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.
A Gram-negative, rod-shaped, weakly motile, non-spore-forming bacterium (D9T) was isolated from the gut of Cylindroiulus fulviceps (Diplopoda) on 1/3-strength nutrient agar plates. On the basis of ...16S rRNA gene sequence similarity, strain D9T was shown to be phylogenetically closely related to the type strain of Budvicia aquatica, the sole species of the genus Budvicia, family Enterobacteriaceae. The similarity of the 16S rRNA gene sequences of strain D9T and B. aquatica DSM 5075T was 98.4 %. Other strains that showed high pairwise similarities with the isolate belonged to the genus Yersinia: Y. frederiksenii ATCC 33641T (96.8 % 16S rRNA gene sequence similarity), Y. massiliensis CCUG 53443T (96.8 %), Y. pestis NCTC 5923T (96.8 %), Y. pseudotuberculosis ATCC 29833T (96.8 %), Y. similis CCUG 52882T (96.7 %) and Y. ruckeri ATCC 29473T (96.5 % ). The similarities of sequences of the housekeeping genes rpoB, hsp60 and gyrB between strain D9T and B. aquatica DSM 5075T and other members of the Enterobacteriaceae were less than 94 %. Phylogenetic trees based on all four gene sequences unequivocally grouped the isolate with the type strain of B. aquatica and separately from the genus Yersinia. Cells contained the quinones Q-8, Q-7 and MK-8. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the DNA (48.3 mol%) and the whole-cell fatty acid composition of strain D9T (C14 : 0, C16 : 1ω7c, C16 : 0, cyclo-C17 : 0 and C18 : 1ω7c as major components) were typical for members of the Enterobacteriaceae. DNA–DNA hybridization of strain D9T with B. aquatica DSM 5075T resulted in a relatedness of 30.4 %, indicating that the isolate did not belong to B. aquatica. Physiological tests allowed the phenotypic differentiation of strain D9T from B. aquatica DSM 5075T as well as from members of the genus Yersinia. From these results, it is concluded that strain D9T represents a novel species, for which the name Budvicia diplopodorum sp. nov. is proposed (type strain D9T = DSM 21983T = CCM 7845T). The description of the genus Budvicia is emended.
The taxonomic status of a nitrogen-fixing bacterium, strain MSSRF38T, isolated from the rhizosphere of mangrove-associated wild rice (Porteresia coarctata Tateoka), in Pichavaram, India, was studied ...using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel strain MSSRF38T was most closely related to Vibrio ruber DSM 16370T (98.3% gene sequence similarity), Vibrio rhizosphaerae DSM 18581T (98.2% sequence similarity) and <96% to the remaining Vibrio species. Multilocus sequence analysis using ftsZ, gapA, gyrB and mreB genes showed low levels of gene sequence similarities (82-90%) with all species of the genus Vibrio with validly published names, indicating that strain MSSRF38T occupies a distinct phylogenetic position. DNA-DNA hybridization experiments showed that strain MSSRF38T had <70% DNA-DNA similarity to its closest neighbours V. ruber DSM 16370T (27.4%) and V. rhizosphaerae DSM 18581T (12.1%). Strain MSSRF38T could be differentiated from its relatives on the basis of several phenotypic characteristics. The major fatty acids were feature 3 (including C₁₆:₁ω7c and/or C₁₅:₀ iso 2-OH), C16:0, C₁₈:₁ω7c, C₁₄:₀ and C₁₂:₀. The DNA G+C content was 45.4 mol%. Based on genotypic, phenotypic, chemotaxonomic and DNA-DNA analyses, the name Vibrio mangrovi sp. nov. (type strain MSSRF38T=LMG 24290T=DSM 19641T) is proposed for this novel taxon.
Two strains of gram-negative bacteria isolated because of their abilities to decompose xenobiotic compounds were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence ...analysis, the two strains were found to belong to the genus Pseudomonas. Benzene degrading strain DSM 8628T was moderately related to P. flavescens NCPP 3063T (98.3% similarity), P. monteilii CIP 104883T, and P. plecoglossicida FPC 951T (98.1%). Strain DSM 9751T capable to grow with cetyltrimethylammonium chloride as the sole carbon source showed the highest similarity values with P. tremae CFBP 2341T and P. meliae MAFF 301463T (98.0%), both related to Pseudomonas syringae. The fatty acid pattern of strain DSM 8628T was distinct from patterns of other members of the genus Pseudomonas in combining a high ratio of 3OH-C₁₂:₁ (5.1%), a low ratio of 2OH-C₁₂:₀ (0.2%) and a relatively low ratio of C₁₈:₁ω7c (23.8%). On the basis of phylogenetic analysis, physiological properties and the composition of whole cell fatty acids, two novel species, Pseudomonas benzenivorans sp. nov. with the type strain DSM 8628T (=CIP 109857T) and Pseudomonas saponiphila sp. nov. with the type strain DSM 9751T (=CIP 109856T), are proposed.
16S rDNA sequence analysis was performed on the type strains of all validly described Acinetobacter species and five unnamed Acinetobacter strains. The phylogenetic analyses confirm that ...Acinetobacter is a coherent genus within the gamma subclass of Proteobacteria and that the species are phylogenetically well defined. A. calcoaceticus, A. lwoffii, A. johnsonii and A. haemolyticus form one cluster of closely related species, the pair A. junii and A. baumannii forms a second cluster. A. radioresistens stands phylogenetically isolated. The study reveals that three undescribed strains can be assigned to individually described species, while strains DSM 30009 and DSM 590 may represent two novel Acinetobacter species.
The City Library of Frankfurt am Main, in cooperation with the Darmstadt University of Applied Sciences, has developed a project to offer a mobile library makerspace. Elke Lang and Elfriede Ludwig ...describe how it works in their BuB article: Here we are – in an oversized space at the branch library in Frankfurt-Höchst, under conditions dictated by the coronavirus. Six participants have come to the workshop and are diligently working on their projects. They are fitting cables and electronic parts (LEDs, sensors, displays, switches, etc.) onto circuit boards, then coding, testing and revising the setups. Their mentors give explanations, ask questions and help the participants. The workshop is scheduled to last three hours, but at the end nobody really wants to leave: »We are not finished yet.« »Next week there will be a second part to the workshop – we'll come again and keep on working.« This is just a small glimpse into the ARDUINO workshop at the City Library of Frankfurt am Main – one building block in the library's digitalisation strategy. The project is the mobile version of the library's plans for a future makerspace. The workshops take place a regular basis. At the moment they are held at one specific location, but in the future they will rotate between a total of 18 different locations within the library system. In this way all residents of the city of Frankfurt will have easier access. Cooperation between the City Library of Frankfurt and the Darmstadt University of Applied Sciences has been beneficial in three ways: providing library users with attractive opportunities, expanding the digital skills of the library staff, and enabling students to have direct experience with practical situations.
Burkholderia xenovorans LB400, Cupriavidus necator H850, and Pseudomonas pseudoalcaligenes KF707 are bacterial strains able to mineralize biphenyl and to co-oxidize many of its halogenated ...derivatives (PCBs). Only strain LB400 also mineralizes a few mono- and dichlorobiphenyls, due to the presence of a functioning chlorocatechol pathway. Here, we used a Tn5-based minitransposon shuttle system to chromosomically introduce genes tcbRCDEF, encoding the chlorocatechol pathway into KF707, and genes cbdABC encoding a 2-chlorobenzoate 1,2-dioxygenase into KF707 and LB400, as well as transposon Tn4653 from the TOL plasmid, providing genes xylXYZL, encoding a broad-range toluate (methylbenzoate) dioxygenase and its dihydrodiol dehydrogenase, to extend the range for the mineralization of halogenated benzoates in LB400 and in KF707 through co-oxidation of halobenzoates into chlorocatechols. The engineered derivatives of LB400 and KF707 thus gained the ability for the mineralization of all isomeric monochloro- and bromobenzoates of the so-called lower pathway which, consequently, also allowed the mineralization of all monochlorobiphenyls and a number of di- and trichlorobiphenyls, thus preventing the accumulation of halobenzoates and of catabolites thereof. LB400 and KF707 also grow with the two commercial PCB formulations, Aroclor 1221 and Aroclor 1232, as the sole carbon and energy sources, but not with higher halogenated PCB mixtures, similar to the already published strain RW112. Repeated exposition of the modified LB400 to short pulses of UV light, over a prolonged period of time, allowed the isolation of a derivative of LB400, termed RW118, capable of growth with Aroclor 1016 still containing only traces of biphenyl, and in co-culture with modified KF707 termed RW120, and modified H850 (RW112) with Aroclor 1242, the commercial mixture already void of biphenyl and monochlorobiphenyls.
DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstr. 7b, 38124 Braunschweig, Germany
Correspondence Elke Lang ela{at}dsmz.de
It is proposed that the type strain of ...Melittangium lichenicola (Thaxter 1892) McCurdy 1971 is ATCC 25946 (=DSM 14877), which was originally designated as a reference strain by McCurdy, and not ATCC 25944 T , as given in the Approved Lists. Swarm appearance, myxospore morphology and 16S rRNA gene sequence data suggest that ATCC 25946 is a representative of the species Melittangium lichenicola , while strain ATCC 25944 is clearly a member of the Myxococcus – Corallococcus clade. A Request for an Opinion to this effect is made to the Judicial Commission of the International Committee on Systematics of Prokaryotes.
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains DSM 14877, ATCC 25944 T and ATCC 25946 are AM930267 –AM930269.
A novel aerobic facultative methylotroph was isolated from contaminated soil. The organism (strain DM16) is a Gram-negative asporogenous non-motile curved rod multiplying by binary fission. Cells are ...neutrophilic and mesophilic. This strain utilized dichloromethane, methanol, formate and formaldehyde along with a variety of polycarbon compounds. Strain DM16 employs the ribulosebisphosphate pathway for C
1 assimilation. The DNA G+C content is 64.5
mol%. The major ubiquinone is Q-10. The dominant cellular fatty acids are 18:1ω7c (58.6%), cyclo-19:0ω8c (34.8%) and 16:0 (3.2%). Sequencing of the 16S rRNA gene and DNA–DNA hybridization experiments clearly indicated that this methylotroph should be classified as a new species within genus
Ancylobacter –
Ancylobacter dichloromethanicus sp. nov. with the type strain DM16
T (DSM 21507
T=VKM B-2484
T).
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