Population genetics and reproductive strategies of two Notostraca (Crustacea) species from winter ponds in Israel

Fluorescent-amplified fragment length polymorphism (FAFLP) fingerprinting assay was used to compare the genetic diversity within and between tadpole shrimps (Notostraca) populations of Lepidurus apus (n=7) and Triops cancriformis (n=2) from rain pools in Israel. Each ephemeral water body has revealed a unique fingerprint pattern with an entailed genetic drift between nearby ponds. High similarity of genotypic diversity within each geographic area led to three clusters of water bodies, north, south and center of Israel. FAFLP assays on several newly hatched individuals of T. cancriformis revealed high identity amongst kin, as compared to L. apus where newly hatched from the same maternal source showed high diversity. Results indicate that T. cancriformis populations from Israel are probably parthenogenetic as indicated by clonal structures. The higher genetic variability in the L. apus populations and in laboratory-hatched specimens indicates the existence of sexual reproduction.     

Genetic stability of strains preserved on LENTICULE discs and by freeze-drying: a comparison using fluorescent amplified fragment length polymorphism analysis

Fluorescent amplified fragment length polymorphism (FAFLP) analysis, a high-resolution genome fingerprinting method, was used to ascertain the DNA integrity of bacterial strains during preservation by lenticulation and by traditional freeze-drying into glass ampoules. This was achieved by comparing FAFLP genotypes of a range of paired bacterial isolates recovered from LENTICULE discs (preserved between 1995 and 2004) and from freeze-dried (FD) cultures in glass ampoules (preserved between 1966 and 2000). A choice of two endonuclease combinations EcoRI/MseI or HindIII/HhaI was used for FAFLP analysis of the five different bacterial genera comprising of 10 strains. Each of these 10 strains exhibited unique FAFLP profiles. However, there were no detectable differences between the FAFLP profiles for each of the individual strains, irrespective of their preservation format or their year of preservation. Thus, the FAFLP data suggests that LENTICULE production does not result in any detectable genetic changes during drying onto LENTICULE discs and storage for at least 5 years. The provision of such FD reference cultures on LENTICULE discs rather than FD glass ampoules will provide a cost-effective format that is easier to use.     

Polyphasic taxonomic study of "Aeromonas eucrenophila-like" isolates from clinical and environmental sources

In the current study, a group of 17 "Aeromonas eucrenophila-like" isolates from clinical and environmental origins was subjected to a polyphasic taxonomic characterization including ribotyping, 16S rDNA sequencing, FAFLP fingerprinting, and biochemical testing. Genotypic, phylogenetic, and phenotypic results were consistent with the conclusion that this group of 17 isolates may represent a currently undescribed Aeromonas taxon most closely related to A. eucrenophila HG6. In addition, comparison of newly obtained 16S rDNA sequencing data with published sequences demonstrated a high phylogenetic heterogeneity among isolates currently classified in the species A. encheleia.     

A FAFLP system for the improved identification of plant-pathogenic and plant-associated species of the genus Pantoea

The majority of Pantoea species are either plant-pathogenic or plant-associated and cause a wide variety of symptoms on a range of hosts. Identification of Pantoea species is difficult due to minor differences in phenotypic characteristics between them and related Enterobacteriaceae. Fluorescent amplified fragment length polymorphism (FAFLP) analysis was investigated for use as a rapid, molecular-based identification technique to the species level of the genus Pantoea. Following analysis of the band patterns generated by FAFLP, seven distinct clusters were observed, one for each validly published species of the genus. FAFLP has proven to be a rapid, reproducible identification technique for all species of the genus Pantoea.     

The coral bleaching Vibrio shiloi Kushmaro et al. 2001 is a later synonym of Vibrio mediterranei Pujalte and Garay 1986

The coral bleaching Vibrio shiloi LMG 19703T was characterized by means of Fluorescent Amplified Fragment Length Polymorphism (FAFLP), DNA-DNA hybridisation, mol% G+C content, fatty acids methyl ester (FAME) analysis and phenotypical tests. Numerical analysis of the FAFLP band patterns indicated that the type strain of V. shiloi in fact belongs to the species V. mediterranei. The type strains of both species shared 77% DNA similarity, as determined by DNA-DNA hybridisation experiments at stringent conditions. Moreover, V. shiloi and V. mediterranei showed almost identical fatty acid composition and phenotypical features. Collectively, the genotypic and phenotypic data presented in this study suggest that V. shiloi Kushmaro et al. 2001 should be considered a later synonym of V. mediterranei Pujalte and Garay 1986. The involvement of V. mediterranei in coral bleaching was unknown until now.     

Genomic diversity amongst Vibrio isolates from different sources determined by fluorescent amplified fragment length polymorphism

The genomic diversity among 506 strains of the family Vibrionaceae was analysed using Fluorescent Amplified Fragments Length Polymorphisms (FAFLP). Isolates were from different sources (e.g. fish, mollusc, shrimp, rotifers, artemia, and their culture water) in different countries, mainly from the aquacultural environment. Clustering of the FAFLP band patterns resulted in 69 clusters. A majority of the actually known species of the family Vibrionaceae formed separate clusters. Certain species e.g. V. alginolyticus, V. cholerae, V. cincinnatiensis, V. diabolicus, V. diazotrophicus, V. harveyi, V. logei, V. natriegens, V. nereis, V. splendidus and V. tubiashii were found to be ubiquitous, whereas V. halioticoli, V. ichthyoenteri, V. pectenicida and V. wodanis appear to be exclusively associated with a particular host or geographical region. Three main categories of isolates could be distinguished: (1) isolates with genomes related (i.e. with > or =45% FAFLP pattern similarity) to one of the known type strains; (2) isolates clustering (> or =45% pattern similarity) with more than one type strain; (3) isolates with genomes unrelated (<45% pattern similarity) to any of the type strains. The latter group consisted of 236 isolates distributed in 31 clusters indicating that many culturable taxa of the Vibrionaceae remain as yet to be described.