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Title: High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer

Abstract

Understanding microbial community structure and function within the subsurface is critical to assessing overall quality and maintenance of groundwater; however, the factors that determine microbial community assembly, structure, and function in groundwater systems and their impact on water quality remains poorly understood. In this study, three shallow wells (FW301, FW303, FW305) in a non-contaminated shallow aquifer in the ENIGMA-Oak Ridge Field Research Center (Oak Ridge, TN) were sampled approximately 3 times a week over a period of three months to measure changes in groundwater geochemistry and microbial diversity. It was expected that the sampled microbial diversity from two historic field wells (FW301, FW303) would be relatively stable, while diversity from a newer well (FW305) would be less stable over time. The wells displayed some degree of hydrochemical variability over time unique to each well, with FW303 being overall the most stable well and FW301 being the most dynamic based upon dissolved oxygen, conductivity, and nitrate. Community analysis via ss-rRNA paired-end sequencing and distribution-based clustering revealed higher OTU richness, diversity, and variability in groundwater communities of FW301 than the other two wells for diversity binned over all time points. Microbial community composition of a given well was on average >50% dissimilarmore » to any other well at a given time (days), yet, functional gene diversity as measured with GeoChip remained relatively constant. Similarities in community structure across wells were observed with respect to the presence of 20 shared bacterial groups in all samples in all wells, although at varying levels over the tested time period. Similarity percentage (SIMPER) analysis revealed that variability in FW301 was largely attributed to low abundance, highly transient populations, while variability in the most hydrochemically stable well (FW303) was due to fluctuations in more highly abundant and frequently present taxa. Additionally, the youngest well FW305 showed a dramatic shift in community composition towards the end of the sampling period that was not observed in the other wells, suggesting possible succession 53 events over time. Time-series analysis using vector auto-regressive models and Granger-causality showed unique relationships between richness and geochemistry over time in each well. These results indicate temporally dynamic microbial communities over short time scales, with day-to-day population shifts in local community structure influenced by available source community diversity and local groundwater hydrochemistry.« less

Authors:
 [1];  [1];  [2];  [3];  [3];  [3]; ORCiD logo [2];  [3]; ORCiD logo [4];  [5]; ORCiD logo [1]
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  1. Montana State Univ., Bozeman, MT (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Univ. of Oklahoma, Norman, OK (United States)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Michigan, Ann Arbor, MI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE National Nuclear Security Administration (NNSA), Office of Nonproliferation and Verification Research and Development (NA-22)
OSTI Identifier:
1607016
Alternate Identifier(s):
OSTI ID: 1562599; OSTI ID: 1777946; OSTI ID: 1804865
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231; NA0003920
Resource Type:
Accepted Manuscript
Journal Name:
Water Research
Additional Journal Information:
Journal Volume: 164; Journal Issue: C; Journal ID: ISSN 0043-1354
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; groundwater; microbial community dynamics; well construction; functional gene array; spatiotemporal; time series; shallow subsurface

Citation Formats

Zelaya, Anna, Parker, Albert, Bailey, Kathryn L., Zhang, Ping, Nostrand, Joy, Ning, Daliang, Elias, Dwayne A., Zhou, Jizhong, Hazen, Terry C., Arkin, Adam, and Fields, Matthew Wayne. High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. United States: N. p., 2019. Web. doi:10.1016/j.watres.2019.114917.
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Zelaya, Anna, Parker, Albert, Bailey, Kathryn L., Zhang, Ping, Nostrand, Joy, Ning, Daliang, Elias, Dwayne A., Zhou, Jizhong, Hazen, Terry C., Arkin, Adam, & Fields, Matthew Wayne. High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer. United States. https://doi.org/10.1016/j.watres.2019.114917
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Zelaya, Anna, Parker, Albert, Bailey, Kathryn L., Zhang, Ping, Nostrand, Joy, Ning, Daliang, Elias, Dwayne A., Zhou, Jizhong, Hazen, Terry C., Arkin, Adam, and Fields, Matthew Wayne. Fri . "High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer". United States. https://doi.org/10.1016/j.watres.2019.114917. https://www.osti.gov/servlets/purl/1607016.
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@article{osti_1607016,
title = {High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer},
author = {Zelaya, Anna and Parker, Albert and Bailey, Kathryn L. and Zhang, Ping and Nostrand, Joy and Ning, Daliang and Elias, Dwayne A. and Zhou, Jizhong and Hazen, Terry C. and Arkin, Adam and Fields, Matthew Wayne},
abstractNote = {Understanding microbial community structure and function within the subsurface is critical to assessing overall quality and maintenance of groundwater; however, the factors that determine microbial community assembly, structure, and function in groundwater systems and their impact on water quality remains poorly understood. In this study, three shallow wells (FW301, FW303, FW305) in a non-contaminated shallow aquifer in the ENIGMA-Oak Ridge Field Research Center (Oak Ridge, TN) were sampled approximately 3 times a week over a period of three months to measure changes in groundwater geochemistry and microbial diversity. It was expected that the sampled microbial diversity from two historic field wells (FW301, FW303) would be relatively stable, while diversity from a newer well (FW305) would be less stable over time. The wells displayed some degree of hydrochemical variability over time unique to each well, with FW303 being overall the most stable well and FW301 being the most dynamic based upon dissolved oxygen, conductivity, and nitrate. Community analysis via ss-rRNA paired-end sequencing and distribution-based clustering revealed higher OTU richness, diversity, and variability in groundwater communities of FW301 than the other two wells for diversity binned over all time points. Microbial community composition of a given well was on average >50% dissimilar to any other well at a given time (days), yet, functional gene diversity as measured with GeoChip remained relatively constant. Similarities in community structure across wells were observed with respect to the presence of 20 shared bacterial groups in all samples in all wells, although at varying levels over the tested time period. Similarity percentage (SIMPER) analysis revealed that variability in FW301 was largely attributed to low abundance, highly transient populations, while variability in the most hydrochemically stable well (FW303) was due to fluctuations in more highly abundant and frequently present taxa. Additionally, the youngest well FW305 showed a dramatic shift in community composition towards the end of the sampling period that was not observed in the other wells, suggesting possible succession 53 events over time. Time-series analysis using vector auto-regressive models and Granger-causality showed unique relationships between richness and geochemistry over time in each well. These results indicate temporally dynamic microbial communities over short time scales, with day-to-day population shifts in local community structure influenced by available source community diversity and local groundwater hydrochemistry.},
doi = {10.1016/j.watres.2019.114917},
journal = {Water Research},
number = C,
volume = 164,
place = {United States},
year = {Fri Jul 26 00:00:00 EDT 2019},
month = {Fri Jul 26 00:00:00 EDT 2019}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.watres.2019.114917
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Cited by: 19 works
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Figures / Tables:

Fig. 1 Fig. 1: Tukey-style boxplots of within-well geochemistry for 3 wells with n= 28 for each well. Mean and median are denoted by a filled-in dark circle and horizontal line, respectively, within each boxplot. Significance testing was carried out via a one-way ANOVA (DF 2). Analysis of variance showed that wellsmore » differed significantly in dissolved oxygen (F(2,81) = 25.49,p= 2.59e-09), pH (F(2,81)= 9.814, p= 0.000153), conductivity (F(2,81)= 51.05, p= 4.52e-15), sulfate (F(2,81) = 16.18, p= 1.23e-06), and nitrate (F(2,80) = 24.82, p= 4.12e-09). Post-hoc analysis (pairwise t-tests with holm adjustment) were used to differentiate differences between groups. All three wells differed significantly from each other. Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘’ 1.« less
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