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Salek MM, Carrara F, Zhou J, Stocker R, Jimenez‐Martinez J. Multiscale Porosity Microfluidics to Study Bacterial Transport in Heterogeneous Chemical Landscapes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310121. [PMID: 38445967 PMCID: PMC11132056 DOI: 10.1002/advs.202310121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Indexed: 03/07/2024]
Abstract
Microfluidic models are proving to be powerful systems to study fundamental processes in porous media, due to their ability to replicate topologically complex environments while allowing detailed, quantitative observations at the pore scale. Yet, while porous media such as living tissues, geological substrates, or industrial systems typically display a porosity that spans multiple scales, most microfluidic models to date are limited to a single porosity or a small range of pore sizes. Here, a novel microfluidic system with multiscale porosity is presented. By embedding polyacrylamide (PAAm) hydrogel structures through in-situ photopolymerization in a landscape of microfabricated polydimethylsiloxane (PDMS) pillars with varying spacing, micromodels with porosity spanning several orders of magnitude, from nanometers to millimeters are created. Experiments conducted at different porosity patterns demonstrate the potential of this approach to characterize fundamental and ubiquitous biological and geochemical transport processes in porous media. Accounting for multiscale porosity allows studies of the resulting heterogeneous fluid flow and concentration fields of transported chemicals, as well as the biological behaviors associated with this heterogeneity, such as bacterial chemotaxis. This approach brings laboratory studies of transport in porous media a step closer to their natural counterparts in the environment, industry, and medicine.
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Affiliation(s)
- M. Mehdi Salek
- Department of Biological Engineering, School of EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Francesco Carrara
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Jiande Zhou
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Microsystems LaboratoryInstitute of MicroengineeringSchool of EngineeringEPFLLausanneSwitzerland
| | - Roman Stocker
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Joaquin Jimenez‐Martinez
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Department of Water Resources and Drinking WaterEawagDubendorfSwitzerland
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2
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Lacroix EM, Aeppli M, Boye K, Brodie E, Fendorf S, Keiluweit M, Naughton HR, Noël V, Sihi D. Consider the Anoxic Microsite: Acknowledging and Appreciating Spatiotemporal Redox Heterogeneity in Soils and Sediments. ACS EARTH & SPACE CHEMISTRY 2023; 7:1592-1609. [PMID: 37753209 PMCID: PMC10519444 DOI: 10.1021/acsearthspacechem.3c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/07/2023] [Accepted: 07/21/2023] [Indexed: 09/28/2023]
Abstract
Reduction-oxidation (redox) reactions underlie essentially all biogeochemical cycles. Like most soil properties and processes, redox is spatiotemporally heterogeneous. However, unlike other soil features, redox heterogeneity has yet to be incorporated into mainstream conceptualizations of soil biogeochemistry. Anoxic microsites, the defining feature of redox heterogeneity in bulk oxic soils and sediments, are zones of oxygen depletion in otherwise oxic environments. In this review, we suggest that anoxic microsites represent a critical component of soil function and that appreciating anoxic microsites promises to advance our understanding of soil and sediment biogeochemistry. In sections 1 and 2, we define anoxic microsites and highlight their dynamic properties, specifically anoxic microsite distribution, redox gradient magnitude, and temporality. In section 3, we describe the influence of anoxic microsites on several key elemental cycles, organic carbon, nitrogen, iron, manganese, and sulfur. In section 4, we evaluate methods for identifying and characterizing anoxic microsites, and in section 5, we highlight past and current approaches to modeling anoxic microsites. Finally, in section 6, we suggest steps for incorporating anoxic microsites and redox heterogeneities more broadly into our understanding of soils and sediments.
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Affiliation(s)
- Emily M. Lacroix
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Meret Aeppli
- Institut
d’ingénierie de l’environnement (IIE), École Polytechnique Fédérale
de Lausanne, 1015 Lausanne, Switzerland
| | - Kristin Boye
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Eoin Brodie
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Scott Fendorf
- Department
of Earth System Science, Stanford University, Stanford, California 94305, United States
| | - Marco Keiluweit
- Institut
des Dynamiques de la Surface Terrestre (IDYST), Université de Lausanne, 1015 Lausanne, Switzerland
| | - Hannah R. Naughton
- Lawrence
Berkeley Laboratory, Earth and Environmental
Sciences Area, Berkeley, California 94720, United States
| | - Vincent Noël
- Environmental
Geochemistry Group, SLAC National Accelerator
Laboratory, Menlo Park, California 94025, United States
| | - Debjani Sihi
- Department
of Environmental Sciences, Emory University, Atlanta, Georgia 30322, United States
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3
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Guex I, Mazza C, Dubey M, Batsch M, Li R, van der Meer JR. Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding. PLoS Comput Biol 2023; 19:e1011402. [PMID: 37603551 PMCID: PMC10470959 DOI: 10.1371/journal.pcbi.1011402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/31/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
When bacterial species with the same resource preferences share the same growth environment, it is commonly believed that direct competition will arise. A large variety of competition and more general 'interaction' models have been formulated, but what is currently lacking are models that link monoculture growth kinetics and community growth under inclusion of emerging biological interactions, such as metabolite cross-feeding. In order to understand and mathematically describe the nature of potential cross-feeding interactions, we design experiments where two bacterial species Pseudomonas putida and Pseudomonas veronii grow in liquid medium either in mono- or as co-culture in a resource-limited environment. We measure population growth under single substrate competition or with double species-specific substrates (substrate 'indifference'), and starting from varying cell ratios of either species. Using experimental data as input, we first consider a mean-field model of resource-based competition, which captures well the empirically observed growth rates for monocultures, but fails to correctly predict growth rates in co-culture mixtures, in particular for skewed starting species ratios. Based on this, we extend the model by cross-feeding interactions where the consumption of substrate by one consumer produces metabolites that in turn are resources for the other consumer, thus leading to positive feedback in the species system. Two different cross-feeding options were considered, which either lead to constant metabolite cross-feeding, or to a regulated form, where metabolite utilization is activated with rates according to either a threshold or a Hill function, dependent on metabolite concentration. Both mathematical proof and experimental data indicate regulated cross-feeding to be the preferred model to constant metabolite utilization, with best co-culture growth predictions in case of high Hill coefficients, close to binary (on/off) activation states. This suggests that species use the appearing metabolite concentrations only when they are becoming high enough; possibly as a consequence of their lower energetic content than the primary substrate. Metabolite sharing was particularly relevant at unbalanced starting cell ratios, causing the minority partner to proliferate more than expected from the competitive substrate because of metabolite release from the majority partner. This effect thus likely quells immediate substrate competition and may be important in natural communities with typical very skewed relative taxa abundances and slower-growing taxa. In conclusion, the regulated bacterial interaction network correctly describes species substrate growth reactions in mixtures with few kinetic parameters that can be obtained from monoculture growth experiments.
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Affiliation(s)
- Isaline Guex
- Department of Mathematics, University of Fribourg, Fribourg, Switzerland
| | - Christian Mazza
- Department of Mathematics, University of Fribourg, Fribourg, Switzerland
| | - Manupriyam Dubey
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Maxime Batsch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Renyi Li
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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4
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Kratz AM, Maier S, Weber J, Kim M, Mele G, Gargiulo L, Leifke AL, Prass M, Abed RMM, Cheng Y, Su H, Pöschl U, Weber B. Reactive Nitrogen Hotspots Related to Microscale Heterogeneity in Biological Soil Crusts. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:11865-11877. [PMID: 35929951 PMCID: PMC9387110 DOI: 10.1021/acs.est.2c02207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Biocrusts covering drylands account for major fractions of terrestrial biological nitrogen fixation and release large amounts of gaseous reactive nitrogen (Nr) as nitrous acid (HONO) and nitric oxide (NO). Recent investigations suggested that aerobic and anaerobic microbial nitrogen transformations occur simultaneously upon desiccation of biocrusts, but the spatio-temporal distribution of seemingly contradictory processes remained unclear. Here, we explore small-scale gradients in chemical concentrations related to structural characteristics and organism distribution. X-ray microtomography and fluorescence microscopy revealed mixed pore size structures, where photoautotrophs and cyanobacterial polysaccharides clustered irregularly in the uppermost millimeter. Microsensor measurements showed strong gradients of pH, oxygen, and nitrite, nitrate, and ammonium ion concentrations at micrometer scales in both vertical and lateral directions. Initial oxygen saturation was mostly low (∼30%) at full water holding capacity, suggesting widely anoxic conditions, and increased rapidly upon desiccation. Nitrite concentrations (∼6 to 800 μM) and pH values (∼6.5 to 9.5) were highest around 70% WHC. During further desiccation they decreased, while emissions of HONO and NO increased, reaching maximum values around 20% WHC. Our results illustrate simultaneous, spatially separated aerobic and anaerobic nitrogen transformations, which are critical for Nr emissions, but might be impacted by future global change and land management.
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Affiliation(s)
- Alexandra Maria Kratz
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Stefanie Maier
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
- Institute
of Biology, Division of Plant Sciences, University of Graz, Graz 8010, Austria
| | - Jens Weber
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
- Institute
of Biology, Division of Plant Sciences, University of Graz, Graz 8010, Austria
| | - Minsu Kim
- Institute
of Biology, Division of Plant Sciences, University of Graz, Graz 8010, Austria
| | - Giacomo Mele
- Institute
for Agriculture and Forestry in the Mediterranean, National Council of Research, 80055 Portici, Italy
| | - Laura Gargiulo
- Institute
for Agriculture and Forestry in the Mediterranean, National Council of Research, 80055 Portici, Italy
| | - Anna Lena Leifke
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Maria Prass
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Raeid M. M. Abed
- College
of Science, Biology Department, Sultan Qaboos
University, P.O. Box 36, Al Khoud, Seeb 123, Sultanate of Oman
| | - Yafang Cheng
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Hang Su
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Ulrich Pöschl
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
| | - Bettina Weber
- Multiphase
Chemistry Department, Max Planck Institute
for Chemistry, Mainz 55128, Germany
- Institute
of Biology, Division of Plant Sciences, University of Graz, Graz 8010, Austria
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5
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Colombi T, Chakrawal A, Herrmann AM. Carbon supply-consumption balance in plant roots: effects of carbon use efficiency and root anatomical plasticity. THE NEW PHYTOLOGIST 2022; 233:1542-1547. [PMID: 34227122 DOI: 10.1111/nph.17598] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Tino Colombi
- Department of Soil & Environment, Swedish University of Agricultural Sciences, PO Box 7014, Uppsala, 75007, Sweden
| | - Arjun Chakrawal
- Department of Physical Geography, Stockholm University, Svante Arrhenius Väg 8C, Frescati, Stockholm, 10691, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, 10691, Sweden
| | - Anke Marianne Herrmann
- Department of Soil & Environment, Swedish University of Agricultural Sciences, PO Box 7014, Uppsala, 75007, Sweden
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6
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Markale I, Cimmarusti GM, Britton MM, Jiménez-Martínez J. Phase Saturation Control on Mixing-Driven Reactions in 3D Porous Media. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8742-8752. [PMID: 34106702 DOI: 10.1021/acs.est.1c01288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Transported chemical reactions in unsaturated porous media are relevant to environmental and industrial applications. Continuum scale models are based on equivalent parameters derived from analogy with saturated conditions and cannot appropriately account for incomplete mixing. It is also unclear how the third dimension controls mixing and reactions. We obtain three-dimensional (3D) images by magnetic resonance imaging using an immiscible nonwetting liquid as a second phase and a fast irreversible bimolecular reaction. We study the impact of phase saturation on the dynamics of mixing and the reaction front. We quantify the temporally resolved effective reaction rate and describe it using the lamellar theory of mixing, which explains faster than Fickian (t0.5) rate of product formation by accounting for the deformation of the mixing interface between the two reacting fluids. For a given Péclet, although stretching and folding of the reactive front enhance as saturation decreases, enhancing the product formation, the product formation is larger as saturation increases. After breakthrough, the extinction of the reaction takes longer as saturation decreases because of the larger nonmixed volume behind the front. These results are the basis for a general model to better predict reactive transport in unsaturated porous media not achievable by the current continuum paradigm.
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Affiliation(s)
- Ishaan Markale
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland
| | | | - Melanie M Britton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Joaquín Jiménez-Martínez
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zürich, Stefano-Franscini-Platz 5, 8093 Zürich, Switzerland
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7
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Microscale pH variations during drying of soils and desert biocrusts affect HONO and NH 3 emissions. Nat Commun 2019; 10:3944. [PMID: 31477724 PMCID: PMC6718665 DOI: 10.1038/s41467-019-11956-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 08/01/2019] [Indexed: 11/08/2022] Open
Abstract
Microscale interactions in soil may give rise to highly localised conditions that disproportionally affect soil nitrogen transformations. We report mechanistic modelling of coupled biotic and abiotic processes during drying of soil surfaces and biocrusts. The model links localised microbial activity with pH variations within thin aqueous films that jointly enhance emissions of nitrous acid (HONO) and ammonia (NH3) during soil drying well above what would be predicted from mean hydration conditions and bulk soil pH. We compared model predictions with case studies in which reactive nitrogen gaseous fluxes from drying biocrusts were measured. Soil and biocrust drying rates affect HONO and NH3 emission dynamics. Additionally, we predict strong effects of atmospheric NH3 levels on reactive nitrogen gas losses. Laboratory measurements confirm the onset of microscale pH localisation and highlight the critical role of micro-environments in the resulting biogeochemical fluxes from terrestrial ecosystems. The mechanisms that determine the composition of nitrogen gas emissions from soil remain unclear. A biocrust mechanistic model was developed to resolve puzzling dynamics of nitrous acid and ammonia emissions from drying soil pointing to previously unknown microscale pH zonation in thinning water films that affect soil biogeochemical fluxes.
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8
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Wang B, Brewer PE, Shugart HH, Lerdau MT, Allison SD. Soil aggregates as biogeochemical reactors and implications for soil-atmosphere exchange of greenhouse gases-A concept. GLOBAL CHANGE BIOLOGY 2019; 25:373-385. [PMID: 30412646 DOI: 10.1111/gcb.14515] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 08/03/2018] [Accepted: 11/02/2018] [Indexed: 05/14/2023]
Abstract
Soil-atmosphere exchange significantly influences the global atmospheric abundances of carbon dioxide (CO2 ), methane (CH4 ), and nitrous oxide (N2 O). These greenhouse gases (GHGs) have been extensively studied at the soil profile level and extrapolated to coarser scales (regional and global). However, finer scale studies of soil aggregation have not received much attention, even though elucidating the GHG activities at the full spectrum of scales rather than just coarse levels is essential for reducing the large uncertainties in the current atmospheric budgets of these gases. Through synthesizing relevant studies, we propose that aggregates, as relatively separate micro-environments embedded in a complex soil matrix, can be viewed as biogeochemical reactors of GHGs. Aggregate reactivity is determined by both aggregate size (which determines the reactor size) and the bulk soil environment including both biotic and abiotic factors (which further influence the reaction conditions). With a systematic, dynamic view of the soil system, implications of aggregate reactors for soil-atmosphere GHG exchange are determined by both an individual reactor's reactivity and dynamics in aggregate size distributions. Emerging evidence supports the contention that aggregate reactors significantly influence soil-atmosphere GHG exchange and may have global implications for carbon and nitrogen cycling. In the context of increasingly frequent and severe disturbances, we advocate more analyses of GHG activities at the aggregate scale. To complement data on aggregate reactors, we suggest developing bottom-up aggregate-based models (ABMs) that apply a trait-based approach and incorporate soil system heterogeneity.
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Affiliation(s)
- Bin Wang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia
| | - Paul E Brewer
- Smithsonian Environmental Research Center, Edgewater, Maryland
| | - Herman H Shugart
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia
| | - Manuel T Lerdau
- Department of Environmental Sciences, University of Virginia, Charlottesville, Virginia
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
- Department of Earth System Science, University of California, Irvine, California
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9
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To what extent do uncertainty and sensitivity analyses help unravel the influence of microscale physical and biological drivers in soil carbon dynamics models? Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Yan Z, Bond-Lamberty B, Todd-Brown KE, Bailey VL, Li S, Liu C, Liu C. A moisture function of soil heterotrophic respiration that incorporates microscale processes. Nat Commun 2018; 9:2562. [PMID: 29967415 PMCID: PMC6028431 DOI: 10.1038/s41467-018-04971-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 06/04/2018] [Indexed: 11/19/2022] Open
Abstract
Soil heterotrophic respiration (HR) is an important source of soil-to-atmosphere CO2 flux, but its response to changes in soil water content (θ) is poorly understood. Earth system models commonly use empirical moisture functions to describe the HR–θ relationship, introducing significant uncertainty in predicting CO2 flux from soils. Generalized, mechanistic models that address this uncertainty are thus urgently needed. Here we derive, test, and calibrate a novel moisture function, fm, that encapsulates primary physicochemical and biological processes controlling soil HR. We validated fm using simulation results and published experimental data, and established the quantitative relationships between parameters of fm and measurable soil properties, which enables fm to predict the HR–θ relationships for different soils across spatial scales. The fm function predicted comparable HR–θ relationships with laboratory and field measurements, and may reduce the uncertainty in predicting the response of soil organic carbon stocks to climate change compared with the empirical moisture functions currently used in Earth system models. Empirical moisture functions that describe the relationship between soil heterotrophic respiration and moisture introduce considerable uncertainty in soil CO2 flux predictions. Here, the authors derive a process-based moisture function by incorporating mechanisms that control soil heterotrophic respiration.
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Affiliation(s)
- Zhifeng Yan
- Institute of Surface-Earth System Science, Tianjin University, 300072, Tianjin, China
| | - Ben Bond-Lamberty
- Pacific Northwest National Laboratory-University of Maryland Joint Global Climate Change Research Institute, College Park, MD, 20740, USA
| | | | | | - SiLiang Li
- Institute of Surface-Earth System Science, Tianjin University, 300072, Tianjin, China
| | - CongQiang Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 550081, Guiyang, China
| | - Chongxuan Liu
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China.
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