Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae.

Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics, revealing a potential role in complementing the host's arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of transmission in this symbiosis which, together with a large effective population size explains the cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the candidate mechanisms enabling a permanent association in the phyllosphere.

Paralcaligenes ginsengisoli sp. nov., isolated from ginseng cultivated soil.

A novel bacterial strain DCY104(T) isolated from soil of a ginseng field in Yeoncheon County, Republic of Korea is described in this study. Cells were short rod-shaped, motile by mean of one polar flagellum, strictly aerobic, Gramreaction negative, oxidase and catalase-positive. 16S rRNA gene sequence analysis showed that strain DCY104(T) shared highest similarity 98.2 % to Paralcaligenes ureilyticus GR24-5(T), and from 97.7 to 97.1 % with other type strains belong to the genera Candidimonas, Pusillimonas and Parapusillimonas Otherwise, phylogenetic trees analyses indicated that strain DCY104(T) belongs to a single group with P. ureilyticus GR24-5(T) that was distinct to other genera. The major polar lipids were phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The major cellular fatty acids consisted of C16:0, cyclo-C17:0, and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). The predominant polyamine was putrescine. The ubiquinone was Q-8. The genomic DNA G+C content was 55.9 mol%. These data in combination with the presence of one polar flagellum and positive activity of urease confirmed the placement of strain DCY104(T) in the genus Paralcaligenes. DNA-DNA relatedness between strain DCY104(T) and P. ureilyticus KACC 13888(T) was 40 %. The differences in the profiles of polar lipids, fatty acids and phenotypic characteristics in combination with DNA-DNA relatedness delineated strain DCY104(T) and P. ureilyticus KACC 13888(T). In summary, taxonomic analyses in this study demonstrated that strain DCY104(T) represents a novel species within the genus Paralcaligenes, for which we propose the name Paralcaligenes ginsengisoli. The type strain is DCY104(T) (= KCTC 42406(T) = JCM 30746(T)).

Modelling of biological Cr(VI) removal in draw-fill reactors using microorganisms in suspended and attached growth systems.

The kinetics of hexavalent chromium bio-reduction in draw-fill suspended and attached growth reactors was examined using sugar as substrate and indigenous microorganisms from the industrial sludge of the Hellenic Aerospace Industry. Initially, experiments in suspended growth batch reactors for Cr (VI) concentrations of 1.4-110 mg/l were carried out, to extensively study the behaviour of a mixed culture. The maximum Cr(VI) reduction rate of 2 mg/l h was achieved for initial concentration 12.85 mg/l with biomass production rate 4.1 mg biomass/l h. Analysis of the microbial structure in the batch reactor culture indicated that the dominant bacterial communities were constituted by bacterial members of Raoultella sp., Citrobacter sp., Klebsiella sp., Salmonella sp., Achromobacter sp. and Kerstersia sp. while the dominant fungal strain was that of Pichia jadinii. Experiments using the same mixed culture were also carried out in packed-bed reactors with plastic support media. High removal rates were achieved (2.0 mg/l h) even in high initial concentrations (109 mg/l). A combination of the model of Tsao and Hanson for growth enhancement and that of Aiba and Shoda for growth inhibition was used in order to describe and predict the process of Cr(VI) bio-reduction in suspended growth and packed-bed reactors. Kinetic constants of the equation obtained from both batch (or draw-fill) culture experiments. In the draw-fill experiments at the packed-bed reactor, hexavalent chromium inhibitory effects were minimized increasing the inhibitory constant value K(i)' at 148.5 mg/l, compared to suspended growth experiments which was K(i) = 8.219 mg/l. The model adequately predicts hexavalent chromium reduction in both batch reactors for all initial concentrations tested.

Pigmentiphaga soli sp. nov., a bacterium isolated from soil.

Strain BS12(T), a Gram-negative motile bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain belonged to the family Alcaligenaceae in the class Betaproteobacteria. The highest degree of sequence similarities of strain BS12(T) were found with Pigmentiphaga litoralis JSM 061001(T) (98.3%), Pigmentiphaga daeguensis K110(T) (98.2%), and Pigmentiphaga kullae K24(T) (98.1%). Chemotaxonomic data revealed that strain BS12(T) possessed ubiquinone-8, which is common in the family Alcaligenaceae, and the predominant fatty acids were C(16:0), C(17:0) cyclo, summed feature 3 (C(16:1) ω6c/ω7c), and summed feature 8 (C(18:1) ω6c/ω7c). The major polar lipids of strain BS12(T) were phosphatidylethanolamine and phosphatidylglycerol. Based on these data, BS12(T) (=KCTC 23577(T) =JCM 17666(T) =KEMB 9004-082(T)) should be classified as a type strain of a novel species, for which the name Pigmentiphaga soli sp. nov. is proposed.

Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field.

A bacterial strain, designated GR24-5(T), was isolated from soil cultivated with Korean ginseng. Cells were Gram-negative, strictly aerobic, catalase- and oxidase-positive, non-spore-forming motile rods. Based on the 16S rRNA gene sequence, strain GR24-5(T) could be assigned to the family Alcaligenaceae. Strain GR24-5(T) showed the highest sequence similarities with Parapusillimonas granuli Ch07(T) (97.1%), Pusillimonas noertemannii BN9(T) (96.9%), Pigmentiphaga kullae DSM 13608(T) (96.5%), and Castellaniella defragrans 54Pin(T) (96.3%). Strain GR24-5(T) demonstrated a low DNA-DNA relatedness (23%) with P. granuli Ch07(T). The major respiratory quinone is ubiquinone 8 (Q-8) and the major fatty acids are C(16:0), C(17:0) cyclo, and summed feature 1 (C(14:0) 3-OH/iso-C(16:1) I/C(12:0) aide). Putrescine, spermidine, and 2-hydroxyputrescine are the major polyamines. The major polar lipids are phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, di-phosphatidylglycerol, and an unknown aminophospholipid. Polar lipid patterns of strain GR24-5(T) were unique in having a large amount of phosphatidylmethylethanolamine. Based on phylogenetic analysis and physiological and biochemical characteristics, strain GR245(T) represents a novel genus and species, for which the name Paralcaligenes ureilyticus gen. nov., sp. nov. is proposed. The type strain of P. aralcaligenes ureilyticus is GR24-5(T) (=KACC 13888 =DSM 24591(T)).

Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost.

Two bacterial strains (SC-089(T) and SC-092(T)) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089(T) and SC-092(T), which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA-DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089(T) = LMG 24812(T) = CCUG 55806(T)) and Candidimonas humi sp. nov. (type strain, SC-092(T) = LMG 24813(T) = CCUG 55807(T)).

Pusillimonas soli sp. nov., isolated from farm soil.

A Gram-negative, motile, non-spore-forming bacterial strain, designated MJ07(T), was isolated from a farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ07(T) belongs to the family Alcaligenaceae, class Betaproteobacteria, and is related most closely to Pusillimonas ginsengisoli KCTC 22046(T) (98.6 % sequence similarity) and Pusillimonas noertemannii BN9(T) (96.9 %). The levels of 16S rRNA gene sequence similarity between strain MJ07(T) and members of all other recognized species of the family Alcaligenaceae were below 95.2 %. The G+C content of the genomic DNA of strain MJ07(T) was 59.4 mol%. The detection of a quinone system with ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown aminolipids as major polar lipids and a fatty acid profile with C16:0 (32.0 %), C17:0cyclo (24.7 %) and C19:0cyclo ω8c (11.5 %) as the major components supported the affiliation of strain MJ07(T) to the genus Pusillimonas. Strain MJ07(T) exhibited relatively low levels of DNA-DNA relatedness with respect to P. ginsengisoli KCTC 22046(T) (50 ± 8 %) and P. noertemannii KACC 13183(T) (18 ± 7 %). On the basis of its phenotypic and genotypic properties together with its phylogenetic distinctiveness, strain MJ07(T) (=KCTC 22455(T) =JCM 16386(T)) should be classified in the genus Pusillimonas as the type strain of a novel species, for which the name Pusillimonas soli sp. nov. is proposed.

Parasutterella excrementihominis gen. nov., sp. nov., a member of the family Alcaligenaceae isolated from human faeces.

A novel, strictly anaerobic, non-spore-forming, Gram-negative coccobacillus (strain YIT 11859(T)) was isolated from human faeces. Biochemically, this strain was largely unreactive and was asaccharolytic. Growth of strain YIT 11859(T) in peptone-yeast extract broth produced no visible turbidity, and a trace amount of propionate was detected as an end product of metabolism. 16S rRNA gene sequence analysis showed that strain YIT 11859(T) was related most closely to the type strains of Sutterella species, with 90.8-88.0 % sequence similarity. Phylogenetic analysis of these and other related sequences confirmed that strain YIT 11859(T) was phylogenetically most closely associated with Sutterella species, but formed a separate cluster, indicating that strain YIT 11859(T) represents a novel member of the family Alcaligenaceae. Fatty acid analysis demonstrated the presence of a high concentration of C(18 : 1)omega9c (75 % of the total). The main respiratory quinones were menaquinone (MK-6) and methylated menaquinone (MMK-6). The G+C content of the DNA was 49.8 mol%. These results suggest that strain YIT 11859(T) represents a novel species of a new genus, for which the name Parasutterella excrementihominis gen. nov., sp. nov. is proposed. The type strain of Parasutterella excrementihominis is YIT 11859(T) (=DSM 21040(T) =JCM 15078(T)).

Pigmentiphaga litoralis sp. nov., a facultatively anaerobic bacterium isolated from a tidal flat sediment.

A novel Gram-negative, facultatively anaerobic, non-sporulating, non-motile, catalase- and oxidase-positive, rod-shaped bacterium (strain JSM 061001(T)) was isolated from a tidal flat in the South China Sea, China. Growth occurred with 0-5 % (w/v) NaCl [optimum, 0.5-1 % (w/v) NaCl], at pH 5.0-10.0 (optimum, pH 7.0) and at 4-35 degrees C (optimum, 25-30 degrees C). The major cellular fatty acids were C(16 : 0), cyclo C(17 : 0), C(18 : 1)omega7c and C(16 : 1). Strain JSM 061001(T) contained ubiquinone Q-8 as the predominant respiratory quinone, and phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the polar lipids. The genomic DNA G+C content was 65.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 061001(T) belongs to the family Alcaligenaceae and was related most closely to the type strains of the two recognized species of the genus Pigmentiphaga. The three strains formed a robust cluster in the neighbour-joining, maximum-parsimony and maximum-likelihood phylogenetic trees. Levels of DNA-DNA relatedness between strain JSM 061001(T) and the type strains of Pigmentiphaga daeguensis and Pigmentiphaga kullae were 15.8 and 10.5 %, respectively. The combination of phylogenetic analysis, DNA-DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strain JSM 061001(T) represents a novel species of the genus Pigmentiphaga, for which the name Pigmentiphaga litoralis sp. nov. is proposed. The type strain is JSM 061001(T) (=CCTCC AA207034(T)=KCTC 22165(T)).

Castellaniella caeni sp. nov., a denitrifying bacterium isolated from sludge of a leachate treatment plant.

A Gram-negative, non-motile, facultatively anaerobic, denitrifying bacterial strain, designated Ho-11(T), was isolated from sludge of a leachate treatment plant and was characterized taxonomically by using a polyphasic approach. The G+C content of the genomic DNA was 63.5 mol%. Strain Ho-11(T) contained ubiquinone Q-8 as the major respiratory lipoquinone and putrescine as the predominant polyamine. The major fatty acids were summed feature 4 (C(16:1)omega7c and/or iso-C(15:0) 2-OH; 29.3%), C(16:0) (28.0%) and summed feature 7 (C(18:1)omega7c, C(18:1)omega9t and/or C(18:1)omega12t; 19.8%). Comparative 16S rRNA gene sequence analysis showed that strain Ho-11(T) belonged to the family Alcaligenaceae, class Betaproteobacteria, and joined the evolutionary radiation enclosed by the genus Castellaniella. 16S rRNA gene sequence similarities between strain Ho-11(T) and the type strains of the two recognized species of the genus, Castellaniella denitrificans DSM 11046(T) and Castellaniella defragrans DSM 12141(T), were 97.8 and 97.4%, respectively. Levels of similarity between strain Ho-11(T) and all other recognized species of the family Alcaligenaceae were below 95.6%. Strain Ho-11(T) exhibited relatively low levels of DNA-DNA relatedness with respect to C. denitrificans DSM 11046(T) (33%) and C. defragrans DSM 12141(T) (28%). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain Ho-11(T) (=KCTC 12197(T)=LMG 23411(T)) should be classified in the genus Castellaniella as the type strain of a novel species, for which the name Castellaniella caeni sp. nov. is proposed.

Pigmentiphaga daeguensis sp. nov., isolated from wastewater of a dye works, and emended description of the genus Pigmentiphaga.

A Gram-negative, non-spore-forming, rod-shaped Pigmentiphaga-like bacterial strain, K110(T), was isolated from wastewater collected from a dye works in Korea and was subjected to a polyphasic taxonomic analysis. Strain K110(T) grew optimally at pH 7.0--8.0 and 37 degrees C in the presence of 0.5 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and C(16 : 0), cyclo C(17 : 0) and cyclo C(19 : 0)omega8c as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and two unidentified aminolipids. The DNA G+C content was 67.4 mol%. In a neighbour-joining phylogenetic tree constructed on the basis of 16S rRNA gene sequences, strain K110(T) joined Pigmentiphaga kullae, the sole species of the genus, at a bootstrap confidence level of 100 %. Strain K110(T) exhibited a 16S rRNA gene sequence similarity of 99.4 % with respect to the type strain of P. kullae. Although strain K110(T) was found to be similar to P. kullae in terms of phenotypic properties, it differed in terms of motility, polar lipids, DNA-DNA relatedness and repetitive extragenic palindromic PCR genomic fingerprinting patterns. On the basis of phenotypic, phylogenetic and genetic data, strain K110(T) represents a novel species of the genus Pigmentiphaga, for which the name Pigmentiphaga daeguensis sp. nov. is proposed. The type strain is K110(T) (=KCTC 12838(T)=JCM 14330(T)).

Pusillimonas noertemannii gen. nov., sp. nov., a new member of the family Alcaligenaceae that degrades substituted salicylates.

The taxonomic position of a Pseudomonas-like strain, designated BN9(T), was investigated. This strain had previously been isolated as a 5-aminosalicylate-degrading organism from a 6-aminonaphthalene-2-sulphonate-degrading mixed bacterial culture. Previously, detection of ubiquinone Q-8, a polyamine pattern with putrescine, spermidine and 2-hydroxyputrescine as the major polyamines, and partial 16S rRNA gene sequencing had suggested that strain BN9(T) belongs to the 'Betaproteobacteria'. This was supported by sequencing the 16S rRNA gene, which demonstrated 94-96 % sequence similarity to different species of the genera Achromobacter, Alcaligenes and Bordetella, and suggested that strain BN9(T) represents a member of the family Alcaligenaceae. Different methods for the construction of phylogenetic dendrograms placed the strain separately from all other genera within the Alcaligenaceae. Fatty acid analysis demonstrated the presence of high concentrations of C(19 : 0) cyclo omega8c. On the basis of low 16S rRNA gene sequence similarity to other members of the Alcaligenaceae, fatty acid and polar lipid profiles, and other unique phenotypic properties of strain BN9(T), the creation of a new genus and species with the name Pusillimonas noertemannii gen. nov., sp. nov. is proposed. The type strain is BN9(T) (= DSM 10065(T) = NCIMB 14020(T)).

Sutterella stercoricanis sp. nov., isolated from canine faeces.

Morphological, biochemical and molecular genetic studies were carried out on an unknown non-spore-forming, Gram-negative, rod-shaped bacterium which was isolated from dog faeces. The bacterium grew under anaerobic conditions, was asaccharolytic, resistant to 20 % (v/v) bile and was oxidase- and urease-negative. Phylogenetic analysis based on comparative 16S rRNA gene sequencing showed that the unidentified bacterium clustered with Sutterella wadsworthensis, although a sequence divergence of >5 % indicated that the bacterium from dog faeces represented a previously unrecognized subline within the genus. On the basis of the presented findings, a novel species, Sutterella stercoricanis sp. nov., is described. The type strain of Sutterella stercoricanis is 5BAC4T (= CCUG 47620T = CIP 108024T).