The use of phospholipid fatty acid analysis to measure impact of acid rock drainage on microbial communities in sediments.

The impact of acid rock drainage (ARD) and eutrophication on microbial communities in stream sediments above and below an abandoned mine site in the Adelaide Hills, South Australia, was quantified by PLFA analysis. Multivariate analysis of water quality parameters, including anions, soluble heavy metals, pH, and conductivity, as well as total extractable metal concentrations in sediments, produced clustering of sample sites into three distinct groups. These groups corresponded with levels of nutrient enrichment and/or concentration of pollutants associated with ARD. Total PLFA concentration, which is indicative of microbial biomass, was reduced by >70% at sites along the stream between the mine site and as far as 18 km downstream. Further downstream, however, recovery of the microbial abundance was apparent, possibly reflecting dilution effect by downstream tributaries. Total PLFA was >40% higher at, and immediately below, the mine site (0-0.1 km), compared with sites further downstream (2.5-18 km), even after accounting for differences in specific surface area of different sediment samples. The increased microbial population in the proximity of the mine source may be associated with the presence of a thriving iron-oxidizing bacteria community as a consequence of optimal conditions for these organisms while the lower microbial population further downstream corresponded with greater sediments' metal concentrations. PCA of relative abundance revealed a number of PLFAs which were most influential in discriminating between ARD-polluted sites and the rest of the sites. These PLFA included the hydroxy fatty acids: 2OH12:0, 3OH12:0, 2OH16:0; the fungal marker: 18:2omega6; the sulfate-reducing bacteria marker 10Me16:1omega7; and the saturated fatty acids 12:0, 16:0, 18:0. Partial constrained ordination revealed that the environmental parameters with the greatest bearing on the PLFA profiles included pH, soluble aluminum, total extractable iron, and zinc. The study demonstrated the successful application of PLFA analysis to rapidly assess the toxicity of ARD-affected waters and sediments and to differentiate this response from the effects of other pollutants, such as increased nutrients and salinity.

Effect of dietary Echinacea purpurea on viremia and performance in porcine reproductive and respiratory syndrome virus-infected nursery pigs.

The effect of dietary Echinacea purpurea on performance, viremia, and ontogeny of the humoral antibody response against porcine reproductive and respiratory syndrome virus (PRRSV) infection was evaluated in weaned pigs. In three replicates, 120 weaned pigs (25 +/- 1 d of age; 8.46 +/- 0.48 kg of BW) from a PRRSV-naive herd were allotted randomly to one of eight pens (diets) in two separate rooms (four pens/room), with each pen containing five pigs. Pigs began one of four dietary treatments (as-fed basis) 1 wk before inoculation with PRRSV: 1) basal diet composed of corn, soybean meal, whey, and essential vitamins and minerals; 2) basal diet plus carbadox (0.055 g/kg of diet; as-fed basis); 3) basal diet plus Echinacea 2% (2% of the total diet); 4) basal diet plus Echinacea 4% (4% of the total diet). The diets were formulated to be isocaloric and isolysinic. Echinacea purpurea was purchased in powder form and determined by chemical analysis to contain 1.35% cichoric acid (as-fed basis). Seven days after starting the diets, all pigs in one room were intranasally inoculated with PRRSV isolate ATCC VR-2332 at a concentration of 10(4) tissue culture infectious dose50/mL. To monitor the effects of Echinacea and PRRSV challenge, BW and blood samples were obtained from all pigs at 7-d intervals. Serum samples were analyzed for the presence of PRRSV and PRRSV-specific antibodies. All challenged pigs became infected with PRRSV, and all unchallenged pigs remained free of infection. No differences (P > 0.10) in ADG, ADFI, or gain:feed (G:F) were observed in PRRSV-challenged compared with unchallenged animals. For PRRSV-challenged animals receiving diets supplemented with Echinacea at 2 or 4%, no differences (P > 0.10) were observed in ADG, ADFI, or G:F ratio. Among PRRSV-challenged pigs, dietary Echinacea did not affect (P > 0.10) the rate or level of the ELISA-detectable antibody response from d 7 to 42 or the level and duration of PRRSV in serum. For PRRSV-unchallenged animals receiving diets supplemented with Echinacea at 2 or 4%, no differences (P > 0.10) were observed in ADG, ADFI, and G:F ratio. Under the conditions of this study, dietary Echinacea did not enhance growth, exhibit antiviral effects to PRRSV, or show any evidence of immune enhancing properties.

Amplification of ribulose biphosphate carboxylase/oxygenase large subunit (RuBisCO LSU) gene fragments from Thiobacillus ferrooxidans and a moderate thermophile using polymerase chain reaction.

Southern blot analysis of DNA from an iron-oxidising moderate thermophile NMW-6 and from Thiobacillus ferrooxidans strain TFI-35 demonstrated sequences homologous to the RuBisCO LSU gene of Synechococcus. DNA fragments (457 bp) encoding part of the RuBisCO LSU gene (amino acids 73-200) were amplified from the genomic DNA of Thiobacillus ferrooxidans and the moderate thermophile NMW-6 using the polymerase chain reaction (PCR) technique (Saiki et al. (1985) Science 233, 1350-1354). A comparison with the LSU sequences from T. ferrooxidans, Alcaligenes eutrophus, Chromatium vinosum, Synechococcus and Spinacea oleracea, which all have RuBisCOs with a hexadecameric structure, showed that the RuBisCO LSU gene sequence from NMW-6 appeared to be most closely related to that of the hydrogen bacterium A. eutrophus which showed 71.9% homology at the amino acid level. Despite its physiological similarity, T. ferrooxidans showed only 64.1% homology to the amino acid sequence from NMW-6 and had the lowest DNA homology (60.9%) of the hexadecameric type RuBisCOs. In the region sequenced, T. ferrooxidans and the RuBisCOs of the phototrophs C. vinosum, Synechococcus and S. oleracea, had 17 residues that were completely conserved which were substituted in both NMW-6 and A. eutrophus, 11 of these being identical substitutions. Comparison of the nucleotide and derived amino acid sequences of the RuBisCO LSU fragment from T. ferrooxidans with other RuBisCO sequences indicated a closer relationship to the hexadecameric type LSU genes of photosynthetic origin than to that of A. eutrophus. The T. ferrooxidans amino acid sequence showed 93.8%, 78.9% and 77.3% homology, respectively, to the C. vinosum, Synechococcus and S. oleracea (spinach) sequences but only 56.2% to A. eutrophus. The DNA sequence from Rhodospirillum rubrum, which has the atypical large subunit dimer RuBisCO structure with no small subunit, showed 39.2% and 42.7% homology, respectively, with the sequences of NMW-6 and T. ferrooxidans, and 25.0% and 29.7% amino acid homology, indicating that the DNA homology was substantially random in nature. PCR fragments (126 bp) that overlaped the last 15 codons of the fragments above were also amplified and sequenced. They showed incomplete homology with the larger fragments, supporting evidence obtained from Southern hybridizations that T. ferrooxidans and the moderate thermophile NMW-6 have multiple copies of RuBisCO LSU genes.