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

Wilkins, Michael J.; Wrighton, Kelly C.; Nicora, Carrie D.; Williams, Kenneth H.; McCue, Lee Ann; Handley, Kim M.; Miller, C. S.; Giloteaux, L.; Montgomery, A. P.; Lovley, Derek R.; Banfield, Jillian F.; Long, Philip E.; Lipton, Mary S.

doi:10.1371/journal.pone.0057819

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

Journal Article · Tue Mar 05 00:00:00 EST 2013 · PLoS One, 8(3):e57819

DOI:https://doi.org/10.1371/journal.pone.0057819· OSTI ID:1076700

Wilkins, Michael J.; Wrighton, Kelly C.; Nicora, Carrie D.; Williams, Kenneth H.; McCue, Lee Ann; Handley, Kim M.; Miller, C. S.; Giloteaux, L.; Montgomery, A. P.; Lovley, Derek R.; Banfield, Jillian F.; Long, Philip E.; Lipton, Mary S.

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.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1076700

Report Number(s):: PNNL-SA-91270; 830403000

Journal Information:: PLoS One, 8(3):e57819, Journal Name: PLoS One, 8(3):e57819

Country of Publication:: United States

Language:: English

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Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system Anantharaman, Karthik; Brown, Christopher T.; Hug, Laura A. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms13219	journal	October 2016
After All, Only Millions? Amann, Rudolf; Rosselló-Móra, Ramon mBio, Vol. 7, Issue 4 https://doi.org/10.1128/mbio.00999-16	journal	July 2016
Environmental Microbial Community Proteomics: Status, Challenges and Perspectives Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan International Journal of Molecular Sciences, Vol. 17, Issue 8 https://doi.org/10.3390/ijms17081275	journal	August 2016
Global transcriptional analysis of Geobacter sulfurreducens under palladium reducing conditions reveals new key cytochromes involved Hernández-Eligio, Alberto; Pat-Espadas, Aurora M.; Vega-Alvarado, Leticia Applied Microbiology and Biotechnology, Vol. 104, Issue 9 https://doi.org/10.1007/s00253-020-10502-5	journal	March 2020
Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer Wrighton, Kelly C.; Castelle, Cindy J.; Wilkins, Michael J. The ISME Journal, Vol. 8, Issue 7 https://doi.org/10.1038/ismej.2013.249	journal	March 2014
Global transcriptional analysis of Geobacter sulfurreducens under palladium reducing conditions reveals new key cytochromes involved Hernández-Eligio, Alberto; Pat-Espadas, Aurora M.; Vega-Alvarado, Leticia Applied Microbiology and Biotechnology https://doi.org/10.1101/319194	journal	May 2018
Reactive transport of uranium in a groundwater bioreduction study: Insights from high-temporal resolution 238U/235U data Shiel, A. E.; Johnson, T. M.; Lundstrom, C. C. Geochimica et Cosmochimica Acta, Vol. 187 https://doi.org/10.1016/j.gca.2016.05.020	journal	August 2016

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