Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow

Merino, Nancy; Jackson, Tracie R.; Campbell, James H.; Kersting, Annie B.; Sackett, Joshua; Fisher, Jenny C.; Bruckner, James C.; Zavarin, Mavrik; Hamilton-Brehm, Scott D.; Moser, Duane P.

doi:10.1016/j.scitotenv.2022.156768

Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow

Journal Article · Tue Jun 21 00:00:00 EDT 2022 · Science of the Total Environment

DOI:https://doi.org/10.1016/j.scitotenv.2022.156768· OSTI ID:1902010

Merino, Nancy ^[1]; Jackson, Tracie R. ^[2]; Campbell, James H. ^[3]; Kersting, Annie B. ^[1]; Sackett, Joshua ^[4]; Fisher, Jenny C. ^[5]; Bruckner, James C. ^[6]; Zavarin, Mavrik ^[1]; Hamilton-Brehm, Scott D. ^[7]; Moser, Duane P. ^[6]

Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
US Geological Survey, Boulder, CO (United States)
Northwest Missouri State University, Maryville, MO (United States)
Desert Research Institute (DRI), Las Vegas, NV (United States); University of Nevada, Las Vegas, NV (United States)
Desert Research Institute (DRI), Las Vegas, NV (United States); Indiana University Northwets, Gary, IN (United States)
Desert Research Institute (DRI), Las Vegas, NV (United States)
Desert Research Institute (DRI), Las Vegas, NV (United States); Southern Illinois University, Carbondale, IL (United States)

Subsurface microbial community distribution patterns are influenced by biogeochemical and groundwater fluxes and may inform hydraulic connections along groundwater-flow paths. This study examined the regional-scale microbial community of the Death Valley Regional Flow System and evaluated whether subsurface communities can be used to identify groundwater-flow paths between recharge and discharge areas. Samples were collected from 36 sites in three groundwater basins: Pahute Mesa–Oasis Valley (PMOV), Ash Meadows (AM), and Alkali Flat–Furnace Creek Ranch (AFFCR). Microbial diversity within and between communities varied by location, and communities were separated into two overall groups that affiliated with the AM and PMOV/AFFCR basins. Network analysis revealed patterns between clusters of common microbes that represented groundwaters with similar geochemical conditions and largely corroborated hydraulic connections between recharge and discharge areas. Null model analyses identified deterministic and stochastic ecological processes contributing to microbial community assemblages. Most communities were more different than expected and governed by dispersal limitation, geochemical differences, or undominating processes. However, certain communities from sites located within or near the Nevada National Security Site were more similar than expected and dominated by homogeneous dispersal or selection. Overall, the (dis)similarities between the microbial communities of DVRFS recharge and discharge areas supported previously documented hydraulic connections between: (1) Spring Mountains and Ash Meadows; (2) Frenchman and Yucca Flat and Amargosa Desert; and (3) Amargosa Desert and Death Valley. However, only a portion of the flow path between Pahute Mesa and Oasis Valley could be supported by microbial community analyses, likely due to well-associated artifacts in samples from the two Oasis Valley sites. This study demonstrates the utility of combining microbial data with hydrologic, geologic, and water-chemistry information to comprehensively characterize groundwater systems, highlighting both strengths and limitations of this approach.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: National Aeronautics and Space Administration (NASA); National Science Foundation (NSF); USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC52-07NA27344; FG02-07ER64406; SC0005306

OSTI ID:: 1902010

Report Number(s):: LLNL-JRNL-823248; 1035849

Journal Information:: Science of the Total Environment, Journal Name: Science of the Total Environment Journal Issue: N/A Vol. 842; ISSN 0048-9697

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (68)

The significance of microbial processes in hydrogeology and geochemistry Chapelle, Francis H. Hydrogeology Journal, Vol. 8, Issue 1 https://doi.org/10.1007/PL00010973	journal	March 2000
Trends, prospects and challenges in quantifying flow and transport through fractured rocks Neuman, Shlomo P. Hydrogeology Journal, Vol. 13, Issue 1 https://doi.org/10.1007/s10040-004-0397-2	journal	February 2005
Potential contaminant transport in the regional Carbonate Aquifer beneath Yucca Mountain, Nevada, USA Bredehoeft, John; King, Michael Hydrogeology Journal, Vol. 18, Issue 3 https://doi.org/10.1007/s10040-009-0550-z	journal	November 2009
The role of interbasin groundwater transfers in geologically complex terranes, demonstrated by the Great Basin in the western United States Nelson, Stephen T.; Mayo, Alan L. Hydrogeology Journal, Vol. 22, Issue 4 https://doi.org/10.1007/s10040-014-1104-6	journal	February 2014
The relative contributions of summer and cool-season precipitation to groundwater recharge, Spring Mountains, Nevada, USA Winograd, Isaac J.; Riggs, Alan C.; Coplen, Tyler B. Hydrogeology Journal, Vol. 6, Issue 1 https://doi.org/10.1007/s100400050135	journal	June 1998
Groundwater as a geologic agent: An overview of the causes, processes, and manifestations Tóth, József Hydrogeology Journal, Vol. 7, Issue 1 https://doi.org/10.1007/s100400050176	journal	February 1999
Current developments in groundwater ecology—from biodiversity to ecosystem function and services Griebler, Christian; Malard, Florian; Lefébure, Tristan Current Opinion in Biotechnology, Vol. 27 https://doi.org/10.1016/j.copbio.2014.01.018	journal	June 2014
Interbasin flow revisited: The contribution of local recharge to high-discharge springs, Death Valley, CA Anderson, Katherine; Nelson, Stephen; Mayo, Alan Journal of Hydrology, Vol. 323, Issue 1-4 https://doi.org/10.1016/j.jhydrol.2005.09.004	journal	May 2006
Regional groundwater flow in structurally-complex extended terranes: An evaluation of the sources of discharge at Ash Meadows, Nevada Bushman, Michelle; Nelson, Stephen T.; Tingey, David Journal of Hydrology, Vol. 386, Issue 1-4 https://doi.org/10.1016/j.jhydrol.2010.03.013	journal	May 2010
Groundwater geochemistry and flow in the Spring Mountains, NV: Implications for the Death Valley Regional Flow System Warix, Sara R.; Rademacher, Laura K.; Meyers, Zachary P. Journal of Hydrology, Vol. 580 https://doi.org/10.1016/j.jhydrol.2019.124313	journal	January 2020
Changes to the microbial communities within groundwater in response to a large crustal earthquake in Kumamoto, southern Japan Morimura, Shigeru; Zeng, Xiangyong; Noboru, Naoki Journal of Hydrology, Vol. 581 https://doi.org/10.1016/j.jhydrol.2019.124341	journal	February 2020
Impact of earthquake on the communities of bacteria and archaea in groundwater ecosystems Kim, Heejung; Kaown, Dugin; Kim, Jeayeon Journal of Hydrology, Vol. 583 https://doi.org/10.1016/j.jhydrol.2020.124563	journal	April 2020
Using Water Chemistry, Isotopes and Microbiology to Evaluate Groundwater Sources, Flow Paths and Geochemical Reactions in the Death Valley Flow System, USA Thomas, James M.; Moser, Duane P.; Fisher, Jenny C. Procedia Earth and Planetary Science, Vol. 7 https://doi.org/10.1016/j.proeps.2013.03.033	journal	January 2013
Groundwater geochemistry and microbial community structure in the aquifer transition from volcanic to alluvial areas Amalfitano, S.; Del Bon, A.; Zoppini, A. Water Research, Vol. 65 https://doi.org/10.1016/j.watres.2014.08.004	journal	November 2014
Groundwater bacterial communities evolve over time in response to recharge Yan, Lijuan; Hermans, Syrie M.; Totsche, Kai Uwe Water Research, Vol. 201 https://doi.org/10.1016/j.watres.2021.117290	journal	August 2021
Groundwater flow and geochemistry in the Southeastern San Juan Basin: Implications for microbial transport and activity Walvoord, Michelle A.; Pegram, Page; Phillips, Fred M. Water Resources Research, Vol. 35, Issue 5 https://doi.org/10.1029/1999WR900017	journal	May 1999
Microbial Community Composition in Deep‐Subsurface Reservoir Fluids Reveals Natural Interwell Connectivity Zhang, Yuran; Dekas, Anne E.; Hawkins, Adam J. Water Resources Research, Vol. 56, Issue 2 https://doi.org/10.1029/2019WR025916	journal	February 2020
A theoretical analysis of groundwater flow in small drainage basins Tóth, J. Journal of Geophysical Research, Vol. 68, Issue 16 https://doi.org/10.1029/JZ068i016p04795	journal	August 1963
Theoretical analysis of regional groundwater flow: 2. Effect of water-table configuration and subsurface permeability variation Freeze, R. Allan; Witherspoon, P. A. Water Resources Research, Vol. 3, Issue 2 https://doi.org/10.1029/WR003i002p00623	journal	June 1967
Major carbon 14 anomaly in a regional carbonate aquifer: Possible evidence for megascale channeling, South Central Great Basin Winograd, Isaac J.; Pearson, F. J. Water Resources Research, Vol. 12, Issue 6 https://doi.org/10.1029/WR012i006p01125	journal	December 1976
Stochastic and deterministic assembly processes in subsurface microbial communities Stegen, James C.; Lin, Xueju; Konopka, Allan E. The ISME Journal, Vol. 6, Issue 9 https://doi.org/10.1038/ismej.2012.22	journal	March 2012
Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes Wang, Jianjun; Shen, Ji; Wu, Yucheng The ISME Journal, Vol. 7, Issue 7 https://doi.org/10.1038/ismej.2013.30	journal	February 2013
Quantifying community assembly processes and identifying features that impose them Stegen, James C.; Lin, Xueju; Fredrickson, Jim K. The ISME Journal, Vol. 7, Issue 11 https://doi.org/10.1038/ismej.2013.93	journal	June 2013
Aquifer environment selects for microbial species cohorts in sediment and groundwater Hug, Laura A.; Thomas, Brian C.; Brown, Christopher T. The ISME Journal, Vol. 9, Issue 8 https://doi.org/10.1038/ismej.2015.2	journal	February 2015
DADA2: High-resolution sample inference from Illumina amplicon data Callahan, Benjamin J.; McMurdie, Paul J.; Rosen, Michael J. Nature Methods, Vol. 13, Issue 7 https://doi.org/10.1038/nmeth.3869	journal	May 2016
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere Wright, Robyn J.; Langille, Morgan G. I.; Walker, Tony R. The ISME Journal, Vol. 15, Issue 3 https://doi.org/10.1038/s41396-020-00814-9	journal	November 2020
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Bolyen, Evan; Rideout, Jai Ram; Dillon, Matthew R. Nature Biotechnology, Vol. 37, Issue 8 https://doi.org/10.1038/s41587-019-0209-9	journal	July 2019
Long-term nitrogen addition affects the phylogenetic turnover of soil microbial community responding to moisture pulse Liu, Chi; Yao, Minjie; Stegen, James C. Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-17736-w	journal	December 2017
Investigation of clogging in porous media induced by microorganisms using a microfluidic application Gaol, Calvin Lumban; Ganzer, Leonhard; Mukherjee, Soujatya Environmental Science: Water Research & Technology, Vol. 7, Issue 2 https://doi.org/10.1039/D0EW00766H	journal	January 2021
Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession Dini-Andreote, Francisco; Stegen, James C.; van Elsas, Jan Dirk Proceedings of the National Academy of Sciences, Vol. 112, Issue 11 https://doi.org/10.1073/pnas.1414261112	journal	March 2015
Environmental Impact and Mechanisms of the Biological Clogging of Saturated Soils and Aquifer Materials Baveye, Philippe; Vandevivere, Philippe; Hoyle, Blythe L. Critical Reviews in Environmental Science and Technology, Vol. 28, Issue 2 https://doi.org/10.1080/10643389891254197	journal	April 1998
Fast unfolding of communities in large networks Blondel, Vincent D.; Guillaume, Jean-Loup; Lambiotte, Renaud Journal of Statistical Mechanics: Theory and Experiment, Vol. 2008, Issue 10 https://doi.org/10.1088/1742-5468/2008/10/P10008	journal	October 2008
Picante: R tools for integrating phylogenies and ecology Kembel, S. W.; Cowan, P. D.; Helmus, M. R. Bioinformatics, Vol. 26, Issue 11 https://doi.org/10.1093/bioinformatics/btq166	journal	April 2010
Spatiotemporal and seasonal dynamics in the microbial communities of a landfill-leachate contaminated aquifer Abiriga, Daniel; Jenkins, Andrew; Alfsnes, Kristian FEMS Microbiology Ecology, Vol. 97, Issue 7 https://doi.org/10.1093/femsec/fiab086	journal	June 2021
Selection imposed by local environmental conditions drives differences in microbial community composition across geographically distinct groundwater aquifers Fillinger, Lucas; Hug, Katrin; Griebler, Christian FEMS Microbiology Ecology, Vol. 95, Issue 11 https://doi.org/10.1093/femsec/fiz160	journal	October 2019
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1219	journal	November 2012
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks Yilmaz, Pelin; Parfrey, Laura Wegener; Yarza, Pablo Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1209	journal	November 2013
Finding community structure in very large networks Clauset, Aaron; Newman, M. E. J.; Moore, Cristopher Physical Review E, Vol. 70, Issue 6 https://doi.org/10.1103/PhysRevE.70.066111	journal	December 2004
iNEXT: an R package for rarefaction and extrapolation of species diversity ( H ill numbers) Hsieh, T. C.; Ma, K. H.; Chao, Anne Methods in Ecology and Evolution, Vol. 7, Issue 12 https://doi.org/10.1111/2041-210X.12613	journal	August 2016
Richness-dependence of phylogenetic diversity indices Sandel, Brody Ecography, Vol. 41, Issue 5 https://doi.org/10.1111/ecog.02967	journal	September 2017
Evaluating Groundwater Interbasin Flow Using Multiple Models and Multiple Types of Data: Groundwater XX, no. XX: XX-XX Ye, Ming; Wang, Liying; Pohlmann, Karl. F. Groundwater, Vol. 54, Issue 6 https://doi.org/10.1111/gwat.12422	journal	April 2016
Testing the spatial phylogenetic structure of local communities: statistical performances of different null models and test statistics on a locally neutral community: Testing spatial community phylogenetic structure Hardy, Olivier J. Journal of Ecology, Vol. 96, Issue 5 https://doi.org/10.1111/j.1365-2745.2008.01421.x	journal	August 2008
Microorganisms as tracers in groundwater injection and recovery experiments: a review Harvey, Ronald W. FEMS Microbiology Reviews, Vol. 20, Issue 3-4 https://doi.org/10.1111/j.1574-6976.1997.tb00330.x	journal	July 1997
Estimating Aquifer Properties from the Water Level Response to Earth Tides Cutillo, Paula A.; Bredehoeft, John D. Ground Water, Vol. 49, Issue 4 https://doi.org/10.1111/j.1745-6584.2010.00778.x	journal	December 2010
Correlations between phylogenetic and functional diversity: mathematical artefacts or true ecological and evolutionary processes? Pavoine, Sandrine; Gasc, Amandine; Bonsall, Michael B. Journal of Vegetation Science, Vol. 24, Issue 5 https://doi.org/10.1111/jvs.12051	journal	August 2013
Stochastic Community Assembly: Does It Matter in Microbial Ecology? Zhou, Jizhong; Ning, Daliang Microbiology and Molecular Biology Reviews, Vol. 81, Issue 4 https://doi.org/10.1128/MMBR.00002-17	journal	October 2017
Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units Glassman, Sydney I.; Martiny, Jennifer B. H. mSphere, Vol. 3, Issue 4 https://doi.org/10.1128/mSphere.00148-18	journal	July 2018
A Novel Sparse Compositional Technique Reveals Microbial Perturbations Martino, Cameron; Morton, James T.; Marotz, Clarisse A. mSystems, Vol. 4, Issue 1 https://doi.org/10.1128/mSystems.00016-19	journal	February 2019
Microbial Community Cohesion Mediates Community Turnover in Unperturbed Aquifers Danczak, Robert E.; Johnston, Michael D.; Kenah, Chris mSystems, Vol. 3, Issue 4 https://doi.org/10.1128/mSystems.00066-18	journal	July 2018
Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems Danczak, R. E.; Daly, R. A.; Borton, M. A. mSystems, Vol. 5, Issue 2 https://doi.org/10.1128/mSystems.00098-20	journal	March 2020
Functional microbial diversity explains groundwater chemistry in a pristine aquifer Flynn, Theodore M.; Sanford, Robert A.; Ryu, Hodon BMC Microbiology, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2180-13-146	journal	January 2013
Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units Joos, Lisa; Beirinckx, Stien; Haegeman, Annelies BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-07126-4	journal	October 2020
Biological observations in microbiota analysis are robust to the choice of 16S rRNA gene sequencing processing algorithm: case study on human milk microbiota Moossavi, Shirin; Atakora, Faisal; Fehr, Kelsey BMC Microbiology, Vol. 20, Issue 1 https://doi.org/10.1186/s12866-020-01949-7	journal	September 2020
Normalization and microbial differential abundance strategies depend upon data characteristics Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0237-y	journal	March 2017
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin Bokulich, Nicholas A.; Kaehler, Benjamin D.; Rideout, Jai Ram Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0470-z	journal	May 2018
A census-based estimate of Earth's bacterial and archaeal diversity Louca, Stilianos; Mazel, Florent; Doebeli, Michael PLOS Biology, Vol. 17, Issue 2 https://doi.org/10.1371/journal.pbio.3000106	journal	February 2019
Sparse and Compositionally Robust Inference of Microbial Ecological Networks Kurtz, Zachary D.; Müller, Christian L.; Miraldi, Emily R. PLOS Computational Biology, Vol. 11, Issue 5 https://doi.org/10.1371/journal.pcbi.1004226	journal	May 2015
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data McMurdie, Paul J.; Holmes, Susan PLoS ONE, Vol. 8, Issue 4 https://doi.org/10.1371/journal.pone.0061217	journal	April 2013
Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing Prodan, Andrei; Tremaroli, Valentina; Brolin, Harald PLOS ONE, Vol. 15, Issue 1 https://doi.org/10.1371/journal.pone.0227434	journal	January 2020
Using null models to disentangle variation in community dissimilarity from variation in α-diversity Chase, Jonathan M.; Kraft, Nathan J. B.; Smith, Kevin G. Ecosphere, Vol. 2, Issue 2 https://doi.org/10.1890/ES10-00117.1	journal	February 2011
An Ordination of the Upland Forest Communities of Southern Wisconsin Bray, J. Roger; Curtis, J. T. Ecological Monographs, Vol. 27, Issue 4 https://doi.org/10.2307/1942268	journal	February 1957
Estimating and mapping ecological processes influencing microbial community assembly Stegen, James C.; Lin, Xueju; Fredrickson, Jim K. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00370	journal	May 2015
Local and Regional Diversity Reveals Dispersal Limitation and Drift as Drivers for Groundwater Bacterial Communities from a Fractured Granite Formation Beaton, E. D.; Stevenson, Bradley S.; King-Sharp, Karen J. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01933	journal	December 2016
Microbiome Datasets Are Compositional: And This Is Not Optional Gloor, Gregory B.; Macklaim, Jean M.; Pawlowsky-Glahn, Vera Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02224	journal	November 2017
The Effect of the 2015 Earthquake on the Bacterial Community Compositions in Water in Nepal Uprety, Sital; Hong, Pei-Ying; Sadik, Nora Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.02380	journal	December 2017
Dynamics of Hydrology and Anaerobic Hydrocarbon Degrader Communities in A Tar-Oil Contaminated Aquifer Pilloni, Giovanni; Bayer, Anne; Ruth-Anneser, Bettina Microorganisms, Vol. 7, Issue 2 https://doi.org/10.3390/microorganisms7020046	journal	February 2019
A phylogenetic transform enhances analysis of compositional microbiota data Silverman, Justin D.; Washburne, Alex D.; Mukherjee, Sayan eLife, Vol. 6 https://doi.org/10.7554/eLife.21887	journal	February 2017
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches Nearing, Jacob T.; Douglas, Gavin M.; Comeau, André M. PeerJ, Vol. 6 https://doi.org/10.7717/peerj.5364	journal	August 2018

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Subsurface microbial communities as a tool for characterizing regional-scale groundwater flow

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