[Show abstract][Hide abstract]ABSTRACT: Meganema perideroedes Gr1(T) is a filamentous bacterium isolated from an activated sludge wastewater treatment plant where it is implicated in poor sludge settleability (bulking). M. perideroedes is the sole described species of the genus Meganema and of the proposed novel family "Meganemaceae". Here we describe the features of the type strain Gr1(T) along with its annotated genome sequence. The 3,409,949 bp long draft genome consists of 22 scaffolds with 3,033 protein-coding and 59 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes KMG project. Notably, genome annotation indicated the potential for facultative methylotrophy. However, the ability to utilize methanol as a carbon source could not be empirically demonstrated for the type strain or for in situ Meganema spp. strains.
Full-text · Article · Feb 2015 · Standards in Genomic Sciences
[Show abstract][Hide abstract]ABSTRACT: A Gram-negative, oxidase and catalase positive bacterium, designated strain EM 4T, which varies in shape from rod shaped to curved or helical with frequently observed bulb-shaped protuberances was isolated from purified water. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the family Chitinophagaceae within the Bacteroidetes; the closest relative among the validly described bacterial species was determined to be Sediminibacterium salmoneum NBRC 103935T with 93.4% sequence identity. Like other Flavobacteria, main fatty acids of strain EM 4T are C15:0 iso, C15:1 iso, and C17:0 iso 3OH. The polar lipid profile consists of phosphatidylethanolamine, aminolipids, aminophospholipids and unknown lipids; the quinone system consists of menaquinone MK-7. The 16S rRNA gene sequence analysis, the polar lipids and the fatty acid profiles suggest that the strain represents a novel genus and species for which the name Hydrobacter penzbergensis sp. nov. is proposed. Type strain is strain EM 4T (= DSM 25353T = CCUG 62278T).
No preview · Article · Jan 2015 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract]ABSTRACT: High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these "orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.
Full-text · Article · Feb 2013 · Systematic and Applied Microbiology
[Show abstract][Hide abstract]ABSTRACT: A novel bacterial strain designated HA-01T was isolated from a freshwater terrestrial hot spring located at Hot Springs National Park, Arkansas, USA. Cells were Gram-negative, rod-shaped, aerobic, chemoorganotrophic, oxidase- and catalase positive, non-spore forming, and motile by means of a single polar flagellum. Growth occurred at 37-60°C with an optimum between 45-50°C, pH 6.5-8.5 with an optimum between pH 6.5-7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that HA-01T closest relatives were Solimonas aquatica NAA-16T (93.8%), Solimonas flavus CW-KD 4T (94.1%), Solimonas soli DCY12T (93.1%), Solimonas variicoloris MN28T (94.0%), Nevskia ramosa Soe1T(91.2%), and Hydrocarboniphaga effusa AP103T (91.1%). Major fatty acids consisted of C16:0, iso-C16:0, C16 w5c, and summed feature 8 (C18:1 w9c, C18:1 w7c, and C18:1 w6c). Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and the major isoprenoid quinone was Q-8. The DNA G+C content was 64.4 mol%. Based on phylogenetic, phenotypic, and chemotaxonomic evidence, it is proposed that the unknown bacterium represents a novel species and genus for which the name Fontimonas thermophila gen. nov., sp. nov. is proposed. The type strain is HA-01T (= DSM 23609T = CCUG 59713T).
Full-text · Article · Jan 2013 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract]ABSTRACT: Thiothrix nivea (Rabenhorst 1865) Winogradsky 1888 (Approved Lists 1980) emend. Larkin and Shinabarger 1983 is the type species of the genus Thiothrix in the family Thiotrichaceae. The species is of interest not only because of its isolated location in the yet to be genomically characterized region of the tree of life, but also because of its life-style with gliding gonidia, the multilayer sheath, rosettes, and the embedded sulfur granules. Strain JP2T is the neotype strain of the species which was first observed by Rabenhorst in 1865 and later reclassified by Winogradsky in 1888 into the then novel genus Thiothrix. This is the first completed (improved-high-quality-draft) genome sequence to be published of a member of the family Thiotrichaceae. The genome in its current assembly consists of 15 contigs in four scaffolds with a total of 4,691,711 bp bearing 4,542 protein-coding and 52 RNA genes and is a part of the Genomic
Full-text · Article · Dec 2011 · Standards in Genomic Sciences
[Show abstract][Hide abstract]ABSTRACT: Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Haliscomenobacter, which belongs to order "Sphingobacteriales". The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically uncharted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The genome of H. hydrossis is the first completed genome sequence reported from a member of the family "Saprospiraceae". The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
[Show abstract][Hide abstract]ABSTRACT: A Gram-positive, spore-forming, aerobic, filamentous bacterium, strain JFMB-ATE(T), was isolated in 2008 during environmental screening of a plastic surface in grade C in a contract manufacturing organization in southern Germany. The isolate grew at temperatures of 25-50 °C and at pH 5.0-8.5, forming ivory-coloured colonies with sparse white aerial mycelia. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the family Thermoactinomycetaceae, except that the cell-wall peptidoglycan contained LL-diaminopimelic acid, while all previously described members of this family display this diagnostic diamino acid in meso-conformation. The DNA G+C content of the novel strain was 54.6 mol%, the main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, and the major menaquinone was MK-7. The major fatty acids had saturated C₁₄-C₁₆ branched chains. No diagnostic sugars were detected. Based on the chemotaxonomic results and 16S rRNA gene sequence analysis, the isolate is proposed to represent a novel genus and species, Kroppenstedtia eburnea gen. nov. sp. nov. The type strain is JFMB-ATE(T) ( = DSM 45196(T) = NRRL B-24804(T) = CCUG 59226(T)).
Full-text · Article · Oct 2010 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract]ABSTRACT: 16S rRNA gene sequenced-based phylogeny indicates that Rhizobacter dauci ATCC 43778(T) branches within the radiation of Methylibium type strains. A comparative chemotaxonomic study including fatty acid methyl esters, polar lipids and polyamines reveals significant differences that, in combination with the topology of phylogenetic trees, support a dissection of the genus Methylibium. The proposals of this study include the transfer of Methylibium fulvum to the genus Rhizobacter as Rhizobacter fulvus comb. nov. (type strain Gsoil 322(T) =KCTC 12591(T) =DSM 19916(T)) and the reclassification of Methylibium aquaticum as Piscinibacter aquaticus gen. nov., comb. nov. (the type strain of Piscinibacter aquaticus is IMCC1728(T) =KCCM 42364(T) =NBRC 102349(T) =DSM 19915(T)) and of Methylibium subsaxonicum as Rivibacter subsaxonicus gen. nov., comb. nov. (the type strain of Rivibacter subsaxonicus is BF49(T) =DSM 19570(T) =CIP 109700(T)). As a consequence of these reclassifications, emended descriptions of the genera Methylibium and Rhizobacter are provided.
Full-text · Article · Aug 2009 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract]ABSTRACT: During a screening of phosphate solubilizing bacteria (PSB) in agricultural soils, two strains, IH9 and OCI1, were isolated from the rhizosphere of grasses in Spain, and they showed a high ability to solubilize phosphate in vitro. Inoculation experiments in chickpea and barley were conducted with both strains and the results demonstrated their ability to promote plant growth. The 16S rRNA gene sequences of these strains were nearly identical to each other and to those of Acinetobacter calcoaceticus DSM 30006(T), as well as the strain CIP 70.29 representing genomospecies 3. Their phenotypic characteristics also coincided with those of strains forming the A. calcoaceticus-baumannii complex. They differed from A. calcoaceticus in the utilization of l-tartrate as a carbon source and from genomospecies 3 in the use of d-asparagine as a carbon source. The 16S-23S intergenic spacer (ITS) sequences of the two isolates showed nearly 98% identities to those of A. calcoaceticus, confirming that they belong to this phylogenetic group. However, the isolates appeared as a separate branch from the A. calcoaceticus sequences, indicating their molecular separation from other A. calcoaceticus strains. The analysis of three housekeeping genes, recA, rpoD and gyrB, confirmed that IH9 and OCI1 form a distinct lineage within A. calcoaceticus. These results were congruent with those from DNA-DNA hybridization, indicating that strains IH9 and OCI1 constitute a new genomovar for which we propose the name A. calcoaceticus genomovar rhizosphaerae.
No preview · Article · Jun 2009 · Systematic and Applied Microbiology
[Show abstract][Hide abstract]ABSTRACT: Bacterial strain BF36T, isolated from the biofilm of a tufa deposit in a hard water rivulet, was characterized by a polyphasic taxonomic approach. Cells of these organisms were Gram-negative, motile, nonpigmented, rod-shaped, non-endospore-forming, and facultatively anaerobic. Cells, organized in loose consortia, were coated by a massive slime layer. Phylogenetic analyses using 16S rRNA gene sequences showed that strain BF36T was a member of the family Enterobacteriaceae, class Gammaproteobacteria, displaying a moderate degree of relationship (96.5% sequence similarity) to Sodalis glossinidius and "Sodalis pallipedes," intracellular symbionts of the tsetse fly Glossinis morsitans morsitans. Dendrograms of relationship generated by different algorithms consistently grouped isolate BF36T with Sodalis glossinidius, Pragia fontium, Budvicia aquatica, Serratia rubideae, and Brenneria spp (94.7-95.8% similarity) which also share many common metabolic properties. Differences between strain BF36T and Sodalis glossinidius DSM 13495T are seen in motility and in the pattern of substrates utilized. Membership to the family was also confirmed by a fatty acid profile consisting of major amounts of C16:0)and C16:1omega7, by the presence of isoprenoids of the ubiquinone Q8 and menaquinone MK8 types and a DNA G + C content of 54.2 mol%. The decision to classify strain BF36T into a new genus Biostraticola gen. nov. is based on its distant phylogenetic position as compared to any other representative of the family and the significant phenotypic differences to its nearest phylogenetic neighbor, Sodalis glossinidius. BF36T represents the type species, for which the name Biostraticola tofi sp. nov. is proposed. The type strain is BF36T (DSM 19580T; CIP109699T).
Full-text · Article · Jul 2008 · Current Microbiology
[Show abstract][Hide abstract]ABSTRACT: A single strain, designated BF49T, was isolated from a biofilm of a tufa deposit from the Westerhöfer rivulet, Lower Saxony, Germany. The G+C content of the genomic DNA of strain BF49T was 69 mol% and the predominant ubiquinone was Q-8. Major fatty acids were C16:1ω7c/15 iso 2OH and C16:0. Comparative 16S rRNA gene sequence analysis indicated that the isolate was placed within the genus Methylibium, class Betaproteobacteria, distantly related to the type strain Methylibium petroleiphilum LMG 22953T (97.4% similarity), Methylibium
fulvum Gsoil 322T (96%), and Methylibium aquaticum IMCC1728T (95.7%). On the basis of phylogenetic and phenotypic distinctness we propose a novel species, Methylibium subsaxonicum sp. nov., with strain BF49T (DSM 19570T, CIP 109700T) as the type strain.
No preview · Article · May 2008 · Current Microbiology
[Show abstract][Hide abstract]ABSTRACT: Three bacterial strains, designated MT1(T), RW10(T) and IpA-2(T), had been isolated previously for their ability to degrade chlorosalicylates or isopimaric acid. 16S rRNA gene sequence analysis demonstrated that these bacteria are related to species of the genus Pseudomonas. Analysis of the results of DNA-DNA hybridization with several close phylogenetic neighbours revealed a low level of hybridization (less than 57 %). On the basis of phenotypic characteristics, phylogenetic analysis, DNA-DNA relatedness data and chemotaxonomic analysis, it is concluded that these isolates represent separate novel species, for which the names Pseudomonas reinekei sp. nov. (type strain MT1(T) =DSM 18361(T)=CCUG 53116(T)), Pseudomonas moorei sp. nov. (type strain RW10(T) =DSM 12647(T)=CCUG 53114(T)) and Pseudomonas mohnii sp. nov. (type strain IpA-2(T) =DSM 18327(T)=CCUG 53115(T)) are proposed.
Preview · Article · Jun 2007 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract]ABSTRACT: Polyphasic characterization of strain DSM 9128, described as 'Pseudomonas azelaica' by Janota-Bassalik et al. [Acta Microbiol Pol B 3, 143-153 (1971)], and four biochemically similar isolates was performed with the aim of validly publishing the name 'Pseudomonas azelaica'. Based on 16S rRNA gene sequence analysis, DNA-DNA hybridization, fatty acid patterns and extensive biochemical testing, it was concluded that DSM 9128, two further strains and the type strains of Pseudomonas nitroreducens and Pseudomonas multiresinivorans form a highly related cluster. However, DNA-DNA binding did not conclusively resolve whether these strains should be regarded as members of one species. Based on results gained with the above-mentioned methods, two other isolates were assigned to the species Pseudomonas citronellolis, a species very close to P. nitroreducens. Based on genetic and biochemical similarities, it is suggested that Pseudomonas multiresinivorans should be considered as a later heterotypic synonym of Pseudomonas nitroreducens. The species descriptions of P. nitroreducens and P. citronellolis are emended.
Preview · Article · Apr 2007 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract]ABSTRACT: In the near future, an increasing number of in situ life detection and sample return missions to planets and other solar system bodies will be launched. The demand to control spacecraft-carried microbial contamination becomes obvious. COSPAR (Committee of Space Research) has defined guidelines and bioburden limits for different types of missions and target bodies. The first step in the implementation of these planetary protection guidelines encompasses a qualitative and quantitative inventory of the bioburden of spacecraft assembly facilities. With information about the composition of these microbial communities the development and/or optimization of adequate cleaning, disinfection, and sterilization procedures for spacecraft preparation before launch will be possible.In the ESA project MiDiv, we started to investigate the diversity of cultivable microorganisms found on spacecraft and spacecraft assembly halls using the satellites SMART-1 and ROSETTA as test objects. The analyses to date include cultivation of microorganisms by varying pH, temperature, oxygen, and pasteurization. A culture collection of bacterial isolates and a database of 16S RNA gene sequences have been established. The results of our preliminary work, including the numbers of colony forming units, differentiated as aerobes and facultative anaerobes as well as their phylogenetic classification, give a first overview of the breadth of physiological potential of the identified microorganisms and their capability to withstand various cleaning and sterilizing procedures currently used for the planetary protection.
No preview · Article · Jan 2006 · Advances in Space Research
[Show abstract][Hide abstract]ABSTRACT: Planetary protection measures are necessary for all space flight missions involved with life detection and or sample return procedures to avoid the contamination of critical spacecraft hardware components with terrestrial organisms Spacecraft are assembled in clean rooms under defined and controlled environmental conditions These conditions might be considered as extreme with respect to controlled air circulation low relative humidity moderately high constant temperature and low nutrient conditions and represent a special artificial environment for microorganisms In the ESA-Project MiDiv the bioburden and the microbial diversity of three different spacecraft assembly and testing facilities has been investigated in periods where the facilities have been in full operation with the assembly and test of European satellites For the selected satellite missions SMART-1 and ROSETTA however no strict planetary protection measures like those required for a landing mission on Mars COSPAR Planetary Protection Category IV have been necessary and taken into consideration The result of this investigation therefore reflects the normal microbial conditions in standard class 100 000 clean rooms used by employees without any special training in planetary protection The investigation in the MiDiv project was restricted to so-called cultivable microorganisms in particular to those microorganisms that are able to grow under the selected conditions The analysis of the samples included cultivation on different media at different pH values and
[Show abstract][Hide abstract]ABSTRACT: Strain CCM 2783, previously classified as representing Arthrobacter aurescens, was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis and chemotaxonomic characteristics such as peptidoglycan type A3alpha Lys-Ala(2), major menaquinone MK-9(H(2)) and fatty acid composition confirmed assignment of the strain to the genus Arthrobacter. The results of phylogenetic analysis, DNA-DNA relatedness experiments and physiological and chemotaxonomic characteristics indicate that CCM 2783 differs from its nearest phylogenetic relative Arthrobacter psychrolactophilus and from other recognized Arthrobacter species. Therefore, a novel species, Arthrobacter stackebrandtii sp. nov., is proposed with the type strain CCM 2783(T) (=DSM 16005(T)).
Full-text · Article · Apr 2005 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract]ABSTRACT: A Gram-positive actinobacterium, previously classified as Kocuria varians, was subjected to a polyphasic taxonomic study. The bacterium showed the peptidoglycan type Lys-Ala3 (variation A3alpha), MK-7(H2) was the major menaquinone and anteiso-C(15 : 0) and anteiso-C(17 : 0) were the major fatty acids. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel species, Kocuria carniphila sp. nov. (type strain, CCM 132T=DSM 16004T), is proposed.
Full-text · Article · Feb 2005 · International Journal of Systematic and Evolutionary Microbiology
[Show abstract][Hide abstract]ABSTRACT: Based on 16S rRNA gene sequence comparison, an isolate that was detected in sterile-filtered vegetable broth was classified as a novel member of the Erysipelothrix line of descent of the Firmicutes. Strain MF-EP02T resembles members of the two species of Erysipelothrix with validly published names, Erysipelothrix rhusiopathiae and Erysipelothrix tonsillarum, in morphology, fatty acid composition, lack of menaquinones in aerobically and anaerobically grown cultures, DNA G+C content and peptidoglycan amino acid composition. Distinct differences in physiological characteristics, however, support the allocation of this isolate to a novel species of the genus Erysipelothrix, for which the name Erysipelothrix inopinata sp. nov. (type strain, MF-EP02T=DSM 15511T=CIP 107935T) is proposed. Members of the Erysipelothrix line of descent are included in the family Erysipelotrichaceae fam. nov.
Preview · Article · Feb 2004 · International Journal of Systematic and Evolutionary Microbiology