Subsurface geochemical and biological transformations often influence fluid flow by altering the pore space morphology and related hydrologic properties such as porosity and permeability. In most coupled-processes models changes in porosity are inferred from geochemical and biological process models using mass-balance. The corresponding evolution of permeability is estimated using (semi-) empirical porosity–permeability functions such as the Kozeny–Carman equation or power-law functions. These equations typically do not account for the heterogeneous spatial distribution and morphological irregularities of the geochemical precipitates and biomass. As a result, predictions of permeability evolution are generally unsatisfactory. In this communication, we demonstrate the significance of pore-scale precipitate distribution on porosity–permeability relations using high resolution simulations of fluid flow through a single pore interspersed with crystals. Based on these simulations, we propose a modification to the Kozeny–Carman model that accounts for the shape of the deposits. Limited comparison with published experimental data suggests the plausibility of the proposed conceptual model.

@article{p2012-Ghezzehei,
  author = {Ghezzehei, T. A.},
  date-modified = {2018-05-27 20:41:59 +0000},
  doi = {10.1016/j.advwatres.2011.12.015},
  journal = {Advances in Water Resources},
  status = {published},
  keywords = {Porosity, Permeability, Clogging, Coupled processes, Mineral precipitation},
  pages = {1-6},
  researchgate = {https://www.researchgate.net/publication/249314234_Linking_sub-pore_scale_heterogeneity_of_biological_and_geochemical_deposits_with_changes_in_permeability},
  title = {Linking sub-pore scale heterogeneity of biological and geochemical deposits with changes in permeability},
  volume = {39},
  year = {2012},
  bdsk-url-1 = {https://doi.org/10.1016/j.advwatres.2011.12.015}
}

Most plants derive their water and nutrient needs from soils, where the resources are often scarce, patchy, and ephemeral. In natural environments, it is not uncommon for plant roots to encounter mismatched patches of water-rich and nutrient-rich regions. Such an uneven distribution of resources necessitates plants to rely on strategies that allow them to explore and acquire nutrients from relatively dry patches. We conducted a laboratory study to provide a mechanistic understanding of the biophysical factors that enable this adaptation. We grew plants in split-root pots that permitted precisely controlled spatial distributions of resources. The results demonstrated that spatial mismatch of water and nutrient availability does not cost plant productivity compared to matched distributions. Specifically, we showed that nutrient uptake is not reduced by overall soil dryness, provided that the whole plant has access to sufficient water elsewhere in the root zone. Essential strategies include extensive root proliferation towards nutrient-rich dry soil patches that allows rapid nutrient capture from brief pulses. Using high-frequency water potential measurements, we also observed nocturnal water release by roots that inhabit dry and nutrient-rich soil patches. Soil water potential gradient is the primary driver of this transfer of water from wet to dry soil parts of the root zone, which is commonly known as hydraulic redistribution (HR). The occurrence of HR prevents the soil drying from approaching the permanent wilting point, and thus supports root functions and enhance nutrient availability. Our results indicate that roots facilitate HR by increasing root-hair density and length and deposition of organic coatings that alter water retention. Therefore, we conclude that biologically-controlled root adaptation involves multiple strategies that compensate for nutrient acquisition under mismatched resource distributions. Based on our findings, we proposed a nature-inspired nutrient management strategy for significantly curtailing water pollution from intensive agricultural systems.

@article{P2020-Yan,
  title = {Root uptake under mismatched distributions of water and nutrients in the root zone},
  author = {Yan, Jing and Bogie, Nathaniel A. and Ghezzehei, Teamrat A.},
  journal = {Biogeosciences},
  volume = {17},
  pages = {6377–6392},
  status = {published},
  doi = {10.5194/bg-17-6377-2020},
  data = {doi:10.6071/M39M2T},
  pdf = {https://bg.copernicus.org/articles/17/6377/2020/bg-17-6377-2020.pdf},
  mendeley = {https://www.mendeley.com/catalogue/f48d8444-28ae-390c-a09d-07f73a0aadb6/},
  year = {2020}
}

Soil water status is one of the most important environmental factors that control microbial activity and rate of soil organic matter decomposition (SOM). Its effect can be partitioned into effect of water energy status (water potential) on cellular activity, effect of water volume on cellular motility and aqueous diffusion of substrate and nutrients, as well as effect of air content and gas-diffusion pathways on concentration of dissolved oxygen. However, moisture functions widely used in SOM decomposition models are often based on empirical functions rather than robust physical foundations that account for these disparate impacts of soil water. The contributions of soil water content and water potential vary from soil to soil according to the soil water characteristic (SWC), which in turn is strongly dependent on soil texture and structure.The overall goal of this study is to introducea physically based modelling framework of aerobic microbial respiration that incorporates the role of SWC under arbitrary soil moisture status.The model was tested by compariing it with published datasets of SOM decomposition under laboratory conditions.

@article{p2019-Ghezzehei-et-al,
  author = {Ghezzehei, Teamrat A. and Sulman, Benjamin and Arnold, Chelsea L. and Bogie, Nathaniel A. and Berhe, Asmeret Asefaw},
  doi = {10.5194/bg-16-1187-2019},
  data = {10.6084/m9.figshare.7749332},
  pdf = {https://bg.copernicus.org/articles/16/1187/2019/bg-16-1187-2019.pdf},
  sort-word = {CO2 flux, Soil respiration, Soil Carbon, aggregation, modeling,biogeoscience},
  journal = {Biogeosciences},
  status = {published},
  volume = {16},
  pages = {1187-1209},
  month = mar,
  title = {On the role of soil water retention characteristic on aerobic microbial respiration},
  mendeley = {https://www.mendeley.com/catalogue/4b76b8fa-36d3-3812-bd2f-086f3faaab4f/},
  year = {2019}
}

A long-term annual crop study in Five Points, California, shows that the combined use of no-tillage, surface residue retention, and cover crops improves soil health compared to conventional practices common to the region. Several chemical, biological, and physical soil health indicators were improved when these practices were combined. Our data suggest that farmers stand to gain multiple synergistic benefits from the integrated use of these practices by increasing soil structural stability, water infiltration and storage, and agroecosystem biodiversity, and improving the efficiencies of the carbon, nitrogen, and water cycles of their production systems.

@article{p2024_micthell,
  title = {No-tillage, surface residue retention, and cover crops improved San Joaquin Valley soil health in the long term},
  author = {Mitchell, Jeffrey P. and Cappellazzi, Shannon B. and Schmidt, Rad and Chiartas, Jessica and Shrestha, Anil and Reicosky, Don and Ferris, Howard and Zhang, Xioake and Ghezzehei, Teamrat and Araya, Samuel and Kelly, Courtney and Fonte, Steve and Light, Sarah and Liles, Garrett and Willey, Tom and Roy, Robert and Bottens, Monte and Crum, Cary and Horwath, William R. and Koch, Geoffrey M. and Scow, Kate M.},
  pages = {},
  doi = {10.3733/001c.94714},
  journal = {California Agriculture},
  year = {2024}
}

To meet the requirements of California’s Sustainable Groundwater Management Act, there is a critical need for crop production strategies with less reliance on irrigation from surface and groundwater sources. One strategy for improving agricultural water use efficiency is reducing tillage and maintaining residues on the soil surface. We evaluated high residue no-till versus standard tillage in the San Joaquin Valley with and without cover crops on the yields of two crops, garbanzo and sorghum, for 4 years. The no-till treatment had no primary or secondary tillage. Sorghum yields were similar in no-till and standard tillage systems while no-till garbanzo yields matched or exceeded those of standard tillage, depending on the year. Cover crops had no effect on crop yields. Soil cover was highest under the no-till with cover crop system, averaging 97% versus 5% for the standard tillage without cover crop system. Our results suggest that garbanzos and sorghum can be grown under no-till practices in the San Joaquin Valley without loss of yield.

@article{Mitchell-2021,
  author = {Mitchell, Jeffrey P. and Shrestha, Anil and Epstein, Lynn and Dahlberg, Jeffery A. and Ghezzehei, Teamrat and Araya, Samuel and Richter, Brian and Kaur, Sukhwinder and Henry, Peter and Munk, Daniel S. and Light, Sarah and Bottens, Monte and Zaccaria, Daniele},
  title = {No-tillage sorghum and garbanzo yields match or exceed standard tillage yields},
  journal = {California Agriculture},
  year = {2022},
  status = {published},
  volume = {75},
  number = {3},
  pages = {112-120},
  pdf = {https://calag.ucanr.edu/archive/?type=pdf&article=ca.2021a0017},
  doi = {10.3733/ca.2021a0017}
}

A new UV spectrophotometry based method for determining the concentration and carbon content of carbohydrate solution was developed. This method depends on the inherent UV absorption potential of hydrolysis byproducts of carbohydrates formed by reaction with concentrated sulfuric acid (furfural derivatives). The proposed method is a major improvement over the widely used Phenol-Sulfuric Acid method developed by DuBois, Gilles, Hamilton, Rebers, and Smith (1956). In the old method, furfural is allowed to develop color by reaction with phenol and its concentration is detected by visible light absorption. Here we present a method that eliminates the coloration step and avoids the health and environmental hazards associated with phenol use. In addition, avoidance of this step was shown to improve measurement accuracy while significantly reducing waiting time prior to light absorption reading. The carbohydrates for which concentrations and carbon content can be reliably estimated with this new rapid Sulfuric Acid-UV technique include: monosaccharides, disaccharides and polysaccharides with very high molecular weight.

@article{p2013-Albalasmeh-Berhe-Ghezzehei,
  author = {Albalasmeh, Ammar A. and Berhe, Asmeret Asefaw and Ghezzehei, Teamrat A.},
  date-modified = {2018-05-31 13:28:00 +0000},
  doi = {10.1016/j.carbpol.2013.04.072},
  journal = {Carbohydrate Polymers},
  status = {published},
  number = {2},
  pages = {253-61},
  researchgate = {https://www.researchgate.net/publication/255176344_A_new_method_for_rapid_determination_of_carbohydrate_and_total_carbon_concentrations_using_UV_spectrophotometry},
  sort-word = {method},
  title = {A new method for rapid determination of carbohydrate and total carbon concentrations using UV spectrophotometry},
  volume = {97},
  year = {2013},
  bdsk-url-1 = {https://doi.org/10.1016/j.carbpol.2013.04.072}
}

Advancing our understanding of Earth system dynamics (ESD) depends on the development of models and other analytical tools that apply physical, biological, and chemical data. This ambition to increase understanding and develop models of ESD based on site observations was the stimulus for creating the networks of Long-Term Ecological Research (LTER), Critical Zone Observatories (CZOs), and others. We organized a survey, the results of which identified pressing gaps in data availability from these networks, in particular for the future development and evaluation of models that represent ESD processes, and provide insights for improvement in both data collection and model integration. From this survey overview of data applications in the context of LTER and CZO research, we identified three challenges: (1) widen application of terrestrial observation network data in Earth system modelling, (2) develop integrated Earth system models that incorporate process representation and data of multiple disciplines, and (3) identify complementarity in measured variables and spatial extent, and promoting synergies in the existing observational networks. These challenges lead to perspectives and recommendations for an improved dialogue between the observation networks and the ESD modelling community, including co-location of sites in the existing networks and further formalizing these recommendations among these communities. Developing these synergies will enable cross-site and cross-network comparison and synthesis studies, which will help produce insights around organizing principles, classifications, and general rules of coupling processes with environmental conditions.

@article{p2018-Baatz,
  author = {Baatz, Roland and Sullivan, Pamela L. and Li, Li and Weintraub, Samantha and Loescher, Henry W. and Mirtl, Michael and Groffman, Peter M. and Wall, Diana H. and Young, Michael and White, Tim and Wen, Hang and Zacharias, Steffen and K{\~A}¼hn, Ingolf and Tang, Jianwu and Gaillardet, J{\'{e}}r{\^{o}}me and Braud, Isabelle and Flores, Alejandro N. and Kumar, Praveen and Lin, Henry and Ghezzehei, Teamrat and Gholz, Henry L. and Vereecken, Harry and Looy, Kris Van},
  date-modified = {2018-11-14 14:16:32 -0800},
  doi = {10.5194/esd-9-593-2018},
  journal = {Earth System Dynamics},
  status = {published},
  month = may,
  pages = {593-609},
  pdf = {https://www.earth-syst-dynam.net/9/593/2018/esd-9-593-2018.pdf},
  researchgate = {https://www.researchgate.net/publication/325313872_Steering_operational_synergies_in_terrestrial_observation_networks_opportunity_for_advancing_Earth_system_dynamics_modelling},
  sort-word = {synthesis},
  title = {Integration of terrestrial observational networks: opportunity for advancing Earth system dynamics modelling},
  volume = {9},
  year = {2018},
  bdsk-url-1 = {https://doi.org/10.5194%2Fesd-2017-94},
  bdsk-url-2 = {http://dx.doi.org/10.5194/esd-2017-94},
  bdsk-url-3 = {https://doi.org/10.5194/esd-9-593-2018}
}

Plant roots alter soil properties at an expensive physiological cost by releasing large quantities of organic carbon (rhizodeposition). The role of rhizodeposits in enhancing beneficial microbial activity and bio-geochemical nutrient mobilization is widely appreciated. But the role of rhizodeposits in water uptake has started gaining modest attention only recently. In this study we present a single root model, which demonstrates the possibility for rhizodeposits to create built-in water potential gradient. The conceptual basis for this model rests on three premises: (a) rhizodeposits are distributed in declining profile with distance from the root surface, (b) considerable fraction of rhizodeposits are strongly adhered to soil particles, and (c) rhizodeposits have the ability to retain water. Thus, variable concentration of affixed rhizodeposits results in a gradient of water potential without commensurate decline in water content with proximity to root surface. To corroborate premises (b) and (c), we conducted experiments using synthetic analog of rhizodeposits (Polygalacturonic Acid, PGA) and glass-bead and sand media. Envi-ronmental scanning electron microscopy was utilized to show affixation of PGA on glass beads during drying as well as pore-scale enhanced water retention. Macroscopic enhancement of water retention was characterized by dew-point potentiametry. We simulated water uptake by a root at constant potential transpiration rates representing high atmospheric demand and considered three distinct spatial distri-bution patterns of rhizodeposits as well as a control (without rhizodeposition). The model simulations indicate that the benefit of such variable distribution of exudates is more pronounced when (a) the poten-tial water uptake rate is high or (b) the rhizodeposits are constrained to a narrow volume of rhizosphere soil.

@article{p2015-Ghezzehei-Albalasmeh,
  author = {Ghezzehei, Teamrat A. and Albalasmeh, Ammar A.},
  doi = {10.1016/j.ecolmodel.2014.10.028},
  journal = {Ecological Modeling},
  status = {published},
  keywords = {Rhizosphere, Roots, Exudates, Water-uptake},
  month = feb,
  pages = {53-63},
  researchgate = {https://www.researchgate.net/publication/271327580_Spatial_distribution_of_rhizodeposits_provides_built-in_water_potential_gradient_in_the_rhizosphere},
  sort-word = {rhizosphere, modeling},
  title = {Spatial distribution of rhizodeposits provides built-in water potential gradient in the rhizosphere},
  volume = {298},
  year = {2015}
}

Livestock are the largest source of anthropogenic methane (CH4) emissions, and in intensive dairy systems, manure management can contribute half of livestock CH4. Recent policies such as California’s short-lived climate pollutant reduction law (SB 1383) and the Global Methane Pledge call for cuts to livestock CH4 by 2030. However, investments in CH4 reduction strategies are primarily aimed at liquid dairy manure, whereas stockpiled solids remain a large source of CH4. Here, we measure the CH4 and net greenhouse gas reduction potential of dairy manure biochar-composting, a novel manure management strategy, through a composting experiment and life-cycle analysis. We found that biochar-composting reduces CH4 by 79%, compared to composting without biochar. In addition to reducing CH4 during composting, we show that the added climate benefit from biochar production and application contributes to a substantially reduced life-cycle global warming potential for biochar-composting: −535 kg CO2e Mg–1 manure compared to −194 kg CO2e Mg–1 for composting and 102 kg CO2e Mg–1 for stockpiling. If biochar-composting replaces manure stockpiling and complements anaerobic digestion, California could meet SB 1383 with 132 less digesters. When scaled up globally, biochar-composting could mitigate 1.59 Tg CH4 yr–1 while doubling the climate change mitigation potential from dairy manure management.

@article{Harrison2022,
  author = {Harrison, Brendan and Gao, Si and Gonzales, Melinda and Thao, Touyee and Bischak, Elena and Ghezzehei, Teamrat and Berhe, Asmeret Asefaw and Diaz, Gerardo and Ryals, Rebecca},
  title = {Dairy Manure Co-composting with Wood Biochar Plays a Critical Role in Meeting Global Methane Goals},
  year = {2022},
  journal = {Environmental Science and Technology},
  volume = {xx-xxxx},
  pages = {},
  abbr = {EST},
  doi = {10.1021/acs.est.2c03467},
  mendeley = {https://www.mendeley.com/catalogue/2d17f05f-9450-3f96-95da-7c06b4153c61/}
}

Soil compaction represents one of the most ubiquitous environmental impacts of human development, decreasing bulk-scale soil porosity and hydraulic conductivity, thereby reducing soil productivity and fertility. At the aggregate-scale however, this study shows that natural root-induced compaction increases contact areas between aggregates, leading to an increase in unsaturated hydraulic conductivity of the soils adjacent to the roots. Contrary to intuition, water flow may therefore be locally enhanced due to root-induced compaction. This study investigates these processes by using recent advances in X-ray microtomography (XMT) imaging and numerical water flow modeling to show evolution in interaggregate contact and its implications for water flow between aggregates under partially saturated conditions. Numerical modeling showed that the effective hydraulic conductivity of a pair of aggregates undergoing uniaxial deformation increased following a nonlinear relationship as the interaggregate contact area increased due to increasing aggregate deformation. Numerical modeling using actual XMT images of aggregated soil around a root surrogate demonstrated how root-induced deformation increases unsaturated water flow toward the root, providing insight into the growth, function, and water uptake patterns of roots in natural soils.

@article{p2011-Aravena-et-al,
  author = {Aravena, Jazmin E. and Berli, Markus and Ghezzehei, Teamrat A. and Tyler, Scott W.},
  date-modified = {2018-05-27 20:36:18 +0000},
  doi = {10.1021/es102566j},
  journal = {Environmental Science and Technology},
  status = {published},
  number = {2},
  pages = {425-431},
  researchgate = {https://www.researchgate.net/publication/49648890_Effects_of_Root-Induced_Compaction_on_Rhizosphere_Hydraulic_Properties_-_X-ray_Microtomography_Imaging_and_Numerical_Simulations},
  title = {Effects of Root-Induced Compaction on Rhizosphere Hydraulic Properties - X-ray Microtomography Imaging and Numerical Simulations},
  volume = {45},
  year = {2011},
  bdsk-url-1 = {https://doi.org/10.1021/es102566j}
}

Soil is a complex ecosystem within which many species interact and where physicochemical and geological processes occur at different spatiotemporal scales, with strong interactions taking place between ecological and management processes. Soil processes affect the qualities of the food and water that we eat and drink, the regulation of greenhouse gases, and are the foundation of our habitation and transportation infrastructures. However, it is estimated that over 2 billion hectares of lands are degraded, with a further 12 million hectares degraded each year causing the annual loss of 24 billion tons of fertile soil. Soil degradation negatively affects the well-being of over 3 billion people, costing more than 10% of the annual global GDP via the loss of ecosystem services, and reducing the productivity of 23% of the global terrestrial area. The sustainable management of soil ecosystems is, therefore, fundamental to global food, water, and energy security, especially under increasingly unpredictable weather patterns caused by climate change. The land–water–food–energy nexus is central to sustainable development and soil inextricably links these critical domains. Stakeholders and decision-makers in all four domains are necessarily focusing on the effects of soil degradation on climate change, water resource management, and food production as key to the development of sustainable agricultural practices and policies. A properly integrated approach to managing rural soils is thus required to ensure global water, food, and energy security, whilst increasing and protecting biodiversity. This special issue collects 15 papers on recent advances on soil physical-, hydrological-, and biological processes, and linkages with agroecosystem sustainability across experiments, field observations, and methodological breakthroughs.

@article{wang2023soil,
  title = {Soil physics matters for the land--water--food--climate nexus and sustainability},
  author = {Wang, Gang and Liu, Ying and Yan, Zhifeng and Chen, Dingjiang and Fan, Jun and Ghezzehei, Teamrat A},
  journal = {European Journal of Soil Science},
  volume = {74},
  number = {6},
  pages = {e13444},
  doi = {10.1111/ejss.13444},
  pdf = {https://bsssjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/ejss.13444},
  year = {2023},
  sort-word = {editorial}
}

Soil science is one of the least diverse fields within science, technology, engineering and mathematics (STEM). Because demographics of groups and institutions provide a window into the culture, climate, equity and inclusion of minoritized scholars, we discuss how lack of diversity continues to affect our science and the scientific community, and its implications for the welfare of the global population. We highlight the role of antiracist practices and policies for improving workplace climate and thereby developing a diverse and inclusive scientific community. We present this article as a starting point for discussions on issues of race and racism in our scientific community and institutions. Highlights Soil science remains one of the least diverse fields in STEM. Workplace climate plays a major role in perpetuating the lack of diversity within soil science and other fields within geosciences. Incorporation of antiracist practices and policies is urgently needed to reverse the current trend and improve representation in our scientific community.

@article{p2021-Berhe-Ghezzehei,
  author = {Berhe, Asmeret Asefaw and Ghezzehei, Teamrat A.},
  title = {Race and racism in soil science (Invited Commentary)},
  journal = {European Journal of Soil Science},
  volume = {},
  year = {2020},
  number = {1-6},
  pages = {},
  keywords = {antiracist, diversity, hostile climates, race, racism},
  doi = {10.1111/ejss.13078},
  pdf = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/ejss.13078},
  mendeley = {https://www.mendeley.com/catalogue/ece86dc5-ed78-3325-96be-74bcc85c7a9f/},
  status = {published}
}

Machine learning (ML) applications in soil science have significantly increased over the past two decades, reflecting a growing trend towards data-driven research addressing soil security. This extensive application has mainly focused on enhancing predictions of soil properties, particularly soil organic carbon, and improving the accuracy of digital soil mapping (DSM). Despite these advancements, the application of ML in soil science faces challenges related to data scarcity and the interpretability of ML models. There is a need for a shift towards Soil Science-Informed ML (SoilML) models that use the power of ML but also incorporate soil science knowledge in the training process to make predictions more reliable and generalisable. This paper proposes methodologies for embedding ML models with soil science knowledge to overcome current limitations. Incorporating soil science knowledge into ML models involves using observational priors to enhance training datasets, designing model structures which reflect soil science principles, and supervising model training with soil science-informed loss functions. The informed loss functions include observational constraints, coherency rules such as regularisation to avoid overfitting, and prior or soil-knowledge constraints that incorporate existing information about the parameters or outputs. By way of illustration, we present examples from four fields: digital soil mapping, soil spectroscopy, pedotransfer functions, and dynamic soil property models. We discuss the potential to integrate process-based models for improved prediction, the use of physics-informed neural networks, limitations, and the issue of overparametrisation. These approaches improve the relevance of ML predictions in soil science and enhance the models’ ability to generalise across different scenarios while maintaining soil science principles, transparency and reliability.

@article{MINASNY2024117094,
  title = {Soil Science-Informed Machine Learning},
  journal = {Geoderma},
  volume = {452},
  pages = {117094},
  year = {2024},
  issn = {0016-7061},
  doi = {https://doi.org/10.1016/j.geoderma.2024.117094},
  url = {https://www.sciencedirect.com/science/article/pii/S0016706124003239},
  author = {Minasny, Budiman and Bandai, Toshiyuki and Ghezzehei, Teamrat A. and Huang, Yin-Chung and Ma, Yuxin and McBratney, Alex B. and Ng, Wartini and Norouzi, Sarem and Padarian, Jose and Rudiyanto and Sharififar, Amin and Styc, Quentin and Widyastuti, Marliana},
  keywords = {Artificial Intelligence, Process-based models, Physics Informed Neural Networks, Informed Machine Learning, Mechanistic models, Pedology}
}

The effect of irrigation with treated wastewater (TWW) on soil physico-chemical and hydraulic properties was evaluated in this study. Field treatments were: non-irrigated (rain-fed) plot (control), rain-fed plot for the first three years and irrigated with TWW for the last two years (2 yr) and plot irrigated with TWW for five years (5 yr). Soil samples were collected from two depth intervals (0–15 and 15–30 cm) in five replicates. Irrigation with TWW significantly increased aggregate stability (AS), exchangeable sodium percentage (ESP), organic matter (OM), and electrical conductivity (EC). Both hydraulic conductivity (HC) and cumulative infiltration (F(t)) were decreased significantly with TWW use and period of application. Moreover, reduction of HC at different tension revealed that pore clogging occurred at both, macro and micro scale. Scanning electron microscopy (SEM) images showed that soil pores were clogged partially and/or fully as a result of suspended particulates and organic matter. Enhanced AS of treated areas indicated that infiltration was more affected by pore clogging than soil dispersion and swelling.

@article{p2016-Gharaibeh-et-al,
  author = {Gharaibeh, Mamoun A. and Ghezzehei, Teamrat A. and Albalasmeh, Ammar A. and Alghzawi, Ma{extquotesingle}in Z.},
  date-modified = {2018-05-27 19:55:55 +0000},
  journal = {Geoderma},
  status = {published},
  keywords = {Aggregate stability, SEM, Infiltration rate, Hydraulic conductivity, Pore clogging},
  month = aug,
  pages = {33--40},
  doi = {10.1016/j.geoderma.2016.04.011},
  publisher = {Elsevier {BV}},
  sort-word = {environmental quality},
  title = {Alteration of physical and chemical characteristics of clayey soils by irrigation with treated waste water},
  volume = {276},
  year = {2016}
}

Low-severity wildfires and prescribed burns have been steadily increasing for over three decades, currently accounting for more than half of total burned area in the Southwestern United States. Most observations immediately after low-severity burns report little adverse impacts on soil properties and processes. In a few studies, however, significant deterioration of soil structure has been observed several months after such fires. Here we show that rapid vaporization of pore water during low-severity burns raises pneumatic gas pressure inside large aggregates (20-30 mm) to damaging levels; on the order of aggregate tensile strength and high-enough to cause visco-plastic deformation. However, the impact on soil structure was not immediately perceptible. This suggests that other natural forces, such as wetting-drying and thermal cycles, are required to disrupt the weakened aggregates. Thus, adverse consequences of the suggested mechanism on soil processes and services (e.g., infiltration, erodibility, and organic matter protection) are likely overlooked.

@article{p2018-Jian-Berli-Ghezzehei,
  author = {Jian, Mathew and Berli, Markus and Ghezzehei, Teamrat A.},
  data = {10.6084/m9.figshare.6349469.v1},
  date-added = {2018-05-27 06:01:51 +0000},
  date-modified = {2018-11-14 14:17:28 -0800},
  doi = {10.1029/2018GL078053},
  journal = {Geophysical Research Letters},
  status = {published},
  month = may,
  number = {5553-5561},
  sort-word = {soil structure, aggregation},
  title = {Soil Structural Degradation during Low-severity Burns},
  volume = {45},
  year = {2018},
  bdsk-url-1 = {https://doi.org/10.1029/2018GL078053}
}

Manure is a leading source of methane (CH4), nitrous oxide (N2O), and ammonia (NH3) emissions, and alternative manure management practices can help society meet climate goals and mitigate air pollution. Recent studies show that biochar-composting can substantially reduce emissions from manure. However, most studies test only one type of biochar applied at a single application rate, leading to high variation in emission reductions between studies. Here, we measured greenhouse gas and NH3 emissions during biochar-composting of dairy manure with biochar applied at 5% or 20%, by mass, and made from walnut shells, almond shells, or almond clippings. We found little difference in emissions between biochar type. However, we found that the 20% application rates increased CH4 emissions and decreased N2O and NH3 emissions, resulting in a net reduction in global warming potential (GWP). We attribute this result to biochar increasing the formation of compost aggregates, which likely acted as anaerobic reactors for methanogenesis and complete denitrification. Biochar may have further fueled CH4 production and N2O consumption by acting as an electron shuttle within aggregates. We recommend lower application rates, as we found that the 5% treatments in our study led to a similar reduction in GWP without increasing CH4 emissions.

@article{harrison2024methane,
  title = {Methane and nitrous oxide emissions during biochar-composting are driven by biochar application rate and aggregate formation},
  author = {Harrison, Brendan P and Gao, Si and Thao, Touyee and Gonzales, Melinda L and Williams, Kennedy L and Scott, Natalie and Hale, Lauren and Ghezzehei, Teamrat and Diaz, Gerardo and Ryals, Rebecca A},
  journal = {Global Change Biology Bioenergy},
  volume = {16},
  number = {1},
  pages = {e13121},
  doi = {10.1111/gcbb.13121},
  pdf = {https://onlinelibrary.wiley.com/doi/epdf/10.1111/gcbb.13121},
  year = {2024},
  keywords = {ammonia, biochar, climate change mitigation, composting, livestock, manure, methane, nitrous oxide},
  sort-word = {biochar, agroecology}
}

Organic amendments, such as compost and biochar, mitigate the environmental burdens associated with wasting organic resources and close nutrient loops by capturing, transforming, and resupplying nutrients to soils. While compost or biochar application to soil can enhance an agroecosystem’s capacity to store carbon and produce food, there have been few field studies investigating the agroecological impacts of amending soil with biochar co-compost, produced through the composting of nitrogen-rich organic material, such as manure, with carbon-rich biochar. Here, we examine the impact of biochar co-compost on soil properties and processes by conducting a field study in which we compare the environmental and agronomic impacts associated with the amendment of either dairy manure co-composted with biochar, dairy manure compost, or biochar to soils in a winter wheat cropping system. Organic amendments were applied at equivalent C rates (8 Mg C ha−1). We found that all three treatments significantly increased soil water holding capacity and total plant biomass relative to the no-amendment control. Soils amended with biochar or biochar co-compost resulted in significantly less greenhouse gas emissions than the compost or control soils. Biochar co-compost also resulted in a significant reduction in nutrient leaching relative to the application of biochar alone or compost alone. Our results suggest that biochar co-composting could optimize organic resource recycling for climate change mitigation and agricultural productivity while minimizing nutrient losses from agroecosystems.

@article{GAO2023,
  title = {Biochar co-compost improves nitrogen retention and reduces carbon emissions in a winter wheat cropping system},
  journal = {Global Change Biology Bioenergy},
  volume = {00},
  doi = {10.1111/gcbb.13028},
  pages = {1-16},
  year = {2023},
  author = {Gao, Si and Harrison, Brendan and Thao, Touyee and Gonzales, Melinda and An, Di and Ghezzehei, Teamrat and Diaz, Gerardo and Ryals, Rebecca}
}

An integrated field, laboratory, and modeling study of the Pena Blanca (Chihuahua, Mexico) natural analogue site is being conducted to evaluate processes that control the mobilization and transport of radionuclides from a uranium ore deposit. One component of this study is an evaluation of the potential for radionuclide transport through the unsaturated zone (UZ) via a seepage study in an adit at the Nopal I uranium mine, excavated 10 m below a mined level surface. Seasonal rainfall on the exposed level surface infiltrates into the fractured rhyolitic ash-flow tuff and seeps into the adit. An instrumented seepage collection system and local automated weather station permit direct correlation between local precipitation events and seepage within the Nopal I +00 adit. Monitoring of seepage within the adit between April 2005 and December 2006 indicates that seepage is highly heterogeneous with respect to time, location, and quantity. Within the back adit area, a few zones where large volumes of water have been collected are linked to fast flow path fractures (0-4 h transit times) presumably associated with focused flow. In most locations, however, there is a 1-6 month time lag between major precipitation events and seepage within the adit, with longer residence times observed for the front adit area. Seepage data obtained from this study will be used to provide input to flow and transport models being developed for the Nopal I hydrogeologic system.

@article{p2012-Dobson-et-al,
  author = {Dobson, P. F. and Ghezzehei, T. A. and Cook, P. J. and Rodriguez-Pineda, J. A. and Villalba, L. and De la Garza, R.},
  date-modified = {2018-05-27 20:46:20 +0000},
  doi = {10.1007/s10040-011-0783-5},
  journal = {Hydrogeology Journal},
  status = {published},
  number = {1},
  pages = {155-166},
  researchgate = {https://www.researchgate.net/publication/255208225_Heterogeneous_seepage_at_the_Nopal_I_natural_analogue_site_Chihuahua_Mexico},
  title = {Heterogeneous seepage at the Nopal I natural analogue site, Chihuahua, Mexico},
  volume = {20},
  year = {2012},
  bdsk-url-1 = {https://doi.org/10.1007/s10040-011-0783-5}
}

Determination of saturated hydraulic conductivity, Ks, and the van Genuchten water retention curve θ(h) parameters is crucial in evaluating unsaturated soil water flow. The aim of this work is to present a method to estimate Ks, α and n from numerical analysis of an upward infiltration process at saturation (Cap0), with (Cap0 + h) and without (Cap0) an overpressure step (h) at the end of the wetting phase, followed by an evaporation process (Evap). The HYDRUS model as well as a brute-force search method were used for theoretical loam soil parameter estimation. The uniqueness and the accuracy of solutions from the response surfaces, Ks–n, α–n and Ks–α, were evaluated for different scenarios. Numerical experiments showed that only the Cap0 + Evap and Cap0 + h + Evap scenarios were univocally able to estimate the hydraulic properties. The method gave reliable results in sand, loam and clay-loam soils.

@article{p2017-Pena-Sancho-et-al,
  author = {Pe{\~{n}}a-Sancho, C. and Ghezzehei, T.A. and Latorre, B. and Gonz{\'{a}}lez-Cebollada, C. and Moret-Fern{\'{a}}ndez, D.},
  date-modified = {2018-11-14 14:03:19 -0800},
  doi = {10.1080/02626667.2017.1343476},
  journal = {Hydrological Sciences Journal},
  status = {published},
  keywords = {soil hydraulic properties, inverse methods, HYDRUS},
  month = jul,
  number = {10},
  pages = {1683--1693},
  sort-word = {method},
  title = {Upward infiltration{extendash}evaporation method to estimate soil hydraulic properties},
  volume = {62},
  year = {2017},
  bdsk-url-1 = {https://doi.org/10.1080%2F02626667.2017.1343476},
  bdsk-url-2 = {http://dx.doi.org/10.1080/02626667.2017.1343476},
  bdsk-url-3 = {https://doi.org/10.1080/02626667.2017.1343476}
}

Modeling water flow in unsaturated soils is vital for describing various hydrological and ecological phenomena. Soil water dynamics is described by well-established physical laws (Richardson–Richards equation – RRE). Solving the RRE is difficult due to the inherent nonlinearity of the processes, and various numerical methods have been proposed to solve the issue. However, applying the methods to practical situations is very challenging because they require well-defined initial and boundary conditions. Recent advances in machine learning and the growing availability of soil moisture data provide new opportunities for addressing the lingering challenges. Specifically, physics-informed machine learning allows both the known physics and data-driven modeling to be taken advantage of. Here, we present a physics-informed neural network (PINN) method that approximates the solution to the RRE using neural networks while concurrently matching available soil moisture data. Although the ability of PINNs to solve partial differential equations, including the RRE, has been demonstrated previously, its potential applications and limitations are not fully known. This study conducted a comprehensive analysis of PINNs and carefully tested the accuracy of the solutions by comparing them with analytical solutions and accepted traditional numerical solutions. We demonstrated that the solutions by PINNs with adaptive activation functions are comparable with those by traditional methods. Furthermore, while a single neural network (NN) is adequate to represent a homogeneous soil, we showed that soil moisture dynamics in layered soils with discontinuous hydraulic conductivities are correctly simulated by PINNs with domain decomposition (using separate NNs for each unique layer). A key advantage of PINNs is the absence of the strict requirement for precisely prescribed initial and boundary conditions. In addition, unlike traditional numerical methods, PINNs provide an inverse solution without repeatedly solving the forward problem. We demonstrated the application of these advantages by successfully simulating infiltration and redistribution constrained by sparse soil moisture measurements. As a free by-product, we gain knowledge of the water flux over the entire flow domain, including the unspecified upper and bottom boundary conditions. Nevertheless, there remain challenges that require further development. Chiefly, PINNs are sensitive to the initialization of NNs and are significantly slower than traditional numerical methods.

@article{C_hess-26-4469-2022,
  author = {Bandai, T. and Ghezzehei, T. A.},
  title = {Forward and inverse modeling of water flow in unsaturated soils with discontinuous hydraulic conductivities using physics-informed neural networks with domain decomposition},
  journal = {Hydrology and Earth System Sciences},
  volume = {26},
  year = {2022},
  number = {16},
  pages = {4469--4495},
  pdf = {https://hess.copernicus.org/articles/26/4469/2022/hess-26-4469-2022.pdf},
  data = {https://doi.org/10.5281/zenodo.6030635},
  doi = {10.5194/hess-26-4469-2022}
}

This study investigates the ability of machine learning models to retrieve the surface soil moisture of a grassland area from multispectral remote sensing carried out using an unoccupied aircraft system (UAS). In addition to multispectral images, we use terrain attributes derived from a digital elevation model and hydrological variables of precipitation and potential evapotranspiration as covariates to predict surface soil moisture. We tested four different machine learning algorithms and interrogated the models to rank the importance of different variables and to understand their relationship with surface soil moisture. All the machine learning algorithms we tested were able to predict soil moisture with good accuracy. The boosted regression tree algorithm was marginally the best, with a mean absolute error of 3.8 % volumetric moisture content. Variable importance analysis revealed that the four most important variables were precipitation, reflectance in the red wavelengths, potential evapotranspiration, and topographic position indices (TPI). Our results demonstrate that the dynamics of soil water status across heterogeneous terrain may be adequately described and predicted by UAS remote sensing and machine learning. Our modeling approach and the variable importance and relationships we have assessed in this study should be useful for management and environmental modeling tasks where spatially explicit soil moisture information is important.

@article{p2019-Araya-et-al-b,
  author = {Araya, S. N. and Fryjoff-Hung, A. and Anderson, A. and Viers, J. H. and Ghezzehei, T. A.},
  journal = {Hydrology and Earth System Sciences},
  volume = {25},
  pages = {2739–2758},
  status = {published},
  title = {Advances in soil moisture retrieval from multispectral remote sensing using unoccupied aircraft systems and machine learning techniques.},
  doi = {10.5194/hess-25-2739-2021},
  mendeley = {https://www.mendeley.com/catalogue/c94110d7-78aa-3804-b08d-409e2acc5e2b/},
  year = {2021}
}

The Nopal I site in the Peña Blanca uranium district has a number of geologic and hydrologic similarities to the proposed high-level radioactive waste repository at Yucca Mountain, making it a useful analogue to evaluate process models for radionuclide transport. The PB-1 well was drilled in 2003 at the Nopal I uranium deposit as part of a DOE-sponsored natural analogue study to constrain processes affecting radionuclide transport. The well penetrates through the Tertiary volcanic section down to Cretaceous limestone and intersects the regional aquifer system. The well, drilled along the margin of the Nopal I ore body, was continuously cored to a depth of 250 m, thus providing an opportunity to document the local stratigraphy. Detailed observations of these units were afforded through petrographic description and rockproperty measurements of the core, together with geophysical logs of the well. The uppermost unit encountered in the PB-1 well is the Nopal Formation, a densely welded, crystal-rich, rhyolitic ashflow tuff. This cored section is highly altered and devitrified, with kaolinite, quartz, chlorite, and montmorillonite replacing feldspars and much of the groundmass. Breccia zones within the tuff contain fracture fillings of hematite, limonite, goethite, jarosite, and opal. A zone of intense clay alteration, encountered in the depth interval 17.45-22.30 m, was interpreted to represent the basal vitrophyre of this unit. Underlying the Nopal Formation is the Coloradas Formation, which consists of a welded lithic-rich rhyolitic ash-flow tuff. The cored section of this unit has undergone devitrification and oxidation, and has a similar alteration mineralogy to that observed in the Nopal tuff. A sharp contact between the Coloradas tuff and the underlying Pozos Formation was observed at a depth of 136.38 m. The Pozos Formation consists of poorly sorted conglomerate containing clasts of subangular to subrounded fragments of volcanic rocks, limestone, and chert. Three thin (2-6 m) intervals of intercalated pumiceous tuffs are present within this unit. The contact between the Pozos Formation and the underlying Cretaceous limestone basement was encountered at a depth of 244.40 m. The water table is located at a depth of  223 m. Several zones with elevated radioactivity in the PB-1 core occur above the current water table. These zones may be associated with changes in redox conditions that could have resulted in the precipitation of uraninite from downward-flowing waters transporting U from the overlying Nopal deposit. All of the intersected units have low (typically submillidarcy) matrix permeability, thus fluid flow in this area is dominated by fracture flow. These stratigraphic and rock-property observations can be used to constrain flow and transport models for the Peña Blanca natural analogue.

@article{p2008-Dobson-et-al,
  author = {Dobson, Patrick F. and Fayek, Mostafa and Goodell, Philip C. and Ghezzehei, Teamrat A. and Melchor, Felipe and Murrell, Michael T. and Oliver, Ronald and Reyes-Cortes, Ignacio A. and de la Garza, Rodrigo and Simmons, Ardyth},
  date-modified = {2018-05-27 20:25:19 +0000},
  doi = {10.2747/0020-6814.50.11.959},
  journal = {International Geology Review},
  status = {published},
  number = {11},
  pages = {959-974},
  researchgate = {https://www.researchgate.net/publication/232914197_Stratigraphy_of_the_PB-1_Well_Nopal_I_Uranium_Deposit_Sierra_Pena_Blanca_Chihuahua_Mexico},
  title = {Stratigraphy of the PB-1 Well, Nopal I Uranium Deposit, Sierra Pena Blanca, Chihuahua, Mexico},
  volume = {50},
  year = {2008},
  bdsk-url-1 = {https://doi.org/10.2747/0020-6814.50.11.959}
}

Recent research has shown that the native shrub, Guiera senegalensis J.F. Gmel, interplanted with crops dramatically increases crop yield in the Sahel. However, little is known about the crop development when grown alongside shrubs. The objectives were to determine the effect of shrub presence on crop development under varying fertilizer rates in northern Senegal. Peanut (\em Arachis hypogaea L.) and pearl millet (\em Pennisetum glaucum (L.)) response in the presence or absence of shrubs was investigated from 2013 to 2016 under low to adequate rainfall. The experiment had a split-plot factorial design with presence or absence shrubs (+shrub, −shrub) as the main plot (elevated densities of 1200 to 1500 shrubs ha−1) and fertilizer rate (0, 0.5, 1 or 1.5 times the recommended N–P–K rate) as the subplot factors. Major developmental phases, leaf counts and plant height were determined. Shrub presence made crops grow up to four times taller and reach 50% flowering when −shrub plots did not reach 50% in 2013 and 2015 (millet). Changes to crop development, even in low rainfall years, indicate that shrub intercropping buffers against crop water stress. Thus, under drought conditions, shrub-based agroforestry can contribute to reduce fertilizer necessity and to mitigate against climate change.

@article{p2021-Bayala-et-al,
  author = {Bayala, Roger and Diedhiou, Ibrahima and Bogie, Nathaniel A. and Bright, Matthew B. H. and Badiane, Y. Ndour and Ghezzehei, Teamrat A. and Dick, Richard P.},
  journal = {Journal of Agronomy and Crop Science},
  volume = {208},
  pages = {158-167},
  status = {published},
  keywords = {crop/stress physiology, drought stress, site specific analysis},
  doi = {10.1111/jac.12568},
  mendeley = {https://www.mendeley.com/catalogue/bc0ee8f8-5d8d-3bfe-b11d-bea72134e194/},
  title = {Intercropping with Guiera senegalensis in a semi-arid area to mitigate early-season abiotic stress in A. hypogea and P. glaucum},
  year = {2022}
}

Emulsions appear in many subsurface applications including bioremediation, surfactant-enhanced remediation, and enhanced oil-recovery. Modeling emulsion transport in porous media is particularly challenging because the rheological and physical properties of emulsions are different from averages of the components. Current modeling approaches are based on filtration theories, which are not suited to adequately address the pore-scale permeability fluctuations and reduction of absolute permeability that are often encountered during emulsion transport. In this communication, we introduce a continuous time random walk based alternative approach that captures these unique features of emulsion transport. Calculations based on the proposed approach resulted in excellent match with experimental observations of emulsion breakthrough from the literature. Specifically, the new approach explains the slow late-time tailing behavior that could not be fitted using the standard approach. The theory presented in this paper also provides an important stepping stone toward a generalized self-consistent modeling of multiphase flow.

@article{p2007-Cortis-Ghezzehei,
  author = {Cortis, Andrea and Ghezzehei, Teamrat A.},
  date-modified = {2018-05-27 20:17:42 +0000},
  doi = {10.1016/j.jcis.2007.04.021},
  journal = {Journal of Colloid and Interface Science},
  status = {published},
  number = {1},
  pages = {1-4},
  researchgate = {https://www.researchgate.net/publication/6337601_On_the_transport_of_emulsions_in_porous_media},
  title = {On the transport of emulsions in porous media [Priority Communications]},
  volume = {313},
  year = {2007},
  bdsk-url-1 = {https://doi.org/10.1016/j.jcis.2007.04.021}
}

The shrink-swell behavior of active clays in response to changes in physicochemical conditions creates great challenges for construction of geotechnical barriers for hazardous waste isolation, and is of significant importance for management of agricultural and natural resources. Initiation and evolution of desiccation cracks in active clays are strongly dependent on physicochemical initial and boundary conditions. To investigate effects of bentonite content (20, 40, 60%), pore fluid chemistry (0.05 and 0.5M NaCl) and drying rates (40 and 60\,^∘C) on cracking behavior, well-controlled dehydration experiments were conducted and X-ray Computed Tomography (CT) was applied to visualize and quantify geometrical features of evolving crack networks. A stochastic model based on the Fokker-Plank equation was adopted to describe the evolution of crack aperture distributions (CAD) and to assess the impact of physicochemical factors on cracking behavior. Analyses of crack porosity and crack specific surface area showed that both clay content and temperature had larger impact on cracking than pore fluid concentration. More cracks formed at high bentonite contents (40 and 60%) and at high drying rate (60\,^∘C). The drift, diffusion and source terms derived from stochastic analysis indicated that evaporative demand had greater influence on the dynamics of the CAD than solution chemistry.

@article{p2011-Gebrenegus-Ghezzehei-Tuller,
  author = {Gebrenegus, T. and Ghezzehei, T. A. and Tuller, M.},
  date-modified = {2018-05-27 20:29:25 +0000},
  doi = {10.1016/j.jconhyd.2011.07.004},
  journal = {Journal of Contaminant Hydrology},
  status = {published},
  number = {1-2},
  pages = {100-112},
  researchgate = {https://www.researchgate.net/publication/51629103_Physicochemical_controls_on_initiation_and_evolution_of_desiccation_cracks_in_sand-bentonite_mixtures_X-ray_CT_imaging_and_stochastic_modeling},
  title = {Physicochemical controls on initiation and evolution of desiccation cracks in sand-bentonite mixtures: X-ray CT imaging and stochastic modeling},
  volume = {126},
  year = {2011},
  bdsk-url-1 = {https://doi.org/10.1016/j.jconhyd.2011.07.004}
}

Wildland fire is an important ecological process in the California Sierra Nevada. Personal accounts from pre-20th century describe a much smokier environment than present day. The policy of suppression beginning in the early 20th century and climate change are contributing to increased megafires. We use a single particulate monitoring site at the wildland urban interface to explore impacts from prescribed, managed, and full suppression wildland fires from 2006 to 2015 producing a contextual assessment of smoke impacts over time at the landscape level. Prescribed fire had little effect on local fine particulate matter (PM2.5) air quality with readings typical of similar non-fire times; hourly and daily good to moderate Air Quality Index (AQI) for PM2.5, maximum hourly concentrations 21–103 μg m−3, and mean concentrations between 7.7 and 13.2 μg m−3. Hourly and daily AQI was typically good or moderate during managed fires with 3 h and one day reaching unhealthy while the site remained below National Ambient Air Quality Standards (NAAQS), with maximum hourly concentrations 27–244 μg m−3, and mean concentrations 6.7–11.7 μg m−3. The large high intensity fire in this area created the highest short term impacts (AQI unhealthy for 4 h and very unhealthy for 1 h), 11 unhealthy for sensitive days, and produced the only annual value (43.9 μg m−3) over the NAAQS 98th percentile for PM2.5 (35 μg m−3). Pinehurst remained below the federal standards for PM2.5 when wildland fire in the local area was managed to 7800 ha (8–22% of the historic burn area). Considering air quality impacts from smoke using the NAAQS at a landscape level over time can give land and air managers a metric for broader evaluation of smoke impacts particularly when assessing ecologically beneficial fire. Allowing managers to control the amount and timing of individual wildland fire emissions can help lessen large smoke impacts to public health from a megafire.

@article{p2017-Schweizer-et-al,
  author = {Schweizer, Don and Cisneros, Ricardo and Traina, Samuel and Ghezzehei, Teamrat A. and Shaw, Glenn},
  date-modified = {2018-11-14 14:00:32 -0800},
  doi = {10.1016/j.jenvman.2017.07.004},
  journal = {Journal of Environmental Management},
  status = {published},
  month = oct,
  pages = {345--356},
  sort-word = {environmental quality},
  title = {Using National Ambient Air Quality Standards for fine particulate matter to assess regional wildland fire smoke and air quality management},
  volume = {201},
  year = {2017},
  bdsk-url-1 = {https://doi.org/10.1016%2Fj.jenvman.2017.07.004},
  bdsk-url-2 = {http://dx.doi.org/10.1016/j.jenvman.2017.07.004},
  bdsk-url-3 = {https://doi.org/10.1016/j.jenvman.2017.07.004}
}

The use of biochar for recovery of excess nutrients in dairy manure effluent and the use of nutrient-enriched biochar as soil amendment can offer a robust solution for multiple environmental issues. In this study we determined the capacity of biochar, produced by pyrolyzing mixed hardwood feedstock at 300\,^∘C, to adsorb and retain or release two major nutrient ions: ammonium (NH4+) and phosphate (PO43−). We conducted the experiment using a range of nutrient concentrations that represent those commonly observed in dairy manure effluent (0–50 mg L−1 for PO43− and 0–1000 mg L−1 for NH4+). Up to 5.3 mg g−1 NH4+ and 0.24 mg g−1 PO43− was adsorbed from manure by biochar (18 and 50% of total amount in the manure slurry, respectively). During the desorption phase of the experiment, biochar retained 78 to 91% of the sorbed NH4+ and 60% of the sorbed PO43− at reaction times <24 h. Our findings confirm that biochar can be used for recovering excess nitrogen and phosphorus from agricultural water, such as dairy manure effluent.

@article{p2013-Sarkhot-Ghezzehei-Berhe,
  author = {Sarkhot, D. V. and Ghezzehei, T. A. and Berhe, A. A.},
  date-modified = {2018-05-27 20:59:26 +0000},
  doi = {10.2134/jeq2012.0482},
  journal = {Journal of Environmental Quality},
  status = {published},
  number = {5},
  pages = {1545},
  publisher = {American Society of Agronomy},
  researchgate = {https://www.researchgate.net/publication/258444056_Effectiveness_of_Biochar_for_Sorption_of_Ammonium_and_Phosphate_from_Dairy_Effluent},
  title = {Effectiveness of Biochar for Sorption of Ammonium and Phosphate from Dairy Effluent},
  volume = {42},
  year = {2013},
  bdsk-url-1 = {https://doi.org/10.2134%2Fjeq2012.0482},
  bdsk-url-2 = {http://dx.doi.org/10.2134/jeq2012.0482},
  bdsk-url-3 = {https://doi.org/10.2134/jeq2012.0482}
}

Amending soils with biochar can have multiple environmental benefits, including improvement in soil physicochemical properties, carbon sequestration, reduction in leaching losses of essential nutrients, and reduction in greenhouse gas (GHG) emissions. This study was conducted to determine the effect of enriched biochar amendments on leaching losses of essential nutrients and GHG emissions from soil. The enriched biochar was prepared by shaking biochar with dairy manure effluent for 24 h, which increased the C and N concentration of biochar by 9.3 and 8.3%, respectively. Incubation and leaching experiments were conducted for 8 wk with three treatments: soil, soil + 1% biochar, and soil + 1% enriched biochar. Amendment with biochar and enriched biochar relative to unamended soil resulted in 68 and 75% reduction in net nitrification, 221 and 229% reduction in net ammonification, 67 and 68% reduction in cumulative CO2 flux, respectively, and 26% reduction in cumulative N2O flux for both biochar treatments. There were no significant differences among treatments in total leaching losses of C, N, and base cations. Our findings suggest that enrichment of biochar with dairy manure effluent can promote C and N storage in soil and provide additional environmental benefits.

@article{p2012-Sarkhot-Berhe-Ghezzehei,
  author = {Sarkhot, D. V. and Berhe, A. A. and Ghezzehei, T. A.},
  date-modified = {2018-05-27 20:44:49 +0000},
  doi = {10.2134/jeq2011.0123},
  journal = {Journal of Environmental Quality},
  status = {published},
  number = {4},
  pages = {1107-1114},
  researchgate = {https://www.researchgate.net/publication/226915424_Impact_of_Biochar_Enriched_with_Dairy_Manure_Effluent_on_Carbon_and_Nitrogen_Dynamics},
  title = {Impact of Biochar Enriched with Dairy Manure Effluent on Carbon and Nitrogen Dynamics},
  volume = {41},
  year = {2012},
  bdsk-url-1 = {https://doi.org/10.2134/jeq2011.0123}
}

Hydrodynamic dispersion is responsible for spreading of dissolved mass within a single phase in porous media. It typically arises because of variability in local flow velocities. Because the pattern of spreading by dispersion is similar to Fickian diffusion, dispersion has been traditionally modeled as a pseudo-diffusive process that depends on the concentration gradient. However, there is no physical basis for this dependence of dispersion on concentration gradient. This unphysical formulation of dispersive flux has led to a number of major shortcomings including (a) lack of a self-consistent, mechanistic, and independent approach for predicting dispersion coefficient; and (b) dependence of the dispersion coefficient on transport distance. In this paper we show that the shape of dispersive spreading can be described using a model based on a variably sized bundle of capillaries and purely advective transport. The model suggests that dispersion can be described in terms of the variance of the pore size distribution only. Breakthrough curves of the proposed model can be exactly matched with the traditional diffusive-type dispersion model. By utilizing this equivalence, we derived relationships between the traditional dispersivity coefficient, pore size variance, and transport distance. The plausibility of the proposed expressions was tested using three illustrative examples that compare aspects of the proposed model with measurements obtained from the literature.

@article{p2013-Arriaza-Ghezzehei,
  author = {Arriaza, Juan Lopez and Ghezzehei, Teamrat A.},
  date-modified = {2018-05-27 21:00:59 +0000},
  doi = {10.1615/JPorMedia.v16.i1.20},
  journal = {Journal of Porous Media},
  status = {published},
  keywords = {porous media, transport, stochastic methods},
  number = {1},
  pages = {11--19},
  researchgate = {https://www.researchgate.net/publication/240613686_Explaining_Longitudinal_Hydrodynamic_Dispersion_Using_Variance_of_Pore_Size_Distribution},
  title = {Explaining longitudinal hydrodynamic dispersion using variance of pore size distribution},
  volume = {16},
  year = {2013},
  bdsk-url-1 = {https://doi.org/10.1615%2Fjpormedia.v16.i1.20},
  bdsk-url-2 = {http://dx.doi.org/10.1615/jpormedia.v16.i1.20},
  bdsk-url-3 = {https://doi.org/10.1615/jpormedia.v16.i1.20},
  bdsk-url-4 = {https://doi.org/10.1615/JPorMedia.v16.i1.20}
}

Most soil hydraulic information used in Earth System Models (ESMs) is derived from pedo-transfer functions that use easy-to-measure soil attributes to estimate hydraulic parameters. This parameterization relies heavily on soil texture, but overlooks the critical role of soil structure originated by soil biophysical activity. Soil structure omission is pervasive also in sampling and measurement methods used to train pedotransfer functions. Here we show how systematic inclusion of salient soil structural features of biophysical origin affect local and global hydrologic and climatic responses. Locally, including soil structure in models significantly alters infiltration-runoff partitioning and recharge in wet and vegetated regions. Globally, the coarse spatial resolution of ESMs and their inability to simulate intense and short rainfall events mask effects of soil structure on surface fluxes and climate. Results suggest that although soil structure affects local hydrologic response, its implications on global-scale climate remains elusive in current ESMs.

@article{p2020-Fatichi-et-al,
  title = {Soil structure is an important omission in Earth System Models},
  author = {Fatichi, Simone and OR, Dani and Walko, Robert and Vereecken, Harry and Young, Michael H. and Ghezzehei, Teamrat A. and Hengl, Tomislav and Kollet, Stefan and Agam, Nurit and Avissar, Roni},
  doi = {10.1038/s41467-020-14411-z},
  sort-word = {CO2 flux, Soil respiration, Soil Carbon, aggregation, modeling,biogeoscience},
  journal = {Nature Communications},
  status = {published},
  pdf = {https://www.nature.com/articles/s41467-020-14411-z.pdf},
  data = {https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-020-14411-z/MediaObjects/41467_2020_14411_MOESM3_ESM.zip},
  mendeley = {https://www.mendeley.com/catalogue/47459482-43dc-319e-95bf-b9110c277f4e/},
  volume = {11},
  pages = {522},
  year = {2020}
}

Water potential directly controls the function of leaves, roots and microbes, and water potential gradients drive water flows throughout the soil-plant-atmosphere continuum. Notwithstanding its clear relevance for many ecosystem processes, soil water potential is rarely measured in-situ, and plant water potential observations are generally discrete, sparse, and not yet aggregated into accessible databases. These gaps limit our conceptual understanding of biophysical responses to moisture stress and inject large uncertainty into hydrologic and land surface models. Here, we outline the conceptual and predictive gains that could be made with more continuous and discoverable observations of water potential in soils and plants. We discuss improvements to sensor technologies that facilitate in situ characterization of water potential, as well as strategies for building new networks that aggregate water potential data across sites. We end by highlighting novel opportunities for linking more representative site-level observations of water potential to remotely-sensed proxies. Together, these considerations offer a roadmap for clearer links between ecohydrological processes and the water potential gradients that have the ‘potential’ to substantially reduce conceptual and modeling uncertainties.

@article{p2021-Novick-et-al,
  author = {Novick, Kim and Ficklin, D and Baldocchi, D and Davis, K and Ghezzehei, TA and Konings, A and MacBean, N and Scott, R and Shi, Y and Sulman, B},
  journal = {Nature Geosciences},
  volume = {15},
  pages = {158–164},
  keywords = {Hydrology, Carbon cycle, Climate and Earth system modelling, Ecosystem ecology, Hydrogeology},
  status = {published},
  doi = {10.1038/s41561-022-00909-2},
  title = {Confronting the water potential information gap},
  year = {2022}
}

Aims\{To investigate the physiological responses of groundnut (Arachis hypogea) and pearl millet (Penisetum glaucum) that were intercropped with the native evergreen woody shrubs Piliostigma reticulatum (D.C.) Hochst and Guiera senegalensis J.F. Gmel compared to control crops throughout two growing seasons at two sites with contrasting climate and soil types in Senegal.Methods\\Shrubs grown in groundnut and millet fields at higher than native density were coppiced annually with aboveground biomass returned to the soil and no additional fertilizer. Crop leaf area index (LAI), handheld normalized difference vegetation index (NDVI), leaf water potential, and soil moisture and temperature were monitored in 2012–2013.Results\\At the drier site, the presence of shrubs reduced soil temperature at 5 cm depth by up to 5 °C during early crop growth. Shrub presence increased LAI by up to 266%, NDVI by up to 217% and increased groundnut leaf water potential throughout the day at the wetter site. Shrub effects on crop physiology were stronger overall at the drier site.Conclusions\\These results improve the understanding of how this unique agroforestry system alters the growing environment and the physiological response of associated crops throughout the season.

@article{p2019-Bogie-et-al-c,
  author = {Bogie, N.A. and Bayala, R. and Diedhiou, I. and Dick, R. and Ghezzehei, T.A.},
  doi = {10.1007/s11104-018-3882-4},
  journal = {Plant and Soil},
  status = {published},
  volume = {1-2},
  pages = {143–159},
  month = jan,
  sort-word = {agroecology},
  mendeley = {https://www.mendeley.com/catalogue/621c9e9c-8372-3721-b62a-c5169e03047a/},
  pdf = {https://link.springer.com/content/pdf/10.1007/s11104-018-3882-4.pdf},
  title = {Intercropping With Two Native Woody Shrubs Improves Water Status and Development of Interplanted Groundnut and Pearl Millet in the Sahel},
  year = {2019}
}

Background and aims:The rhizosphere, the soil immediately surrounding roots, provides a critical bridge for water and nutrient uptake. The rhizosphere is influenced by various forms of root–soil interactions of which mechanical deformation due to root growth and its effects on the hydraulics of the rhizosphere are the least studied. In this work, we focus on developing new experimental and numerical tools to assess these changes. \{Methods: This study combines X-ray micro-tomography (XMT) with coupled numerical simulation of fluid and soil deformation in the rhizosphere. The study provides a new set of tools to mechanistically investigate root-induced rhizosphere compaction and its effect on root water uptake. The numerical simulator was tested on highly deformable soil to document its ability to handle a large degree of strain. \{Results: Our experimental results indicate that measured rhizosphere compaction by roots via localized soil compaction increased the simulated water flow to the roots by 27 % as compared to an uncompacted fine-textured soil of low bulk density characteristic of seed beds or forest topsoils. This increased water flow primarily occurred due to local deformation of the soil aggregates as seen in the XMT images, which increased hydraulic conductivity of the soil. Further simulated root growth and deformation beyond that observed in the XMT images led to water uptake enhancement of  50 % beyond that due to root diameter increase alone and demonstrated the positive benefits of root compaction in low density soils. \{Conclusions: The development of numerical models to quantify the coupling of root driven compaction and fluid flow provides new tools to improve the understanding of plant water uptake, nutrient availability and agricultural efficiency. This study demonstrated that plants, particularly during early growth in highly deformable low density soils, are involved in active mechanical management of their surroundings. These modeling approaches may now be used to quantify compaction and root growth impacts in a wide range of soils.

@article{p2013-Aravena-et-al,
  author = {Aravena, Jazm{\'{\i}}n E. and Berli, Markus and Ruiz, Siul and Su{\'{a}}rez, Francisco and Ghezzehei, Teamrat A. and Tyler, Scott W.},
  date-modified = {2018-05-27 21:13:46 +0000},
  doi = {10.1007/s11104-013-1946-z},
  journal = {Plant and Soil},
  status = {published},
  keywords = {Rhizosphere, Growth, Mechanical deformation, Uptake, X-ray microtomography},
  month = nov,
  number = {1-2},
  pages = {95--110},
  publisher = {Springer Nature},
  researchgate = {https://www.researchgate.net/publication/268743485_Quantifying_coupled_deformation_and_water_flow_in_the_rhizosphere_using_X-ray_microtomography_and_numerical_simulations},
  title = {Quantifying coupled deformation and water flow in the rhizosphere using X-ray microtomography and numerical simulations},
  volume = {376},
  year = {2013}
}

Background and Aims: Wetting-drying cycles are important environmental processes known to enhance aggregation. However, very little attention has been given to drying as a process that transports mucilage to inter-particle contacts where it is deposited and serves as binding glue. The objective of this study was to formulate and test conceptual and mathematical models that describe the role of drying in soil aggregation through transportation and deposition of binding agents. \{Methods: We used an ESEM to visualize aggregate formation of pair of glass beads. To test our model, we subjected three different sizes of sand to multiple wetting-drying cycles of PGA solution as a mimic of root exudates to form artificial aggregates. Water stable aggregate was determined using wet sieving apparatus. \{Results: A model to predict aggregate stability in presence of organic matter was developed, where aggregate stability depends on soil texture as well as the strength, density and mass fraction of organic matter, which was confirmed experimentally. The ESEM images emphasize the role of wetting-drying cycles on soil aggregate formation. \{Conclusions: Our experimental results confirmed the mathematical model predictions as well as the ESEM images on the role of drying in soil aggregation as an agent for transport and deposition of binding agents.

@article{p2013-Albalasmeh-Ghezzehei,
  author = {Albalasmeh, Ammar A. and Ghezzehei, Teamrat A.},
  date-modified = {2018-05-27 21:12:15 +0000},
  doi = {10.1007/s11104-013-1910-y},
  journal = {Plant and Soil},
  status = {published},
  keywords = {Rhizosheath, Aggregate formation/stabilization, Root exudate, Rhizosphere water content, Polygalacturonic Acid (PGA)},
  month = oct,
  number = {1-2},
  pages = {739--751},
  publisher = {Springer Nature},
  researchgate = {https://www.researchgate.net/publication/255176344_A_new_method_for_rapid_determination_of_carbohydrate_and_total_carbon_concentrations_using_UV_spectrophotometry},
  title = {Interplay between soil drying and root exudation in rhizosheath development},
  volume = {374},
  year = {2013},
  bdsk-url-1 = {https://doi.org/10.1007%2Fs11104-013-1910-y},
  bdsk-url-2 = {http://dx.doi.org/10.1007/s11104-013-1910-y},
  bdsk-url-3 = {https://doi.org/10.1007/s11104-013-1910-y}
}

Soil structure degradation by fire is usually attributed to qualitative and quantitative change of organic and inorganic binding agents, especially in high severity burns (> 300 A degrees C) that last for prolonged periods (> 1 hour). In contrast, controlled burns are typically managed to be low in intensity and severity. Such burns are considered benign to soil structural stability because organic matter and inorganic binding agents (e.g., gypsum) are relatively stable at such low temperatures. Recent observations at a controlled burn site in the eastern Great Basin (Nevada) showed soil aggregate breakdown found in shrub canopies where soil temperatures briefly exceeded 300 A degrees C as well as interspaces between shrubs, where the temperatures were likely lower than beneath shrubs because of less surface biomass. These alterations cannot be explained in terms of thermal alteration of binding agents. This study was designed to test whether pressure created by rapidly vaporized pore water can cause aggregate breakdown. We subjected three different sizes of aggregates (0.25-1, 1-2 and 2-4 mm) of soils derived from the eastern Great Basin burn site as well as from a forest and urban garden in California to rapid and slow (3 A degrees C/min) heating rates. These treatments were conducted at 5 peak temperatures (75, 100, 125, 150 and 175 A degrees C). Post-burn water stability of the aggregates showed that rapid heating rate caused more pronounced degradation of aggregate stability than slow heating. Moreover, the heating-rate dependent structural degradation increased with peak temperature. For the majority of the aggregates, the effect also increased with initial water content. In all the soils tested, there was no preferential loss of organic matter in the rapid-heating treatment that can explain the observed enhanced breakdown of aggregates. Our observations indicate that soil structural degradation under low-intensity fire occurs as a result of mechanical stresses extorted by rapidly escaping steam from soil pores under rapid heating rate.

@article{p2013-Albalasmeh-et-al,
  author = {Albalasmeh, A. A. and Berli, M. and Shafer, D. S. and Ghezzehei, T. A.},
  date-modified = {2018-05-27 21:09:37 +0000},
  doi = {10.1007/s11104-012-1408-z},
  journal = {Plant and Soil},
  status = {published},
  number = {1-2},
  pages = {335-344},
  researchgate = {https://www.researchgate.net/publication/236455238_Degradation_of_moist_soil_aggregates_by_rapid_temperature_rise_under_low_intensity_fire},
  title = {Degradation of moist soil aggregates by rapid temperature rise under low intensity fire},
  volume = {362},
  year = {2013},
  bdsk-url-1 = {https://doi.org/10.1007/s11104-012-1408-z}
}

By the end of the 20th century, the onset of spring in the Sierra Nevada mountain range of California has been occurring on average three weeks earlier than historic records. Superimposed on this trend is an increase in the presence of highly anomalous “extreme years, where spring arrives either significantly late or early. The timing of the onset of continuous snowpack coupled to the date at which the snowmelt season is initiated play an important role in the development and sustainability of mountain ecosystems. In this study, we assess the impact of extreme winter precipitation variation on aboveground net primary productivity and soil respiration over three years (2011 to 2013). We found that the duration of snow cover, particularly the timing of the onset of a continuous snowpack and presence of early spring frost events contributed to a dramatic change in ecosystem processes. We found an average 100% increase in soil respiration in 2012 and 2103, compared to 2011, and an average 39% decline in aboveground net primary productivity observed over the same time period. The overall growing season length increased by 57 days in 2012 and 61 days in 2013. These results demonstrate the dependency of these keystone ecosystems on a stable climate and indicate that even small changes in climate can potentially alter their resiliency.

@article{p2014-Arnold-Ghezzehei-Berhe,
  author = {Arnold, Chelsea and Ghezzehei, Teamrat A. and Berhe, Asmeret Asefaw},
  data = {10.6084/m9.figshare.1113179.v19},
  date-modified = {2018-05-27 21:16:54 +0000},
  doi = {10.1371/journal.pone.0106058},
  journal = {PLoS ONE},
  status = {published},
  keywords = {Ecosystems, Seasons, Soil respiration, Productivity, Spring, Winter, Carbon dioxide, Ecosystem functioning},
  month = sep,
  number = {9},
  pages = {e106058},
  researchgate = {https://www.researchgate.net/publication/265509769_Early_Spring_Severe_Frost_Events_and_Drought_Induce_Rapid_Carbon_Loss_in_High_Elevation_Meadows},
  sort-word = {biogeoscience},
  title = {Early Spring, Severe Frost Events, and Drought Induce Rapid Carbon Loss in High Elevation Meadows},
  volume = {9},
  year = {2014}
}

Soil structure is a key attribute of soil quality and health that significantly impacts water infiltration. Structure can be significantly altered by natural or anthropogenic drivers including soil management practices and can in turn impact soil infiltration. Those changes in soil structure are often complex to quantify and can lead to conflicting impacts on water infiltration into soils. Here, we present a narrative systematic review (SR) of the impacts of soil structure on water infiltration. Based on inclusion and exclusion criteria, as well as defined methods for literature search and data extraction, our systematic review led to a total of 153 papers divided into two sets: experimental (131) and theoretical (22) papers. That implied a significant number of in-situ and field experiments that were conducted to assess the impacts of soil structure on water infiltration under the influence of different land uses and soil practices. Analysis of the metadata extracted from the collected papers revealed significant impacts of soil structure on water infiltration. Those effects were further attributed to land use and management, where we demonstrate the impact of three unique categories: soil amendments, crop management and tillage. Furthermore, significant correlations were established between infiltration rate and soil structural properties, with R2 values ranging from 0.51 to 0.80 and for saturated hydraulic conductivity and soil structural properties, with R2 values ranging from 0.21 to 0.78. Finally, our review highlighted the significant absence of and the need for theoretical frameworks studying the impacts of soil structure on water infiltration.

@article{BASSET2023105577,
  title = {How does soil structure affect water infiltration? A meta-data systematic review},
  journal = {Soil and Tillage Research},
  volume = {226},
  pages = {105577},
  year = {2023},
  issn = {0167-1987},
  doi = {10.1016/j.still.2022.105577},
  pdf = {https://www.sciencedirect.com/science/article/pii/S016719872200263X},
  author = {Basset, Christelle and {Abou Najm}, Majdi and Ghezzehei, Teamrat and Hao, Xiaoxiao and Daccache, André},
  keywords = {Soil structure, Soil infiltration, Pedotransfer functions, Infiltration capacity}
}

Scarcity of plant available water is a major challenge for rainfed agriculture throughout the Sahel. At two long-term experiments in Central and Southern Senegal, optimized intercropping with native woody shrubs, Piliostigma reticulatum (DC.) Hochst or Guiera senegalensis J.F. Gmel, (elevated densities and annual coppiced biomass returned to soils) have shown significant improvement of soil-plant-water relations, nutrient availability, and crop yields. The objective was to investigate soil physical properties to develop a mechanistic understanding for the observed improvement of water dynamics due to optimized shrub intercropping. The field experiments had a split-plot factorial design with shrubs as the main factor and fertilizer rate (0, 0.5, 1.0. 1.5 times the recommended addition of N-P-K fertilizer) as the subplot factor. This experiment was carried out at the sites of Keur Matar Arame (Keur Matar) with G. senegalensis and Nioro du Rip (Nioro) with P. reticulatum. Water retention characteristic, unsaturated hydraulic conductivity, surface evaporation, and surface infiltration were measured in the zero fertilizer treatment. At Keur Matar samples were collected from crop + shrub plots near (<0.5 m) the shrub canopy (CSn), crop + shrub plots far (>1 m) from the canopy (CSf) and in crop only plots (CO). At Nioro samples were taken in CSn, CSf, CO, and also from bare soil with no crops or shrubs growing (BS). Infiltration in CO plots compared to CSn plots was 75% and 28% higher at Keur Matar and Nioro, respectively. At Keur Matar water retention was significantly higher at wilting point (−1.5 MPa) in the CSn treatment than in the CSf treatment with values of 0.030 and 0.016 m3 m−3, respectively. At Nioro there was no significant difference in wilting point water content between treatments. These results indicate that shrubs slow down soil water as it infiltrates in the sandy soils and that the large additions of shrub biomass over a ten year period has had a small but significant effect on water retention at wilting point. This study highlights the role that shrub presence and biomass additions play in altering centimeter-scale soil properties.

@article{p2018-Bogie-et-al,
  author = {Bogie, N and Bayala, R. and Diedhiou, I. and Dick, R.P. and Ghezzehei, T. A.},
  doi = {10.1016/j.still.2018.05.010},
  status = {published},
  journal = {Soil and Tillage Research},
  keywords = {Soil structure, Sahel, Agroforestry},
  month = may,
  pages = {153--163},
  sort-word = {agroecology},
  title = {Alteration of soil physical properties and processes after ten years of intercropping with native shrubs in the Sahel},
  volume = {182},
  year = {2018},
  bdsk-url-1 = {https://doi.org/10.1016/j.still.2018.05.010}
}

Tillage modifies the soil structure to create conditions favorable for plant growth. However, the resulting loose structure is susceptible to collapse by internal capillary forces and external compactive stresses with concurrent changes in soil hydraulic properties. Presently, limited understanding of these complex processes often leads to consideration of the soil plow-layer as a static porous medium. Our objective is to provide a review of recent progress in modeling soil structural dynamics at the pore-scale, based on soil mechanical and rheological properties. The basic geometrical framework of the models was a cubic arrangement of monosized spherical aggregates (other arrangements are discussed). The process of soil aggregate rejoining by capillary forces was modeled by considering the rate of energy dissipation due to viscous deformation of wet soil, and corresponding energy release due to reconfiguration of water capillary menisci. The model was complemented by independent rheological characterization of soil that provides control on the rate as well as the onset and termination of aggregate coalescence. The model was also adapted for consideration of steady stress (such as overburden) acting upon the unit cells. Unlike steady stress, transient stress (such as traffic) is applied for too short of a period to allow for total energy dissipation by viscous deformation. Hence, a portion of the deformation is elastic (with a recoverable portion of the applied energy). Rheological characterization under transient (oscillatory) stress provided coupled elastic and viscous properties under several loading frequencies. Effects of transient stresses on the geometrical model were modeled by considering a combination of (i) Hertzian-type elastic strain and (ii) viscous flow of soil at the contacts. Application of the models is demonstrated using illustrative examples and rheological measurements of Millville silt loam soil. Finally, we provide an outlook for upscaling the unit cell results to an aggregate bed scale.

@article{p2002-Or-Ghezzehei,
  author = {Or, D and Ghezzehei, T. A.},
  date-modified = {2018-05-31 01:36:51 +0000},
  journal = {Soil and Tillage Research},
  status = {published},
  keywords = {Rheology, Soil-structure, Compaction, Aggregate},
  number = {1-2},
  pages = {41-59},
  researchgate = {https://www.researchgate.net/publication/222697340_Modeling_post-tillage_soil_structural_dynamics_A_review},
  sort-word = {aggregation},
  title = {Modeling post-tillage soil structural dynamics: a review},
  volume = {64},
  doi = {10.1016/S0167-1987(01)00256-2},
  year = {2002}
}

Soil tillage often results in a structurally unstable soil layer with an elevated inter-aggregate porosity that is gradually decreased by the interplay of capillary and rheological processes. We have previously proposed to describe the evolution of the pore-size distribution (PSD) with the Fokker–Planck equation (FPE). The coefficients of this equation quantify the drift, dispersion, and degradation processes acting upon the PSD. An analytical solution for the PSD is presented for the case where drift and degradation coefficients depend on time, and the dispersion coefficient is proportional to the drift coefficient. These coefficients can be estimated from independent measurements of the PSD or (surrogate) water retention data or from mechanistic models. In this paper, we illustrate the application of the pore-size evolution model for: (i) a generic drift coefficient, (ii) static water retention data for soils under different tillage regimes, and (iii) dynamic hydraulic data for a soil subject to a sequence of wetting and drying cycles. These applications show the viability of our approach to model pore-size evolution. However, the development and application of the model is hampered by a lack of definitive data on soil structural and hydraulic dynamics.

@article{p2002-Leij-Ghezzehei-Or,
  author = {Leij, FJ and Ghezzehei, TA and Or, D},
  date-modified = {2018-05-31 01:36:25 +0000},
  journal = {Soil and Tillage Research},
  status = {published},
  keywords = {Soil hydraulic properties, Compaction, Wetting, Drying, Pore-size distribution, Analytical solution},
  number = {1-2},
  pages = {61-78},
  researchgate = {https://www.researchgate.net/publication/222696315_Modeling_the_dynamics_of_the_soil_pore-size_distribution_Soil_Tillage_Reseach},
  pdf = {https://www.sciencedirect.com/science/article/pii/S0167198701002574/pdfft?md5=4b527e89a8a8936c6acaf6c4e53e2470&pid=1-s2.0-S0167198701002574-main.pdf},
  doi = {10.1016/S0167-1987(01)00257-4},
  sort-word = {aggregation},
  title = {Modeling the dynamics of the soil pore-size distribution},
  volume = {64},
  year = {2002}
}

We studied the long-term impact of contrasting tillage and cover cropping systems on soil structure and hydraulic properties. Complete water retention and conductivity curves for the top (0–5 cm) and subsurface (20–25 cm) soils were characterized and contrasted. Dynamic water storage and retention were evaluated using numerical simulations in HYDRUS-2D software. Compared with standard-till (ST) and no-cover-crop (NO) systems, soils under no-till (NT) and cover cropping (CC) systems showed improved soil structure in terms of pore size distribution (PSD). Changes in hydraulic conductivity (K) under these systems led to an increased infiltration rate and water retention. However, NT and CC plots had lower water content at field capacity (33 kPa suction) and lower plant-available water (PAW) compared with ST and NO plots. Numerical simulations, however, showed that NT and CC plots have higher water storage (albeit marginal in magnitude) and water availability following irrigation. Because the numerical simulations considered retention and conductivity functions simultaneously and dynamically through time, they allow the capture of hydraulic states that are arguably more relevant to crops. The study concludes that the long-term practices of NT and CC systems were beneficial in terms of changes to the PSD. NT and CC systems also marginally improved soil water conductivity and storage at the plot scale.

@article{p2022-Araya-et-al-a,
  title = {Long-Term Impact of Cover Crop and Reduced Disturbance Tillage on Soil Pore Size and Soil Water Storage},
  author = {Araya, S. N. and Mitchell, J. P. and W., Hopmeans J. and Ghezzehei, T. A.},
  journal = {SOIL},
  volume = {8},
  pages = {177–198},
  status = {published},
  doi = {10.5194/soil-8-177-2022},
  pdf = {https://soil.copernicus.org/articles/8/177/2022/soil-8-177-2022.pdf},
  year = {2022}
}

Subsurface carbon stocks are a prime target for efforts to increase soil carbon storage for climate change mitigation and improving soil health. However, subsurface carbon (C) dynamics are not well understood, especially in soils under long term intensive agricultural management. We compared subsurface C dynamics in tomato-corn rotations after 25 years of differing C and nutrient management in the California Central Valley: CONV (mineral fertilizer), CONV+WCC (mineral fertilizer + cover crops) and ORG (composted poultry manure + cover crops). Our results showed a  19 Mg/ha increase in SOC stocks down to 1 m under ORG systems, no significant SOC increases under CONV+WCC or CONV systems, and the accumulation of carboxyl rich C in the subsurface (60–100 cm) horizons of all systems. Systems also had greater amounts of aromatic carbon in the order ORG>CONV+WCC>CONV. We identified a potential interaction between cover crops and compost, theorizing that increased macropores from cover crop roots facilitate the transport of soluble C and nutrients into the subsurface, thereby increasing stocks. These results demonstrate the potential for subsurface carbon storage in tilled agricultural systems and highlight a potential pathway for increasing carbon transport and storage in subsurface soil layers.

@article{soil-2021-19,
  author = {Rath, D. and Bogie, N. and Deiss, L. and Parikh, S. and Wang, D. and Ying, S. and Tautges, N. and Berhe, A. A. and Ghezzehei, Teamrat A. and Scow, K.},
  title = {Synergy between compost and cover crops leads to increased subsurface soil carbon storage},
  journal = {SOIL},
  year = {2022},
  status = {published},
  volume = {8},
  pages = {59–83},
  pdf = {https://soil.copernicus.org/articles/8/59/2022/soil-8-59-2022.pdf},
  mendeley = {https://www.mendeley.com/catalogue/642cdcb9-42d7-3bf0-b926-29c1f2eb24c5/},
  doi = {10.5194/soil-8-59-2022}
}

Soil science is one of the least diverse subdisciplines within the agricultural, earth, and natural sciences. Representation within soil science does not currently reflect demographic trends in the U.S. We synthesize available data on the representation of historically marginalized groups in soil science in the U.S. and identify historical mechanisms contributing to these trends. We review education and employment information within academic and the federal government, land‐grant university participation, and available Soil Science Society of America (SSSA) membership data to gain insight into the current state of representation within soil sciences and implications for the future of this discipline. Across all domains of diversity, historically marginalized groups are underrepresented in soil science. We provide recommendations toward recognizing diversity within the field, improving and encouraging diversity within the SSSA, and suggested responses for both individuals and institutions toward improving diversity, equity, and inclusion.

@article{p2021-Carteret-al,
  author = {Carter, T.L. and Jennings, L.L. and Pressler, Y. and Gallo, A. C. and Berhe, A. A. and Marín-Spiotta, E. and Shepard, C. and Ghezzehei, T. A. and Vaughan., K. L.},
  title = {Towards diverse representation and inclusion in soil science in the United States.(Invited Commentary)},
  journal = {Soil Science Society of America Journal},
  volume = {},
  year = {2020},
  number = {1-6},
  pages = {},
  keywords = {antiracist, diversity, hostile climates, race, racism},
  doi = {10.1002/saj2.20210},
  pdf = {https://acsess.onlinelibrary.wiley.com/doi/epdf/10.1002/saj2.20210},
  mendeley = {https://www.mendeley.com/catalogue/c94110d7-78aa-3804-b08d-409e2acc5e2b/},
  status = {published}
}

Silt-sized aggregates (2–53 μm) can store a high percentage of organic matter (OM) in agricultural soils. This study aimed to determine whether additions of charcoal and CaCO3 may enhance the retention of organic C (OC) and total N (Nt) in silt-sized aggregates. We used artificial soil mixtures without a silt component (89% sand, 10% clay, 1% OM) to emulate sandy soils with little natural structure. Charcoal and/or CaCO3 were added, and the resulting mixtures were incubated for 16 wk in the dark. The newly formed silt-sized fraction was separated and analyzed for OC and Nt concentrations and characterized using FTIR and scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS). Compared to the control treatment, CaCO3 addition had no positive effects on C and N retention in the silt-sized fraction (17–20 g kg−1 OC, 0.15–0.17 g kg−1 Nt) whereas the silt-sized fraction from treatments with charcoal additions showed significantly higher OC and Nt concentrations (50–56 g kg−1 OC, 0.31–0.85 g kg−1 Nt). Silt-sized fractions from the charcoal treatments also showed a significant increase in the proportion of C=O groups. These initial results justify more detailed investigations into the improvement of the structure and nutrient retention of sandy soils by charcoal and CaCO3 applications.

@article{p2014-Kaiser-et-al,
  author = {Kaiser, Michael and Ghezzehei, Teamrat A. and Kleber, Markus and Myrold, David D. and Berhe, Asmeret Asefaw},
  date-modified = {2018-05-27 21:14:46 +0000},
  doi = {10.2136/sssaj2014.04.0146},
  journal = {Soil Science Society of America Journal},
  status = {published},
  number = {5},
  pages = {1624-1631},
  researchgate = {https://www.researchgate.net/publication/265602694_Influence_of_Calcium_Carbonate_and_Charcoal_Applications_on_Organic_Matter_Storage_in_Silt-Sized_Aggregates_Formed_during_a_Microcosm_Experiment},
  title = {Influence of Calcium Carbonate and Charcoal Applications on Organic Matter Storage in Silt-Sized Aggregates Formed during a Microcosm Experiment},
  volume = {78},
  year = {2014},
  bdsk-url-1 = {https://doi.org/10.2136%2Fsssaj2014.04.0146},
  bdsk-url-2 = {http://dx.doi.org/10.2136/sssaj2014.04.0146},
  bdsk-url-3 = {https://doi.org/10.2136/sssaj2014.04.0146}
}

Direct characterization of hysteresis in water retention (WR) is typically cumbersome and time consuming. Thus, such data are scarce, and even when available are typically ignored in unsaturated flow modeling. One reason for disregard of this ubiquitous and significant feature of WR is lack of a universally applicable index for the degree of hysteresis that allows a priori assessment of its effect on flow. In this note we show that the mismatch between the hydraulic capacity functions of the primary drainage and imbibition curves can serve as generalized index for degree of hysteresis (H). Moreover, we showed that hysteresis indices of a broad range of soils are linearly related with the natural-logarithm of the van Genuchten n parameter (r^2 = 0.73). This model allows predicting the degree of hysteresis and the missing hysteresis branch using only wetting or drying water retention data. The robustness of the proposed index was illustrated by comparing it with error in simulated moisture redistribution in a horizontal column that arises from ignoring hysteresis.

@article{p2011-Gebrenegus-Ghezzehei,
  author = {Gebrenegus, Thomas and Ghezzehei, Teamrat A.},
  date-modified = {2018-05-30 21:20:08 +0000},
  doi = {10.2136/sssaj2011.0082N},
  journal = {Soil Science Society of America Journal},
  status = {published},
  number = {6},
  pages = {2122-2127},
  researchgate = {https://www.researchgate.net/publication/274221936_An_Index_for_Degree_of_Hysteresis_in_Water_Retention},
  sort-word = {method},
  title = {An Index for Degree of Hysteresis in Water Retention},
  volume = {75},
  year = {2011},
  bdsk-url-1 = {https://doi.org/10.2136/sssaj2011.0082N}
}

@article{p2008-Ghezzehei-b,
  author = {Ghezzehei, Teamrat A.},
  date-modified = {2018-05-27 20:01:54 +0000},
  journal = {Soil Science Society of America Journal},
  status = {published},
  number = {1},
  pages = {277},
  publisher = {Soil Science Society of America},
  title = {Book Review: Clay Swelling and Colloid Stability},
  volume = {72},
  sort-word = {review},
  year = {2008},
  bdsk-url-1 = {https://doi.org/10.2136%2Fsssaj2007.0024br},
  bdsk-url-2 = {http://dx.doi.org/10.2136/sssaj2007.0024br},
  bdsk-url-3 = {https://doi.org/10.2136/sssaj2007.0024br}
}

The loose and fragmented soil structure that results from tillage operations provides favorable physical conditions for plant growth. This desirable state is structurally unstable and deteriorates with time because of overburden, external stresses, and capillary forces. The objective of this study was to model these structural changes by coupling soil intrinsic rheological properties with geometry and arrangement of aggregates represented as monosized spheres. Calculations of interaggregate stresses and strains, and associated changes in density and porosity, were performed for a rhombohedral unit cell. Soil rheological properties determined by application of steady shear stress were used for calculations of strains under steady interaggregate stresses. The models developed herein correspond to the initial stage of deformation when discrete aggregates exist. At strains exceeding 0.12 the interaggregate voids are isolated and the current model no longer applies and an alternative approach is presented elsewhere. Unit cell calculations were up scaled to an aggregate-bed scale by considering a one-dimensional stack of unit cells, which allows only vertical stress transmission. The stress acting at an interaggregate contact is fully accommodated (dissipated) by viscous flow when it exceeds the yield stress (strength) of the aggregates. The stress is fully transmitted to subsequent unit cells when it is less than the yield stress. Plausibility of the models was demonstrated by illustrative examples that highlight the different features of the models. The results were in qualitative agreement with observations from the literature for deformation of either loose structure, and for highly dense cases close to maximal bulk density.

@article{p2003-Ghezzehei-Or,
  author = {Ghezzehei, Teamrat A. and Or, Dani},
  date-modified = {2018-05-27 19:55:55 +0000},
  journal = {Soil Science Society of America Journal},
  status = {published},
  number = {1},
  pages = {12},
  researchgate = {https://www.researchgate.net/publication/37450858_Pore-Space_Dynamics_in_a_Soil_Aggregate_Bed_under_a_Static_External_Load},
  title = {Pore-Space Dynamics in a Soil Aggregate Bed under a Static External Load},
  volume = {67},
  year = {2003}
}

Tillage causes soil fragmentation thereby increasing the proportion of interaggregate (structural) pore space. The resulting tilled layer tends to be structurally unstable as manifested by a gradual decrease in interaggregate porosity until a new equilibrium has been reached between external loads and internal capillary forces at a rate governed by the soil rheological properties. The soil pore-size distribution (PSD) will change accordingly with time. We have previously applied the Fokker-Planck equation (FPE) to describe the evolution of the PSD as the result of drift, dispersion, and degradation processes that affect the pore space in unstable soils. In this study, we provide closed-form solutions for PSD evolution, which can be used to predict temporal behavior of unsaturated soil hydraulic properties. Solutions and moments of the PSD were obtained in case: (i) drift and degradation coefficients depend on time and the dispersivity is constant and (ii) drift and dispersivity are also linearly related to pore size. Both solutions can model the reduction in pore size during the growing season while the second solution can account for a reduction in the dispersion of the PSD. The solutions for PSD were plotted for a mathematically convenient expression for the drift and degradation coefficients and for an expression derived from a model for soil aggregate coalescence. Experimental data on the settlement of a Millville (coarse-silty, carbonatic, mesic Typic Haploxeroll) silt loam during wetting and drying cycles were used to determine time-dependent drift and degradation coefficients according to this coalescence model. The solution for the PSD was used to independently predict the water retention curve, which exhibited a satisfactory agreement with experimental retention data at the end of two drying cycles.

@article{p2002-Leij-Ghezzehei-Or-b,
  author = {Leij, Feike J. and Ghezzehei, Teamrat A. and Or, Dani},
  date-modified = {2018-05-31 01:37:35 +0000},
  journal = {Soil Science Society of America Journal},
  status = {published},
  number = {4},
  pages = {1104},
  pdf = {https://www.researchgate.net/publication/37450945_Analytical_Models_for_Soil_Pore-Size_Distribution_After_Tillage},
  doi = {10.2136/sssaj2002.1104},
  sort-word = {aggregation},
  title = {Analytical Models for Soil Pore-Size Distribution After Tillage},
  volume = {66},
  year = {2002}
}

Tilled agricultural soils are in a constant state of change induced by variations in soil strength due to wetting and drying and compaction by farm implements. Changes in soil structure affect many hydraulic and transport properties; hence their quantification is critical for accu- rate hydrological and environmental modeling. This study highlights the role of soil rheology in determining time-dependent stress–strain relationships that are essential for prediction and analysis of structural changes in soils. The primary objectives of this study were (i) to extend a previously proposed aggregate-pair model to prediction of compaction under external steady or transient stresses and (ii) to provide experimentally determined rheological information for the above models. Rheological properties of soils and clay minerals were measured with a rotational rheometer with parallel-plate sensors. These measurements, under controlled steady shear stress application, have shown that wet soils have viscoplastic behavior with well-defined yield stress and nearly constant plastic viscosity. In contrast, rapid transient loading (e.g., passage of a tractor) is often too short for complete viscous dissipation of applied stress, resulting in an elastic (recoverable) component of deformation (viscoelastic behavior). Measured viscoelastic properties were expressed by complex viscosity and shear modulus whose components denote viscous energy dissipa- tion, and energy storage (elastic). Results show that for low water contents and fast loading (tractor speed), the elastic component of deformation increases, whereas with higher water contents, viscosity and shear modulus decrease. Steady and oscillatory stress application to an aggregate pair model illustrates potential use of rheological properties towards obtaining predictions of strains in soils.

@article{p2001-Ghezzehei-Or,
  author = {Ghezzehei, Teamrat A. and Or, Dani},
  date-modified = {2018-05-30 21:37:12 +0000},
  journal = {Soil Science Society of America Journal},
  status = {published},
  number = {3},
  pages = {624},
  pdf = {https://www.researchgate.net/publication/37450913_Rheological_Properties_of_Wet_Soils_and_Clays_under_Steady_and_Oscillatory_Stresses},
  sort-word = {aggregation, mechanics},
  title = {Rheological Properties of Wet Soils and Clays under Steady and Oscillatory Stresses},
  doi = {10.2136/sssaj2001.653624x},
  volume = {65},
  year = {2001}
}

Interplay between capillary, gravity and viscous forces in unsaturated fractures gives rise to a range of complex flow phenomena. Evidence of highly intermittent fluxes, preferential and sustainable flow pathways lead to potentially significant flow focusing of concern for regulatory and management of water resources in fractured rock formations. In previous work[Ghezzehei TA,Or D.: Water Resour. Res. In Review(2005)] we developed mechanistic models for formation, growth and detachment of liquid bridges in geometrical irregularities within fractures. Such discrete and intermittent flows present a challenge to standard continuum theories. Our focus here is on predicting travel velocities of detached liquid elements and their interactions with fracture walls. The scaling relationships proposed by Podgorski et al. [Podgorski, T., et al.: Phys. Rev. Lett. 8703(3), 6102-NIL_95 (2001)] provide a general framework for processes affecting travel velocities of discrete liquid elements in fractures, tubes, and in coarse porous media. Comparison of travel velocity and distance by discrete bridges relative to equivalent continuous film flow reveal significantly faster and considerably larger distances traversed by liquid bridges relative to liquid films. Coalescence and interactions between liquid bridges result in complex patterns of travel times and distances. Mass loss on rough fracture surfaces shortens travel distances of an element; however, results show that such retardation provides new opportunities for coalescence of subsequent liquid elements traveling along the same path, resulting in mass accumulation and formation of larger liquid elements traveling larger distances relative to smooth fracture surfaces. Such flow focusing processes may be amplified considering a population of liquid bridges within a fracture plane and mass accumulation in fracture intersections.

@article{p2007-Or-Ghezzehei,
  author = {Or, Dani and Ghezzehei, Teamrat A.},
  date-modified = {2018-05-27 20:16:57 +0000},
  doi = {10.1007/s11242-006-9060-9},
  journal = {Transport in Porous Media},
  status = {published},
  keywords = {Intermittent flow, Fracture ,Dripping, Liquid bridge, Transport},
  number = {1},
  pages = {129-151},
  researchgate = {https://www.researchgate.net/publication/226126078_Traveling_liquid_bridges_in_unsaturated_fractured_porous_media},
  title = {Traveling liquid bridges in unsaturated fractured porous media},
  volume = {68},
  year = {2007},
  bdsk-url-1 = {https://doi.org/10.1007/s11242-006-9060-9}
}

Soil water infiltration is a critical process in the soil water cycle and agricultural practices, especially when wastewater is used for irrigation. Although research has been conducted to evaluate the changes in the physical and chemical characteristics of soils irrigated by treated wastewater, a quantitative analysis of the effects produced on the infiltration process is still lacking. The objective of this study is to address this issue. Field experiments previously conducted on three adjacent field plots characterized by the same clayey soil but subjected to three different irrigation treatments have been used. The three irrigation conditions were: non-irrigated (natural conditions) plot, irrigated plot with treated wastewater for two years, and irrigated plot with treated wastewater for five years. Infiltration measurements performed by the Hood infiltrometer have been used to estimate soil hydraulic properties useful to calibrate a simplified infiltration model widely used under ponding conditions, that were existing during the irrigation stage. Our simulations highlight the relevant effect of wastewater usage as an irrigation source in reducing cumulative infiltration and increasing overland flow as a result of modified hydraulic properties of soils characterized by a lower capacity of water drainage. These outcomes can provide important insights for the optimization of irrigation techniques in arid areas where the use of wastewater is often required due to the chronic shortage of freshwater.

@article{p2020-Albalasmeh-et-al,
  title = {Using Wastewater in Irrigation: The Effects on Infiltration Process in a Clayey Soil},
  author = {Albalasmeh, Ammar A. and Gharaibeh, Mamoun A. and Alghzawi, Ma’in Z. and Morbidelli, Renato and Saltalippi, Carla and Ghezzehei, Teamrat A. and Flammini, Alessia.},
  doi = {10.3390/w12040968},
  pdf = {https://www.mdpi.com/2073-4441/12/4/968/pdf},
  sort-word = {CO2 flux, Soil respiration, Soil Carbon, aggregation, modeling,biogeoscience},
  journal = {Water},
  status = {published},
  volume = {12},
  number = {4},
  pages = {968},
  year = {2020}
}

Abstract The constitutive relations of the Richardson-Richards equation encode the macroscopic properties of soil water retention and conductivity. These soil hydraulic functions are commonly represented by models with a handful of parameters. The limited degrees of freedom of such soil hydraulic models constrain our ability to extract soil hydraulic properties from soil moisture data via inverse modeling. We present a new free-form approach to learning the constitutive relations using physically constrained neural networks. We implemented the inverse modeling framework in a differentiable modeling framework, JAX, to ensure scalability and extensibility. For efficient gradient computations, we implemented implicit differentiation through a nonlinear solver for the Richardson-Richards equation. We tested the framework against synthetic noisy data and demonstrated its robustness against varying magnitudes of noise and degrees of freedom of the neural networks. We applied the framework to soil moisture data from an upward infiltration experiment and demonstrated that the neural network-based approach was better fitted to the experimental data than a parametric model and that the framework can learn the constitutive relations.

@article{p2024_bandai-b,
  author = {Bandai, Toshiyuki and Ghezzehei, Teamrat A. and Jiang, Peishi and Kidger, Patrick and Chen, Xingyuan and Steefel, Carl I.},
  title = {Learning Constitutive Relations From Soil Moisture Data via Physically Constrained Neural Networks},
  journal = {Water Resources Research},
  volume = {60},
  number = {7},
  pages = {e2024WR037318},
  keywords = {inverse modeling, soil hydraulic functions, physics-informed machine learning, neural networks, soil moisture},
  doi = {10.1029/2024WR037318},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2024WR037318},
  note = {e2024WR037318 2024WR037318},
  year = {2024}
}

Water retention curve (WRC) and hydraulic conductivity function (HCF) are essential information to model the movement of water in the soil using the Richardson-Richards equation (RRE). Although laboratory measurement methods of WRC and HCF have been well established, the lab-based WRC and HCF can not be used to model soil moisture dynamics in the field because of the scale mismatch. Therefore, it is necessary to derive the inverse solution of the RRE and estimate WRC and HCF from field measurement data. We are proposing a physics-informed neural networks (PINNs) framework to obtain the inverse solution of the RRE and estimate WRC and HCF from only volumetric water content measurements. The PINNs was constructed using three feedforward neural networks, two of which were constrained to be monotonic functions to reflect the monotonicity of WRC and HCF. The PINNs was trained using noisy synthetic volumetric water content data derived from the simulation of soil moisture dynamics for three soils with distinct textures. The PINNs could reconstruct the true soil moisture dynamics from the noisy data. As for WRC, the PINN could not precisely determine the WRCs. However, it was shown that the PINNs could estimate the HCFs from only the noisy volumetric water content data without specifying initial and boundary conditions and assuming any information about the HCF (e.g., saturated hydraulic conductivity). Additionally, we showed that the PINNs framework could be used to estimate soil water flux density with a broader range of estimation than the currently available methods.

@article{P2020-Bandai,
  author = {Bandai, Toshiyuki and Ghezzehei, Teamrat},
  title = {Physics-informed neural networks with monotocnicity constraints for Richardson-Richards equation--Estimation of constitutive relationships and soil water flux density from volumetric water content measurements.},
  journal = {Water Resources Research},
  volume = {57},
  number = {2},
  pages = {e2020WR027642},
  year = {2021},
  doi = {10.1029/2020WR027642},
  data = {https://github.com/ToshiyukiBandai/PINNs_RRE},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2020WR027642},
  keywords = {inverse method, machine learning , partial differential equation,physics‐informed neural networks,soil moisture,soil water flux density},
  status = {published},
  mendeley = {https://www.mendeley.com/catalogue/792322df-e0b2-3cc2-8826-2c8730d232f4/}
}

Water retention curve (WRC) and hydraulic conductivity function (HCF) are essential information to model the movement of water in the soil using the Richardson-Richards equation (RRE). Although laboratory measurement methods of WRC and HCF have been well established, the lab-based WRC and HCF can not be used to model soil moisture dynamics in the field because of the scale mismatch. Therefore, it is necessary to derive the inverse solution of the RRE and estimate WRC and HCF from field measurement data. We are proposing a physics-informed neural networks (PINNs) framework to obtain the inverse solution of the RRE and estimate WRC and HCF from only volumetric water content measurements. The PINNs was constructed using three feedforward neural networks, two of which were constrained to be monotonic functions to reflect the monotonicity of WRC and HCF. The PINNs was trained using noisy synthetic volumetric water content data derived from the simulation of soil moisture dynamics for three soils with distinct textures. The PINNs could reconstruct the true soil moisture dynamics from the noisy data. As for WRC, the PINN could not precisely determine the WRCs. However, it was shown that the PINNs could estimate the HCFs from only the noisy volumetric water content data without specifying initial and boundary conditions and assuming any information about the HCF (e.g., saturated hydraulic conductivity). Additionally, we showed that the PINNs framework could be used to estimate soil water flux density with a broader range of estimation than the currently available methods.

@article{p2020-Shillito,
  author = {Shillito, Rose and Berli, Markus and Ghezzehei, Teamrat},
  title = {Quantifying the Effect of Subcritical Water-repellency on Sorptivity: A Physically-based Model},
  journal = {Water Resources Research},
  doi = {10.1029/2020WR027942},
  volume = {56},
  number = {11},
  pages = {e2020WR027942},
  year = {2020},
  status = {published},
  pdf = {https://onlinelibrary.wiley.com/share/author/ZZEUQBHVP4JZ5ZJI2RIG?target=10.1029/2020WR027942},
  mendeley = {https://www.mendeley.com/catalogue/e9581a1c-e288-3004-a6ae-1bf642b02ed7/},
  data = {https://doi.org/10.21079/11681/38202},
  keywords = {soil water repellency, hydrophobicity ,contact angle, sorptivity, infiltration, post‐fire runoff}
}

Saturated hydraulic conductivity (Ks) is a fundamental soil property that regulates the fate of water in soils. Its measurement, however, is cumbersome and instead pedotransfer functions (PTFs) are routinely used to estimate it. Despite much progress over the years, the performance of current generic PTFs estimating Ks remains poor. Using machine learning, high‐performance computing, and a large database of over 18,000 soils, we developed new PTFs to predict Ks. We compared the performances of four machine learning algorithms and different predictor sets. We evaluated the relative importance of soil properties in explaining Ks. PTF models based on boosted regression tree algorithm produced the best models with root‐mean‐squared log‐transformed error in ranges of 0.4 to 0.3 (log10(cm/day)). The 10th percentile particle diameter (d10) was found to be the most important predictor followed by clay content, bulk density (ρb), and organic carbon content (C). The sensitivity of Ks to soil structure was investigated using ρb and C as proxies for soil structure. An inverse relationship was observed between ρb and Ks, with the highest sensitivity at around 1.8 g/cm3 for most textural classes. Soil C showed a complex relationship with Ks with an overall positive relation for fine‐textured and midtextured soils but an inverse relation for coarse‐textured soils. This study sought to maximize the extraction of information from a large database to develop generic machine learning‐based PTFs for estimating Ks. Models developed here have been made publicly available and can be readily used to predict Ks.

@article{p2019-Araya-Ghezzehei,
  author = {Araya, Samuel N. and Ghezzehei, Teamrat A.},
  journal = {Water Resources Research},
  status = {published},
  doi = {10.1029/2018WR024357},
  mendeley = {https://www.mendeley.com/catalogue/1d6f2e16-3c52-32b5-ae9a-70d1a5d1adff/},
  data = {10.6071/M3T95H},
  volume = {55},
  pages = {5715-5737},
  month = jul,
  sort-word = {modeling},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2018WR024357},
  keywords = {soil hydraulic conductivity, machine learning, pedotransfer function, soil structure, bulk density, organic carbon},
  title = {Using Machine Learning for Prediction of Saturated Hydraulic Conductivity and Its Sensitivity to Soil Structural Perturbations},
  year = {2019}
}

A new method was developed to measure soil consolidation by capillary suction in organic soils. This method differs from previous methods of measuring soil consolidation in that no external load is utilized and only the forces generated via capillary suction consolidate the soil matrix. This limits the degree of consolidation that can occur, but gives a more realistic ecological perspective on the response of organic soils to desiccation in the field. This new method combines the principles behind a traditional triaxial cell (for measurements of volume change), a pressure plate apparatus, (to facilitate drainage by capillary suction), and the permeameter, (to measure saturated hydraulic conductivity), and allows for simultaneous desaturation of the soil while monitoring desiccation induced volume change in the soil. This method also enables detection of historic limit of dryness. The historic limit of dryness is a novel concept that is unique to soils that have never experienced drying since their formation. It is fundamentally equivalent to the pre-compression stress of externally loaded soils. This method is particularly important for forecasting structural and hydrologic changes that may occur in soils that were formed in very wet regimes (e.g., wet meadows at the foot of persistent snow packs and permafrost peats) as they respond to a changing climate.

@article{p2015-Arnold-Ghezzehei,
  author = {Arnold, Chelsea and Ghezzehei, Teamrat A.},
  data = {10.6084/m9.figshare.1243716.v1},
  doi = {10.1002/2014WR015745},
  journal = {Water Resources Research},
  status = {published},
  keywords = {Ecosystems, Seasons, Soil respiration, Productivity, Spring, Winter, Carbon dioxide, Ecosystem functioning},
  month = sep,
  number = {1},
  pages = {e106058},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1002/2014WR015745},
  researchgate = {https://www.researchgate.net/publication/267875649_A_method_for_characterizing_desiccation-induced_consolidation_and_permeability_loss_of_organic_soils},
  sort-word = {method, mechanics},
  title = {A method for characterizing desiccation-induced consolidation and permeability loss of organic soils},
  volume = {51},
  year = {2015}
}

Prediction of water flow and transport processes in soils susceptible to structural alteration such as compaction of tilled agricultural lands or newly constructed landfills rely on accurate description of changes in soil unsaturated hydraulic conductivity. Recent studies have documented the critical impact of aggregate contact characteristics on water flow rates and pathways in unsaturated aggregated soils. We developed an analytical model for aggregate contact size evolution as a basis for quantifying effects of compression on saturated and unsaturated hydraulic conductivity of aggregated soil. Relating confined one‐dimensional sample strain with aggregate deformation facilitates prediction of the increase in interaggregate contact area and concurrent decrease in macropore size with degree of sample compression. The hydrologic component of the model predicts unsaturated hydraulic conductivity of a pack of idealized aggregates (spheres) on the basis of contact size and saturation conditions under prescribed sample deformation. Calculated contact areas and hydraulic conductivity for pairs of aggregates agreed surprisingly well with measured values, determined from compaction experiments employing neutron and X‐ray‐radiography and image analysis. Model calculations for a unit cell of uniform spherical aggregates in cubic packing were able to mimic some of the differences in saturated and unsaturated hydraulic conductivity observed for aggregates and bulk soil.

@article{p2008-Berli-et-al,
  author = {Berli, M. and Carminati, A. and Ghezzehei, T. A. and Or, D.},
  date-modified = {2018-05-27 20:26:59 +0000},
  doi = {10.1029/2007WR006501},
  journal = {Water Resources Research},
  status = {published},
  month = may,
  number = {5},
  pages = {W00C09},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2007WR006501},
  publisher = {American Geophysical Union ({AGU})},
  title = {Evolution of unsaturated hydraulic conductivity of aggregated soils due to compressive forces},
  volume = {44},
  year = {2008},
  bdsk-url-1 = {https://doi.org/10.1029%2F2007wr006501},
  bdsk-url-2 = {http://dx.doi.org/10.1029/2007wr006501},
  bdsk-url-3 = {https://doi.org/10.1029/2007wr006501}
}

One potential consequence of global climate change and rapid changes in land use is an increased risk of flooding. Proper understanding of floodwater infiltration thus becomes a crucial component of our preparedness to meet the environmental challenges of projected climate change. In this paper, we present the results of a long‐term infiltration experiment performed on fractured ash flow tuff. Water was released from a 3 × 4 m2 infiltration plot (divided into 12 square subplots) with a head of ∼0.04 m, over a period of ∼800 days. This experiment revealed peculiar infiltration patterns not amenable to current infiltration models, which were originally developed for infiltration into soils over a short duration. In particular, we observed that in part of the infiltration plot, the infiltration rate abruptly increased a few weeks into the infiltration tests. We suggest that these anomalies result from increases in fracture permeability during infiltration, which may be caused by swelling of clay fillings and/or erosion of infill debris. Interaction of the infiltration water with subsurface natural cavities (lithophysal cavities) could also contribute to such anomalies. This paper provides a conceptual model that partly describes the observed infiltration patterns in fractured rock and highlights some of the pitfalls associated with direct extension of soil infiltration models to fractured rock over a long period.

@article{p2008-Salve-Ghezzehei-Jones,
  author = {Salve, Rohit and Ghezzehei, Teamrat A. and Jones, Robert},
  date-modified = {2018-05-27 20:04:15 +0000},
  doi = {10.1029/2006WR005701},
  journal = {Water Resources Research},
  status = {published},
  keywords = {Infiltration, fractures, rock},
  month = jan,
  number = {1},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2006WR005701},
  researchgate = {https://www.researchgate.net/publication/251422689_Infiltration_into_fractured_bedrock},
  title = {Infiltration into fractured bedrock},
  volume = {44},
  year = {2008},
  bdsk-url-1 = {https://doi.org/10.1029%2F2006wr005701},
  bdsk-url-2 = {http://dx.doi.org/10.1029/2006wr005701},
  bdsk-url-3 = {https://doi.org/10.1029/2006wr005701}
}

Application of time domain reflectometry (TDR) in soil hydrology often involves the conversion of TDR‐measured dielectric permittivity to water content using universal calibration equations (empirical or physically based). Deviations of soil‐specific calibrations from the universal calibrations have been noted and are usually attributed to peculiar composition of soil constituents, such as high content of clay and/or organic matter. Although it is recognized that soil disturbance by TDR waveguides may have impact on measurement errors, to our knowledge, there has not been any quantification of this effect. In this paper, we introduce a method that estimates this error by combining two models: one that describes soil compaction around cylindrical objects and another that translates change in bulk density to evolution of soil water retention characteristics. Our analysis indicates that the compaction pattern depends on the mechanical properties of the soil at the time of installation. The relative error in water content measurement depends on the compaction pattern as well as the water content and water retention properties of the soil. Illustrative calculations based on measured soil mechanical and hydrologic properties from the literature indicate that the measurement errors of using a standard three‐prong TDR waveguide could be up to 10%. We also show that the error scales linearly with the ratio of rod radius to the interradius spacing.

@article{p2008-Ghezzehei,
  author = {Ghezzehei, Teamrat A.},
  date-modified = {2018-05-31 13:28:50 +0000},
  doi = {10.1029/2007WR006502},
  journal = {Water Resources Research},
  status = {published},
  keywords = {TDR, water content, compaction, measurement error},
  number = {8},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2007WR006502},
  sort-word = {method},
  title = {Errors in determination of soil water content using time domain reflectometry caused by soil compaction around waveguides},
  volume = {44},
  year = {2008},
  bdsk-url-1 = {https://doi.org/10.1029/2007WR006502}
}

The Gardner and van Genuchten models of relativepermeability are widely used in analytical and numerical solutions toflow problems. However, the applicability of the Gardner model to realproblems is usually limited, because empirical relative permeability datato calibrate the model are not routinely available. In contrast, vanGenuchten parameters can be estimated using more routinely availablematric potential and saturation data. However, the van Genuchten model isnot amenable to analytical solutions. In this paper, we introducegeneralized conversion formulae that reconcile these two models. Ingeneral, we find that the Gardner parameter alpha G is related to the vanGenuchten parameters alpha vG and n by alpha G/alpha vG  ; 1.3 n. Thisconversion rule will allow direct recasting of Gardner-based analyticalsolutions in the van Genuchten parameter space. The validity of theproposed formulae was tested by comparing the predicted relativepermeability of various porous media with measured values.

@article{p2007-Ghezzehei-Kneafsey-Su,
  author = {Ghezzehei, Teamrat A. and Kneafsey, Timothy J. and Su, Grace W.},
  date-modified = {2018-05-27 20:24:43 +0000},
  doi = {10.1029/2006WR005339},
  journal = {Water Resources Research},
  status = {published},
  month = oct,
  number = {10},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2006WR005339},
  researchgate = {https://www.researchgate.net/publication/236496415_Correspondence_of_the_Gardner_and_van_Genuchten-Mualem_relative_permeability_function_parameters},
  title = {Correspondence of the Gardner and van Genuchten-Mualem relative permeability function parameters},
  volume = {43},
  year = {2007},
  bdsk-url-1 = {https://doi.org/10.1029%2F2006wr005339},
  bdsk-url-2 = {http://dx.doi.org/10.1029/2006wr005339},
  bdsk-url-3 = {https://doi.org/10.1029/2006wr005339},
  bdsk-url-4 = {https://doi.org/10.1029/2006WR005339}
}

@article{p2006-Or-Ghezzehei,
  author = {Or, Dani and Ghezzehei, Teamrat A.},
  date-modified = {2018-05-27 20:15:53 +0000},
  doi = {10.1029/2006WR004994},
  journal = {Water Resources Research},
  status = {published},
  month = jul,
  number = {7},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2006WR004994},
  researchgate = {https://www.researchgate.net/publication/37451052_Comment_on_Computer_simulation_of_two-phase_immiscible_fluid_motion_in_unsaturated_complex_fractures_using_a_volume_of_fluid_method_by_Hai_Huang_Paul_Meakin_and_Moubin_Liu},
  sort-word = {commentary},
  title = {Comment on "Computer simulation of two-phase immiscible fluid motion in unsaturated complex fractures using a volume of fluid method" by Hai Huang, Paul Meakin, and Moubin Liu},
  volume = {42},
  year = {2006}
}

Flow diversion around subsurface cavities in unsaturated fractured media is important to numerous environmental and engineering applications. This paper provides analytical solutions to partial and complete flow diversion around cavities intersected by fractures under steady state conditions. It is focused on a typical trifracture junction located upstream from a cavity surface. Fractures are modeled as two‐dimensional porous media with an exponential relationship between the capillary pressure and unsaturated hydraulic conductivity. The solutions show that the vertical distance between the fracture end and the nearest junction (Z) and the slope of the unsaturated hydraulic conductivity (α) are by far the most important determinants of flow diversion. In fact, the product of Z and α enters the threshold flux and liquid entry flux equations as a dimensionless sorptive length (s). This relationship between Z and α is shown to have important implications for uncertainty and scalability of calibrated model parameters. The solutions given in this paper are expected to be directly applicable to cavities on the order of the fracture spacing.

@article{p2005-Ghezzehei-b,
  author = {Ghezzehei, Teamrat A.},
  date-modified = {2018-05-27 20:15:11 +0000},
  doi = {10.1029/2004WR003860},
  journal = {Water Resources Research},
  status = {published},
  month = nov,
  number = {11},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2004WR003860},
  researchgate = {https://www.researchgate.net/publication/228661472_Flow_diversion_around_cavities_in_fractured_media},
  title = {Flow diversion around cavities in fractured media},
  volume = {41},
  year = {2005}
}

In recent years, significant advances have been made in our understanding of the complex flow processes in individual fractures, aided by flow visualization experiments and conceptual modeling efforts. These advances have led to the recognition of several flow regimes in unsaturated individual fractures subjected to different initial and boundary conditions. For an idealized smooth fracture surface the most important regimes are film flow, rivulet flow, and sliding of droplets. The existence of such significantly dissimilar flow regimes has been a major hindrance in the development of self-consistent conceptual models of flow for single fracture surfaces that encompass all the flow regimes. The objective of this study is to delineate the existence of the different flow regimes in individual fracture surfaces. For steady state flow conditions, we developed physical constraints on the different flow regimes that satisfy minimum energy configurations, which enabled us to segregate the wide range of fracture flux (volumetric flow rate per fracture width) into several flow regimes. These are, in increasing order of flow rate, flow of adsorbed films, flow of sliding drops, rivulet flow, stable film flow, and unstable (turbulent) film flow. The scope of this study is limited to wide-aperture smooth fractures with the flow on the opposing sides of fracture being independent.

@article{p2005-Ghezzehei,
  author = {Ghezzehei, Teamrat A.},
  date-modified = {2018-05-27 20:14:34 +0000},
  doi = {10.1029/2004WR003164},
  journal = {Water Resources Research},
  status = {published},
  month = nov,
  number = {11},
  pages = {W11503},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/2004WR003164},
  researchgate = {https://www.researchgate.net/publication/228979913_Constraints_for_flow_regimes_on_smooth_fracture_surfaces},
  title = {Constraints for flow regimes on smooth fracture surfaces},
  volume = {40},
  year = {2005}
}

Flow processes in unsaturated fractures considerably differ from flow in rock matrix because of the dominance of gravitational forces, accentuated by variations in fracture geometry. This gives rise to liquid fragmentation, fingering, and intermittent flow regimes that are not amenable to standard continuum representation. We develop an alternative modeling framework to describe the onset of liquid fragmentation and subsequent flow behavior of discrete liquid clusters. The transition from a slowly growing anchored liquid element to a finger‐forming mobile liquid element is estimated from the force balance between retarding capillary forces dominated by contact angle hysteresis and suspended liquid weight. A model for liquid fragmentation within the fracture plane (smooth and parallel walled fractures) for given a steady input flux and aperture size is developed and tested. Predictions of sizes and detachment intervals of liquid elements are in good agreement with experimental results. The results show that the mass of detached liquid element is only weakly related to flow rate but increases with fracture aperture size. Periodic discharge similar to that experimentally observed is a result of the interplay between capillary, viscous, and gravitational forces. We show that the presence of even a few irregularities in a fracture plane may induce complicated flux patterns downstream. Similar erratic fluxes are observed in studies involving gravity‐driven unsaturated flow.

@article{p2005-Ghezzehei-Or,
  author = {Ghezzehei, TA and Or, D},
  date-modified = {2018-05-27 20:11:40 +0000},
  doi = {10.1029/2004WR003834},
  journal = {Water Resources Research},
  status = {published},
  keywords = {fracture, intermittent, episodic, finger, dripping, vadose zone},
  number = {12},
  pages = {W12406},
  researchgate = {https://www.researchgate.net/publication/37451025_Liquid_fragmentation_and_intermittent_flow_regimes_in_unsaturated_fractured_media},
  title = {Liquid fragmentation and intermittent flow regimes in unsaturated fractured media},
  volume = {41},
  year = {2005}
}

This study deals with deformation of small pores in wet soils of relatively high bulk density such as in the final settlement phase of tilled or disturbed soils. Pore deformation was modeled by volume reduction of spherical voids embedded in a homogenous soil matrix. External constant stress and overburden were considered as steady stresses because the change in interaggregate contact stress under overburden is slow compared to the associated strain rate. In contrast, stress due to passage of farm implements was considered as transient because the rate of change of interaggregate stress is comparable with the strain rate. Rheological behavior of the soil matrix under steady and transient stresses was obtained from independent rheological measurements. Experimental data from the literature were used to illustrate the model. Model predictions of relative density compared favorably with experimental data for constant stress application as well as for constant strain rate experiments. Results showed that the rate of densification decreased as the relative density approached unity (complete pore closure) and the relative stress required for driving densification increased exponentially with increasing relative density.

@article{p2003-Ghezzehei-Or-b,
  author = {Ghezzehei, Teamrat A. and Or, Dani},
  date-modified = {2018-05-27 19:55:55 +0000},
  journal = {Water Resources Research},
  status = {published},
  month = mar,
  number = {3},
  sort-word = {aggregation},
  title = {Stress-induced volume reduction of isolated pores in wet soil},
  doi = {10.1029/2001wr001137},
  volume = {39},
  year = {2003}
}

Tillage operations disrupt surface layers of agricultural soils, creating a loosened structure with a substantial proportion of interaggregate porosity that enhances liquid and gaseous exchange properties favorable for plant growth. Unfortunately, such desirable soil tilth is structurally unstable and is susceptible to change by subsequent wetting and drying processes and other mechanical stresses that reduce total porosity and modify pore size distribution (PSD). Ability to model posttillage dynamics of soil pore space and concurrent changes in hydraulic properties is important for realistic predictions of transport processes through this surface layer. We propose a stochastic modeling framework that couples the probabilistic nature of pore space distributions with physically based soil deformation models using the Fokker‐Planck equation (FPE) formalism. Three important features of soil pore space evolution are addressed: (1) reduction of the total porosity, (2) reduction of mean pore radius, and (3) changes in the variance of the PSD. The proposed framework may be used to provide input to hydrological models concerning temporal variations in near‐surface soil hydraulic properties. In a preliminary investigation of this approach we link a previously proposed mechanistic model of soil aggregate coalescence to the stochastic FPE framework to determine the FPE coefficients. An illustrative example is presented which describes changes in interaggregate pore size due to wetting‐drying cycles and the resulting effects on dynamics of the soil water characteristic curve and hydraulic conductivity functions.

@article{p2000-Or-etal,
  author = {Or, D and Leij, FJ and Snyder, V and Ghezzehei, T. A.},
  date-modified = {2018-05-30 21:36:47 +0000},
  journal = {Water Resources Research},
  status = {published},
  month = jul,
  number = {7},
  pages = {1641-1652},
  researchgate = {https://www.researchgate.net/publication/37450896_Stochastic_model_for_post-tillage_soil_pore_size_evolution},
  sort-word = {aggregation},
  title = {Stochastic model for posttillage soil pore space evolution},
  volume = {36},
  year = {2000},
  doi = {10.1029/2000WR900092}
}

Water dripping into subterranean cavities within fractured porous media is studied in order to improve estimates of dripping rates, drop sizes, and chemical composition of droplets that could affect long‐term integrity of waste disposal canisters placed in caverns. Steady state liquid flux in fracture surfaces supported by flow in partially liquid‐filled grooves and liquid films in adjacent planes was calculated as a function of the matric potential (vapor pressure) of the fracture. At an intersection of a vertical fracture with a wider cavity the liquid flux feeds a growing pendant drop that eventually detaches. Equilibrium state size and approximate shape of liquid drops suspended from the cavity ceiling were determined from lateral and vertical force balance considering capillarity, gravity, and hydrostatic pressure. A one‐dimensional, viscous extension model with appropriate gravitational and surface tension components was employed to determine dripping rate from specified fracture roughness geometry as a function of matric potential (flux). The effect of evaporation from drop surface during drop formation was incorporated; the resulting alterations in drop volume, dripping rate, and drop solute concentration were determined. To facilitate experimental testing of the proposed model, a decoupled solution that considers independently controlled flux and evaporation is presented. Under evaporative conditions, dripping in finite period is possible only when volumetric flux exceeds evaporative demand. Calculations indicate that dripping rate and solute concentration are extremely sensitive to ambient matric potential. The results of this work may be extended to study other phenomena including formation and growth of stalactites and rivulet flow in cave ceilings.

@article{p2000-Or-Ghezzehei,
  author = {Or, D and Ghezzehei, T. A.},
  date-modified = {2018-05-30 21:36:21 +0000},
  journal = {Water Resources Research},
  status = {published},
  month = feb,
  number = {2},
  pages = {381-393},
  researchgate = {https://www.researchgate.net/publication/37450895_Dripping_into_cavities_from_unsaturated_fractures_under_evaporative_conditions},
  sort-word = {nuclear},
  title = {Dripping into subterranean cavities from unsaturated fractures under evaporative conditions},
  volume = {36},
  year = {2000},
  pdf = {https://agupubs.onlinelibrary.wiley.com/doi/epdf/10.1029/1999WR900311},
  doi = {10.1029/1999WR900311}
}

The desired soil structure following tillage of agricultural soils is often unstable and susceptible to coalescence of aggregates and reduction of interaggregate porosity due to wetting and drying cycles. This process of aggregate rejoining was modeled by equating the rate of work done by liquid‐vapor menisci, to the rate of energy dissipation due to viscous deformation of a pair of spherical aggregates. The nonlinearity of wet soil viscous flow behavior was accounted for by introducing a Bingham rheological model. A natural outcome of the analysis was the formulation of a mathematical condition for the onset and termination of coalescence based on soil strength at specified water content. The condition states that sufficient energy in excess of soil strength (yield stress) must be available for coalescence to proceed. The rate of aggregate coalescence is proportional to available energy and is inversely related to the coefficient of plastic viscosity. Transport of wet soil to the periphery of the interaggregate contact by viscous flow leads to smoothing of the neck, resulting in pore closure, on the one hand, and restricting the minimum matric potential that can be achieved, on the other. The interplay between rheology and geometry prevent coalescence from proceeding indefinitely. Independently determined soil rheological properties were used to illustrate the use of the model. Coalescence under constant water content and during wetting‐drying cycles was calculated. Comparison of data from experiments on one‐dimensional, aggregate bed settlement has shown reasonable agreement with the model predictions.

@article{p2000-Ghezzehei-Or,
  author = {Ghezzehei, T. A. and Or, D.},
  date-modified = {2018-05-30 21:21:45 +0000},
  journal = {Water Resources Research},
  status = {published},
  month = feb,
  number = {2},
  pages = {367-379},
  researchgate = {https://www.researchgate.net/publication/37450893_Dynamics_of_soil_aggregate_coalescence_governed_by_capillary_and_rheological_processes},
  sort-word = {soil structure, aggregation},
  title = {Dynamics of soil aggregate coalescence governed by capillary and rheological processes},
  volume = {36},
  year = {2000},
  doi = {10.1029/1999WR900316}
}

Application of biochar amendments in agricultural systems has received much attention in recent years. In this study, we assess the 5-year impacts of biochar application on soil water and plant interactions for an irrigated fresh market tomato (Solanum lycopersicum) and a rainfed pasture (Poaceae) cropping system. In particular, we focus on three varieties of locally produced biochar from agricultural waste materials—almond shell, walnut shell, and almond pruning residues that are pyrolyzed using a mobile pyrolysis unit. We used the soil hydrological model HYDRUS-1D to explicitly track seasonal and annual soil water fluxes through changes in water retention, drainage, evaporation, and plant water uptake under biochar application. Modeling results show that the application of biochar at 5% increased soil water availability within the top 20 cm for a rainfed system, irrespective of biochar amendment type. This is clearly indicative of higher plant water uptake and greater water use efficiency (WUE) under biochar application. In contrast, a similar biochar amendment for the irrigated system did not affect WUE, instead reducing seasonal soil evaporation loss and thereby reducing irrigation demand. In both cropping systems, year-to-year variability in precipitation significantly impacted the total amount of water saved under biochar application with certain amendments retaining more water than others. Given that biochar application increased water retention irrespective of cropping systems, we further used a simple approach to determine yield trade-off, if any, between control and biochar treatments. Our economic balance clearly demonstrates that the water saved by amending soil with biochar does not offset the yield disparity if compensated with carbon credits and therefore, application of biochar should be actively considered for both its direct and indirect benefits to potential greenhouse gas mitigation (e.g., diverting orchard waste from open burning), water savings, and soil health.

@article{p2023-Taho-et-al,
  author = {Thao, Touyee and Arora, Bhavna and Ghezzehei, Teamrat A.},
  journal = {Vadose Zone Journal},
  pages = {e20266},
  title = {Impact of biochar amendments on soil water and plant uptake dynamics under different cropping systems},
  year = {2023},
  doi = {10.1002/vzj2.20266},
  pdf = {https://acsess.onlinelibrary.wiley.com/doi/epdf/10.1002/vzj2.20266}
}

Despite the vast extent of desert soils on the Earth’s surface, our understanding of the moisture dynamics of near-surface desert soils (top centimeters to a few meters) remains limited. A recent study introduced a HYDRUS-1D model to simulate water redistribution in a bare, sandy desert soil as a function of infiltration and evaporation. For soil conditions drier than pF 2, the model consistently underestimated evaporative fluxes and subsequently overestimated moisture content in the near-surface soil. The goal of this study was to explore the use of the Peters-Durner-Iden (or PDI) instead of the original bimodal van Genuchten (or BVG) water retention and hydraulic conductivity functions to improve water redistribution simulations for drier soils in desert environments. By comparing measured and simulated moisture redistribution data, we found that the simulations of moisture redistribution were improved by employing PDI soil water retention functions instead of BVG soil water retention functions. In particular, simulations for volumetric moisture contents ranging between 6% and 10% (suction heads between pF 2 and pF 3.8 and saturation degrees between 19% and 32%, respectively) improved using PDI. Interestingly, using PDI instead of BVG hydraulic conductivity functions had no noticeable effect on the simulation results. This study also emphasized the importance of good-quality soil water retention data for the relevant soil moisture content range. In conclusion, the HYDRUS-1D model using PDI hydraulic functions can accurately predict moisture redistribution for bare, sandy soil at volumetric moisture contents as low as 6% (pF 3.8 or 19% saturation, respectively).

@article{p2020-Luo-et-al-b,
  title = {Modeling Near-surface Water Redistribution in a Desert Soil},
  author = {Luo, Yuan and Ghezzehei, Teamrat A. and Yu, Zhongbo and Berli, Markus},
  journal = {Vadose Zone Journal},
  status = {published},
  year = {2020},
  volume = {19},
  number = {1},
  pages = {e20081},
  doi = {10.1002/vzj2.20081},
  pdf = {https://acsess.onlinelibrary.wiley.com/doi/epdf/10.1002/vzj2.20081},
  mendeley = {https://www.mendeley.com/catalogue/2498ed79-9bbd-32b8-99b5-47e9e01996c5/}
}

Although desert soils cover approximately one third of the Earth’s land surface, surprisingly little is known about their physical properties and how those properties affect the ecology and hydrology of arid environments. The main goal of this study was to advance our understanding of desert soil hydrodynamics. For this purpose, we developed a process-based component within HYDRUS-1D to describe the moisture dynamics of an arid zone soil as a function of water fluxes through the soil surface. A modified van Genuchten model for the dry end of the soil water retention curve was developed to better capture the basic flow processes for very dry conditions. A scaling method was further used to account for variabilities in water retention because of changes in the bulk density vs. depth. The model was calibrated and validated using hourly soil moisture, temperature, and mass data from a 3-m-deep weighing lysimeter of the Scaling Environmental Processes in Heterogeneous Arid Soils facility at the Desert Research Institute (Las Vegas, NV). Measurements and simulations during a 1-yr period agreed better under precipitation (wetting) than under evaporation (drying) conditions. Evaporation was better simulated for wet than for dry soil surface conditions. This was probably caused by vapor-phase exchange processes with the atmosphere, which were unaccounted for and need to be further explored. Overall, the model provides a promising first step toward developing a more realistic numerical tool to quantify the moisture dynamics of arid ecosystems and their role in climate change, plant growth, erosion, and recharge patterns.

@article{p2018-Dijkema-et-al,
  author = {Dijkema, J. and Koonce, J.E. and Shillito, R.M. and Ghezzehei, T.A. and Berli, M. and van der Ploeg, M.J. and van Genuchten, M.Th.},
  date-modified = {2018-11-14 13:15:15 -0800},
  doi = {10.2136/vzj2017.01.0035},
  journal = {Vadose Zone Journal},
  status = {published},
  number = {1},
  sort-word = {modeling},
  title = {Water Distribution in an Arid Zone Soil: Numerical Analysis of Data from a Large Weighing Lysimeter},
  volume = {17},
  year = {2018},
  bdsk-url-1 = {https://doi.org/10.2136%2Fvzj2017.01.0035},
  bdsk-url-2 = {http://dx.doi.org/10.2136/vzj2017.01.0035},
  bdsk-url-3 = {https://doi.org/10.2136/vzj2017.01.0035}
}

The remarkable complexity of soil and its importance to a wide range of ecosystem services presents major challenges to the modeling of soil processes. Although major progress in soil models has occurred in the last decades, models of soil processes remain disjointed between disciplines or ecosystem services, with considerable uncertainty remaining in the quality of predictions and several challenges that remain yet to be addressed. First, there is a need to improve exchange of knowledge and experience among the different disciplines in soil science and to reach out to other Earth science communities. Second, the community needs to develop a new generation of soil models based on a systemic approach comprising relevant physical, chemical, and biological processes to address critical knowledge gaps in our understanding of soil processes and their interactions. Overcoming these challenges will facilitate exchanges between soil modeling and climate, plant, and social science modeling communities. It will allow us to contribute to preserve and improve our assessment of ecosystem services and advance our understanding of climate-change feedback mechanisms, among others, thereby facilitating and strengthening communication among scientific disciplines and society. We review the role of modeling soil processes in quantifying key soil processes that shape ecosystem services, with a focus on provisioning and regulating services. We then identify key challenges in modeling soil processes, including the systematic incorporation of heterogeneity and uncertainty, the integration of data and models, and strategies for effective integration of knowledge on physical, chemical, and biological soil processes. We discuss how the soil modeling community could best interface with modern modeling activities in other disciplines, such as climate, ecology, and plant research, and how to weave novel observation and measurement techniques into soil models. We propose the establishment of an international soil modeling consortium to coherently advance soil modeling activities and foster communication with other Earth science disciplines. Such a consortium should promote soil modeling platforms and data repository for model development, calibration and intercomparison essential for addressing contemporary challenges.

@article{p2016-Vereecken-et-al,
  author = {Vereecken, H. and Schnepf, A. and Hopmans, J.W. and Javaux, M. and Or, D. and Roose, T. and Vanderborght, J. and Young, M.H. and Amelung, W. and Aitkenhead, M. and Allison, S.D. and Assouline, S. and Baveye, P. and Berli, M. and Br{\"u}ggemann, N. and Finke, P. and Flury, M. and Gaiser, T. and Govers, G. and Ghezzehei, T. and Hallett, P. and Franssen, H.J. Hendricks and Heppell, J. and Horn, R. and Huisman, J.A. and Jacques, D. and Jonard, F. and Kollet, S. and Lafolie, F. and Lamorski, K. and Leitner, D. and McBratney, A. and Minasny, B. and Montzka, C. and Nowak, W. and Pachepsky, Y. and Padarian, J. and Romano, N. and Roth, K. and Rothfuss, Y. and Rowe, E.C. and Schwen, A. and {\v{S}}im{\r{u}}nek, J. and Tiktak, A. and Dam, J. Van and van der Zee, S.E.A.T.M. and Vogel, H.J. and Vrugt, J.A. and W{\"o}hling, T. and Young, I.M.},
  date-modified = {2018-05-27 19:55:55 +0000},
  journal = {Vadose Zone Journal},
  status = {published},
  keywords = {Akaike information criterion, Bayesian model evidence, Bayesian information criterion, Bayesian model averaging, CLM, Community Land Model, DEM, digital elevation model, EnKF, Ensemble Kalman Filter, ET, evapotranspiration, GHG, greenhouse gases, GIS, geographic information system, GPS, global positioning system, IC, information criteria, ISMC, International Soil Modeling Consortium, KIC, Kashyap information criterion, LIDAR, Light Detection and Ranging, MCMC, Markov chain Monte Carlo, MRI, magnetic resonance imaging, MW, microwave spectrum, MWIR, mid-wave infrared spectrum, NIR, near-infrared spectrum, OTU, operational taxonomic units, pdf, probability density function, PSS, proximal soil sensing, PTF, pedotransfer function, SAR, Synthetic Aperture Radar, SDA, sequential data assimilation, SVAT, soil--vegetation--atmosphere transfer, SWIR, short-wave infrared spectrum, TE, treated effluents, TIR, thermal infrared spectrum, UAV, unmanned air vehicles, μCT, microcomputed tomography, VIS, visible spectrum, VSP, virtual soil platform},
  number = {5},
  researchgate = {https://www.researchgate.net/publication/303017539_Modeling_Soil_Processes_Review_Key_Challenges_and_New_Perspectives},
  sort-word = {synthesis, review},
  title = {Modeling Soil Processes: Review, Key Challenges, and New Perspectives},
  volume = {15},
  doi = {10.2136/vzj2015.09.0131},
  year = {2016},
  bdsk-url-1 = {https://doi.org/10.2136%2Fvzj2015.09.0131},
  bdsk-url-2 = {http://dx.doi.org/10.2136/vzj2015.09.0131},
  bdsk-url-3 = {https://doi.org/10.2136/vzj2015.09.0131}
}

Plant roots exude approximately 10% of the carbon assimilated through photosynthesis into the soil, a process referred to as rhizodeposition. Here, we show that the mucilaginous fraction of the rhizodeposits, referred to as mucilage, plays a crucial role on soil–plant water relation and it has the potential to increase plant drought tolerance. Mucilage is a gel that can absorb large volumes of water, altering the physical properties of the rhizosphere and maintaining the rhizosphere wet and conductive when the soil dries. It is hypothesized that mucilage acts as a hydraulic bridge between roots and the soil, facilitating root water uptake and maintaining transpiration in dry soils. By employing a simplified model of root water uptake coupled with mucilage dynamics, we found that in a sandy soil the benefit of mucilage in maintaining root water uptake commenced to manifest when the soil matric potential dropped below approximately −0.8 MPa. This critical matric potential varied with transpiration rate, root length, and exudation rate. Below the critical potential, mucilage maintained photosynthesis and resulted in a net gain of carbon. In summary, rhizodeposition modifies the physical soil environment and has an impact on transpiration and photosynthesis. In other words: water for carbon, but also carbon for water.

@article{p2016-Carminati-et-al,
  author = {Carminati, Andrea and Kroener, Eva and Ahmed, Mutez A. and Zarebanadkouki, Mohsen and Holz, Maire and Ghezzehei, Teamrat},
  date-modified = {2018-05-27 19:55:55 +0000},
  journal = {Vadose Zone Journal},
  status = {published},
  number = {2},
  researchgate = {https://www.researchgate.net/publication/298640122_Water_for_carbon_carbon_for_water},
  sort-word = {rhizosphere},
  title = {Water for Carbon, Carbon for Water},
  volume = {15},
  year = {2016}
}

Cavities excavated in unsaturated geological formations are important to activities such as nuclear waste disposal and mining. Such cavities provide a unique setting for simultaneous occurrence of seepage and evaporation. Previously, inverse numerical modeling of field liquid-release tests and associated seepage into cavities were used to provide seepage-related large-scale formation properties, ignoring the impact of evaporation. The applicability of such models was limited to the narrow range of ventilation conditions under which the models were calibrated. The objective of this study was to alleviate this limitation by incorporating evaporation into the seepage models. We modeled evaporation as an isothermal vapor diffusion process. The semiphysical model accounts for the relative humidity (RH), temperature, and ventilation conditions of the cavities. The evaporation boundary layer thickness (BLT) over which diffusion occurs was estimated by calibration against free-water evaporation data collected inside the experimental cavities. The estimated values of BLT were 5 to 7 mm for the open underground drifts and 20 mm for niches closed off by bulkheads. Compared with previous models that neglected the effect of evaporation, this new approach showed significant improvement in capturing seepage fluctuations into open cavities of low RH. At high relative-humidity values (>85%), the effect of evaporation on seepage was very small.

@article{p2004-Ghezzehei-et-al,
  author = {Ghezzehei, T. A. and Trautz, R. C. and Finsterle, S. and Cook, P. J. and Ahlers, C. F.},
  date-modified = {2018-05-27 20:09:29 +0000},
  doi = {10.2136/vzj2004.0806},
  journal = {Vadose Zone Journal},
  status = {published},
  month = aug,
  number = {3},
  pages = {806--818},
  researchgate = {https://www.researchgate.net/publication/236570656_Modeling_coupled_evaporation_and_seepage_in_ventilated_tunnels},
  sort-word = {nuclear waste},
  title = {Modeling Coupled Evaporation and Seepage in Ventilated Cavities},
  volume = {3},
  year = {2004}
}

Aggregation is a vital characteristic of soil structure that affects its physical and biogeochemical properties. Aggregation results from the cohesion of primary minerals with organic or inorganic constituents. It depends on the dynamic balance between binding and fragmentation. There are two classes of aggregation. Mechanical aggregates are formed instantly by external forces and are often unstable. Hierarchical aggregates result from slow binding and are stable. Characterization of aggregation includes size, shape, stability, configuration, and their arrangement within soil. The nature of hierarchical aggregation is inferred from size separation of aggregates. Aggregate stability indicates their ability to persist under disruptive forces.

@incollection{GHEZZEHEI2023,
  title = {Aggregation},
  booktitle = {Encyclopedia of Soils in the Environment},
  volume = {5: Soil Physics},
  edition = {2nd},
  publisher = {Elsevier},
  editor = {Goss, Michael J. and Oliver, Margaret},
  year = {2023},
  isbn = {978-0-12-409548-9},
  doi = {10.1016/B978-0-12-822974-3.00277-9},
  author = {Ghezzehei, Teamrat A.},
  keywords = {Aeration, Aggregate, Cementation, Clod, Imaging, Organic matter, Rhizosheath, Rhizosphere, Root, Sequestration, Soil health, Tillage, X-racy CT},
  sort-word = {aggregation}
}

@incollection{p2020-Berhe-Ghezzehei,
  author = {Berhe, A.A. and Ghezzehei, T. A.},
  booktitle = {In Multi-scale Biogeochemical Processes in Soil Ecosystems: Critical Reactions and Resilience to Climate Changes. },
  status = {published},
  editor = {Yang, Y. and Keiluweit, M. and Senesi, N. and Xing, B.},
  publisher = {CRC Press, Boca Raton, Fla.,},
  title = {Biogeochemistry in dynamic landscapes: Geochemical and mathematical constraints on the erosion-induced terrestrial carbon sink (Invited)},
  volume = {Volume 5: Biophysico-Chemical Processes in Environmental Systems},
  year = {2020}
}

@incollection{2018-Santos-et-al,
  author = {Santos, F. and Moreland, K. and Barnes, M. and Abney, R. and Jin, L. and Bogie, N. and Ghezzehei, T.A. and Berhe, A. A.},
  booktitle = {Ecosystem Consequences of Soil Warming: microbes, vegetation, fauna, and soil biogeochemistry},
  status = {published},
  editor = {Mohan, J.},
  publisher = {Elsevier},
  sort-word = {biogeoscience},
  title = {Response of soil physical properties to warming and implications for biogeochemical cycling of essential elements},
  year = {2018}
}

The rhizosphere, a thin layer of soil surrounding plant roots, plays a dynamic role in the hydrologic cycle by governing plant water and nutrient uptake. Study of rhizosphere soil structure formation due to mechanical processes has been limited by a lack of nondestructive techniques to quantify the dynamic nature of this region. In this chapter, we present recent developments in visualizing how growing roots modify their physical environment by moving soil particles, deforming aggregates and decreasing the amount of inter-aggregate pores while creating hydraulic pathways that connect neighboring soil aggregates using noninvasive, synchrotron X-ray microtomography (XMT). Image-processing tools were applied for quantifying root-induced rhizosphere alterations from XMT grayscale images as well as to transform XMT images into finite element meshes, building a bridge from nondestructive rhizosphere visualization to micromechanical and hydraulic simulations.

@incollection{2013-Arevena-et-al,
  author = {Aravena, Jazm{\'{\i}}n E. and Berli, Markus and Menon, Manoj and Ghezzehei, Teamrat A. and Mandava, Ajay K. and Regentova, Emma E. and Pillai, Natarajan S. and Steude, John and Young, Michael H. and Nico, Peter S. and Tyler, Scott W.},
  booktitle = {Soil{extendash}Water{extendash}Root Processes: Advances in Tomography and Imaging},
  status = {published},
  date-modified = {2018-06-01 19:47:40 +0000},
  doi = {10.2136/sssaspecpub61.c3},
  editor = {Anderson, Stephen H. and Hopmans, Jan W.},
  pages = {39-67},
  publisher = {Soil Science Society of America},
  title = {Synchrotron X-Ray Microtomography{extemdash}New Means to Quantify Root Induced Changes of Rhizosphere Physical Properties},
  year = {2013},
  bdsk-url-1 = {https://doi.org/10.2136%2Fsssaspecpub61.c3},
  bdsk-url-2 = {http://dx.doi.org/10.2136/sssaspecpub61.c3},
  bdsk-url-3 = {https://doi.org/10.2136/sssaspecpub61.c3}
}

@incollection{2012-Berhe-Ghezzehei-a,
  author = {Berhe, Asmeret Asefaw and Ghezzehei, Teamrat A.},
  booktitle = {Encyclopedia of Global Warming \& Climate Change},
  status = {published},
  date-modified = {2018-05-27 20:39:37 +0000},
  doi = {10.4135/9781452218564.n166},
  editor = {Philander, S. George},
  publisher = {SAGE},
  sort-word = {review},
  title = {Climatic Data, Sediment Records},
  year = {2012},
  bdsk-url-1 = {http://doi.org/10.4135/9781452218564.n166}
}

@incollection{2012-Ghezzehei-b,
  author = {Ghezzehei, TA},
  booktitle = {Handbook of Soil Sciences},
  status = {published},
  editor = {Huang, P.M. and Li, Y. and Sumner, M.E.},
  publisher = {CRC Press, Boca Raton, Fla.,},
  researchgate = {https://www.researchgate.net/publication/285160921_Soil_Structure},
  sort-word = {aggregation, review},
  title = {Soil Structure},
  volume = {1. Properties and Processes},
  year = {2012}
}

@incollection{2012-Berhe-Ghezzehei-b,
  author = {Berhe, Asmeret Asefaw and Ghezzehei, Teamrat A.},
  booktitle = {Encyclopedia of Global Warming \& Climate Change},
  status = {published},
  date-modified = {2018-05-27 20:40:35 +0000},
  doi = {10.4135/9781452218564.n70},
  editor = {Philander, S. George},
  publisher = {SAGE},
  sort-word = {review},
  title = {Biogeochemical Feedbacks},
  year = {2012},
  bdsk-url-1 = {http://doi.org/10.4135/9781452218564.n70}
}

The presence of subterranean holes creates a capillary barrier in an unsaturated environment. This phenomenon has been referred to as "Drift Shadow" and indicates a region that is sheltered from the downward percolating water. If the lateral hydraulic conductivity is insufficient to divert the water, fully saturated conditions are reached locally, and seepage occurs as the capillary barrier fails. Natural heterogeneities in hydrological properties can reduce the probability of seepage only if the flux is largely diverted around the drift. Previous numerical studies have been performed investigating various aspects of capillary barrier performance in engineered or naturally layered systems. Many authors examined the impact of heterogeneity on the distribution and rate of water seepage across a capillary barrier and into a drift, but the seepage exclusion problem has not been formally analyzed for fractured formations, in which the physical processes governing seepage in porous media also represent key factors. This paper analyzes the effect that a fracture network can have on the drift shadow. In a fractured environment, the effectiveness of the capillary barrier is determined by the capability of individual fractures to hold water by capillary forces and by the permeability and connectivity of the fracture network, which allow water to be diverted around the drift. The orientation of any individual fracture in relation to the opening, the discreteness and the anisotropy of\ldots

@incollection{2008-Cherubini-et-al,
  author = {Cherubini, Claudia and Ghezzehei, T. A. and Su, G. W.},
  booktitle = {Unsaturated Soils. Advances in Geo-Engineering},
  date-modified = {2018-05-27 16:47:52 +0000},
  editor = {Toll, DG and Augarde, CE and Gallipoli, D and Wheeler, SJ},
  journal = {Unsaturated Soils: Advances in Geo-Engineering},
  status = {published},
  pages = {761-764},
  publisher = {CRC Press},
  title = {The drift shadow phenomenon in an unsaturated fractured environment},
  year = {2008}
}

@incollection{2003-Berli-Ghezzehei-Or,
  author = {Berli, M. and Ghezzehei, Teamrat A. and Or, Dani},
  booktitle = {Environmental Geomechanics},
  status = {published},
  editor = {Vulliet, Laurent and Schrefler, Bernard and Laloui, Lyesse},
  pages = {245-},
  pdf = {https://books.google.com/books?id=41_SS4BOsV0C&pg=PA245&lpg=PA245&dq=Modeling+bulk+soil+compaction+using+a+Rheologically-based+pore+closure+model&source=bl&ots=79mQ6URRF3&sig=pvs9O0E7-hGDLVOnY7d-XyBKvi0&hl=en&sa=X&ved=0ahUKEwilh9vnnKbbAhX1FjQIHQQcC0QQ6AEILjAB},
  publisher = {EPFL Press},
  sort-word = {mechanics},
  title = {Modeling bulk soil compaction using a Rheologically-based pore closure model},
  year = {2003}
}

Aggregation is a vital characteristic of soil structure that affects its physical and biogeochemical properties. Aggregation results from the cohesion of primary minerals with organic or inorganic constituents. It depends on the dynamic balance between binding and fragmentation. There are two classes of aggregation. Mechanical aggregates are formed instantly by external forces and are often unstable. Hierarchical aggregates result from slow binding and are stable. Characterization of aggregation includes size, shape, stability, configuration, and their arrangement within soil. The nature of hierarchical aggregation is inferred from size separation of aggregates. Aggregate stability indicates their ability to persist under disruptive forces.

@incollection{GHEZZEHEI2023,
  title = {Aggregation},
  booktitle = {Encyclopedia of Soils in the Environment},
  volume = {5: Soil Physics},
  edition = {2nd},
  publisher = {Elsevier},
  editor = {Goss, Michael J. and Oliver, Margaret},
  year = {2023},
  isbn = {978-0-12-409548-9},
  doi = {10.1016/B978-0-12-822974-3.00277-9},
  author = {Ghezzehei, Teamrat A.},
  keywords = {Aeration, Aggregate, Cementation, Clod, Imaging, Organic matter, Rhizosheath, Rhizosphere, Root, Sequestration, Soil health, Tillage, X-racy CT},
  sort-word = {aggregation}
}

@incollection{p2020-Berhe-Ghezzehei,
  author = {Berhe, A.A. and Ghezzehei, T. A.},
  booktitle = {In Multi-scale Biogeochemical Processes in Soil Ecosystems: Critical Reactions and Resilience to Climate Changes. },
  status = {published},
  editor = {Yang, Y. and Keiluweit, M. and Senesi, N. and Xing, B.},
  publisher = {CRC Press, Boca Raton, Fla.,},
  title = {Biogeochemistry in dynamic landscapes: Geochemical and mathematical constraints on the erosion-induced terrestrial carbon sink (Invited)},
  volume = {Volume 5: Biophysico-Chemical Processes in Environmental Systems},
  year = {2020}
}

@incollection{2018-Santos-et-al,
  author = {Santos, F. and Moreland, K. and Barnes, M. and Abney, R. and Jin, L. and Bogie, N. and Ghezzehei, T.A. and Berhe, A. A.},
  booktitle = {Ecosystem Consequences of Soil Warming: microbes, vegetation, fauna, and soil biogeochemistry},
  status = {published},
  editor = {Mohan, J.},
  publisher = {Elsevier},
  sort-word = {biogeoscience},
  title = {Response of soil physical properties to warming and implications for biogeochemical cycling of essential elements},
  year = {2018}
}

The rhizosphere, a thin layer of soil surrounding plant roots, plays a dynamic role in the hydrologic cycle by governing plant water and nutrient uptake. Study of rhizosphere soil structure formation due to mechanical processes has been limited by a lack of nondestructive techniques to quantify the dynamic nature of this region. In this chapter, we present recent developments in visualizing how growing roots modify their physical environment by moving soil particles, deforming aggregates and decreasing the amount of inter-aggregate pores while creating hydraulic pathways that connect neighboring soil aggregates using noninvasive, synchrotron X-ray microtomography (XMT). Image-processing tools were applied for quantifying root-induced rhizosphere alterations from XMT grayscale images as well as to transform XMT images into finite element meshes, building a bridge from nondestructive rhizosphere visualization to micromechanical and hydraulic simulations.

@incollection{2013-Arevena-et-al,
  author = {Aravena, Jazm{\'{\i}}n E. and Berli, Markus and Menon, Manoj and Ghezzehei, Teamrat A. and Mandava, Ajay K. and Regentova, Emma E. and Pillai, Natarajan S. and Steude, John and Young, Michael H. and Nico, Peter S. and Tyler, Scott W.},
  booktitle = {Soil{extendash}Water{extendash}Root Processes: Advances in Tomography and Imaging},
  status = {published},
  date-modified = {2018-06-01 19:47:40 +0000},
  doi = {10.2136/sssaspecpub61.c3},
  editor = {Anderson, Stephen H. and Hopmans, Jan W.},
  pages = {39-67},
  publisher = {Soil Science Society of America},
  title = {Synchrotron X-Ray Microtomography{extemdash}New Means to Quantify Root Induced Changes of Rhizosphere Physical Properties},
  year = {2013},
  bdsk-url-1 = {https://doi.org/10.2136%2Fsssaspecpub61.c3},
  bdsk-url-2 = {http://dx.doi.org/10.2136/sssaspecpub61.c3},
  bdsk-url-3 = {https://doi.org/10.2136/sssaspecpub61.c3}
}

@incollection{2012-Berhe-Ghezzehei-a,
  author = {Berhe, Asmeret Asefaw and Ghezzehei, Teamrat A.},
  booktitle = {Encyclopedia of Global Warming \& Climate Change},
  status = {published},
  date-modified = {2018-05-27 20:39:37 +0000},
  doi = {10.4135/9781452218564.n166},
  editor = {Philander, S. George},
  publisher = {SAGE},
  sort-word = {review},
  title = {Climatic Data, Sediment Records},
  year = {2012},
  bdsk-url-1 = {http://doi.org/10.4135/9781452218564.n166}
}

@incollection{2012-Ghezzehei-b,
  author = {Ghezzehei, TA},
  booktitle = {Handbook of Soil Sciences},
  status = {published},
  editor = {Huang, P.M. and Li, Y. and Sumner, M.E.},
  publisher = {CRC Press, Boca Raton, Fla.,},
  researchgate = {https://www.researchgate.net/publication/285160921_Soil_Structure},
  sort-word = {aggregation, review},
  title = {Soil Structure},
  volume = {1. Properties and Processes},
  year = {2012}
}

@incollection{2012-Berhe-Ghezzehei-b,
  author = {Berhe, Asmeret Asefaw and Ghezzehei, Teamrat A.},
  booktitle = {Encyclopedia of Global Warming \& Climate Change},
  status = {published},
  date-modified = {2018-05-27 20:40:35 +0000},
  doi = {10.4135/9781452218564.n70},
  editor = {Philander, S. George},
  publisher = {SAGE},
  sort-word = {review},
  title = {Biogeochemical Feedbacks},
  year = {2012},
  bdsk-url-1 = {http://doi.org/10.4135/9781452218564.n70}
}

The presence of subterranean holes creates a capillary barrier in an unsaturated environment. This phenomenon has been referred to as "Drift Shadow" and indicates a region that is sheltered from the downward percolating water. If the lateral hydraulic conductivity is insufficient to divert the water, fully saturated conditions are reached locally, and seepage occurs as the capillary barrier fails. Natural heterogeneities in hydrological properties can reduce the probability of seepage only if the flux is largely diverted around the drift. Previous numerical studies have been performed investigating various aspects of capillary barrier performance in engineered or naturally layered systems. Many authors examined the impact of heterogeneity on the distribution and rate of water seepage across a capillary barrier and into a drift, but the seepage exclusion problem has not been formally analyzed for fractured formations, in which the physical processes governing seepage in porous media also represent key factors. This paper analyzes the effect that a fracture network can have on the drift shadow. In a fractured environment, the effectiveness of the capillary barrier is determined by the capability of individual fractures to hold water by capillary forces and by the permeability and connectivity of the fracture network, which allow water to be diverted around the drift. The orientation of any individual fracture in relation to the opening, the discreteness and the anisotropy of\ldots

@incollection{2008-Cherubini-et-al,
  author = {Cherubini, Claudia and Ghezzehei, T. A. and Su, G. W.},
  booktitle = {Unsaturated Soils. Advances in Geo-Engineering},
  date-modified = {2018-05-27 16:47:52 +0000},
  editor = {Toll, DG and Augarde, CE and Gallipoli, D and Wheeler, SJ},
  journal = {Unsaturated Soils: Advances in Geo-Engineering},
  status = {published},
  pages = {761-764},
  publisher = {CRC Press},
  title = {The drift shadow phenomenon in an unsaturated fractured environment},
  year = {2008}
}

@incollection{2003-Berli-Ghezzehei-Or,
  author = {Berli, M. and Ghezzehei, Teamrat A. and Or, Dani},
  booktitle = {Environmental Geomechanics},
  status = {published},
  editor = {Vulliet, Laurent and Schrefler, Bernard and Laloui, Lyesse},
  pages = {245-},
  pdf = {https://books.google.com/books?id=41_SS4BOsV0C&pg=PA245&lpg=PA245&dq=Modeling+bulk+soil+compaction+using+a+Rheologically-based+pore+closure+model&source=bl&ots=79mQ6URRF3&sig=pvs9O0E7-hGDLVOnY7d-XyBKvi0&hl=en&sa=X&ved=0ahUKEwilh9vnnKbbAhX1FjQIHQQcC0QQ6AEILjAB},
  publisher = {EPFL Press},
  sort-word = {mechanics},
  title = {Modeling bulk soil compaction using a Rheologically-based pore closure model},
  year = {2003}
}