The impact of heavy metal contamination on soil bacterial communities was studied in soils amended for many years with sewage sludge contaminated with heavy metals to varying extents. At the broad level of resolution, DNA reassociation analysis indicated a dramatic decrease in bacterial diversity from 16{ omitted}000 bacterial genomes (g soil [wet wt])(-1) in the non-contaminated soil to 6400 bacterial genomes (g soil [wet wt])(-1) in soil with low metal amendments and only 2000 bacterial genomes (g soil [wet wt])(-1) in soil with high metal amendments. No differences between bacterial communities of these soils, however, were displayed in the %G+C profiles analysed by thermal denaturation. At a coarse level of characterisation, in situ hybridisation analysing larger phylogenetic groups of bacteria revealed a general decrease in the percentage of cells detected with probes ARCH915, BET42a, GAM42a, SRB385, CF319a, LGCb and HGC69a with increasing metal amendment. Only cells detected with probe ALF1b increased significantly from 3.1+/-0.8% of the cells detected by the domain-specific probe EUB338 in the non-contaminated soil to 6.5+/-1.3% in soil with high metal amendments. These shifts in populations of larger phylogenetic groups were largely confirmed by dot blot analysis of 16S and 23S rDNA clone libraries from bacteria in soil with low metal and high metal amendments, respectively. For a fine-level characterisation, 72 clones of 16S rDNA libraries were identified by comparative sequence analysis. A few sequences could not be assigned to the major taxa described. Most of the sequences were assigned to the Gram-positive bacteria with a high DNA G+C content (45%) and the alpha-subdivision of Proteobacteria (24%). However, only minor differences were seen between bacterial communities from the low and high metal soils. In the soil with high metal amendment, more sequences clustered to the alpha-subdivision of Proteobacteria, while in the low metal soil, more sequences clustered to the Gram-positive bacteria with a high DNA G+C content.

No abstract

The impact of heavy-metal contamination on archaean communities was studied in soils amended with sewage sludge contaminated with heavy metals to varying extents. Fluorescent in situ hybridization showed a decrease in the percentage of Archaea from 1.3% ± 0.3% of 4′,6-diamidino-2-phenylindole-stained cells in untreated soil to below the detection limit in soils amended with heavy metals. A comparison of the archaean communities of the different plots by denaturing gradient gel electrophoresis revealed differences in the structure of the archaean communities in soils with increasing heavy-metal contamination. Analysis of cloned 16S ribosomal DNA showed close similarities to a unique and globally distributed lineage of the kingdom Crenarchaeota that is phylogenetically distinct from currently characterized crenarchaeotal species.

No abstract

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.