title: Functional gene array-based analysis of microbial communities in heavy metals-contaminated lake sediments.
abstract: Lake DePue (IL, USA) has been contaminated for > 80 years by an adjacent Zn-smelting facility. Previous work indicated that sulfate reduction increased and biomass declined as pore-water metal concentrations increased, while 16S rRNA gene profiles remained relatively stable. To better understand this phenomenon, the sediment microbial community structure and functional potential were investigated using a functional gene microarray (GeoChip) targeting > 10,000 functional genes. Nonmetric multidimensional scaling and clustering analyses showed that the overall community structure was similar across all sites based on the relative abundance of all detected genes, but some individual gene categories did show differences. A subset of sulfate reduction genes (dsr) and the most relevant metal resistance genes were more abundant than other categories and were highly correlated with metal contamination. The most significant correlations were between pore-water metal concentrations and dsr, with Zn, Cd, and Mn as the most predictive for the presence of dsr. These results suggest that metal contamination influences sediment microbial community structure and function by increasing the abundance of relevant metal-resistant and sulfate-reducing populations. These populations therefore appear to contribute significantly to the resistance and stability of the microbial communities throughout the gradient of metal contamination in Lake DePue.
authors.affiliation: Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK, USA.
authors.forename: Sanghoon
authors.initials: S
authors.lastname: Kang
authors.forename: Joy D
authors.initials: JD
authors.lastname: Van Nostrand
authors.forename: Heidi L
authors.initials: HL
authors.lastname: Gough
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.forename: David A
authors.initials: DA
authors.lastname: Stahl
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D016000:Cluster Analysis; D004785:Environmental Pollutants / Q000032:analysis*; D005798:Genes, Bacterial; D014644:Genetic Variation; D019015:Geologic Sediments / Q000737:chemistry / Q000382:microbiology*; D060106:Lakes / Q000382:microbiology*; D019216:Metals, Heavy / Q000032:analysis*; D020411:Oligonucleotide Array Sequence Analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D004785:Environmental Pollutants; D019216:Metals, Heavy; D012336:RNA, Ribosomal, 16S
keywords: GeoChip; functional gene microarray; metal resistance; metals contamination; microbial communities; sulfate-reducing bacteria