Abstract
While microbial activities in environmental systems play a key role in the utilization and cycling of essential elements and compounds, microbial activity and growth frequently fluctuates in response to environmental stimuli and perturbations. To investigate these fluctuations within a saturated aquifer system, we monitored a carbon-stimulated in situ Geobacter population while iron reduction was occurring, using 16S rRNA abundances and high-resolution tandem mass spectrometry proteome measurements. Following carbon amendment, 16S rRNA analysis of temporally separated samples revealed the rapid enrichment of Geobacter-like environmental strains with strong similarity to G. bemidjiensis. Tandem mass spectrometry proteomics measurements suggest high carbon flux through Geobacter respiratory pathways, and the synthesis of anapleurotic four carbon compounds from acetyl-CoA via pyruvate ferredoxin oxidoreductase activity. Across a 40-day period where Fe(III) reduction was occurring, fluctuations in protein expression reflected changes in anabolic versus catabolic reactions, with increased levels of biosynthesis occurring soon after acetate arrival in the aquifer. In addition, localized shifts in nutrient limitation were inferred based on expression of nitrogenase enzymes and phosphate uptake proteins. These temporal data offer the first example of differing microbial protein expression associated with changing geochemical conditions in a subsurface environment.
Highlights
The activities of microbial populations play an important role in the cycling of metals and nutrients in environmental systems, where processes including element uptake, excretion and transformations catalyzed by microorganisms contribute to dynamic fluxes of C, P, N, S, and Fe [1]
Understanding the physiology and metabolism of Geobacter spp. in environmental systems is important for predicting biogeochemical processes and bioremediation efforts in the subsurface; these species and strains can couple the oxidation of organic carbon to the reduction of a range of metals including Fe, U, V, and Se [7,8,9,10]
Nine proteomic samples were collected from well CD-01 and binned into three different phases of carbon amendment; Early, Middle, and Late. (Figure 1A)
Summary
The activities of microbial populations play an important role in the cycling of metals and nutrients in environmental systems, where processes including element uptake, excretion and transformations catalyzed by microorganisms contribute to dynamic fluxes of C, P, N, S, and Fe [1] Given that these fluxes are closely linked to the physiological state of microbial community members, the interrogation of in situ microbial metabolism and activity may offer an opportunity to better understand biogeochemical cycles. The stimulation of in situ microbial activity via carbon amendment allows shifts in global protein and mRNA profiles to be measured under controlled conditions, where the enrichment of specific microbial groups can be predicted and subsequently monitored [4,5] This approach has been applied at the Rifle Integrated Field Research Challenge (IFRC) site in Western Colorado, where the use of in situ carbon amendment experiments over the past decade has allowed both microbiological and geochemical responses to be better predicted [6]. These data offer the potential to link metabolic and physiological inferences to geochemical measurements, and obtain a greater predictive understanding of subsurface processes
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