Abstract
Stimulation of subsurface microorganisms to induce reductive immobilization of metals is a promising approach for bioremediation, yet the overall microbial community response is typically poorly understood. Here we used proteogenomics to test the hypothesis that excess input of acetate activates complex community functioning and syntrophic interactions among autotrophs and heterotrophs. A flow-through sediment column was incubated in a groundwater well of an acetate-amended aquifer and recovered during microbial sulfate reduction. De novo reconstruction of community sequences yielded near-complete genomes of Desulfobacter (Deltaproteobacteria), Sulfurovum- and Sulfurimonas-like Epsilonproteobacteria and Bacteroidetes. Partial genomes were obtained for Clostridiales (Firmicutes) and Desulfuromonadales-like Deltaproteobacteria. The majority of proteins identified by mass spectrometry corresponded to Desulfobacter-like species, and demonstrate the role of this organism in sulfate reduction (Dsr and APS), nitrogen fixation and acetate oxidation to CO2 during amendment. Results indicate less abundant Desulfuromonadales, and possibly Bacteroidetes, also actively contributed to CO2 production via the tricarboxylic acid (TCA) cycle. Proteomic data indicate that sulfide was partially re-oxidized by Epsilonproteobacteria through nitrate-dependent sulfide oxidation (using Nap, Nir, Nos, SQR and Sox), with CO2 fixed using the reverse TCA cycle. We infer that high acetate concentrations, aimed at stimulating anaerobic heterotrophy, led to the co-enrichment of, and carbon fixation in Epsilonproteobacteria. Results give an insight into ecosystem behavior following addition of simple organic carbon to the subsurface, and demonstrate a range of biological processes and community interactions were stimulated.
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Acknowledgements
Funding was provided through the IFRC, Subsurface Biogeochemical Research Program, Office of Science, Biological and Environmental Research, the US Department of Energy (DOE), with equal support for LBNL employees through LBNL’s Sustainable Systems Scientific Focus Area (contract DE-AC02-05CH11231); and an EMBO Long-Term Fellowship (I Sharon). Genomic sequencing was performed at the W M Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign. We thank S Chan (University of California, LA, USA) for help with field implementation, and K Campbell (the US Geological Survey, Menlo Park) and J Bargar (Stanford Synchrotron Radiation Lightsource, Menlo Park, USA) for assistance with column design. We also thank our anonymous reviewer's for their helpful comments.
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Handley, K., VerBerkmoes, N., Steefel, C. et al. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J 7, 800–816 (2013). https://doi.org/10.1038/ismej.2012.148
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