title: Fluctuations in species-level protein expression occur during element and nutrient cycling in the subsurface.
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.
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA. michael.wilkins@pnnl.gov
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Wilkins
authors.forename: Kelly C
authors.initials: KC
authors.lastname: Wrighton
authors.forename: Carrie D
authors.initials: CD
authors.lastname: Nicora
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Williams
authors.forename: Lee Ann
authors.initials: LA
authors.lastname: McCue
authors.forename: Kim M
authors.initials: KM
authors.lastname: Handley
authors.forename: Chris S
authors.initials: CS
authors.lastname: Miller
authors.forename: Ludovic
authors.initials: L
authors.lastname: Giloteaux
authors.forename: Alison P
authors.initials: AP
authors.lastname: Montgomery
authors.forename: Derek R
authors.initials: DR
authors.lastname: Lovley
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
authors.forename: Philip E
authors.initials: PE
authors.lastname: Long
authors.forename: Mary S
authors.initials: MS
authors.lastname: Lipton
mesh_terms: D018533:Biomass; D002244:Carbon / Q000737:chemistry; D004777:Environment; D015964:Gene Expression Regulation, Bacterial; D045302:Geobacter / Q000378:metabolism* / Q000502:physiology*; D060587:Groundwater; D006812:Humic Substances; D007501:Iron / Q000737:chemistry; D010084:Oxidation-Reduction; D010710:Phosphates / Q000737:chemistry; D010933:Plankton / Q000378:metabolism; D040901:Proteomics; D012336:RNA, Ribosomal, 16S / Q000378:metabolism; D053719:Tandem Mass Spectrometry; D014501:Uranium / Q000737:chemistry; D014639:Vanadium / Q000737:chemistry; D014871:Water Microbiology
chemical_list: D006812:Humic Substances; D010710:Phosphates; D012336:RNA, Ribosomal, 16S; D014639:Vanadium; D014501:Uranium; D002244:Carbon; D007501:Iron