Versatile soil gas concentration and isotope monitoring: optimization and integration of novel soil gas probes with online trace gas detection

Gil-Loaiza, Juliana; Roscioli, Joseph R.; Shorter, Joanne H.; Volkmann, Till H. M.; Ng, Wei-Ren; Krechmer, Jordan E.; Meredith, Laura K.

doi:10.5194/bg-19-165-2022

Title: Versatile soil gas concentration and isotope monitoring: optimization and integration of novel soil gas probes with online trace gas detection

Journal Article · Mon Jan 10 00:00:00 EST 2022 · Biogeosciences (Online)

DOI:https://doi.org/10.5194/bg-19-165-2022· OSTI ID:1839102

; Roscioli, Joseph R.;

; Volkmann, Till H. M.; Ng, Wei-Ren;

;

Gas concentrations and isotopic signatures can unveil microbial metabolisms and their responses to environmental changes in soil. Currently, few methods measure in situ soil trace gases such as the products of nitrogen and carbon cycling or volatile organic compounds (VOCs) that constrain microbial biochemical processes like nitrification, methanogenesis, respiration, and microbial communication. Versatile trace gas sampling systems that integrate soil probes with sensitive trace gas analyzers could fill this gap with in situ soil gas measurements that resolve spatial (centimeters) and temporal (minutes) patterns. We developed a system that integrates new porous and hydrophobic sintered polytetrafluoroethylene (sPTFE) diffusive soil gas probes that non-disruptively collect soil gas samples with a transfer system to direct gas from multiple probes to one or more central gas analyzer(s) such as laser and mass spectrometers. Here, we demonstrate the feasibility and versatility of this automated multiprobe system for soil gas measurements of isotopic ratios of nitrous oxide (δ¹⁸O, δ¹⁵N, and the ¹⁵N site preference of N₂O), methane, carbon dioxide (δ¹³C), and VOCs. First, we used an inert silica matrix to challenge probe measurements under controlled gas conditions. By changing and controlling system flow parameters, including the probe flow rate, we optimized recovery of representative soil gas samples while reducing sampling artifacts on subsurface concentrations. Second, we used this system to provide a real-time window into the impact of environmental manipulation of irrigation and soil redox conditions on in situ N₂O and VOC concentrations. Moreover, to reveal the dynamics in the stable isotope ratios of N₂O (i.e., ¹⁴N¹⁴N¹⁶O, ¹⁴N¹⁵N¹⁶O, ¹⁵N¹⁴N¹⁶O, and ¹⁴N¹⁴N¹⁸O), we developed a new high-precision laser spectrometer with a reduced sample volume demand. Our integrated system – a tunable infrared laser direct absorption spectrometry (TILDAS) in parallel with Vocus proton transfer reaction mass spectrometry (PTR-MS), in line with sPTFE soil gas probes – successfully quantified isotopic signatures for N₂O, CO₂, and VOCs in real time as responses to changes in the dry–wetting cycle and redox conditions. Broadening the collection of trace gases that can be monitored in the subsurface is critical for monitoring biogeochemical cycles, ecosystem health, and management practices at scales relevant to the soil system.

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Research Organization:: Aerodyne Research, Inc., Billerica, MA (United States); Univ. of Arizona, Tucson, AZ (United States)

Sponsoring Organization:: USDOE Office of Science (SC); University of Arizona; Philecology Foundation; Landscape Evolutionary Observatory

Grant/Contract Number:: SC0018459

OSTI ID:: 1839102

Alternate ID(s):: OSTI ID: 1981295

Journal Information:: Biogeosciences (Online), Journal Name: Biogeosciences (Online) Vol. 19 Journal Issue: 1; ISSN 1726-4189

Publisher:: Copernicus GmbHCopyright Statement

Country of Publication:: Germany

Language:: English

References (63)

Turbulence Effect on Gas Transport in Three Contrasting Forest Soils Maier, Martin; Schack-Kirchner, Helmer; Aubinet, Marc Soil Science Society of America Journal, Vol. 76, Issue 5 https://doi.org/10.2136/sssaj2011.0376	journal	September 2012
Long-term and high-frequency non-destructive monitoring of water stable isotope profiles in an evaporating soil column Rothfuss, Y.; Merz, S.; Vanderborght, J. Hydrology and Earth System Sciences, Vol. 19, Issue 10 https://doi.org/10.5194/hess-19-4067-2015	journal	January 2015
Biogenic volatile emissions from the soil: Biogenic volatile emissions from the soil PeÑUelas, J.; Asensio, D.; Tholl, D. Plant, Cell & Environment, Vol. 37, Issue 8 https://doi.org/10.1111/pce.12340	journal	May 2014
A fragrant neighborhood: volatile mediated bacterial interactions in soil Schulz-Bohm, Kristin; Zweers, Hans; de Boer, Wietse Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01212	journal	November 2015
Mechanistic insights on the responses of plant and ecosystem gas exchange to global environmental change: Lessons from Biosphere 2 Gonzalez-Meler, Miquel A.; Rucks, Jessica S.; Aubanell, Gerard Plant Science, Vol. 226 https://doi.org/10.1016/j.plantsci.2014.05.002	journal	September 2014
The Volatilome: A Vital Piece of the Complete Soil Metabolome Honeker, Linnea K.; Graves, Kelsey R.; Tfaily, Malak M. Frontiers in Environmental Science, Vol. 9 https://doi.org/10.3389/fenvs.2021.649905	journal	April 2021
The limits of signal averaging in atmospheric trace-gas monitoring by tunable diode-laser absorption spectroscopy (TDLAS) Werle, P.; M�cke, R.; Slemr, F. Applied Physics B Photophysics and Laser Chemistry, Vol. 57, Issue 2 https://doi.org/10.1007/BF00425997	journal	August 1993
Profile Nitrous Oxide and Carbon Dioxide Concentrations in a Soil Subject to Freezing Burton, D. L.; Beauchamp, E. G. Soil Science Society of America Journal, Vol. 58, Issue 1 https://doi.org/10.2136/sssaj1994.03615995005800010016x	journal	January 1994
A new sampling technique to monitor concentrations of CH ₄ , N ₂ O and CO ₂ in air at well-defined depths in soils with varied water potential Kammann, C.; Grünhage, L.; Jäger, H. -J. European Journal of Soil Science, Vol. 52, Issue 2 https://doi.org/10.1046/j.1365-2389.2001.00380.x	journal	June 2001
Measuring techniques for concentration and stable isotopologues of CO2 in a terrestrial ecosystem: A review Voglar, Grega E.; Zavadlav, Saša; Levanič, Tom Earth-Science Reviews, Vol. 199 https://doi.org/10.1016/j.earscirev.2019.102978	journal	December 2019
Distinguishing Nitrous Oxide Production from Nitrification and Denitrification on the Basis of Isotopomer Abundances Sutka, R. L.; Ostrom, N. E.; Ostrom, P. H. Applied and Environmental Microbiology, Vol. 72, Issue 1 https://doi.org/10.1128/AEM.72.1.638-644.2006	journal	January 2006
Reduced microbial diversity induces larger volatile organic compound emissions from soils Abis, Letizia; Loubet, Benjamin; Ciuraru, Raluca Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-63091-8	journal	April 2020
Monitoring water stable isotopic composition in soils using gas-permeable tubing and infrared laser absorption spectroscopy: Monitoring Water Stable Isotopic Composition in Soils Rothfuss, Youri; Vereecken, Harry; Brüggemann, Nicolas Water Resources Research, Vol. 49, Issue 6 https://doi.org/10.1002/wrcr.20311	journal	June 2013
What are the instrumentation requirements for measuring the isotopic composition of net ecosystem exchange of CO ₂ using eddy covariance methods?† Saleska, Scott R.; Shorter, Joanne H.; Herndon, Scott Isotopes in Environmental and Health Studies, Vol. 42, Issue 2 https://doi.org/10.1080/10256010600672959	journal	June 2006
Porous tubing for use in monitoring soil CO2 concentrations Desutter, T.; Sauer, T.; Parkin, T. Soil Biology and Biochemistry, Vol. 38, Issue 9 https://doi.org/10.1016/j.soilbio.2006.04.022	journal	September 2006
A multi-layer, closed-loop system for continuous measurement of soil CO ₂ concentration Jochheim, Hubert; Wirth, Stephan; von Unold, Georg Journal of Plant Nutrition and Soil Science, Vol. 181, Issue 1 https://doi.org/10.1002/jpln.201700259	journal	August 2017
Development of a gas diffusion probe for the determination of methane concentrations and diffusion characteristics in flooded paddy soil Rothfuss, Franz; Conrad, Ralf FEMS Microbiology Ecology, Vol. 14, Issue 4 https://doi.org/10.1111/j.1574-6941.1994.tb00116.x	journal	September 1994
Continual in situ monitoring of pore water stable isotopes in the subsurface Volkmann, T. H. M.; Weiler, M. Hydrology and Earth System Sciences, Vol. 18, Issue 5 https://doi.org/10.5194/hess-18-1819-2014	journal	January 2014
Volatile organic compounds (VOCs) in soils Insam, Heribert; Seewald, Martin S. A. Biology and Fertility of Soils, Vol. 46, Issue 3 https://doi.org/10.1007/s00374-010-0442-3	journal	February 2010
A global model of natural volatile organic compound emissions Guenther, Alex; Hewitt, C. Nicholas; Erickson, David Journal of Geophysical Research, Vol. 100, Issue D5 https://doi.org/10.1029/94JD02950	journal	January 1995
The surface CO ₂ gradient and pore-space storage flux in a high-porosity litter layer Hirsch, Adam I.; Trumbore, Susan E. :; Goulden, Michael L. Tellus B: Chemical and Physical Meteorology, Vol. 56, Issue 4 https://doi.org/10.3402/tellusb.v56i4.16449	journal	January 2004
From the Ground Up: Global Nitrous Oxide Sources are Constrained by Stable Isotope Values Snider, David M.; Venkiteswaran, Jason J.; Schiff, Sherry L. PLOS ONE, Vol. 10, Issue 3 https://doi.org/10.1371/journal.pone.0118954	journal	March 2015
High-resolution isotope measurements resolve rapid ecohydrological dynamics at the soil-plant interface Volkmann, Till H. M.; Haberer, Kristine; Gessler, Arthur New Phytologist, Vol. 210, Issue 3 https://doi.org/10.1111/nph.13868	journal	February 2016
Constraining the atmospheric N2O budget from intramolecular site preference in N2O isotopomers Yoshida, Naohiro; Toyoda, Sakae Nature, Vol. 405, Issue 6784 https://doi.org/10.1038/35012558	journal	May 2000
Terpenoids are Widespread in Actinomycetes: A Correlation of Secondary Metabolism and Genome Data Citron, Christian A.; Gleitzmann, Julia; Laurenzano, Gianfranco ChemBioChem, Vol. 13, Issue 2 https://doi.org/10.1002/cbic.201100641	journal	December 2011
Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems Jiao, Shuo; Chen, Weimin; Wang, Jieli Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0526-0	journal	August 2018
Biogenic Volatile Organic Compounds in Arctic Soil: A Field Study of Concentrations and Variability With Vegetation Cover Wester‐Larsen, Lærke; Kramshøj, Magnus; Albers, Christian N. Journal of Geophysical Research: Biogeosciences, Vol. 125, Issue 7 https://doi.org/10.1029/2019JG005551	journal	July 2020
A new method for continuously measuring the δ ¹³ C of soil CO ₂ concentrations at different depths by laser spectrometry: Automatic measurement of soil CO ₂ isotopic signature Parent, F.; Plain, C.; Epron, D. European Journal of Soil Science, Vol. 64, Issue 4 https://doi.org/10.1111/ejss.12047	journal	May 2013
Drought-induced nitrous oxide flux dynamics in an enclosed tropical forest van Haren, Joost L. M.; Handley, Linda L.; Biel, Karl Y. Global Change Biology, Vol. 11, Issue 8 https://doi.org/10.1111/j.1365-2486.2005.00987.x	journal	August 2005
Continuous analysis of δ ¹⁸ O and δD values of water by diffusion sampling cavity ring-down spectrometry: a novel sampling device for unattended field monitoring of precipitation, ground and surface waters : Continuous analysis of δ Munksgaard, Niels C.; Wurster, Chris M.; Bird, Michael I. Rapid Communications in Mass Spectrometry, Vol. 25, Issue 24 https://doi.org/10.1002/rcm.5282	journal	November 2011
Measurement of dissolved H2 concentrations in methanogenic environments with a gas diffusion probe Kramer, H. FEMS Microbiology Ecology, Vol. 12, Issue 3 https://doi.org/10.1016/0168-6496(93)90010-5	journal	July 1993
Use of silicone tubing to sample nitrous oxide in the soil atmosphere Jacinthe, P. -A.; Dick, W. A. Soil Biology and Biochemistry, Vol. 28, Issue 6 https://doi.org/10.1016/0038-0717(95)00176-X	journal	June 1996
A method for in situ monitoring of the isotope composition of tree xylem water using laser spectroscopy Volkmann, Till H. M.; Kühnhammer, Kathrin; Herbstritt, Barbara Plant, Cell & Environment, Vol. 39, Issue 9 https://doi.org/10.1111/pce.12725	journal	June 2016
Measurements of methane emissions from natural gas gathering facilities and processing plants: measurement methods Roscioli, J. R.; Yacovitch, T. I.; Floerchinger, C. Atmospheric Measurement Techniques, Vol. 8, Issue 5 https://doi.org/10.5194/amt-8-2017-2015	journal	January 2015
Stable Carbon Isotope Fractionation by Methylotrophic Methanogenic Archaea Penger, Jörn; Conrad, Ralf; Blaser, Martin Applied and Environmental Microbiology, Vol. 78, Issue 21 https://doi.org/10.1128/AEM.01773-12	journal	August 2012
Methane, Carbon Dioxide and Nitrous Oxide Fluxes in Soil Profile under a Winter Wheat-Summer Maize Rotation in the North China Plain Wang, Yuying; Hu, Chunsheng; Ming, Hua PLoS ONE, Vol. 9, Issue 6 https://doi.org/10.1371/journal.pone.0098445	journal	June 2014
Differential effects of redox conditions on the decomposition of litter and soil organic matter Lin, Yang; Campbell, Ashley N.; Bhattacharyya, Amrita Biogeochemistry, Vol. 154, Issue 1 https://doi.org/10.1007/s10533-021-00790-y	journal	April 2021
An in situ method for real-time measurement of gas transport in soil: Monitoring of gas transport in soil Laemmel, T.; Maier, M.; Schack-Kirchner, H. European Journal of Soil Science, Vol. 68, Issue 2 https://doi.org/10.1111/ejss.12412	journal	March 2017
Design and performance of a dual-laser instrument for multiple isotopologues of carbon dioxide and water McManus, J. Barry; Nelson, David D.; Zahniser, Mark S. Optics Express, Vol. 23, Issue 5 https://doi.org/10.1364/OE.23.006569	journal	January 2015
Calling from distance: attraction of soil bacteria by plant root volatiles Schulz-Bohm, Kristin; Gerards, Saskia; Hundscheid, Maria The ISME Journal, Vol. 12, Issue 5 https://doi.org/10.1038/s41396-017-0035-3	journal	January 2018
Diffusion probe for gas sampling in undisturbed soil: Diffusion probe for soil gas sampling Petersen, S. O. European Journal of Soil Science, Vol. 65, Issue 5 https://doi.org/10.1111/ejss.12170	journal	September 2014
Linking NO and N 2 O emission pulses with the mobilization of mineral and organic N upon rewetting dry soils Leitner, Sonja; Homyak, Peter M.; Blankinship, Joseph C. Soil Biology and Biochemistry, Vol. 115 https://doi.org/10.1016/j.soilbio.2017.09.005	journal	December 2017
Profiling of soil volatile organic compounds after long-term application of inorganic, organic and organic-inorganic mixed fertilizers and their effect on plant growth Raza, Waseem; Mei, Xinlan; Wei, Zhong Science of The Total Environment, Vol. 607-608 https://doi.org/10.1016/j.scitotenv.2017.07.023	journal	December 2017
Life in Dry Soils: Effects of Drought on Soil Microbial Communities and Processes Schimel, Joshua P. Annual Review of Ecology, Evolution, and Systematics, Vol. 49, Issue 1 https://doi.org/10.1146/annurev-ecolsys-110617-062614	journal	November 2018
Interlaboratory assessment of nitrous oxide isotopomer analysis by isotope ratio mass spectrometry and laser spectroscopy: current status and perspectives: Interlaboratory assessment of nitrous oxide isotopomer analysis Mohn, Joachim; Wolf, Benjamin; Toyoda, Sakae Rapid Communications in Mass Spectrometry, Vol. 28, Issue 18 https://doi.org/10.1002/rcm.6982	journal	August 2014
Isotopocule analysis of biologically produced nitrous oxide in various environments: ISOTOPOCULE ANALYSIS OF BIOLOGICAL N Toyoda, Sakae; Yoshida, Naohiro; Koba, Keisuke Mass Spectrometry Reviews, Vol. 36, Issue 2 https://doi.org/10.1002/mas.21459	journal	April 2015
First real-time isotopic characterisation of N2O from chemodenitrification Wei, Jing; Ibraim, Erkan; Brüggemann, Nicolas Geochimica et Cosmochimica Acta, Vol. 267 https://doi.org/10.1016/j.gca.2019.09.018	journal	December 2019
Membrane probe array: Technique development and observation of CO2 and CH4 diurnal oscillations in peat profile Panikov, N. S.; Mastepanov, M. A.; Christensen, T. R. Soil Biology and Biochemistry, Vol. 39, Issue 7 https://doi.org/10.1016/j.soilbio.2007.01.034	journal	July 2007
The effect of soil drying on humus decomposition and nitrogen availability Birch, H. F. Plant and Soil, Vol. 10, Issue 1 https://doi.org/10.1007/BF01343734	journal	September 1958
Methane dynamics regulated by microbial community response to permafrost thaw McCalley, Carmody K.; Woodcroft, Ben J.; Hodgkins, Suzanne B. Nature, Vol. 514, Issue 7523 https://doi.org/10.1038/nature13798	journal	October 2014
Performance properties and applications of polytetrafluoroethylene (PTFE)—a review Dhanumalayan, E.; Joshi, Girish M. Advanced Composites and Hybrid Materials, Vol. 1, Issue 2 https://doi.org/10.1007/s42114-018-0023-8	journal	February 2018
A New Method for In Situ Measurements of Oxygen Isotopologues of Soil Water and Carbon Dioxide with High Time Resolution Gangi, Laura; Rothfuss, Youri; Ogée, Jerôme Vadose Zone Journal, Vol. 14, Issue 8 https://doi.org/10.2136/vzj2014.11.0169	journal	January 2015
The HITRAN2012 molecular spectroscopic database Rothman, L. S.; Gordon, I. E.; Babikov, Y. Journal of Quantitative Spectroscopy and Radiative Transfer, Vol. 130, p. 4-50 https://doi.org/10.1016/j.jqsrt.2013.07.002	journal	November 2013
Quantification of methanogenic pathways using stable carbon isotopic signatures: a review and a proposal Conrad, Ralf Organic Geochemistry, Vol. 36, Issue 5 https://doi.org/10.1016/j.orggeochem.2004.09.006	journal	May 2005
Isotopic composition of tropospheric and soil N ₂ O from successive depths of agricultural plots with contrasting crops and nitrogen amendments Rock, L.; Ellert, B. H.; Mayer, B. Journal of Geophysical Research, Vol. 112, Issue D18 https://doi.org/10.1029/2006JD008330	journal	January 2007
Effects of Long-Term CO2 Enrichment on Soil-Atmosphere CH4 Fluxes and the Spatial Micro-Distribution of Methanotrophic Bacteria Karbin, Saeed; Guillet, Cécile; Kammann, Claudia I. PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0131665	journal	July 2015
Temporal changes in soil pore space CO2 concentration and storage under permanent grassland Flechard, C. R.; Neftel, A.; Jocher, M. Agricultural and Forest Meteorology, Vol. 142, Issue 1 https://doi.org/10.1016/j.agrformet.2006.11.006	journal	January 2007
Challenges to incorporating spatially and temporally explicit phenomena (hotspots and hot moments) in denitrification models Groffman, Peter M.; Butterbach-Bahl, Klaus; Fulweiler, Robinson W. Biogeochemistry, Vol. 93, Issue 1-2 https://doi.org/10.1007/s10533-008-9277-5	journal	January 2009
Diffusion of 15N-labelled N2O into soil columns: a promising method to examine the fate of N2O in subsoils Clough, T. J.; Kelliher, F. M.; Wang, Y. P. Soil Biology and Biochemistry, Vol. 38, Issue 6 https://doi.org/10.1016/j.soilbio.2005.11.002	journal	June 2006
Evaluation of a New Reagent-Ion Source and Focusing Ion–Molecule Reactor for Use in Proton-Transfer-Reaction Mass Spectrometry Krechmer, Jordan; Lopez-Hilfiker, Felipe; Koss, Abigail Analytical Chemistry, Vol. 90, Issue 20 https://doi.org/10.1021/acs.analchem.8b02641	journal	September 2018
Sampling air from dung pats by silicone rubber diffusion chambers Holter, Peter Soil Biology and Biochemistry, Vol. 22, Issue 7 https://doi.org/10.1016/0038-0717(90)90143-N	journal	January 1990
A review of the molecular diffusivities of H2O, CO2, CH4, CO, O3, SO2, NH3, N2O, NO, and NO2 in air, O2 and N2 near STP Massman, W. J. Atmospheric Environment, Vol. 32, Issue 6 https://doi.org/10.1016/S1352-2310(97)00391-9	journal	March 1998
Equilibrium and Transport Properties of Gas Mixtures at Low Density: Eleven Polyatomic Gases and Five Noble Gases Bzowski, J.; Kestin, J.; Mason, E. A. Journal of Physical and Chemical Reference Data, Vol. 19, Issue 5 https://doi.org/10.1063/1.555867	journal	September 1990

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