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2. Continuum modeling of bioclogging of soil aquifer treatment systems segregating active and inactive biomass.

Author

Cifuentes, Edwin Saavedra, Furman, Alex, Rosenzweig, Ravid, and Packman, Aaron I.

Abstract

Soil aquifer treatment (SAT) systems are used to remove pollutants from treated wastewater and store freshwater for reclamation and reuse. However, the accumulation of microbial biomass in the soil pore space, bioclogging, reduces water infiltration and hinders SAT efficiency. Since SAT systems play a crucial role in maintaining water resilience by providing an alternative to freshwater supply, optimizing their operation is essential to ensure their effectiveness. However, SAT systems are complex and dynamic systems that involve coupled interactions between microbial activity, water infiltration, and bioclogging in unsaturated media. This work proposes a continuum model that accounts for all these processes while distinguishing between active and inactive biomass, with the latter split into labile and recalcitrant fractions. The model is used to replicate a laboratory column experiment of bioclogging under unsaturated conditions and to explore how to optimize the operation of SAT systems. Specifically, we determined optimal wetting and drying periods that maximize water input to the SAT system while maintaining nutrient transformation rates. Our simulations show that the dry/wet time ratio controls biomass spatial distribution over depth. In contrast, the dry time extent dictates the degree of recovery of the soil relative to its initial (clean) infiltration capacity. We discuss the potential of this model to be extended to larger-scale experiments and to inform daily SAT operations in the field. [ABSTRACT FROM AUTHOR]

Published
2024
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15. A Science Gateway for Wastewater-based Epidemiology - a Case Study of the World's Largest Wastewater Treatment Plant in Chicago

Author

Anuj Tiwari, Leisman, Katelyn Plaisier, Shrestha, Abhilasha, Poretsky, Rachel, Owens, Sarah, Dorevitch, Samuel, Grippo, Mark, Packman, Aaron I., Gesing, Sandra, and Catlett, Charlie

Subjects
Wastewater-based Epidemiology (WBE), COVID-19, Wastewater Treatment Plants (WWTPs), Gateways 2022, Gateways22, Science Gateway
Abstract

Wastewater-based epidemiology (WBE), got its start with polio and ascended in acceptance with COVID-19 pandemic has reaffirmed its potential to sound the alarm on both old opponents and new threats like monkeypox, which has been stated a public health emergency by the World Health Organization [Nelson 2022; Taylor 2022]. The revelations in our sewage have offered evidence for why developing and maintaining the infrastructure necessary for wastewater-data analysis, modeling, and visualization should be an urgent public health priority. Critical to success for WBE is the capability to rapidly translate data into results that are visualized and presented such that public health officials can make timely decisions, where the officials are typically accustomed to clinical data, and rarely have data science, microbiology, genetic sequencing, or environmental science experience. Science gateways uniquely equip research communities with shared data, applications, and resources, usually in a graphical user interface, that can be further customized to meet the requirements of a specific project. In the current study, we present the design of a science gateway-based WBE data analysis and visualization framework for accomplishing Centers for Disease Control and Prevention (CDC) standard weekly (or short-term) pandemic/disease reporting and an effective investigation report. This framework incorporates heterogeneous datasets that come in many varied formats from different organizations like sewer-specific information from the water resources department, wastewater treatment geographical details from wastewater treatment plants (WWTPs), clinical information from the health department, sequencing data and PCR data. The challenge is to clean up the data, check whether the values make sense or might have errors included to create profiles with information for CDC and in a further step to the public. Currently, we have developed a set of data analytic scripts and visualizations via Python, which can be started manually on command line. The logical workflow and the different data sources are complex to integrate. Thus, we have designed a framework based on Galaxy to automate steps and support the researchers in the project to access data and analysis without needing to use the command line. The design uses access via RESTful APIs or via FTP to different resources where appropriate. To demonstrate the feasibility of the proposed framework, a case study is presented with wastewater data collected from OCT 2020 to AUG 2021 in one of the world’s largest WWTP, Stickney WWTP, Chicago, USA. The Stickney WWTP serves 2 million residents in the central part of Chicago as well as 46 other communities within a 260-square-mile-area. Once deployed, the proposed framework can be immediately utilized by WBE scientists and commercial vendors as an on-demand science gateway for providing COVID-19 WBE services. This can also be further customized for adding new services for opioids, polio, monkeypox, etc.

Published
2022
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18. Organizational Principles of Hyporheic Exchange Flow and Biogeochemical Cycling in River Networks Across Scales

Author

Krause, Stefan, Abbott, Benjamin W., Baranov, Viktor, Bernal, Susana, Blaen, Phillip J., Datry, Thibault, Drummond, Jennifer D., Fleckenstein, Jan H., Gómez Vélez, Jesús, Hannah, David M., Knapp, Julia L.A., Kurz, Marie J., Lewandowski, Jörg, Martí, Eugènia, Mendoza-Lera, Clara, Milner, Alexander, Packman, Aaron I., Pinay, Gilles, Ward, Adam S., Zarnetske, Jay P., Krause, Stefan, Abbott, Benjamin W., Baranov, Viktor, Bernal, Susana, Blaen, Phillip J., Datry, Thibault, Drummond, Jennifer D., Fleckenstein, Jan H., Gómez Vélez, Jesús, Hannah, David M., Knapp, Julia L.A., Kurz, Marie J., Lewandowski, Jörg, Martí, Eugènia, Mendoza-Lera, Clara, Milner, Alexander, Packman, Aaron I., Pinay, Gilles, Ward, Adam S., and Zarnetske, Jay P.

Abstract

Hyporheic zones increase freshwater ecosystem resilience to hydrological extremes and global environmental change. However, current conceptualizations of hyporheic exchange, residence time distributions, and the associated biogeochemical cycling in streambed sediments do not always accurately explain the hydrological and biogeochemical complexity observed in streams and rivers. Specifically, existing conceptual models insufficiently represent the coupled transport and reactivity along groundwater and surface water flow paths, the role of autochthonous organic matter in streambed biogeochemical functioning, and the feedbacks between surface-subsurface ecological processes, both within and across spatial and temporal scales. While simplified approaches to these issues are justifiable and necessary for transferability, the exclusion of important hyporheic processes from our conceptualizations can lead to erroneous conclusions and inadequate understanding and management of interconnected surface water and groundwater environments. This is particularly true at the landscape scale, where the organizational principles of spatio-temporal dynamics of hyporheic exchange flow (HEF) and biogeochemical processes remain largely uncharacterized. This article seeks to identify the most important drivers and controls of HEF and biogeochemical cycling based on a comprehensive synthesis of findings from a wide range of river systems. We use these observations to test current paradigms and conceptual models, discussing the interactions of local-to-regional hydrological, geomorphological, and ecological controls of hyporheic zone functioning. This improved conceptualization of the landscape organizational principles of drivers of HEF and biogeochemical processes from reach to catchment scales will inform future river research directions and watershed management strategies.

Published
2022

20. Waking from Paralysis: Revitalizing Conceptions of Climate Knowledge and Justice for More Effective Climate Action

Author

Marion Suiseeya, Kimberly R., primary, O’connell, Margaret G., additional, Leoso, Edith, additional, Defoe, Marvin Shingwe Biness Neme, additional, Anderson, Alexandra, additional, Bang, Megan, additional, Beckman, Pete, additional, Boyer, Anne-Marie, additional, Dunn, Jennifer, additional, Gilbert, Jonathan, additional, Hester, Josiah, additional, Horton, Daniel E., additional, Jennings, Dylan Bizhikiins, additional, Kebec, Philomena, additional, Loeb, Nancy C., additional, Loew, Patricia, additional, Miller, William M., additional, Moffitt, Katie, additional, Packman, Aaron I., additional, Waasegiizhig Price, Michael, additional, Redbird, Beth, additional, Rogers, Jennie, additional, Sankaran, Rajesh, additional, Schwoch, James, additional, Silas, Pamala, additional, Twardowski, Weston, additional, and Zerega, Nyree, additional

Published
2022
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21. Microplastic accumulation in riverbed sediment via hyporheic exchange from headwaters to mainstems

Author

Drummond, Jennifer D., Schneidewind, Uwe, Li, Angang, Hoellein, Timothy J., Krause, Stefan, and Packman, Aaron I.

Subjects
Earth, Environmental, Ecological, and Space Sciences, Multidisciplinary, Environmental Studies, SciAdv r-articles, Research Article
Abstract

Description, Bidirectional flow between surface water and sediment leads to high accumulation of small and lightweight microplastics in rivers., In rivers, small and lightweight microplastics are transported downstream, but they are also found frequently in riverbed sediment, demonstrating long-term retention. To better understand microplastic dynamics in global rivers from headwaters to mainstems, we developed a model that includes hyporheic exchange processes, i.e., transport between surface water and riverbed sediment, where microplastic retention is facilitated. Our simulations indicate that the longest microplastic residence times occur in headwaters, the most abundant stream classification. In headwaters, residence times averaged 5 hours/km but increased to 7 years/km during low-flow conditions. Long-term accumulation for all stream classifications averaged ~5% of microplastic inputs per river kilometer. Our estimates isolated the impact of hyporheic exchange processes, which are known to influence dynamics of naturally occurring particles in streams, but rarely applied to microplastics. The identified mechanisms and time scales for small and lightweight microplastic accumulation in riverbed sediment reveal that these often-unaccounted components are likely a pollution legacy that is crucial to include in global assessments.

Published
2022
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26. Critical Capability Needs for Reduction of Transmission of SARS-CoV-2 Indoors

Author

Morrow, Jayne B., primary, Packman, Aaron I., additional, Martinez, Kenneth F., additional, Van Den Wymelenberg, Kevin, additional, Goeres, Darla, additional, Farmer, Delphine K., additional, Mitchell, Jade, additional, Ng, Lisa, additional, Hazi, Yair, additional, Schoch-Spana, Monica, additional, Quinn, Sandra, additional, Bahnfleth, William, additional, and Olsiewski, Paula, additional

Published
2021
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29. Residence Time in Hyporheic Bioactive Layers Explains Nitrate Uptake in Streams

Author

Li, Angang, Bernal, Susana, Kohler, Brady, Thomas, Steven A., Martí, Eugènia, Packman, Aaron I., Li, Angang, Bernal, Susana, Kohler, Brady, Thomas, Steven A., Martí, Eugènia, and Packman, Aaron I.

Abstract

The Tracer Additions for Spiraling Curve Characterization (TASCC) model has been rapidly adopted to interpret in‐stream nutrient spiraling metrics over a range of concentrations from breakthrough curves (BTCs) obtained during pulse solute injection experiments. TASCC analyses often identify hysteresis in the relationship between spiraling metrics and concentration as nutrient concentration in BTCs rises and falls. The mechanisms behind these hysteresis patterns have yet to be determined. We hypothesized that differences in the time a solute is exposed to bioactive environments (i.e. biophysical opportunity) between the rising and falling limbs of BTCs causes hysteresis in TASCCs. We tested this hypothesis using nitrate data from Elkhorn Creek (CO) combined with a process‐based particle tracking model representing travel times and transformations along each flow path in the water column and hyporheic zone, from which the bioactive zone comprised only a thin superficial layer. In‐stream nitrate uptake was controlled by hyporheic exchange and the cumulative time nitrate spend in the bioactive layer. This bioactive residence time generally increased from the rising to the falling limb of the BTC, systematically generating hysteresis in the TASCC curves. Hysteresis decreased when nutrient uptake primarily occurred in the water column compared to the hyporheic zone, and with increasing the distance between the injection and sampling points. Hysteresis increased with the depth of the hyporheic bioactive layer. Our results emphasize that good characterization of spatial heterogeneity of surface‐subsurface flow paths and bioactive hot spots within streams is essential to understanding the mechanisms of in‐stream nutrient uptake.

Published
2021

34. Deposition of cryptosporidium oocysts in streambeds

Author

Searcy, Kristin E., Packman, Aaron I., Atwill, Edward R., and Harter, Thomas

Subjects
Cryptosporidium -- Genetic aspects, Acclimatization -- Research, Biological sciences
Abstract

The results of laboratory flume experiments designed to investigate the stream-subsurface exchange of Cryptosporidium parvum oocysts is presented. The results indicate that the interactions reduce oocyst concentrations in surface waters and they also concentrate oocysts in sediment beds, which then represent a reservoir for pathogens that could be released during high-flow events.

Published
2006

37. Gathering at the top? Environmental controls of microplastic uptake and biomagnification in freshwater food webs

Author

Krause, Stefan, primary, Baranov, Viktor, additional, Nel, Holly A., additional, Drummond, Jennifer D., additional, Kukkola, Anna, additional, Hoellein, Timothy, additional, Sambrook Smith, Gregory H., additional, Lewandowski, Joerg, additional, Bonet, Berta, additional, Packman, Aaron I., additional, Sadler, Jon, additional, Inshyna, Valentyna, additional, Allen, Steve, additional, Allen, Deonie, additional, Simon, Laurent, additional, Mermillod-Blondin, Florian, additional, and Lynch, Iseult, additional

Published
2021
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38. Standardizing data reporting in the research community to enhance the utility of open data for SARS-CoV-2 wastewater surveillance

Author

McClary-Gutierrez, Jill S., primary, Aanderud, Zachary T., additional, Al-faliti, Mitham, additional, Duvallet, Claire, additional, Gonzalez, Raul, additional, Guzman, Joe, additional, Holm, Rochelle H., additional, Jahne, Michael A., additional, Kantor, Rose S., additional, Katsivelis, Panagis, additional, Kuhn, Katrin Gaardbo, additional, Langan, Laura M., additional, Mansfeldt, Cresten, additional, McLellan, Sandra L., additional, Mendoza Grijalva, Lorelay M., additional, Murnane, Kevin S., additional, Naughton, Colleen C., additional, Packman, Aaron I., additional, Paraskevopoulos, Sotirios, additional, Radniecki, Tyler S., additional, Roman, Fernando A., additional, Shrestha, Abhilasha, additional, Stadler, Lauren B., additional, Steele, Joshua A., additional, Swalla, Brian M., additional, Vikesland, Peter, additional, Wartell, Brian, additional, Wilusz, Carol J., additional, Wong, Judith Chui Ching, additional, Boehm, Alexandria B., additional, Halden, Rolf U., additional, Bibby, Kyle, additional, and Delgado Vela, Jeseth, additional

Published
2021
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39. Hyporheic exchange with gravel beds: basic hydrodynamic interactions and bedform-induced advective flows

Author

Packman, Aaron I., Salehin, Mashfiqus, and Zaramella, Mattia

Subjects
Hydraulic engineering -- Research, Bedforms, Engineering and manufacturing industries, Science and technology
Abstract

Stream-subsurface exchange processes are important because of their role in controlling the transport of contaminants and ecologically relevant substances in streams. Laboratory flume experiments were conducted to examine solute exchange with gravel streambeds. Two morphologies were studied: flat beds and beds covered by dune-shaped bedforms. High rates of exchange were observed with flat beds under a wide range of stream flow conditions, indicating that there was considerable turbulent coupling of stream and pore water flows. The presence of bedforms produced additional exchange under all flow conditions. The exchange with bedforms could be represented well by considering solute flux caused by bedform-induced advective pumping. Pumping exchange was enhanced by inertial effects, including non-Darcy flow and turbulent diffusion. For the flat bed case, dye injections showed that exchange also occurred by a combination of advective pore water flow and turbulent diffusion near the stream subsurface interface. The relative effects of advective and diffusive transport processes could not be separated due to the complex nature of the induced flows in the gravel bed. However, exchange was found to scale with the square of the stream Reynolds number in all cases. Comparison of these results with those obtained with coarser and finer sediments demonstrated that the exchange rate is also proportional to the square of the characteristic bed sediment size. These scaling relationships can be used to improve interpretation of solute transport observed in natural rivers. CE Database subject headings: Streambeds; Streams; Porous media; Turbulent diffusion; Pore water; Interfaces.

Published
2004

41. Parameter estimation of the transient storage model for stream-subsurface exchange

Author

Marion, Andrea, Zaramella, Mattia, and Packman, Aaron I.

Subjects
River sediments, Sediment transport -- Models, Engineering and manufacturing industries, Environmental issues
Abstract

The transient storage model (TSM) is the most commonly used model for stream-subsurface exchange of solutes. The TSM provides a convenient, simplified representation of hyporheic exchange, but its lack of a true physical basis causes its parameters to be difficult to predict. However, the simple formulation makes the model a useful practical tool for many applications. This work compares the TSM with a physically based pumping model. This comparison is advantageous for two reasons: Advective pumping is known to be an important hyporheic exchange process in many streams, and the pumping model can be used to derive dimensionless transient storage parameters that are properly scaled with important physical stream parameters. Transient storage model parameters are shown to be dependent on both the timescale of observation and the shape of the breakthrough curve, i.e., on the temporal evolution of the solute concentration in the surface water. This indicates that the transient storage model can, in practice, lead to incorrect predictions when model parameters are obtained without consideration of the stream flow dynamics, the properties of the stream bed, or the process timescale. This work emphasizes the limitations of simplified models for hyporheic transport, and indicates that such models need to be carefully applied. CE Database subject headings: Models; Subsurface environment; Solutes; Hydraulic transients; Streams.

Published
2003

44. Effects of background water composition on stream--subsurface exchange of submicron colloids

Author

Ren, Jianhong and Packman, Aaron I.

Subjects
Environmental engineering -- Research, Colloids -- Environmental aspects, Sediment transport -- Environmental aspects, Rivers -- Environmental aspects, Engineering and manufacturing industries, Environmental issues
Abstract

While very fine sediments (colloids) are normally assumed to be readily transported downstream without deposition, recent evidence suggests that these particles will often deposit into streambeds due to a combination of physical and chemical mechanisms. This study investigates a regime of particle deposition where settling is unimportant and thus where particle deposition can only result from advective stream--subsurface exchange followed by deep-bed filtration. Laboratory flume experiments were conducted to examine the deposition of 0.45 [micro]m diameter silica colloids into a silica sand bed. This system was selected for study because submicron sized colloids will not settle and silica colloid filtration by silica sand is generally quite low. Despite the lack of settling and the weak particle--particle interactions, the ongoing interfacial flux of colloids to the subsurface still produced significant filtration of silica colloids over the course of the experiments. Variation of the background ionic strength caused significant modification of filtration behavior and silica colloid deposition. In addition, cleaning the sand surface with mild acid and base washes reduced both filtration and net colloid exchange. These experimental results are interpreted in terms of a fundamentally based physicochemical model which predicts net particle deposition based on stream and subsurface hydrodynamic conditions and subsurface filtration. These results show that both particle surface chemical conditions and background water chemistry play a critical role in controlling the net transport and deposition of fine sediments. It is important to recognize the effects of physicochemical processes both when designing laboratory experiments and when analyzing environmental particle transport. CE Database keywords: Colloids; Sediment transport; Sediment deposits; Streams.

Published
2002

49. Spatial and temporal variation in river corridor exchange across a 5th-order mountain stream network

Author

Ward, Adam S., primary, Wondzell, Steven M., additional, Schmadel, Noah M., additional, Herzog, Skuyler, additional, Zarnetske, Jay P., additional, Baranov, Viktor, additional, Blaen, Phillip J., additional, Brekenfeld, Nicolai, additional, Chu, Rosalie, additional, Derelle, Romain, additional, Drummond, Jennifer, additional, Fleckenstein, Jan H., additional, Garayburu-Caruso, Vanessa, additional, Graham, Emily, additional, Hannah, David, additional, Harman, Ciaran J., additional, Hixson, Jase, additional, Knapp, Julia L. A., additional, Krause, Stefan, additional, Kurz, Marie J., additional, Lewandowski, Jörg, additional, Li, Angang, additional, Martí, Eugènia, additional, Miller, Melinda, additional, Milner, Alexander M., additional, Neil, Kerry, additional, Orsini, Luisa, additional, Packman, Aaron I., additional, Plont, Stephen, additional, Renteria, Lupita, additional, Roche, Kevin, additional, Royer, Todd, additional, Segura, Catalina, additional, Stegen, James, additional, Toyoda, Jason, additional, Hager, Jacqueline, additional, and Wisnoski, Nathan I., additional

Published
2019
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