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

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

doi:10.1093/femsec/fiy191

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

Journal Article · 26 September 2018 · FEMS Microbiology Ecology (Online)

DOI: https://doi.org/10.1093/femsec/fiy191 · OSTI ID:1493269

Smith, H. J. ^[1]; Zelaya, Anna J. ^[2]; De León, K. B. ^[3]; Chakraborty, R. ^[4];

^[5];

^[6]; Arkin, A. P. ^[7]; Cunningham, A. B. ^[8];

^[9]

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
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
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
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Climate and Ecosystems Science Division, and ENIGMA, Environmental Genomics and Systems Biology Division
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
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
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Bioengineering, and ENIGMA, Environmental Genomics and Systems Biology Division
Montana State Univ., Bozeman, MT (United States). Center for Biofilm Engineering, and Dept. of Civil Engineering
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

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231; AC05-00OR22725

OSTI ID:: 1493269

Journal Information:: FEMS Microbiology Ecology (Online), Journal Name: FEMS Microbiology Ecology (Online) Journal Issue: 12 Vol. 94; ISSN 1574-6941

Publisher:: Federation of European Microbiological SocietiesCopyright Statement

Country of Publication:: United States

Language:: English

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