L. I. Evtushenko

Rathayibacter gen, nov., Including the Species Rathayibacter rathayi comb , nov,, Rathayibacter tritici comb , nov,, Rathayibacter iranicus comb, nov., and Six Strains from Annual Grasses

A new genus, Rathayibacter, is proposed to accommodate three species of gram-positive, aerobic, coryneform bacteria previously placed in the genus Clavibacter (Rathayibacter rathayi comb. nov., Rathayibacter tritici comb. nov., and Rathayibacter iranicus comb. nov.), as well as six strains that were isolated from annual cereal grasses, may be responsible for ryegrass toxicity, and are very similar to the recently described organism Clavibacter toxicus sp. nov. (I. T. Riley and K. M. Ophel, Int. J. Syst. Bacteriol. 42:64-68, 1992). The properties of members of the genus Rathayibacter include coryneform morphology, peptidoglycan based on 2,4-diaminobutyric acid (type B2γ), predominant menaquinones of the MK-10 type, and phosphatidylglycerol and diphosphatidylglycerol as basic polar lipids. The DNA base compositions range from 63 to 72 mol% G+C. The members of the new genus form a phenetic cluster distinct from Clavibacter spp. at a level of 71% (simple matching coefficient) and exhibit 7 to 9% DNA-DNA reassociation with strains of Clavibacter spp. In contrast to Clavibacter spp., most Rathayibacter strains are associated with nematodes belonging to the genus Anguina. The Rathayibacter species differ from species belonging to related genera (e.g., Clavibacter and Agromyces species) in the following characteristics: Menaquinone and whole-cell sugar compositions, results of lysozyme-sodium dodecyl sulfate test (which indicates differences in cell wall composition), ability to utilize a number carbon sources, resistance to bacteriocins of some Clavibacter spp., and other characteristics. The Rathayibacter species can be differentiated from each other by following characteristics: Presence or absence of xylose and galactose in the cell walls, fatty acid composition, ability to assimilate various sources of carbon and nitrogen, hydrolytic activity, tolerance to 5% NaCI and 0.03% potassium tellurite, susceptibility to iranicin, and absence or presence of plasmids of certain sizes. The type species of the genus Rathayibacter is R. rathayi. The type strains of the species are R. rathayi VKM Ac-1601 (= ICMP 2574), R. iranicus VKM Ac-1602 (= ICMP 3496), and R. tritici VKM Ac-1603 (= ICMP 2626).

Three New Species of Brevibacteria, Brevibacterium antiquum sp. nov., Brevibacterium aurantiacum sp. nov., and Brevibacterium permense sp. nov.

This work deals with the taxonomic study of orange-pigmented bacteria isolated from permafrost sediments, rice plots, and soils contaminated with wastes from the chemical and salt industries that were assigned to the genus Brevibacterium on the basis of phenotypic characteristics, as well as of some strains described previously as Brevibacterium linens. The study revealed three genomic species, whose members and the type strains of the closest species of Brevibacterium had DNA similarity levels between 24 and 59%. The strains of the genomic species differed from each other and from the known species of Brevibacterium in some physiological and biochemical characteristics, as well as in the sugar and polyol composition of their teichoic acids. The 16S rDNA sequence analysis confirmed the assignment of the environmental isolates to the genus Brevibacterium and showed the phylogenetic distinction of the three genomic species. The results obtained in this study allow three new Brevibacterium species to be described: Brevibacterium antiquum (type strain VKM Ac-2118T = UCM Ac-411T), Brevibacterium aurantiacum (type strain VKM Ac-2111T = NCDO 739T = ATCC 9175T), and Brevibacterium permense (type strain VKM Ac-2280T = UCM Ac-413T).

Proposed minimal standards for describing new genera and species of the suborder Micrococcineae.

The Subcommittee on the Taxonomy of the Suborder Micrococcineae of the International Committee on Systematics of Prokaryotes has agreed on minimal standards for describing new genera and species of the suborder Micrococcineae. The minimal standards are intended to provide bacteriologists involved in the taxonomy of members of the suborder Micrococcineae with a set of essential requirements for the description of new taxa. In addition to sequence data comparisons of 16S rRNA genes or other appropriate conservative genes, phenotypic and genotypic criteria are compiled which are considered essential for the comprehensive characterization of new members of the suborder Micrococcineae. Additional features are recommended for the characterization and differentiation of genera and species with validly published names.

Nitriliruptor alkaliphilus gen. nov., sp. nov., a deep-lineage haloalkaliphilic actinobacterium from soda lakes capable of growth on aliphatic nitriles, and proposal of Nitriliruptoraceae fam. nov. and Nitriliruptorales ord. nov.

A novel bacterial strain, designated ANL-iso2(T), was obtained from an enrichment culture inoculated with a mixture of soda lake sediments by using isobutyronitrile (iBN) as the carbon, energy and nitrogen source at pH 10. The enrichment resulted in a stable binary culture containing iBN-degrading Gram-positive rods and a satellite Gram-negative gammaproteobacterium Marinospirillum sp. strain (ANL-isoa) scavenging the products of nitrile hydrolysis. Cells of the iBN-degrading strain, ANL-iso2(T), were short, non-motile, non-spore-forming rods. Strain ANL-iso2(T) was capable of utilizing propionitrile (C(3)), butyronitrile (C(4)), isobutyronitrile (C(4)), valeronitrile (C(5)) and capronitrile (C(6)) as the only growth substrate. Growth on nitriles was biphasic with fast initial hydrolysis of nitriles to the corresponding amides, carboxylic acids and ammonia and slow further utilization of these products resulting in biomass growth. Cells of strain ANL-iso2(T) grown with iBN were capable of extremely active hydration of a wide range of nitriles into the corresponding amides and much slower hydrolysis of these amides to the corresponding carboxylic acids. This indicated the presence of the nitrile hydratase/amidase pathway of nitrile degradation in the novel bacterium. Strain ANL-iso2(T) showed obligately alkaliphilic growth on iBN within the pH range 8.4-10.6, with optimum growth at 9.0-9.5. It was moderately salt-tolerant, with a salt range for growth of 0.1-2.0 M Na(+) and an optimum salt concentration for growth of 0.2-0.3 M. The dominant fatty acids in the polar lipids were C(16 : 0), iso-C(14), C(14 : 0), iso-C(16) and C(16 : 1)omega7. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid. Phylogenetic analysis placed strain ANL-iso2(T) within the class Actinobacteria as an independent lineage with only uncultured bacteria from soda lakes as its nearest relatives. On the basis of its unique phenotype and distinct phylogeny, strain ANL-iso2(T) is considered to represent a novel species of a new genus, for which the name Nitriliruptor alkaliphilus gen. nov., sp. nov. is proposed. The type strain of the type species, Nitriliruptor alkaliphilus, is ANL-iso2(T) (=DSM 45188(T)=NCCB 100119(T)=UNIQEM U239(T)). Phylogenetic data suggest that the novel bacterium forms the basis of a new family Nitriliruptoraceae fam. nov. and a novel order Nitriliruptorales ord. nov. within the class Actinobacteria.

Survival of Micromycetes and Actinobacteria under Conditions of Long-Term Natural Cryopreservation

Almost all of the investigated samples of the Arctic and Antarctic permafrost sediments of different genesis with ages from 5–10 thousand to 2–3 million years were found to contain viable micromycete and bacterial cells. The maximum amounts of viable cells of fungi (up to 104CFU/g air-dried sample) and bacteria (up to 107–109CFU/g air-dried sample) were present in fine peaty sediment samples taken from different depths. The identified micromycetes belonged to more than 20 genera of the divisions Basidiomycota, Ascomycota, and Zygomycota, and some represented mitosporic fungi. Thawing the samples at 35 and 52°C allowed the number of detected fungal genera to be increased by more than 30%. Aerobic heterotrophic prokaryotes were dominated by coryneform, nocardioform, and spore-forming microorganisms of the order Actinomycetales.Analysis of the isolated fungi and actinomycetes showed that most of them originated from the microbial communities of ancient terrestrial biocenoses.

Agreia bicolorata gen. nov., sp. nov., to accommodate actinobacteria isolated from narrow reed grass infected by the nematode Heteroanguina graminophila

Agreia bicolorata gen. nov., sp. nov. (type strain VKM Ac-1804T=UCM Ac-620T) is proposed to accommodate aerobic, oxidase- and catalase-positive, weakly motile, coryneform actinobacteria isolated from leaf galls induced by the plant-parasitic nematode Heteroanguina graminophila in narrow reed grass, Calamagrostis neglecta. Bacteria assigned to Agreia bicolorata gen. nov., sp. nov. form a distinct lineage within the phylogenetic branch of the family Microbacteriaceae and possess the following chemotaxonomic characteristics: B-type peptidoglycan containing 2,4-diaminobutyric acid, ornithine, alanine, glycine, glutamate and hydroxyglutamate; cell wall sugars rhamnose, fucose and mannose; MK-10 as major menaquinone; phosphatidylglycerol and diphosphatidylglycerol as principal phospholipids; and 12-methyltetradecanoic acid (anteiso-15:0), 14-methyl-pentadecanoic acid (iso-16:0) and 14-methyl-hexadecanoic acid (anteiso-17:0) as predominant fatty acids. The DNA G+C content of Agreia bicolorata is about 67.0 mol %.

Salinicola socius gen. nov., sp. nov., a moderately halophilic bacterium from a naphthalene-utilizing microbial association

A chemoorganotrophic, moderately halophilic bacterium (strain SMB35) has been isolated from a naphthalene-utilizing microbial community obtained from salt mines (Perm region of Russia). Strain SMB35 grows in a wide salinity range, 0.5 to 30% (wt/vol) NaCl. Cells are gram-negative rods motile by means of a single polar flagellum. The predominant fatty acids are 16:1ω7, 16:0, 18:1ω7, and 19 cy. The major lipoquinone is an unsaturated ubiquinone with nine isoprene units (Q9). The DNA G+C content is 63.0 mol %. The 16S rDNA-based phylogenetic analysis has shown that strain SMB35 formed a separate clade in the cluster of the family Halomonadaceae. The 16S rDNA sequence similarity of the isolate to the members of the family is in the range from 90.6 to 95.1%. The phylogenetic and phenotypic differences from Halomonas elongata (the type species of the genus) and from other members of the family suggest that the isolate represents a novel genus and species, for which the name Salinicola socius gen. nov., sp. nov. is proposed. The type strain is SMB35T(=VKM B-2397T).

Okibacterium fritillariae gen. nov., sp. nov., a novel genus of the family Microbacteriaceae.

Okibacterium fritillariae gen. nov., sp. nov. (type strain VKM Ac-2059T = IFO 16404T) is proposed for aerobic, oxidase- and catalase-positive, coryneform bacteria isolated from seeds of Fritillaria ruthenica Wikstr. and Clematis recta L. Strains of the new genus form a distinct branch within the phylogenetic cluster composed of members of the family Microbacteriaceae and are characterized by B-type peptidoglycan containing amino acids glycine, glutamate, homoserine, alanine and lysine, the glycolyl type of muramic acid, the major menaquinones MK-10 and MK-11, the principal phospholipids phosphatidylglycerol and diphosphatidylglycerol, and a DNA G+C content of approximately 67 mol %.

A new species of actinomycete, Amycolata alni

A new species of the genus Amycolata, Amycolata alni, is proposed for strains which were mostly isolated from root nodules and rhizospheres of alder trees and were formerly assigned to the species Amycolata autotrophica. Strains of this new species could be differentiated from representatives of A. autotrophica by deoxyribonucleic acid homology data (17 to 29% relatedness), as well as by their ability to grow on salicin and D-gluconate, their failure to produce acid from cellobiose and meso-inositol, their resistance to penicillin and carbenicillin (10 g/ml), and other characteristics. Phenotypic features and low levels of deoxyribonucleic acid homology distinguish A. alni from two other species of the genus Amycolata, Amycolata saturnea and Amycolata hydrocarbonoxydans. The type strain of A. alni is strain 3LS (= VKM Ac-901).

Glycomyces tenuis sp. nov.

Chemotaxonomic, genetic, and phenotypic characteristics of strain VKM Ac-1250T (T = type strain), which was isolated from an association with Streptomyces galilaeus INA 5888, revealed that this actinomycete is a new Glycomyces species, for which the name Glycomyces tenuis is proposed. This new species could be differentiated from Glycomyces harbinensis and Glycomyces rutgersensis by the following characteristics: Thin hyphae (diameter, 0.15 to 0.40 μm) on the substrate mycelium, absence of aerial hyphae, major menaquinone composition [MK-9(H6), MK-10(H6), and MK-11(H6)], certain physiological properties, and high levels of susceptibility to some antibiotics and growth inhibitors. The type strain of G. tenuis is strain VKM Ac-1250 (= INA n-5888).