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

Abstract

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? In this study, 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. Subsidiesmore » and stressors related to changes in a set of functional genes and pathways, but differences were not consistently predictable using thermodynamic expectations. Laslty, 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.« less

Authors:
ORCiD logo [1];  [2];  [2]; ORCiD logo [3]; ORCiD logo [2]
  1. Stroud Water Research Center, Avondale, PA (United States); Duke Univ., Durham, NC (United States)
  2. Duke Univ., Durham, NC (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1561663
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Limnology and Oceanography
Additional Journal Information:
Journal Name: Limnology and Oceanography; Journal ID: ISSN 0024-3590
Publisher:
Association for the Sciences of Limnology and Oceanography - Wiley
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES

Citation Formats

Bier, Raven L., Wernegreen, Jennifer J., Vilgalys, Rytas J., Ellis, Joseph Christopher, and Bernhardt, Emily S. Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage. United States: N. p., 2019. Web. doi:10.1002/lno.11301.
Bier, Raven L., Wernegreen, Jennifer J., Vilgalys, Rytas J., Ellis, Joseph Christopher, & Bernhardt, Emily S. Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage. United States. doi:10.1002/lno.11301.
Bier, Raven L., Wernegreen, Jennifer J., Vilgalys, Rytas J., Ellis, Joseph Christopher, and Bernhardt, Emily S. Thu . "Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage". United States. doi:10.1002/lno.11301.
@article{osti_1561663,
title = {Subsidized or stressed? Shifts in freshwater benthic microbial metagenomics along a gradient of alkaline coal mine drainage},
author = {Bier, Raven L. and Wernegreen, Jennifer J. and Vilgalys, Rytas J. and Ellis, Joseph Christopher and Bernhardt, Emily S.},
abstractNote = {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? In this study, 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. Laslty, 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.},
doi = {10.1002/lno.11301},
journal = {Limnology and Oceanography},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {8}
}

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