Integrative analysis of the interactions between <i>Geobacter</i> spp. and sulfate-reducing bacteria during uranium bioremediation

Abstract

Enhancing microbial U(VI) reduction with the addition of organic electron donors is a promising strategy for immobilizing uranium in contaminated groundwaters, but has yet to be optimized because of a poor understanding of the factors controlling the growth of various microbial communities during bioremediation. In previous field trials in which acetate was added to the subsurface, there were two distinct phases: an initial phase in which acetate-oxidizing, U(VI)-reducing <i>Geobacter</i> predominated and U(VI) was effectively reduced and a second phase in which acetate-oxidizing sulfate reducing bacteria (SRB) predominated and U(VI) reduction was poor. The interaction of <i>Geobacter</i> and SRB was investigated both in sediment incubations that mimicked in situ bioremediation and with in silico metabolic modeling. In sediment incubations, <i>Geobacter</i> grew quickly but then declined in numbers as the microbially reducible Fe(III) was depleted whereas the SRB grow more slowly and reached dominance after 30–40 days. Modeling predicted a similar outcome. Additional modeling in which the relative initial percentages of the <i>Geobacter</i> and SRB were varied indicated that there was little to no competitive interaction between <i>Geobacter</i> and SRB when acetate was abundant. Further simulations suggested that the addition of Fe(III) would revive the <i>Geobacter</i>, but have little to no effect on the SRB. This result was confirmed experimentally. The results demonstrate that it is possible to predict the impact of amendments on important components of the subsurface microbial community during groundwater bioremediation. The finding that Fe(III) availability, rather than competition with SRB, is the key factor limiting the activity of <i>Geobacter</i> during in situ uranium bioremediation will aid in the design of improved uranium bioremediation strategies

Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface

“…However, these strains have the potential to dump electrons onto a wide range of redox-active metals and compounds, including organic matter (humic compounds), vanadium, and uranium, and therefore alter their physical and chemical behavior. Concurrently, decreasing biosynthesis in Geobacter strains may be linked indirectly to increasing activity of sulfate-reducing bacteria (SRB), as has been reported previously [12], [38]. Greater activity of SRB results in rising aqueous sulfide concentrations which can subsequently react with other metal cations to form precipitates and clog pore networks, catalyze the dissolution of Fe(III) phases, and release adsorbed metal cations from Fe(III) mineral surfaces.…”

“…Following this period, the development of sulfate-reducing conditions in the aquifer is linked to decreasing abundances and activity of planktonic Geobacter [11], [12]. To date, a number of approaches have been used to interrogate the physiology and ecology of Geobacter in the subsurface, including quantification of specific genes associated with N, P and acetate limitation [13], [14], [15].…”

Molecular Analysis of theIn SituGrowth Rates of Subsurface Geobacter Species

“…It seems likely that a similar approach may also be useful for monitoring the growth of other subsurface microorganisms, such as the Dehalococcoides species involved in reductive dechlorination (57), or to monitor the growth of microorganisms added to the subsurface to promote bioremediation (58)(59)(60). Furthermore, as the ability to predictively model the growth of subsurface microorganisms at the genome scale advances (16,17,(61)(62)(63), it will be increasingly important to have better methods for monitoring key aspects of microbial physiology, such as growth rate for model validation.…”

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

“…Efforts to model the in situ bioremediation of uranium-contaminated water have become increasingly sophisticated with the introduction of genome-scale metabolic models to predict the growth and metabolic activity of the microorganisms thought to influence the bioremediation process (Scheibe et al, 2009;Fang et al, 2011;Lovley et al, 2011;Mahadevan et al, 2011;Zhuang et al, 2011;Barlett et al, 2012). However, these modeling efforts have not considered the potential role of protozoa in influencing microbial community dynamics.…”