<Emphasis Type="Italic">Chryseobacterium nankingense</Emphasis> sp. nov. WR21 effectively suppresses <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> growth via intensive root exudates competition

Previous studies demonstrated that the Chryseobacterium sp. WR21 could effectively control the bacterial wilt disease caused by Ralstonia solanacearum through effective root colonization. The strain WR21 exhibited a low level of DNA homology with Chryseobacterium strains DSM 15235^T (24.1%), DSM 17724^T (24.8%), and DSM 18014^T (10.4%), suggesting that WR21 may represent a novel species, for which the name Chryseobacterium nankingense sp. nov. is proposed. The in vitro competition experiments with strain WR21 indicated it significantly inhibited growth of the pathogen in co-culture with six of nine tested nutrients (e.g. root exudates) that could be utilized by strain WR21 and R. solanacearum. Similar trends were observed in co-culturing experiments using tissue exudates of tomato. A positive relationship (r = 0.785) was noticed between the differences in the average growth rate of both strains and the disease suppression effects. In conclusion, Chryseobacterium nankingense sp. nov. WR21 exhibits antagonism through nutrient competition that might be used for achieving biocontrol of Ralstonia solanacearum induced wilts.     

Identification of the di-<Emphasis Type="Italic">n</Emphasis>-butyl phthalate-biodegrading strains and the biodegradation pathway in strain LMB-1

DNA isolated from a greenhouse soil (Nanjing, Jiangsu Province, China) was suitable for PCR amplification of gene segment coding for the 16S rRNA. Diverse PCR products were characterized by cloning and sequencing, and analysis of bacterial colonies showed the presence over 26 phyla. The most bacteria belonged to Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria and Planctomycetes. Furthermore, after the enrichment procedure of DBP-degrading microorganisms, 4 strains were isolated from the soil sample with di-n-butyl phthalate (DBP) biodegradability, and they were identified to be Rhizobium sp., Streptomyces sp., Pseudomonas sp. and Acinetobacter sp. Analysis of the degradation products by LC-MS led to identification of metabolites of DBP in strain LMB-1 (identified as Rhizobium sp.) which suggests that DBP was degraded through β-oxidation, demethylation, de-esterification and cleavage of aromatic ring.     

Taxonomic description and draft genome of <Emphasis Type="Italic">Pseudomonas sediminis</Emphasis> sp. nov., isolated from the rhizospheric sediment of <Emphasis Type="Italic">Phragmites karka</Emphasis>

The taxonomic position of a Gram-stain-negative, rod-shaped bacterial strain, designated PI11^T, isolated from the rhizospheric sediment of Phragmites karka was characterized using a polyphasic approach. Strain PI11^T could grow optimally at 1.0% NaCl concentration with pH 7.0 at 30°C and was positive for oxidase and catalase but negative for hydrolysis of starch, casein, and esculin ferric citrate. Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain PI11^T belonged to the genus Pseudomonas sharing the highest sequence similarities with Pseudomonas indoloxydans JCM 14246^T (99.72%), followed by, Pseudomonas oleovorans subsp. oleovorans DSM 1045^T (99.29%), Pseudomonas toyotomiensis JCM 15604^T (99.15%), Pseudomonas chengduensis DSM 26382^T (99.08%), Pseudomonas oleovorans subsp. lubricantis DSM 21016^T (99.08%), and Pseudomonas alcaliphila JCM 10630^T (99.01%). Experimental DNA-DNA relatedness between strain PI11^T and P. indoloxydans JCM 14246^T was 49.4%. The draft genome of strain PI11^T consisted of 4,884,839 bp. Average nucleotide identity between the genome of strain PI11^T and other closely related type strains ranged between 77.25–90.74%. The polar lipid pattern comprised of phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major (> 10%) cellular fatty acids were C_18:1ω6c/ω7c, C_16:1ω6c/ω7c, and C_16:0. The DNA G + C content of strain PI11^T was 62.4 mol%. Based on the results of polyphasic analysis, strain PI11^T was delineated from other closely related type strains. It is proposed that strain PI11^T represents represents a novel species of the genus Pseudomonas, for which the name Pseudomonas sediminis sp. nov. is proposed. The type strain is PI11^T (= KCTC 42576^T = DSMZ 100245^T).     

<Emphasis Type="Italic">Nonomuraea insulae</Emphasis> sp. nov., isolated from forest soil

Strain H2R21^T, a novel actinobacterium, isolated from a forest soil sample collected from Heybeliada, Istanbul, Turkey, and a polyphasic approach was used for characterisation of the strain. Chemotaxonomic and morphological characterisation of strain H2R21^T indicated that it belongs to the genus Nonomuraea. 16S rRNA gene sequence similarity showed that the strain is closely related to Nonomuraea purpurea 1SM4-01^T (99.1%) and Nonomuraea solani CGMCC 4.7037^T (98.4%). DNA–DNA relatedness values were found to be lower than 70% between the isolate and its phylogenetic neighbours N. purpurea 1SM4-01^T, N. solani CGMCC 4.7037^T and Nonomuraea rhizophila YIM 67092^T. The whole cell hydrolysates of strain H2R21^T were found to contain meso-diaminopimelic acid as the diagnostic diamino acid and glucose, madurose, mannose and ribose as the cell sugars. The polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, dihydroxy-phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, two glycophospholipids and two unidentified lipids. The predominant menaquinones were identified as MK-9(H₄) and MK-9(H₆). The major fatty acids were found to be iso-C_16:0, iso-C_16:0 2OH and C_17:0 10-methyl. On the basis of DNA–DNA relatedness data and some phenotypic characteristics, it is evident that strain H2R21^T can be distinguished from the closely related species in the genus Nonomuraea. Thus, it is concluded that strain H2R21^T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea insulae sp. nov. is proposed. The type strain is H2R21^T (= DSM 102915^T = CGMCC 4.7338^T = KCTC 39769^T).     

Indole acetic acid overproduction transformants of the rhizobacterium <Emphasis Type="Italic">Pseudomonas</Emphasis> sp. UW4

The plant growth-promoting rhizobacterium Pseudomonas sp. UW4 was transformed to increase the biosynthesis of the auxin, indole-3-acetic acid (IAA). Four native IAA biosynthesis genes from strain UW4 were individually cloned into an expression vector and introduced back into the wild-type strain. Quantitative real-time polymerase chain reaction analysis revealed that the introduced genes ami, nit, nthAB and phe were all overexpressed in these transformants. A significant increase in the production of IAA was observed for all modified strains. Canola plants inoculated with the modified strains showed enhanced root elongation under gnotobiotic conditions. The growth rate and 1-aminocyclopropane-1-carboxylate deaminase activity of transformant strains was lower compared to the wild-type. The indoleacetic acid biosynthesis pathways and the role of this phytohormone in the mechanism of plant growth stimulation by Pseudomonas sp. UW4 is discussed.     

Engineering of <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> to utilize xylan as a sole carbohydrate source by co-expression of an endoxylanase,xylosidase and a bacterial xylose isomerase

Xylan represents a major component of lignocellulosic biomass, and its utilization by Saccharomyces cerevisiae is crucial for the cost effective production of ethanol from plant biomass. A recombinant xylan-degrading and xylose-assimilating Saccharomyces cerevisiae strain was engineered by co-expression of the xylanase (xyn2) of Trichoderma reesei, the xylosidase (xlnD) of Aspergillus niger, the Scheffersomyces stipitis xylulose kinase (xyl3) together with the codon-optimized xylose isomerase (xylA) from Bacteroides thetaiotaomicron. Under aerobic conditions, the recombinant strain displayed a complete respiratory mode, resulting in higher yeast biomass production and consequently higher enzyme production during growth on xylose as carbohydrate source. Under oxygen limitation, the strain produced ethanol from xylose at a maximum theoretical yield of ~90 %. This study is one of only a few that demonstrates the construction of a S. cerevisiae strain capable of growth on xylan as sole carbohydrate source by means of recombinant enzymes.     

<Emphasis Type="Italic">Streptomyces luozhongensis</Emphasis> sp. nov., a novel actinomycete with antifungal activity and antibacterial activity

A novel actinomycete strain, designated TRM 49605^T, was isolated from a desert soil sample from Lop Nur, Xinjiang, north-west China, and characterised using a polyphasic taxonomic approach. The strain exhibited antifungal activity against the following strains: Saccharomyces cerevisiae, Curvularia lunata, Aspergillus flavus, Aspergillus niger, Fusarium oxysporum, Penicillium citrinum, Candida albicans and Candida tropicalis; Antibacterial activity against Bacillus subtilis, Staphylococcus epidermidis and Micrococcus luteus; and no antibacterial activity against Escherichia coli. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain TRM 49605^T to the genus Streptomyces. Strain TRM 49605^T shows high sequence similarities to Streptomyces roseolilacinus NBRC 12815^T (98.62 %), Streptomyces flavovariabilis NRRL B-16367^T (98.45 %) and Streptomyces variegatus NRRL B-16380^T (98.45 %). Whole cell hydrolysates of strain TRM 49605^T were found to contain ll-diaminopimelic acid as the diagnostic diamino acid and galactose, glucose, xylose and mannose as the major whole cell sugars. The major fatty acids in strain TRM 49605^T were identified as iso C_16:0, anteiso C_15:0, C_16:0 and Summed Feature 5 as defined by MIDI. The main menaquinones were identified as MK-9(H₄), MK-9(H₆), MK-9(H₈) and MK-10(H₆). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The G+C content of the genomic DNA was determined to be 71.2 %. The DNA–DNA relatedness between strain TRM 49605^T and the phylogenetically related strain S. roseolilacinus NBRC 12815^T was 60.12 ± 0.06 %, which is lower than the 70 % threshold value for delineation of genomic prokaryotic species. Based on the phenotypic, chemotaxonomic and phylogenetic data, strain TRM 49605^T (=CCTCC AA2015026^T = KCTC 39666^T) should be designated as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces luozhongensis sp. nov. is proposed.     

<Emphasis Type="Italic">Kribbella podocarpi</Emphasis> sp. nov., isolated from the leaves of a yellowwood tree (<Emphasis Type="Italic">Podocarpus latifolius</Emphasis>)

An endophytic actinobacterial strain was isolated from a yellowwood tree growing on the slope of Devil’s Peak, Cape Town, South Africa. Analysis of the 16S rRNA gene showed that the strain belongs to the genus Kribbella. Phylogenetic analyses using the 16S rRNA gene and multilocus sequence analysis using the concatenated gene sequences of the gyrB, rpoB, relA, recA and atpD genes showed that strain YPL1^T is closely related to the type strains of Kribbella karoonensis and Kribbella shirazensis. DDH experiments showed that strain YPL1^T is a distinct genomic species from its close phylogenetic relative, K. karoonensis Q41^T. Physiological comparisons further showed that strain YPL1^T is phenotypically distinct from the type strains of Kribbella jejuensis, Kribbella aluminosa, K. karoonensis, K. shirazensis and Kribbella swartbergensis. Strain YPL1^T is thus presented as the type strain of a novel species, for which the name Kribbella podocarpi sp. nov. (= DSM 29424^T = NRRL B-65063^T), is proposed.     

Effects of macrophyte leachate on <Emphasis Type="Italic">Anabaena</Emphasis> sp. and <Emphasis Type="Italic">Chlamydomonas moewusii</Emphasis> growth in freshwater tropical ecosystems

This study reports on the effects of dissolved organic matter (DOM) derived from the aquatic macrophyte Pistia stratiotes (collected from a tropical reservoir) on the mixotrophic growth of two phytoplankton species (Chlamydomonas moewusii and Anabaena sp.). The DOM from P. stratiotes had a mainly aliphatic structure, low molecular weight, low cellulose and lignin content and high carbon content. The addition of DOM (5% v/v) significantly decreased the growth rate of Anabaena sp. but increased the chlorophyll a concentration of C. moewusii. Higher light intensity (100 versus 30 µmol m^?2 s^?1) was important for Anabaena sp., increasing its growth rate and chlorophyll content. The use of DOM from P. stratiotes to mitigate cyanobacterial blooms should be further explored in future studies.     

Plant growth-promoting potential of endophytic bacteria isolated from roots of wild <Emphasis Type="Italic">Dodonaea viscosa</Emphasis> L.

Dodonaea viscosa, a wild and perennial shrub that can tolerate harsh environmental conditions, was used for the isolation of its endophytic bacteria and their potential was explored for the promotion of Canola growth. The bacteria identified through 16S rRNA gene sequencing, belonged to ten different genera namely Inquilinus, Xanthomonas, Pseudomonas, Rhizobium, Brevundimonas, Microbacterium, Bacillus, Streptomyces, Agrococcus and Stenotrophomonas. All the strains produced small amount of IAA (indole acetic acid) in the absence of tryptophan and comparatively more in the presence of tryptophan. All the bacterial strains were positive for ammonia production, cellulase and pectinase activity, but few of them showed phosphate solubilization, siderophore and hydrogen cyanide production. Only three strains showed ACC (1-aminocyclopropane-1-carboxylate) deaminase activity when tested using in-vitro enzyme assay. Members of genera Bacillus, Pseudomonas and Streptomyces showed positive chitinase, protease and antifungal activity against two phytopathogenic fungi Aspergillus niger and Fusarium oxysoprum, while members of Xanthomonas, Pseudomonas and Bacillus showed significant root elongation of Canola which could be related with their positive plant-growth-promoting (PGP) traits. Among the three plant growth promoting Bacillus strains, B. idriensis is never reported before for its PGP activities. These results showed the potential of Dodonaea viscosa endophytic bacteria as PGPBs, which in future can be further explored for their host range/molecular mechanisms.     

<Emphasis Type="Italic">Streptomyces xiangluensis</Emphasis> sp. nov., a novel actinomycete isolated from soil

A novel actinomycete, designated strain NEAU-LA29^T, was isolated from soil collected from Xianglu Mountain and subjected to a polyphasic taxonomic study. Based on a polyphasic taxonomic approach comprising chemotaxonomic, phylogenetic, morphological and physiological characterisation, the isolate has been affiliated to the genus Streptomyces. 16S rRNA gene sequence analysis showed that the isolate is closely related to Streptomyces vastus JCM4524^T (98.8% identity) and Streptomyces cinereus DSM43033^T (97.9%). However, multilocus sequence analysis based on five other house-keeping genes (atpD, gyrB, rpoB, recA and trpB) and low DNA–DNA relatedness values enabled the strain to be differentiated from these closely related species of the genus Streptomyces. Thus, strain NEAU-LA29^T is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces xiangluensis sp. nov. is proposed. The type strain is NEAU-LA29^T (=?CGMCC 4.7466^T?=?DSM 105786^T).     

<Emphasis Type="Italic">Streptomyces gamaensis</Emphasis> sp. nov., a novel actinomycete with antifungal activity isolated from soil in Gama,Chad

During an investigation exploring potential sources of novel species and natural products, a novel actinomycete with antifungal activity, designated strain NEAU-Gz11^T, was isolated from a soil sample, which was collected from Gama, Chad. The isolate was found to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. 16S rRNA gene sequence similarity studies showed that strain NEAU-Gz11^T belongs to the genus Streptomyces with high sequence similarity to Streptomyces hiroshimensis JCM 4098^T (98.0 %). Similarities to other type strains of the genus Streptomyces were lower than 98.0 %. However, the physiological and biochemical characteristics and low levels of DNA–DNA relatedness could differentiate the isolate genotypically and phenotypically from S. hiroshimensis JCM 4098^T. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces gamaensis sp. nov. is proposed. The type strain is NEAU-Gz11^T (=CGMCC 4.7304^T=DSM 101531^T).     

<Emphasis Type="Italic">Novosphingobium profundi</Emphasis> sp. nov. isolated from a deep-sea seamount

A marine bacterial strain, F72^T, was isolated from a solitary scleractinian coral, collected in Yap seamounts in the Pacific Ocean. Strain F72^T is a Gram-negative, light-yellow-pigmented, motile, rod-shaped bacterium. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F72^T is related to the genus Novosphingobium and has high 16S rRNA gene sequence similarities with the type strains of Novosphingobium pentaromativorans US6-1^T (97.7 %), Novosphingobium panipatense SM16^T (97.6 %), Novosphingobium mathurense SM117^T (97.2 %) and Novosphingobium barchaimii LL02^T (97.1 %). Ubiquinone Q-10 was detected as the dominant quinone. The predominant cellular fatty acids were C_18:1ω7c and C_17:1ω6c. The genomic DNA G+C content of strain F72^T was 63.4 mol %. The polar lipids profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, sphingoglycolipid and one uncharacterized lipid. Strain F72^T shared DNA relatedness of 25 % with N. pentaromativorans JCM 12182^T, 31 % with N. panipatense DSM 22890^T, 21 % with N. mathurense DSM 23374^T and 26 % with N. barchaimii DSM 25411^T. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that the strain F72^T is a representative of a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium profundi sp. nov. (type strain F72^T = KACC 18566^T = CGMCC 1.15390^T).     

<Emphasis Type="Italic">Saccharothrix tharensis</Emphasis> sp. nov., an actinobacterium isolated from the Thar Desert,India

The taxonomic provenance of a filamentous actinobacterial strain isolated from a desert soil was established using a polyphasic approach. The strain has chemotaxonomic and morphological properties consistent with its classification in the genus Saccharothrix. It forms a distinct branch in the Saccharothrix 16S rRNA gene tree, related to the type strain of Saccharothrix saharensis (96.7%) but was distinguished readily from it using a combination of phenotypic properties. The genotypic and phenotypic data show that the strain represents a novel species in the genus Saccharothrix, for which the name Saccharothrix tharensis sp. nov. is proposed with the type strain TD-093^T (=?KCTC 39724^T?=?MCC 2832^T).     

Improved production of carotenoid-free welan gum in a genetic-engineered <Emphasis Type="Italic">Alcaligenes</Emphasis> sp. ATCC31555

Objective

To improve the production of welan gum and obtain a carotenoid-free strain while reducing the fermentation and post-treatment costs.

Results

The vitreoscilla globin (vgb) gene combined with the β-galactosidase (lacZ) promoter was inserted into the phytoene synthase (crtB) gene region of the chromosome in Alcaligenes sp. ATCC31555. When the recombinant strain was grown in a 5 l fermentor, welan gum was produced at 24 ± 0.4 g l^?1 compared to 21 g ± 0.4 g l^?1 in the wild type. Furthermore, the carotenoid-free welan gum produced using Alcaligenes sp. ATCC31555 VHb strain was less expensive with improved properties.

Conclusions

Alcaligenes sp. ATCC31555 VHb strain was a better neutral welan-producing strain with a higher production than the wild-type strain.

     

Growth and wax ester production of an <Emphasis Type="Italic">Acinetobacter baylyi</Emphasis> ADP1 mutant deficient in exopolysaccharide capsule synthesis

Acinetobacter baylyi ADP1 naturally produces wax esters that could be used as a raw material in industrial applications. We attempted to improve wax ester yield of A. baylyi ADP1 by removing rmlA, a gene involved in exopolysaccharide production. Growth rate, biomass formation and wax ester yield on 4-hydroxybenzoate were not affected, but the rmlA ^? strain grew slower on acetate, while reaching similar biomass and wax ester yield. The rmlA ^? cells had malformed shape and large size and grew poorly on glucose without expression of the gene for pyruvate kinase (pykF) from Escherichia coli. The pykF-expressing rmlA ^? strain had similar growth rate, lowered biomass formation and improved wax ester production on glucose as compared to the wild-type strain expressing pykF. Cultivation of the pykF-expressing rmlA ^? strain on an elevated glucose concentration in a medium supplemented with amino acids resulted in doubled molar wax ester yield and acetate production.     

<Emphasis Type="Italic">Ponticoccus alexandrii</Emphasis> sp. nov., a novel bacterium isolated from the marine toxigenic dinoflagellate <Emphasis Type="Italic">Alexandrium minutum</Emphasis>

During an investigation of the biodiversity of the cultivable bacterial community associated with paralytic shellfish poisoning toxin-producing marine dinoflagellate, Alexandrium minutum a novel algal-associated bacterium, designated strain AT2-A^T was isolated. 16S rRNA gene sequence similarity analysis showed that the strain is a member of the genus Ponticoccus, with high sequence similarity to Ponticoccus litoralis DSM 18986^T (97.9%) and Ponticoccus lacteus JCM 30379^T (96.0%). However, based on the data obtained for the physiological and biochemical characteristics, and low level of DNA–DNA relatedness analysis, the strain could be genotypically and phenotypically differentiated from two type strains of the genus Ponticoccus. Therefore, this algal-associated bacterial strain is concluded to represent a novel species of the genus Ponticoccus, for which the name Ponticoccus alexandrii sp. nov. is proposed. The type strain is AT2-A^T (CCTCC AB 2017228 ^T = KCTC 52626 ^T ).     

Molecular characterization of <Emphasis Type="Italic">bmyC</Emphasis> gene of the mosquito pupicidal bacteria, <Emphasis Type="Italic">Bacillus amyloliquefaciens</Emphasis> (VCRC B483) and in silico analysis of bacillomycin D synthetase C protein

A strain of Bacillus amyloliquefaciens (VCRC B483) exhibiting mosquito pupicidal, keratinase and antimicrobial activities was isolated from mangrove forest ecosystem of Andaman and Nicobar Islands. Molecular characterization of the strain showed the presence of lipopeptide encoding bmyC gene. Phylogenetic tree based on protein sequence of this gene exhibited homology with mycosubtilin synthetase of Bacilus atropheus and Iturin synthetase of Bacillus subtilis and B. amyloliquefaciens. This is the first report on the evolutionary conservation of amino acids concerned with the function and structure of bmyC protein of B. amyloliquefaciens. The presence of valine at the 1197th position in our strain was found to be unique and different from the existing strains of B. subtilis and B. amyloliquefaciens. Molecular modelling studies revealed significant changes in the structure of epimerization domain of the bmyC protein with A1197V variation. Crude metabolite of this strain exhibited antifungal activity against Fusarium sp. and Carvularia sp.