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PubMed2002

Two novel psychrotolerant species, Bacillus psychrotolerans sp. nov. and Bacillus psychrodurans sp. nov., which contain ornithine in their cell walls.

Eleven psychrotolerant Bacillus strains with ornithine as diamino acid in position 3 of the peptide side chain of the cell wall and a G+C range of 35.7-38.4 mol% were characterized taxonomically. DNA-DNA hybridization studies confirmed previously physiologically established groups. High DNA-binding values (> 70%) were found within groups I A (consisting of the type strain of Bacillus insolitus DSM 5(T) and Bacillus insolitus DSM 2272), I B (consisting of isolates 3H1(T0, 71H1, 84E1, 87H2 and 4H2) and I C (consisting of isolates 68E39T), 61E1, 4E3 and 67E1). Low DNA-binding values (< 60%) were revealed between the three groups. Consequently, strains of groups I B and I C were considered as being representatives of new psychrotolerant species. For group I B strains the name Bacillus psychrotolerans sp. nov. is proposed with the type strain 3H1(T) (= DSM 11706(T) = NCIMB 13838(T)) and for group I C strains the name Bacillus psychrodurans sp. nov. is proposed with the type strain 68E3(T) (= DSM 11713(T) = NCIMB 13837(T)).

Bacillus↗
PubMed2001

Microbacterium gubbeenense sp. nov., from the surface of a smear-ripened cheese.

Phenotypic and phylogenetic studies were performed on 11 strains of a Microbacterium-like organism isolated from the surface of a smear-ripened cheese. The isolates were Gram-positive, catalase-positive, facultatively anaerobic, oxidase-negative, non-spore-forming, non-motile, small, slender rods and grew in 12% (w/v) NaCl. Chemotaxonomic investigation revealed that all the isolates belonged unambiguously to the genus Microbacterium. They contained type B1 peptidoglycans with L-lysine as the diamino acid and glycolyl acyl types; rhamnose and galactose were the cell wall sugars. The G+C content ranged from 69 to 72 mol%. The major menaquinones were MK-11 and MK-12 and the major fatty acids were anteiso C15:0 and C17:0 and iso C16:0. Phylogenetic analysis of the 16S rRNA sequences of four isolates showed that they represented a new subline in the genus Microbacterium, with Microbacterium barkeri as their nearest phylogenetic neighbour. M. barkeri showed the highest sequence similarity to the isolates; however, DNA-DNA hybridization showed that the isolates had only 38% chromosomal similarity to M. barkeri. Based on the phylogenetic and phenotypic distinctiveness of the isolates, it is proposed that they be classified as a new Microbacterium species, for which the name Microbacterium gubbeenense sp. nov. is suggested. The type strain has been deposited as LMG S-19263T (= NCIMB 30129T). The GenBank accession number for the 16S rDNA sequence of the type strain is AF263563.

Actinomycetales↗
PubMed1997

Demetria terragena gen. nov., sp. nov., a new genus of actinomycetes isolated from compost soil.

A novel actinomycete was isolated from compost soil and was studied taxonomically and phylogenetically. Cells of this organism were gram positive, not acid fast, nonmotile, nonsporulating, irregular coccoid to short rod shaped, and microaerophilic. The cell wall peptidoglycan contained lysine and was cross-linked via an L-Lys<--L-Ser<--D-Asp interpeptide bridge. The major menaquinone was MK-8(H4). The polar lipids were phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and two unknown phospholipids. Mycolic acids were absent. The cellular fatty acid profile was complex, with large amounts of saturated and monounsaturated straight-chain acids and smaller amounts of iso and anteiso branched-chain acids. The G+C content of the DNA was 66 mol%. Comparative 16S ribosomal DNA studies revealed that strain HKI 0089T represents a novel lineage within Actinobacteria (32) distinct from all previously described genera and most closely related to members of the genera Kytococcus, Dermacoccus, and Dermatophilus of the family Dermatophilaceae. On the basis of our results, we suggest that strain HKI 0089 should be classified in a new genus and species, for which we propose the name Demetria terragena. The type strain and the only strain of the genus and species is HKI 0089 (DSM 11295).

Actinomycetaceae↗
PubMed1997

A new genus of the order Actinomycetales, Spirilliplanes gen. nov., with description of Spirilliplanes yamanashiensis sp. nov.

Actinomycete strain YU127-1T (T = type strain), which produces zoospores, was isolated from a soil sample. The aerial mycelium of this organism at maturity forms short chains of spores. The hyphae form coils, and sporangia are not observed. Strain YU127-1T contains glutamic acid, glucosamine, glycine, alanine, and meso-diaminopimelic acid in its cell wall (wall chemotype II), 3-O-methylmannose, mannose, xylose, and glucose as whole-cell sugars, meanaquinone 10(H4), and glycolyl cell wall polysaccharides and has a guanine-plus-cytosine content of 69.0 mol%. Mycolic acids are absent. Phosphatidylinositol and phosphatidylethanolamine are diagnostic phospholipids. The chemotaxonomic data, except for the lack of arabinose in the whole-cell sugars, indicate that this strain belongs to the family Micromonosporaceae. The morphological and physiological characteristics and chemotaxonomic and phylogenetic data for this strain differ from those of the previously described actinomycetes. We therefore propose a new genus, spirilliplanes, for this organism; the type species of the genus is Spirilliplanes yamanashiensis sp. nov., and the type strain of S. yamanashiensis is strain YU127-1 (= IFO 15828).

Actinomyces↗
PubMed1997

Chemical Composition of Hypodermal and Endodermal Cell Walls and Xylem Vessels Isolated from Clivia miniata (Identification of the Biopolymers Lignin and Suberin).

The occurrence of the biopolymers lignin and suberin was investigated with hypodermal (HCW) and endodermal cell walls (ECW) and xylem vessels (XV) isolated from Clivia miniata Reg. roots. Both biopolymers were detected in HCW and ECW, whereas in XV, typical aliphatic suberin monomers were missing and only representative lignin monomers such as guaiacyl (G) and syringyl (S) units could be detected. The absolute amounts of lignin were about one order of magnitude higher compared with suberin in both HCW and ECW. The ratios of the two aromatic lignin units (G/S) decreased from 39 in XV and 10 in HCW to about 1 in ECW, indicating significant differences in lignin structure and function between the three investigated samples. Additionally, compared with the detectable lignin-derived aromatic units G and S, significantly higher amounts of esterified p-coumaric acid-derived aromatic monomers were obtained with HCW, but not with ECW. This is interpreted as a functional adaption of HCW toward pathogen defense at the root/soil interface. The final aim of this study was to provide a thorough chemical characterization of the composition of HCW, ECW, and XV, which in turn will form the basis for a better understanding of the relevant barriers toward the passive, radial, and apoplastic diffusion of solutes from the soil across the root cortex into the root cylinder.

Journal Article↗
PubMed2004

Janibacter melonis sp. nov., isolated from abnormally spoiled oriental melon in Korea.

Two Gram-positive bacterial strains, CM2104(T) and CM2110, isolated from the inner part of abnormally spoiled oriental melon (Cucumis melo) in Korea, were subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan of strains CM2104(T) and CM2110 contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H(4)). The major fatty acids detected in the two strains were iso-C(16 : 0), C(17 : 1)omega8c and C(18 : 1)omega9c or C(17 : 0). The DNA G+C content of the two strains was 73 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a coherent cluster with a clade comprising two Janibacter species, Janibacter limosus and Janibacter terrae. Strains CM2104(T) and CM2110 exhibited a 16S rRNA gene sequence similarity value of 99.7 % and a mean DNA-DNA relatedness level of 89 %. Strains CM2104(T) and CM2110 showed 16S rRNA gene sequence similarity levels of 97.8-98.4 % to the type strains of J. limosus and J. terrae. DNA-DNA relatedness between strains CM2104(T) and CM2110 and the type strains of these two Janibacter species was 7-11 %. On the basis of the phenotypic and phylogenetic data and genomic distinctiveness, strains CM2104(T) and CM2110 should be placed within the genus Janibacter as members of a novel species, for which the name Janibacter melonis sp. nov. is proposed. The type strain is CM2104(T) (=KCTC 9987(T)=DSM 16063(T)=JCM 12321(T)).

Actinomycetales↗
PubMed2004

Bacillus hwajinpoensis sp. nov. and an unnamed Bacillus genomospecies, novel members of Bacillus rRNA group 6 isolated from sea water of the East Sea and the Yellow Sea in Korea.

Two Gram-positive or -variable, endospore-forming, slightly halophilic strains (SW-72(T) and SW-93) were isolated from sea water of the East Sea and the Yellow Sea in Korea, respectively, and subjected to polyphasic taxonomic study. Both strains had cell-wall peptidoglycan that was based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The two strains contained large amounts of saturated and branched fatty acids, with anteiso-C(15 : 0) as the major fatty acid. The DNA G+C contents of strains SW-72(T) and SW-93 were 40.9 and 41.0 mol%, respectively. Phylogenetic analysis based on 16S rDNA sequences showed that strains SW-72(T) and SW-93 fall within the radiation of the cluster that comprises members of the genus Bacillus, particularly Bacillus rRNA group 6. There were five nucleotide differences between the 16S rDNA sequences of strains SW-72(T) and SW-93. The mean level of DNA-DNA relatedness between strains SW-72(T) and SW-93 was 21.5 %. Strains SW-72(T) and SW-93 showed 93.1-95.2 % 16S rDNA sequence similarity to the type strains of Bacillus species that are assigned to rRNA group 6. Strains SW-72(T) and SW-93 could not be differentiated clearly by using their phenotypic properties. On the basis of phenotypic properties, phylogeny and genomic data, it is proposed that strain SW-72(T) (=KCCM 41641(T)=JCM 11807(T)) should be placed in the genus Bacillus as the type strain of a novel species, Bacillus hwajinpoensis sp. nov., and that strain SW-93 (=KCCM 41640=JCM 11806) should be placed in the genus Bacillus as an unnamed Bacillus genomospecies.

Bacillus↗
PubMed2000

Hongia gen. nov., a new genus of the order Actinomycetales.

An aerobic, nocardioform actinomycete, named LM 161T, was isolated from a soil sample obtained from a gold mine in Kongiu, Republic of Korea. This organism formed well-differentiated aerial and substrate mycelia and produced branched hyphae that fragmented into short or elongated rods. The cell wall contains major amounts of LL-diaminopimelic acid, alanine, glycine, glutamic acid, mannose, glucose, galactose, ribose and acetyl muramic acid. The major phospholipids of this isolate are phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, and the major isoprenologue is a tetrahydrogenated menaquinone with nine isoprene units. The whole-cell hydrolysate of strain LM 161T contains 12-methyltetradecanoic and 14-methylpentadecanoic acids as the predominant fatty acids, but does not contain mycolic acids. The G+C content of the DNA is 71.3 mol%. The phylogenetic position of the test strain was investigated using an almost complete 16S rDNA sequence. The isolate formed the deepest branch in the clade encompassing the members of the suborder Propionibacterineae Rainey et al. 1997. On the basis of chemical, phenotypic and genealogical data, it is proposed that this isolate be classified within a new genus as Hongia koreensis gen. nov., sp. nov. in the order Actinomycetales. The type strain is LM 161T (= IMSNU 50530T).

Actinomycetales↗
PubMed1975

[Isolation of new species of the genus Actinomadura on selective media with rubomycin].

In the screening programme of organisms producing new antibiotics on selective media with rubomycin (5, 10, 20 gamma/ml) 4 unusual actinomyceteus cultures forming short, straight, hook-like and monospiral spore chains on the aerial mycelium were isolated. The study of the composition of the cell walls showed that they contained meso-diaminopimelic acid and madurose, a differentiating sugar. On the basis of the morphological structure and composition of the cell walls the isolates were classified as belonging to Actinomadura. Comparison of the isolates with the species of Actinomadura described in the literature showed that the isolates were new species of the genera, i.e. Am. roseola sp. nov., Am, aurantiaca sp. nov., Am. vinacea sp. nov. and Am. livida sp. nov.

Actinomycetales↗
PubMed2006

Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains L-lysine in its cell wall.

A halotolerant, round-endospore-forming, aerobic, Gram-positive bacterium, designated BH724(T), was isolated from a solar saltern at Taean in Korea. Cells of this strain were rod-shaped and found to be non-motile. Strain BH724(T) grew at salinities of 0-10 % (w/v) NaCl with an optimum of 3 % (w/v) NaCl and at temperatures of 15-50 degrees C with an optimum of 40 degrees C. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH724(T) belonged to the genus Bacillus and that Bacillus aquimaris TF-12(T), Bacillus marisflavi TF-11(T) and Bacillus vietnamensis JCM 11124(T) were its closest neighbours, sharing 97.3, 97.2 and 97.0 % 16S rRNA gene sequence similarity, respectively. The genomic DNA G+C content was 39 mol% and the predominant menaquinone was MK-7. Its major cellular fatty acids were anteiso-C(15 : 0), iso-C(15 : 0), iso-C(16 : 0) and iso-C(14 : 0). The peptidoglycan type was A1alpha, linked directly through l-lysine. On the basis of morphological, chemotaxonomic, physiological and phylogenetic properties, strain BH724(T) represents a novel species of the genus Bacillus, for which the name Bacillus seohaeanensis sp. nov. is proposed. The type strain is BH724(T) (=KCTC 3913(T)=DSM 16464(T)).

Bacillus↗
PubMed2001

Ultrastructural effects of cellulose biosynthesis inhibitor herbicides on developing cotton fibers.

Cotton fibers are often utilized as a model system to investigate cellulose biosynthesis and cell wall elongation. In this study, we grew cotton fibers in vitro, with ovules dissected at day zero post anthesis as the explant source, in the presence of three herbicides that inhibit cellulose biosynthesis. Cultures were sampled for electron microscopy and immunocytochemistry 1-2 days after beginning the treatments. After dichlobenil treatment, the fibers were much shorter than the controls and assumed a variety of abnormal shapes, from shortened versions of the control fiber to nearly spherical. The inner layers of the fiber wall often contained juxtaposed electron-translucent and -transparent areas; this layer reacted strongly with antibodies to callose. Cellulase-gold labeling in these newly developed fibers grown in the presence of dichlobenil was present at only about 3% of the control labeling. After treatment with either isoxaben or flupoxam, the fibers assumed spherical shapes and frequently (more than 60% of fibers) exhibited a new cell plate within the fiber, indicating that cell division had occurred, a process that rarely occurred in the controls. Unlike the dichlobenil-treated fibers, fibers grown in the presence of isoxaben or flupoxam contained an extensive accumulation of chiefly deesterified pectins, replacing the entire wall with an elaborated version of the pectin sheath found in control cotton fibers. These data indicate that all three herbicides are effective disrupters of cellulose biosynthesis and cause radical changes in cell wall structure and composition. Moreover, these data indicate that the composition of the walls may influence indirectly cell cycle kinetics, keeping these fiber cells in a more meristematic mode.

Benzamides↗
PubMed2002

Identification of QTLs influencing wood property traits in loblolly pine ( Pinus taeda L.). II. Chemical wood properties.

Chemical wood property traits were analyzed for the presence of quantitative trait loci (QTLs) in a three-generation outbred pedigree of loblolly pine ( Pinus taeda L.). These traits were assayed using pyrolysis molecular beam mass spectrometry and include mass spectrum peak intensities associated with carbohydrates, alpha-cellulose and hemicellulose sugars, and lignin. Models for projection to latent structures (PLS) were used to also estimate the chemical composition of cell walls (i.e., alpha-cellulose, galactan and lignin) from mass spectrum data using multivariate regression. Both earlywood and latewood fractions from the fifth annual ring were analyzed for each trait. An interval mapping approach designed for an outbred pedigree was used to estimate the number of QTLs, the magnitude of QTL effects, and their genomic position. Eight unique QTLs influencing cell wall chemistry were detected from multiple peak intensities and/or PLS estimates using the one- and two-QTL models. Significant differences in chemical contents were observed among the populations from North Carolina vs Oklahoma, and results from QTLxenvironment analyses suggest that QTLs interact with environmental location. QTLs should be verified in larger experiments and in different genetic and environmental backgrounds. QTL mapping will help towards eventually identifying genes having a major effect on chemical wood properties.

Journal Article↗
PubMed2002

Isolation and characterization of bile salts-sensitive mutants of Enterococcus faecalis.

A library of insertional mutants of Enterococcus faecalis was constructed; it allowed the isolation and the characterization of 10 mutants affected in resistance to bile salts. Insertion loci of two mutants corresponded to genes of unknown function, while the amino acid sequences deduced from the other loci were homologous to proteins related to DNA repair, oxidative response, transcriptional regulation, dGTP hydrolysis, membrane composition, or cell wall synthesis. Further characterization of one mutant revealed that the insertion within the E. faecalis sagA gene led to a decrease of the resistance towards numerous independent physicochemical stresses, to modifications of the cell wall integrity, and to perturbations of cell division with septation anomalies.

Bacterial Proteins↗
PubMed2004

Structure of the cinnamyl-alcohol dehydrogenase gene family in rice and promoter activity of a member associated with lignification.

Analysis of lignification in rice has been facilitated by the availability of the recently completed rice genome sequence, and rice will serve as an important model for understanding the relationship of grass lignin composition to cell wall digestibility. Cinnamyl-alcohol dehydrogenase (CAD) is an enzyme important in lignin biosynthesis. The rice genome contains 12 distinct genes present at nine different loci that encode products with significant similarity to CAD. The rice gene family is diverse with respect to other angiosperm and gymnosperm CAD genes isolated to date and includes one member (OsCAD6) that contains a peroxisomal targeting signal and is substantially diverged relative to other family members. Four closely related family members (OsCAD8A-D) are present at the same locus and represent the product of a localized gene duplication and inversion. Promoter-reporter gene fusions to OsCAD2, an orthologue of the CAD gene present at the bm1 (brown midrib 1) locus of maize, reveal that in rice expression is associated with vascular tissue in aerial parts of the plant and is correlated with the onset of lignification. In root tissue, expression is primarily in the cortical parenchyma adjacent to the exodermis and in vascular tissue.

Alcohol Oxidoreductases↗
PubMed2006

Reproductive isolation among sympatric cryptic species in marine diatoms.

Pseudo-nitzschia is a marine cosmopolitan genus of chain-forming planktonic diatoms. As for the vast majority of phytoplankton organisms, species identification within this genus mostly relies upon morphological features. Taxa were initially identified based on cell shape and gross morphology of their composite silica cell wall, called the frustule. Yet, observations of the frustule in electron microscopy showed many additional characters for species identification and results of molecular studies have demonstrated that genetically distinct groups might exist within morpho-species. However, these studies have not addressed the biological meaning of these genetic differences. Here, we bridge that gap by comparing ultrastructural features and sequence data (three ribosomal and one plastid marker) of 95 strains with results of mating experiments among these strains. Experiments were performed on two morphologically distinct entities: P. delicatissima and P. pseudodelicatissima. Each of the two entities consisted of multiple genetically distinct and reproductively isolated taxa, all occurring in sympatry: P. delicatissima was composed of three phylogenetic and reproductively distinct groups, whereas P. pseudodelicatissima consisted of up to five. Once these taxa had been defined both genetically and biologically, subtle ultrastructural differences could be detected as well. Our findings not only show that cryptic genetic variants abound in sympatry, but also that they are reproductively isolated and, therefore, biologically distinct units.

DNA, Ribosomal Spacer↗