- Volume 53, Issue 5, 2003

Actinomycete strains isolated from lesions on equine placentas from two horses in Kentucky and one in South Africa were subjected to a polyphasic taxonomic study. Chemotaxonomic and morphological characteristics indicated that the isolates are members of the genus Amycolatopsis. On the basis of phylogenetic analysis of 16S rDNA sequences, the isolates are related most closely to Amycolatopsis mediterranei. Physiological characteristics of these strains indicated that they do not belong to A. mediterranei and DNA relatedness determinations confirmed that these strains represent three novel species of the genus Amycolatopsis, for which the names Amycolatopsis kentuckyensis (type strain, NRRL B-24129T=LDDC 9447-99T=DSM 44652T), Amycolatopsis lexingtonensis (type strain, NRRL B-24131T=LDDC 12275-99T=DSM 44653T) and Amycolatopsis pretoriensis (type strain, NRRL B-24133T=ARC OV1 0181T=DSM 44654T) are proposed.

Sequence homology of partial 60 kDa heat-shock protein (HSP60) genes was analysed for 50 Bifidobacterium strains that represent 12 Bifidobacterium species and subspecies with validly published names. Sequence similarities were 96·5–100 % within the same species, 95·5–97 % at the subspecies level and 80–96 % (mean, 88 %) at the interspecies level among the 10 Bifidobacterium species. Hence, the HSP60 gene was a more accurate tool for species identification within the genus Bifidobacterium than 16S rDNA. Two new Bifidobacterium strains isolated from piglet faeces were shown to be closely related to the thermophilic bifidobacterial group, based on 16S rDNA sequence analysis: strain P3-14T (=AS 1.3009T=LMG 21689T) exhibited 97·9 % similarity to Bifidobacterium boum JCM 1211T, 97·2 % similarity to Bifidobacterium thermacidophilum AS 1.2282T and 97 % similarity to Bifidobacterium thermophilum JCM 1207T. However, higher levels of DNA–DNA relatedness (83 %) and HSP60 gene sequence similarity (97 %) were determined between B. thermacidophilum AS 1.2282T and strain P3-14T, indicating a closer relationship between them. The new strains differed from B. thermacidophilum AS 1.2282T in some phenotypic characteristics, such as growth at a lower temperature (46·5 °C), as well as different sugar-fermentation patterns. Hence, a novel Bifidobacterium subspecies, Bifidobacterium thermacidophilum subsp. porcinum subsp. nov., is designated.

The taxonomic position of an actinomycete, strain HD321T, isolated from an oil-producing well of Daqing oilfield, was clarified using a polyphasic taxonomic approach. The strain possessed cell-wall chemotype IV, MK-9(H2) as the predominant menaquinone, relatively long-chain mycolic acids (52–62 carbon atoms) of the Gordonia type, straight-chain saturated and monounsaturated fatty acids and tuberculostearic acid. The G+C content of the DNA was 66 mol%. 16S rDNA analyses as well as chemotaxonomic and physiological properties indicated that strain HD321T represents a novel species within the genus Gordonia, for which the name Gordonia paraffinivorans sp. nov. is proposed; the type strain is HD321T (=AS 4.1730T=DSM 44604T).

Eight strains of Gram-positive, catalase- and oxidase-positive cocci were isolated from the skin of llamas (Lama glama L.) and characterized using a polyphasic approach. These strains were assigned to the genus Macrococcus on the basis of their phenotypic properties (resistance to bacitracin and sensitivity to furazolidone) and DNA base content (40–42 mol% G+C). Phylogenetic analysis based on 16S rDNA confirmed that the strains are members of the genus Macrococcus. They differed from all hitherto described macrococcal species in their production of phosphatase and reduction of nitrate (most strains) and the inability to produce acid from glycerol or to grow in 7·5 % NaCl. Ribotyping (EcoRI), macrorestriction analysis (XbaI) and fatty acid methyl ester analysis divided the strains from llamas into three stable clusters. Moreover, ribotyping differentiated the strains analysed not only from previously described macrococcal species but also from oxidase-positive staphylococci. DNA–DNA hybridization confirmed that the three clusters represent separate genomic groups (similarity values<54 %). All the results showed that the strains represent three novel species, for which the names Macrococcus hajekii sp. nov. (type strain CCM 4809T=LMG 21711T), Macrococcus brunensis sp. nov. (type strain CCM 4811T=LMG 21712T) and Macrococcus lamae sp. nov. (type strain CCM 4815T=LMG 21713T) are proposed.

Three novel mite-associated basidiomycetous species are described in two new anamorph genera as Meira geulakonigii gen. nov., sp. nov. (type CBS 110052T=NRRL Y-27483T=AS 004T), Meira argovae sp. nov. (type CBS 110053T=NRRL Y-27482T=AS 005T) and Acaromyces ingoldii gen. nov., sp. nov. (type CBS 110050T=NRRL Y-27484T=AS 001T). Morphologically, these fungi are similar to the yeast-like fungi classified in the Ustilaginales, such as Pseudozyma species. However, analysis of the D1/D2 domain of the LSU rDNA suggests that they belong to two different lineages within the Exobasidiomycetidae of the Ustilaginomycetes (Basidiomycota). Furthermore, these fungi may be of interest for the biocontrol of mites, as they reduced mite numbers by approximately 80 % after inoculation.

Two new species of the ascosporic yeast genus Metschnikowia were isolated from nectaries and associated muscoid flies of flowers from the common milkweed (Asclepias syriaca) in North America, and are described as Metschnikowia vanudenii [type strain=PYCC 4650T=CBS 9134T=NRRL Y-27243T=UWO(PS) 86A4.1T] and Metschnikowia lachancei [type strain=PYCC 4605T=CBS 9131T=NRRL Y-27242T=UWO(PS) 7ASB2.3T]. As with the previously described Metschnikowia gruessii, M. vanudenii has vegetative cells with an ‘aeroplane’ or cross-like configuration, produces ovoid chlamydospores and forms ellipsoidopedunculate asci with two acicular ascospores. Metschnikowia lachancei is distinguished from other Metschnikowia species by formation of club-shaped asci with 1–2 thick clavate ascospores. The phylogenetic positions of the proposed new species within Metschnikowia were determined from sequence analysis of the D1/D2 domain of 26S rDNA. The new species show low nuclear DNA relatedness with neighbouring taxa.

Fourteen apiculate yeast strains isolated from various sources in South Africa, North America and the Hawaiian islands were found to be genetically divergent from other Hanseniaspora–Kloeckera species by using randomly amplified polymorphic DNA (RAPD)-PCR. After cluster analysis of the RAPD-PCR fingerprints, five groups were recognized. DNA reassociation values among representatives of these groups and strains of Hanseniaspora–Kloeckera species revealed that the strains represent five novel species. Four are described here as novel species of Hanseniaspora: Hanseniaspora meyeri sp. nov. (type CBS 8734T), Hanseniaspora clermontiae sp. nov. (type CBS 8821T), Hanseniaspora lachancei sp. nov. (type CBS 8818T) and Hanseniaspora opuntiae sp. nov. (type CBS 8733T). The fifth novel species, which is represented by only a single strain, CBS 8772, is not introduced as a new taxon. Phylogenetic analyses of the D1/D2 region of the 26S rDNA and internal transcribed spacer (ITS) regions with 5·8S rDNA sequences placed H. meyeri, H. clermontiae, H. lachancei, H. opuntiae and strain CBS 8772 close to Hanseniaspora uvarum and Hanseniaspora guilliermondii. The key characteristics for standard physiological identification of H. clermontiae and H. lachancei were respectively maximal growth temperature and assimilation of 2-keto-d-gluconate. However, physiological characteristics did not allow the distinction of H. opuntiae and strain CBS 8772 from H. guilliermondii or H. meyeri from H. uvarum. These three novel taxa can be identified by either ITS sequencing or PCR-RFLP of ITS regions using restriction enzymes MboII and HinfI.

The phylogenetic relationship of 12 ammonia-oxidizing isolates (eight nitrosospiras and four nitrosomonads), for which no gene sequence information was available previously, was investigated based on their genes encoding 16S rRNA and the active site subunit of ammonia monooxygenase (AmoA). Almost full-length 16S rRNA gene sequences were determined for the 12 isolates. In addition, 16S rRNA gene sequences of 15 ammonia-oxidizing bacteria (AOB) published previously were completed to allow for a more reliable phylogeny inference of members of this guild. Moreover, sequences of 453 bp fragments of the amoA gene were determined from 15 AOB, including the 12 isolates, and completed for 10 additional AOB. 16S rRNA gene and amoA-based analyses, including all available sequences of AOB pure cultures, were performed to determine the position of the newly retrieved sequences within the established phylogenetic framework. The resulting 16S rRNA gene and amoA tree topologies were similar but not identical and demonstrated a superior resolution of 16S rRNA versus amoA analysis. While 11 of the 12 isolates could be assigned to different phylogenetic groups recognized within the betaproteobacterial AOB, the estuarine isolate Nitrosomonas sp. Nm143 formed a separate lineage together with three other marine isolates whose 16S rRNA sequences have not been published but have been deposited in public databases. In addition, 17 environmentally retrieved 16S rRNA gene sequences not assigned previously and all originating exclusively from marine or estuarine sites clearly belong to this lineage.

Flow cytometric sorting based on its large cell size enabled an enriched fraction of Oscillospira guillermondii cells to be obtained from the rumen contents of a sheep. Phylogenetic analysis based on cloned 16S rDNA sequences indicated that the bacterium is a member of the low-G+C Gram-positive bacterial cluster. Sporobacter termitidis and Papillibacter cinnamivorans were the most closely related known species, with sequence similarities of only 86·3–88·1 %. Fluorescently labelled 16S rRNA-targeted oligonucleotide probes specific for Oscillospira were designed and applied to the rumen sample from which the enriched fraction was obtained. The probes hybridized specifically with the large, morphologically conspicuous Oscillospira cells.

Farrand et al. [Int J Syst Evol Microbiol 53 (2003), 1681–1687] have presented a critique of the proposal of Young et al. [Int J Syst Evol Microbiol 51 (2001), 89–103] to revise the nomenclature and classification of Rhizobium. They argued that Young et al. (2001) are mistaken in their reclassification of all Agrobacterium species within Rhizobium, and that the resulting nomenclatural revision is ‘unnecessary and unwarranted’. These objections arise because the authors appear not to understand the role of formal nomenclature, and fail to distinguish between formal and special-purpose nomenclatures (Bacteriological Code, 1990 Revision). The arguments set out by Farrand et al. (2003) can be addressed in terms of (1) the taxonomic status of the genera Agrobacterium and Rhizobium; (2) the status of species and biovars and their nomenclature; and (3) the role of transmissible genomic elements in classification and nomenclature. Finally, an attempt is made to unravel the confusion underpinning their discussion with a consideration of the relationship between formal and special-purpose nomenclatures.

Data currently available on members of the genera Haloterrigena and Natrinema suggest that some strains of the species Haloterrigena turkmenica that have been shown by DNA–DNA hybridization to belong to this species show a high degree of 16S rDNA sequence similarity to members of the genus Natrinema. However, closer examination of the data presented in the original publications and in subsequent publications suggests that there may be a number of problems associated with some of the published data.

The genus Deleya was created to encompass a number of marine organisms that had previously been classified in diverse genera. Deleya aesta was designated as the type species of the genus. Subsequent work indicated that Deleya aesta, Alcaligenes aquamarinus and Alcaligenes faecalis subsp. homari were heterotypic synonyms. Consequently, Akagawa & Yamasato (Int J Syst Bacteriol 39, 462–466, 1989) concluded that, based on Rules 23a and 51b of the Bacteriological Code (1975 Revision), the oldest legitimate species epithet was aquamarinus and the type species of the genus Deleya should therefore be changed to Deleya aquamarina. Dobson & Franzmann (Int J Syst Bacteriol 46, 550–558, 1996) concluded that it was not possible to distinguish between members of the genus Deleya and members of the genus Halomonas Vreeland et al. 1980 , leading them to transfer members of the genus Deleya to the genus Halomonas and resulting in the creation of a new combination, Halomonas aquamarina. Closer examination of some of these changes indicates that they are not all in accordance with the Rules of the Bacteriological Code (1975 or 1990 Revisions).