Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments
- Smith, Heidi J. [ Montana State University: Center for Biofilm Engineering ] [ MTENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720 ]
- Zelaya, Anna J. [ Montana State University: Microbiology & Cell Biology ] [ MTENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720 ]
- De Leon, K. B. [ Department of Biochemistry, University of Missouri, Columbia ] [ MOENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720 ]
- Chakraborty, R. [ Climate and Ecosystems Science Division, Lawrence Berkeley National Laboratory, Berkeley, CAENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, ]
- Elias, D. A. [ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TNENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720 ]
- Hazen, T. C. [ Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TNENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Be ]
- Arkin, A. P. [ Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CAENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, ]
- Cunningham, Al B. [ Montana State University: Civil Engineering ]
- Fields, M. W. [ Montana State University: Microbiology & Cell Biology ] [ MTENIGMA (www.enigma.lbl.gov) Environmental Genomics and Systems Biology Division, Biosciences Area, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS:977, Berkeley, CA 94720 ]
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.