Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community

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 acetateamended 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 CO 2 during amendment. Results indicate less abundant Desulfuromonadales, and possibly Bacteroidetes, also actively contributed to CO 2 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 CO 2 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.

Snowmelt Induced Hydrologic Perturbations Drive Dynamic Microbiological and Geochemical Behaviors across a Shallow Riparian Aquifer

“…Groups representing known sulfate reducing bacteria (SRB) previously identified as active at the site (Miletto et al, 2011;Handley et al, 2013)-including members of the Desulfobacteraceae and Desulfobulbaceae-were present in all samples collected during this study, and exhibited dynamic relative abundance fluctuations in many locations. In many instances, relative abundance changes varied over orders of magnitude (Figure 6) despite relatively constant groundwater sulfate concentrations (typically between 8 and 10 mM with slightly elevated concentrations in BND between 8 and 15 mM).…”

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

“…Sulfate reduction in the Rifle sediments and groundwater has been previously attributed to Desulfobacter spp. (Milleto et al, 2011;Handley et al, 2012Handley et al, , 2013, while metagenome reconstruction suggested sulfide re-oxidation was attributed to Sulfurovum-and Sulfurimonas-like Epsilonproteobacteria . None of these genomically characterized sulfur-cycling organisms were identified in these samples, indicating the value of sampling different material (planktonic vs sediment-attached) under varying geochemical conditions (iron reduction vs sulfate reduction) to capture the vast physiological diversity in subsurface communities.…”

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction

“…To remediate these sites, various fast-degrading substrates (e.g., acetate, ethanol, and lactate) have been used. The substrate injection stimulated microbial populations important to U(VI) reduction, resulting in distinct microbial communities whose functions were dependent upon the choice of substrate (6)(7)(8)(9)(10)(11)(12)(13). However, the use of these fast-degrading, simple substrates has several drawbacks.…”