity with members of the family Xanthomonadaceae, and was related most closely to the genera Dyella and Dokdonella. In its biochemical characteristics, strain KIS3-4T was clearly separable from other genera within the family Xanthomonadaceae on the basis of the hydrolysis of cellulose and urea, high G+C content (64 mol%) and fatty acid profile. Major fatty acids (>10% of the total fatty acids) were iso-C17:1omega9c (32.8%), iso-C17:0 (18.0%) and iso-C16:0 (12.7%). Q-8 was the predominant respiratory quinone. Phosphatidylethanolamine and several unidentified aminophospholipids and phospholipids were present. Based on its unique phenotypic, genotypic and phylogenetic features, strain KIS3-4T represents a novel genus and species, for which the name Rudaea cellulosilytica gen. nov., sp. nov. is proposed. The type strain of Rudaea cellulosilytica is KIS3-4T (=KACC 12734T=JCM 15422T).

Dyella marensis sp. nov., isolated from cliff soil.

A novel, Gram-negative bacterium, designated CS5-B2(T), was isolated from soil that had been collected from a cliff on Mara Island, Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the radiation of the genus Dyella. The closest relatives were the type strains of Dyella koreensis, Dyella ginsengisoli and Dyella japonica and 16S rRNA gene sequence similarities between strain CS5-B2(T) and these strains were 99.0, 97.9 and 97.8 %, respectively. The sequence similarities between the novel isolate and other related taxa compared in the phylogenetic analysis were less than 96.7 %. The cells of strain CS5-B2(T) were aerobic, oxidase-negative, catalase-positive, motile rods. The temperature range for growth was 20-37 degrees C, with optimal growth at 30-37 degrees C. Growth occurred at pH 5.1-9.1, with optimal growth at pH 6.1-9.1. NaCl tolerance for growth was from 1 to 2 % (w/v). Ubiquinone-8 was the predominant respiratory lipoquinone. The major fatty acids were iso-C(15 : 0) and iso-C(17 : 1)omega9c. The G+C content of the DNA was 65.7-66.6 mol%. The level of DNA-DNA relatedness with D. koreensis KCTC 12359(T) was 20.2 and 29.6 % in duplicate measurements. On the basis of phenotypic features, phylogenetic analysis and DNA-DNA relatedness, a novel species of the genus Dyella is proposed, with the name Dyella marensis sp. nov. The type strain is CS5-B2(T) (=JCM 14959(T) =KCTC 22144(T)).

Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil.

Two novel strains isolated from soils, JS12-10(T) and JS14-6(T), were characterized using a polyphasic approach to determine their taxonomic positions. These isolates were found to be aerobic, Gram-negative, motile with one polar flagellum, non-spore-forming and rod-shaped. Phenotypic and fatty acid data supported the affiliation of JS12-10(T) and JS14-6(T) to the genus Dyella. However, chemotaxonomic data and DNA-DNA relatedness values allowed differentiation of these strains from other Dyella species with validly published names. Strains JS12-10(T) and JS14-6(T) showed the highest 16S rRNA gene sequence similarities with Dyella ginsengisoli Gsoil 3046(T) (98.4 %) and Dyella japonica XD53(T) (97.9 %), respectively, and the 16S rRNA gene sequence similarity between them was 97.1 %. DNA-DNA hybridization values between the novel isolates and strains of other recognized Dyella species were 29-38 %. Therefore, strains JS12-10(T) and JS14-6(T) represent two novel species of the genus Dyella, for which the names Dyella soli sp. nov. (type strain JS12-10(T) =KACC 12747(T) =JCM 15423(T)) and Dyella terrae sp. nov. (type strain JS14-6(T) =KACC 12748(T) =JCM 15424(T)) are proposed.

Rhodanobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field in South Korea.

A novel gammaproteobacterium, designated Gsoil 3054(T), was isolated from soil of a ginseng field in Pocheon province, South Korea, and was characterized using a polyphasic approach to determine its taxonomic position. The strain was Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Rhodanobacter; it was most closely related to Rhodanobacter fulvus Jip2(T) and Rhodanobacter thiooxydans LCS2(T) (97.9 and 97.2 % 16S rRNA gene sequence similarity, respectively). Chemotaxonomic data, i.e. Q-8 as the predominant ubiquinone and iso-C(15 : 0), 10-methyl C(16 : 0) and iso-C(17 : 0) as major fatty acids, also supported classification of strain Gsoil 3054(T) in the genus Rhodanobacter. However, DNA-DNA hybridization values of Gsoil 3054(T) with R. fulvus Jip2(T) and R. thiooxydans LCS2(T) were 45 and 31 %, respectively. Moreover, physiological and biochemical tests enabled strain Gsoil 3054(T) to be differentiated phenotypically from other established species of Rhodanobacter. Therefore, the isolate represents a novel species, for which the name Rhodanobacter ginsenosidimutans sp. nov. is proposed; the type strain is Gsoil 3054(T) (=KACC 12822(T) =DSM 21013(T) =KCTC 22231(T) =LMG 24457(T)).