High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment

Journal Article · Fri Apr 13 00:00:00 EDT 2012 · FEMS Microbiology Ecology

DOI:https://doi.org/10.1111/j.1574-6941.2012.01363.x· OSTI ID:1126367

Handley, Kim M. ^[1]; Wrighton, Kelly C. ^[1]; Piceno, Yvette M. ^[2]; Andersen, Gary L. ^[2]; DeSantis, Todd Z. ^[2]; Williams, Kenneth H. ^[2]; Wilkins, Michael J. ^[3]; N'Guessan, A. Lucie ^[4]; Peacock, Aaron ^[5]; Bargar, John ^[6]; Long, Philip E. ^[7]; Banfield, Jillian F.

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1. Univ. of California, Berkeley, CA (United States)
2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
4. Univ. of Massachusetts, Amherst, MA (United States)
5. Haley & Aldrich, Oak Ridge, TN (United States)
6. SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
7. Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99353, USA

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 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 (for example, Desulfovibrionales; Syntrophobacterales; Peptococcaceae) and autotrophic sulfur oxidation (Sulfurovum; Campylobacterales). These data imply complex membership among highly stimulated taxa, and by inference biogeochemical responses to acetate, a non-fermentable substrate.

• Research Organization: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1126367
• Report Number(s): PNNL-SA-86541; 830403000
• Journal Information: FEMS Microbiology Ecology, Vol. 81, Issue 1; ISSN 0168-6496
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
phylochip
stimulated aquifer
acetate amendment