- Volume 60, Issue 1, 2010

A taxonomic study was carried out on strain LMC2up-L3T, which was isolated from a polycyclic aromatic hydrocarbon-degrading consortium enriched with a sediment sample collected from a hydrothermal field of the south-west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LMC2up-L3T belonged to the genus Oceanibaculum, with the highest sequence similarity of 98.4 % to Oceanibaculum indicum P24T; similarity to other strains was below 93.1 %. DNA–DNA hybridization between strain LMC2up-L3T and O. indicum P24T was 31 %. rep-PCR fingerprints also differentiated strain LMC2up-L3T from O. indicum P24T. The G+C content of the chromosomal DNA was 67.7 mol%. The principal fatty acids were C16 : 1 (17.8 %), C16 : 0 (21.2 %), C18 : 1 ω7c (23.6 %), C18 : 0 (4.1 %), C18 : 1 2-OH (4.5 %) and C19 : 0 cyclo ω8c (17.4 %). The combined genotypic and phenotypic data show that strain LMC2up-L3T represents a novel species of the genus Oceanibaculum, for which the name Oceanibaculum pacificum sp. nov. is proposed, with the type strain LMC2up-L3T (=CCTCC AB 209059T =LMG 24859T =MCCC 1A02656T). An emended description of the genus Oceanibaculum is also provided.

Four strains isolated from cultured Manila clam, Ruditapes philippinarum, in the north-western coast of Spain were characterized phenotypically and genotypically. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that these bacteria were closely related to Aliivibrio wodanis, Aliivibrio salmonicida, Aliivibrio fischeri and Aliivibrio logei with sequence similarities between 98.1 and 96.0 %. Phylogenetic analysis based on the RNA polymerase alpha chain (rpoA), RecA protein (recA), the α-subunit of bacterial ATP synthase (atpA) and the uridine monophosphate (UMP) kinase (pyrH) genes and fluorescent amplified fragment length polymorphism experiments clearly showed that these novel isolates form a tight genomic group different from any currently known Aliivibrio species. On the basis of phylogenetic analysis and phenotypic data, the four strains represent a novel taxon, for which the name Aliivibrio finisterrensis sp. nov. is proposed. Several phenotypic features were revealed that discriminate A. finisterrensis from other Aliivibrio species. The type strain is CMJ 11.1T (=CECT 7228T=LMG 23869T).

Few studies using modern methods have been carried out on ciliated protozoa in tropical marine waters. In the present work, two hypotrichs, Parabirojimia multinucleata spec. nov. and Anteholosticha scutellum (Cohn, 1866) Berger, 2003, collected from Daya Bay in southern China, were investigated morphologically. P. multinucleata is distinguished by the following combination of characters: slender body, without a snout-like protrusion in the frontal field, and about 50 macronuclear nodules. The poorly known A. scutellum has never been investigated using modern methods; hence, a redescription is needed. During the present study, observations of specimens in vivo and following protargol impregnation revealed new information concerning structures such as the cortical granules and the infraciliature. A redescription and improved diagnosis are supplied based on the China population. The small-subunit (SSU) rRNA gene was sequenced for both organisms and comparisons with those of similar congeners clearly support the findings based on morphological studies.

Two novel yeast species, Candida aechmeae sp. nov. and Candida vrieseae sp. nov., were isolated from bromeliads in Itapuã Park, Rio Grande do Sul, Brazil. These species are genetically isolated from all other currently recognized ascomycetous yeasts based on their sequence divergence in the D1/D2 domain of the LSU rRNA gene. C. aechmeae sp. nov. is phylogenetically close to Candida ubatubensis, a species also isolated from bromeliads in Brazil, but the novel species can be differentiated on the basis of differences in the D1/D2 domain and positive results for the assimilation of l-arabinose, raffinose, inulin and citrate. Candida vrieseae sp. nov. is phylogenetically placed in a clade near Candida membranifaciens that is composed of several species associated with insects, but the novel species can be differentiated from them by the D1/D2 and ITS gene sequences, positive results for the assimilation of nitrite and a negative result for the assimilation of ethylamine. The type strain for Candida aechmeae sp. nov. is BI153T (=CBS 10831T=NRRL Y-48456T) and the type strain for C. vrieseae sp. nov. is BI146T (=CBS 10829T=NRRL Y-48461T).

The central clade of the genus Vibrio, also called the Vibrio core group, comprises six species that are tightly related (DNA–DNA reassociation values are very close to 70 % for most species pairs). Identification of novel strains to the species level within this group is troublesome and results are quite often dependent on the methodology employed. Therefore, this group represents an excellent framework to test the robustness of multilocus sequence analysis (MLSA) not only for inferring phylogeny but also as an identification tool without the need for DNA–DNA hybridization assays. The genes selected, 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR, were amplified by direct PCR from 44 Vibrio core-group strains. Subsequent analysis allowed us to recognize toxR and rpoD as the most resolving individual genes and showed that concatenated sequences of rpoD, rctB and toxR were more useful than concatenated sequences of all seven genes. To validate our conclusions, MLSA similarities have been correlated with DNA–DNA relatedness values obtained in this study and values taken from the literature. Although the seven concatenated genes gave the best correlation, the concatenated sequences of rpoD, rctB and toxR have the practical advantage of showing a considerable gap between the maximal interspecies similarity and the minimal intraspecies similarity recorded, meaning that they can be used quite conveniently for species identification of vibrios.

Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years. The purpose of the present article is to outline the key elements in the way that prokaryotes are characterized, with a view to providing an overview of some of the pitfalls commonly encountered in taxonomic papers.