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Heavy-metal contamination of soil has a detrimental effect on Archaea. This bacteria was thought to exist only in extreme environments, but has been found in marine, freshwater, and terrestrial habitats. 16S rRNA sequence analysis shows it belongs to the Crenarchaeota kingdom.

A study was conducted to evaluate the reproducibility and suitability of of competitive polymerase chain reaction (PCR) in soil ecosystems for characterizing population dynamics of indigenous Pseudomonas populations in soil hot spots. Results indicate that competitive PCR accurately quantifies DNA in soil reproducibly even when differences between DNA content and the number of culturable bacteria is only about one order of magnitude.

Microcosm experiments in the fish-pathogenic bacterium Aeromonas salmonicida that serves as a donor reveal the high frequency transfer of the promiscuous plasmid RAS1 in marine sediments, even without a selective factor. DNA probe hybridization reveals that 86.8% of oxytetracycline-sensitive bacterial isolates and 45.8% of oxytetracycline-resistant isolates transfer plasmids, indicating that oxytetracycline promotes transfer frequency. The transconjugants from a oxytetracycline-containing microcosm exhibit less diversity than those from a microcosm lacking a selective agent.

Three strains of Yersinia ruckeri were studied to determine the effect of salinity on growth and survival. Populations of all strains showed an ability to survive at salinities less than or equal to 20%. At 35% salinity, the survival capacity significantly decreased. Direct viable counts (DVC, viable but nonculturable cells) greater than colony-forming units were not detected. Flow cytometry was determined effective in differentiating viable and nonviable cells, as well as for demonstrating genome replication. Six genomes were detected in starved cells of Y. ruckeri.

A method to detect low levels of infectious salmon anemia virus (ISAV) in environmental samples has been developed. The method is based on concentrating the viruses by tangential flow filtration and ultracentrifugation prior to amplification of the extracted viral RNA by nested reverse transcription polymerase chain reaction (RT-PCR). In the current investigation, seawater samples from salmon holdings were used for ISAV identification. ISAV was detected in seawater samples from a salmon holding site and from a vessel transporting salmon in 2 consecutive trials of the methodology. When known concentrations of ISAV were added to 21 of sea water, 5.5 viruses ml(-1) (corresponding to a tissue culture titer of TCID50 1.6 x 10(-2) ml(-1)) were detected using this method.

Small subunit ribosomal genes were explored using PCR-RFLP to facilitate the characterization of bacteria cultured from reared fry of the Atlantic halibut (Hippoglossus hippoglossus). Concern has been expressed about pathogen invasion in larvae lacking a counteracting normal flora that may aid the immune system in producing robust noninfected individuals. In this study, pure cultured representatives of normal flora that were previously found to be antagonistic towards a pathogenic Vibrio sp. were subjected to a whole cell PCR protocol amplifying approximately 1500 bp of 16S rDNA. Amplified DNA was digested by AluI, BstUI, CfoI, and RsaI, to generate restriction profiles. Before the isolates were characterized, a survey was performed to test the discriminative efficiency of the RFLP. Efficient detection of polymorphism and the resolution of species and subspecies were achieved. Using the RFLP on 103 isolates generated as many as 22 genotypes. Based on the restriction profiles, a taxonomic tree incorporating 19 reference strains was constructed. Partial sequencing found this tree to be dominated by gamma-Proteobacteria in clusters of Vibrio-, Pseudomonas-, and Alteromonas-affiliated species. Only nine isolates fell outside these genera, including the three isolates Shewanella alga, Deleya marina, and Marinomonas protea. These species have not previously been reported as halibut flora. The most frequently isolated genotype resembled Vibrio salmonicida.