Microbial diversity and zinc toxicity to Pseudomonas sp. from Coeur d'Alene River sediment

Abstract

Coeur d'Alene River (CDAR) in northern Idaho is one of the metal contaminated rivers in US. The sediments of the river are enriched with As, Cd, Cu, Pb, and Zn which are toxic metals to humans and animals. It is hypothesized that microorganisms living in this river sediment can remove the metals and thus detoxify their environment. The objective of this work is to investigate the microbial communities existing in CDAR sediment using 16S ribosomal RNA (rRNA) gene sequencing and 16S rRNA gene microarray (PhyloChip) analysis. According to our phylogenetic analysis, the CDAR clones fell into 13 distinct phylogenetic classes including 2 environmental samples, 1 uncultured bacterium, and an unclassified Chloroflexi. The major representative genera found were Thiobacillus (7 of 91), Azoarcus (7/91), Acidobacterium (6/91), Burkholderia (5/91), Flavobacterium (5/91) and Janthinobacterium (5/91). PhyloChip data showed the presence of 1551 operational taxonomic units (OTUs). 97% of the clone library sequences matched at various taxonomic levels with the microarray results.

The results from the clone library and PhyloChip have provided the broad picture of the microorganisms found in the metal polluted CDAR sediment. To better understand the metal toxicity kinetics of specific isolates, Pseudomonas sp. strain JM001 from the CDAR sediment was selected for further study. Cell growth and aqueous Zn removal rate of strain JM001 was observed in batch kinetic experiments. It was found that cell growth rate depends on substrate and nutrient concentration and incubation temperature. The minimum inhibitory concentration (MIC) of Zn to the cells was 0.024 mM and the 50% inhibition in specific growth rate was found at 0.011 mM Zn when cells were grown in nutrient limited defined media at 22 °C. The MIC was 1 mM Zn and 50% inhibition occurred at 0.515 mM Zn in minimal salts medium with vitamin solutions at 35 °C. The results are significant to develop a dose-response model that will quantify the effects of toxic metals on microbial growth and inhibition in complex CDAR environment.