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Title: Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

Abstract

Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.

Authors:
 [1];  [2];  [3];  [4]; ORCiD logo [5]; ORCiD logo [6];  [7];  [8]; ORCiD logo [9]
  1. Montana State Univ., Bozeman, MT (United States). Center for Biofilm Engineering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). ENIGMA, Environmental Genomics and Systems Biology Division
  2. Montana State Univ., Bozeman, MT (United States). Center for Biofilm Engineering; Montana State Univ., Bozeman, MT (United States). Dept. of Microbiology & Immunology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). ENIGMA, Environmental Genomics and Systems Biology Division
  3. Univ. of Missouri, Columbia, MO (United States). Dept. of Biochemistry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). ENIGMA, Environmental Genomics and Systems Biology Division
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Climate and Ecosystems Science Division, and ENIGMA, Environmental Genomics and Systems Biology Division
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). ENIGMA, Environmental Genomics and Systems Biology Division
  6. Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). ENIGMA, Environmental Genomics and Systems Biology Division
  7. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Bioengineering, and ENIGMA, Environmental Genomics and Systems Biology Division
  8. Montana State Univ., Bozeman, MT (United States). Center for Biofilm Engineering, and Dept. of Civil Engineering
  9. Montana State Univ., Bozeman, MT (United States). Center for Biofilm Engineering; Montana State Univ., Bozeman, MT (United States). Dept. of Microbiology & Immunology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). ENIGMA, Environmental Genomics and Systems Biology Division
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); 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:
1493269
Alternate Identifier(s):
OSTI ID: 1528688
Grant/Contract Number:  
AC02-05CH11231; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
FEMS Microbiology Ecology (Online)
Additional Journal Information:
Journal Name: FEMS Microbiology Ecology (Online); Journal Volume: 94; Journal Issue: 12; Journal ID: ISSN 1574-6941
Publisher:
Federation of European Microbiological Societies
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; groundwater; sediment; aquifer; ecology; activity

Citation Formats

Smith, H. J., Zelaya, Anna J., De León, K. B., Chakraborty, R., Elias, Dwayne A., Hazen, Terry C., Arkin, A. P., Cunningham, A. B., and Fields, Matthew Wayne. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. United States: N. p., 2018. Web. doi:10.1093/femsec/fiy191.
Smith, H. J., Zelaya, Anna J., De León, K. B., Chakraborty, R., Elias, Dwayne A., Hazen, Terry C., Arkin, A. P., Cunningham, A. B., & Fields, Matthew Wayne. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments. United States. doi:10.1093/femsec/fiy191.
Smith, H. J., Zelaya, Anna J., De León, K. B., Chakraborty, R., Elias, Dwayne A., Hazen, Terry C., Arkin, A. P., Cunningham, A. B., and Fields, Matthew Wayne. Thu . "Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments". United States. doi:10.1093/femsec/fiy191. https://www.osti.gov/servlets/purl/1493269.
@article{osti_1493269,
title = {Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments},
author = {Smith, H. J. and Zelaya, Anna J. and De León, K. B. and Chakraborty, R. and Elias, Dwayne A. and Hazen, Terry C. and Arkin, A. P. and Cunningham, A. B. and Fields, Matthew Wayne},
abstractNote = {Subsurface environments contain a large proportion of planetary microbial biomass and harbor diverse communities responsible for mediating biogeochemical cycles important to groundwater used by human society for consumption, irrigation, agriculture and industry. Within the saturated zone, capillary fringe and vadose zones, microorganisms can reside in two distinct phases (planktonic or biofilm), and significant differences in community composition, structure and activity between free-living and attached communities are commonly accepted. However, largely due to sampling constraints and the challenges of working with solid substrata, the contribution of each phase to subsurface processes is largely unresolved. Here, we synthesize current information on the diversity and activity of shallow freshwater subsurface habitats, discuss the challenges associated with sampling planktonic and biofilm communities across spatial, temporal and geological gradients, and discuss how biofilms may be constrained within shallow terrestrial subsurface aquifers. We suggest that merging traditional activity measurements and sequencing/-omics technologies with hydrological parameters important to sediment biofilm assembly and stability will help delineate key system parameters. Ultimately, integration will enhance our understanding of shallow subsurface ecophysiology in terms of bulk-flow through porous media and distinguish the respective activities of sessile microbial communities from more transient planktonic communities to ecosystem service and maintenance.},
doi = {10.1093/femsec/fiy191},
journal = {FEMS Microbiology Ecology (Online)},
number = 12,
volume = 94,
place = {United States},
year = {2018},
month = {9}
}

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