title: High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment.
abstract: There is increasing interest in harnessing the functional capacities of indigenous microbial communities to transform and remediate a wide range of environmental contaminants. Information about which community members respond to stimulation can guide the interpretation and development of remediation approaches. To comprehensively determine community membership and abundance patterns among a suite of samples associated with uranium bioremediation experiments, we employed a high-density microarray (PhyloChip). Samples were unstimulated, naturally reducing, or collected during Fe(III) (early) and sulfate reduction (late biostimulation) from an acetate re-amended/amended aquifer in Rifle, Colorado, and from laboratory experiments using field-collected materials. Deep community sampling with PhyloChip identified hundreds-to-thousands of operational taxonomic units (OTUs) present during amendment, and revealed close similarity among highly enriched taxa from drill core and groundwater well-deployed column sediment. Overall, phylogenetic data suggested that stimulated community membership was most affected by a carryover effect between annual stimulation events. Nevertheless, OTUs within the Fe(III)- and sulfate-reducing lineages, Desulfuromonadales and Desulfobacterales, were repeatedly stimulated. Less consistent, co-enriched taxa represented additional lineages associated with Fe(III) and sulfate reduction (e.g. Desulfovibrionales; Syntrophobacterales; Peptococcaceae) and autotrophic sulfur oxidation (Sulfurovum; Campylobacterales). Data implies complex membership among highly stimulated taxa and, by inference, biogeochemical responses to acetate, a nonfermentable substrate.
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, CA 94720, USA.
authors.forename: Kim M
authors.initials: KM
authors.lastname: Handley
authors.forename: Kelly C
authors.initials: KC
authors.lastname: Wrighton
authors.forename: Yvette M
authors.initials: YM
authors.lastname: Piceno
authors.forename: Gary L
authors.initials: GL
authors.lastname: Andersen
authors.forename: Todd Z
authors.initials: TZ
authors.lastname: DeSantis
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Williams
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Wilkins
authors.forename: A Lucie
authors.initials: AL
authors.lastname: N'Guessan
authors.forename: Aaron
authors.initials: A
authors.lastname: Peacock
authors.forename: John
authors.initials: J
authors.lastname: Bargar
authors.forename: Philip E
authors.initials: PE
authors.lastname: Long
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D000085:Acetates / Q000378:metabolism*; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D001673:Biodegradation, Environmental; D044822:Biodiversity; D003120:Colorado; D020564:Deltaproteobacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D005290:Ferric Compounds / Q000378:metabolism; D060587:Groundwater / Q000382:microbiology*; D020411:Oligonucleotide Array Sequence Analysis; D010084:Oxidation-Reduction; D010802:Phylogeny; D013455:Sulfur / Q000378:metabolism; D014501:Uranium / Q000378:metabolism*; D014875:Water Pollutants, Radioactive / Q000378:metabolism*
chemical_list: D000085:Acetates; D005290:Ferric Compounds; D014875:Water Pollutants, Radioactive; D014501:Uranium; D013455:Sulfur