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Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage

Publication ,  Journal Article
Bier, RL; Wernegreen, JJ; Vilgalys, RJ; Ellis, JC; Bernhardt, ES
Published in: Limnology and Oceanography
January 1, 2020

Chemical pollution mixtures enter aquatic environments and interact with microorganisms in eclectic ways with disparate consequences for microbial ecosystem services. Can using a thermodynamic framework help to determine the net influence of a chemical mixture on the functional capacity of benthic microbial communities? We examined this question by comparing benthic stream microbial communities exposed to a gradient of neutral-alkaline coalmine effluent. Using a combination of approaches (metagenomics, quantitative polymerase chain reaction [qPCR], and functional assays), we show that functional genes and pathways of microbial communities growing in mine effluent differed in composition, but not diversity. The majority of functional genes and pathways that changed decreased at sites exposed to mine effluent, resulting in lower abundances of nitrogenase and methanogen genes and fermentation pathways. However, selenate reductase gene abundance increased with water and sediment concentration of an ecologically important contaminant at mined sites: selenium. Denitrification genes nosZ and nirK differed between sites: metagenome-based nosZ increased with dissolved nitrate concentration and qPCR-based nirK had a hump-shaped pattern across the mining gradient. Osmoprotectant gene abundance did not change. Extracellular enzyme assays and alkaline phosphatase gene relative abundance suggested that mined stream microbial communities may be constrained by phosphorus bioavailability. Subsidies and stressors related to changes in a set of functional genes and pathways, but differences were not consistently predictable using thermodynamic expectations. This suggests that pairing hypotheses for expected subsidies and stressors with post hoc explorations can yield valuable directions for future study of how microbial functional capacity responds to pollutant mixtures.

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Published In

Limnology and Oceanography

DOI

EISSN

1939-5590

Publication Date

January 1, 2020

Volume

65

Issue

S1

Start / End Page

S277 / S292

Related Subject Headings

  • Marine Biology & Hydrobiology
  • 41 Environmental sciences
  • 37 Earth sciences
  • 31 Biological sciences
  • 06 Biological Sciences
  • 05 Environmental Sciences
  • 04 Earth Sciences
 

Citation

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Bier, R. L., Wernegreen, J. J., Vilgalys, R. J., Ellis, J. C., & Bernhardt, E. S. (2020). Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage. Limnology and Oceanography, 65(S1), S277–S292. https://doi.org/10.1002/lno.11301
Bier, R. L., J. J. Wernegreen, R. J. Vilgalys, J. C. Ellis, and E. S. Bernhardt. “Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage.” Limnology and Oceanography 65, no. S1 (January 1, 2020): S277–92. https://doi.org/10.1002/lno.11301.
Bier RL, Wernegreen JJ, Vilgalys RJ, Ellis JC, Bernhardt ES. Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage. Limnology and Oceanography. 2020 Jan 1;65(S1):S277–92.
Bier, R. L., et al. “Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage.” Limnology and Oceanography, vol. 65, no. S1, Jan. 2020, pp. S277–92. Scopus, doi:10.1002/lno.11301.
Bier RL, Wernegreen JJ, Vilgalys RJ, Ellis JC, Bernhardt ES. Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage. Limnology and Oceanography. 2020 Jan 1;65(S1):S277–S292.
Journal cover image

Published In

Limnology and Oceanography

DOI

EISSN

1939-5590

Publication Date

January 1, 2020

Volume

65

Issue

S1

Start / End Page

S277 / S292

Related Subject Headings

  • Marine Biology & Hydrobiology
  • 41 Environmental sciences
  • 37 Earth sciences
  • 31 Biological sciences
  • 06 Biological Sciences
  • 05 Environmental Sciences
  • 04 Earth Sciences