Thomas C. Harmon

University of California, Merced | UCM · Department of Civil & Environmental Engineering, Environmental Systems Graduate Program, and Sierra Nevada Research Institute (SNRI)

Leaf-cutter ants (LCAs) are widely distributed and alter the physical and biotic architecture above and below ground. In neotropical rainforests, they create aboveground and belowground disturbance gaps that facilitate oxygen and carbon dioxide exchange. Within the hyperdiverse neotropical rainforests, arbuscular mycorrhizal (AM) fungi occupy nearl...

Collaborations between ecosystem ecologists and engineers have led to impressive progress in developing complex models of biogeochemical fluxes in response to global climate change. Ecology and engineering iteratively inform and transform each other in these efforts. Nested data streams from local sources, adjacent networks, and remote sensing sour...

Low-income, rural frontline communities of California's Central Valley experience environmental and socioeconomic injustice, water insecurity, extremely poor air quality, and lack of fundamental infrastructure (sewage, green areas, health services), which makes them less resilient. Many communities depend financially on agriculture, while water sca...

Low-income, rural frontline communities of California’s Central Valley experience environmental and socioeconomic injustice that makes them less resilient, including lack of fundamental infrastructure (sewage, green areas, health services), water insecurity, and the lowest air quality in the United States. These communities often depend financially...

Tobacco and cannabis product use can result in debris (a.k.a. litter) on the landscape, with implications to soil and water quality and thus potential impacts to ecosystems. More information is needed regarding how much debris exists on the landscape, such that the magnitude of potential associated environment problems can be quantified. Such infor...

While the impacts of cigarette smoking on human health are widely known, a less recognized impact of tobacco product use and disposal is environmental pollution. This review discusses the current literature related to cigarette and e-cigarette contamination in the context of environmental sources and impacts, with a focus on the documented influenc...

Riding the global waves of decriminalization, medical or recreational use of cannabis (Cannabis sativa spp.) is now legal in more than 50 countries and U.S. states. As governments regulate this formerly illegal crop, there is an urgent need to understand how cannabis may impact the environment. Due to the challenges of researching quasi-legal commo...

Achieving water security for humans and ecosystems is a pervasive challenge globally. Extensive areas of the Americas are at significant risk of water insecurity, resulting from global-change processes coupled with regional and local impacts. Drought, flooding, and water quality challenges pose significant threats, while at the same time, rapid urb...

Maintaining and restoring freshwater ecosystem services in the face of local and global change requires adaptive research that effectively engages stakeholders. However, there is a lack of understanding and consensus in the research community regarding where, when, and which stakeholders should be engaged and what kind of researcher should do the e...

Soil CO2 concentrations and emissions from tropical forests are modulated seasonally by precipitation. However, sub‐seasonal responses to meteorological events (for example, storms, drought) are less well‐known. Here we present the effects of meteorological variability on short‐term (hours to months) dynamics of soil CO2 concentrations and emission...

Research on carbon gas flux to and from inland waters has increased over the past two decades, driven mainly by the need to understand (1) the global carbon budget in regard to stabilizing earth’s climate, and (2) how aquatic ecosystems and the services they provide change in response to anthropogenic pressures like climate and land use change. Thi...

Leaf-cutter ant nests are biogeochemical hot spots where ants live and import vegetation to grow fungus. Metabolic activity and (in wet tropical forests) soil gas flux to the nest may result in high nest CO2 concentrations if not adequately ventilated. Wind-driven ventilation mitigates high CO2 concentrations in grasslands, but little is known abou...

A number of studies using the so‐called space‐for‐time substitution (STS) approach have predicted that climate warming of snow‐influenced watersheds would result in alarming increases in long‐term ET and concurrent decreases in runoff. This empirical approach implicitly assumes that any spatial covariation of factors across the landscape would rema...

Global atmospheric methane growth rates have wildly fluctuated over the past three decades, which may be driven by the proportion of tropical land surface saturated by water. The El Niño/Southern Oscillation Event (ENSO) cycle drives large‐scale climatic trends globally, with El Niño events typically bringing drier weather than La Niña. In a lowlan...

Leaf‐cutter ants are a prominent feature in Neotropical ecosystems, but a comprehensive assessment of their effects on ecosystem functions is lacking. We reviewed the literature and used our own recent findings to identify knowledge gaps and develop a framework to quantify the effects of leaf‐cutter ants on ecosystem processes. Leaf‐cutter ants dis...

Leaf‐cutter ants are dominant herbivores that disturb the soil and create biogeochemical hot spots. We studied how leaf‐cutter ant Atta cephalotes impacts soil CO2 dynamics in a wet Neotropical forest. We measured soil CO2 concentration monthly over 2.5 years at multiple depths in nonnest and nest soils (some of which were abandoned during the stud...

In this work, we develop and test proxy-based diagnostic tools for comparing freshwater ecosystem services (FWES) risks across an international array of freshwater ecosystems. FWES threats are increasing rapidly under pressure from population, climate change, pollution, land use change, and other factors. We identified spatially explicit FWES threa...

Catchment hydro-physical controls on the interannual variability of dissolved organic carbon (DOC) in terrestrial watershed runoff, important for water quality, ecosystem structure, and foodweb dynamics, are not well understood. To address this, we simulated water residence time (“age”) and flow path of terrestrial runoff and analyzed their mediati...

Paleoenvironmental reconstructions are increasingly being used in conservation biology, ecosystem management, and evaluations of ecosystem services (ES), but their potential to contribute to the ES risk assessment process has not been explored. We propose that the long-term history of the ecosystem provides valuable information that augments and st...

The US and Mexico share a common history in many areas, including language and culture. They face ecological changes due to the increased frequency and severity of droughts and rising energy demands; trends that entail economic costs for both nations and major implications for human well being. We describe an ongoing effort by the Environment Worki...

Changes in long-term, montane actual evapotranspiration (ET) in response to climate change could impact future water supplies and forest species composition. For scenarios of atmospheric warming, predicted changes in long-term ET tend to differ between studies using space-for-time substitution (STS) models and integrated watershed models, and the i...

Delineating pollutant reactive transport pathways that connect local land use patterns to surface water is an important goal. This work illustrates high-resolution river mapping of salinity or specific conductance (SC) and nitrate ( NO3−) as a potential part of achieving this goal. We observed longitudinal river SC and nitrate distributions using h...

One main problem of the spectral decomposition-based change detection method is the lack of efficient automatic techniques for developing the difference image. Traditional techniques generally assume that gray-level values in a difference image are independent and multitemporal images are co-registered/rectified perfectly without error. However, su...

Calibration of watershed models to the shape of the baseflow recession curve is a way to capture the important relationship between groundwater discharge and subsurface water storage in a catchment. In some montane Mediterranean regions, such as the mid-elevation Providence Creek catchment in the southern Sierra Nevada of California (USA), nearly a...

California’s Central Valley (CV) water crisis has increased in severity due to a prolonged drought. The drought is directly contributing to the overexploitation of groundwater, along with deficiency in agricultural, recreational and aesthetic water services. The population of the CV, home to about 6.5 million people, is projected to be 12 million b...

Measuring CO 2 concentrations and fluxes is key to the evaluation of terrestrial ecosystem carbon dynamics. Both the high cost and low portability of currently available sensors and field instruments are constraints to achieving adequate spatial and temporal coverage in characterizing ecosystem CO 2 fluxes and point concentrations. We used commerci...

Quantifying distributed lateral groundwater contributions to surface water (GW-SW discharges) is a key aspect of tracking nonpoint-source pollution (NPSP) within a watershed. In this study, we characterized distributed GW-SW discharges and associated salt loading using elevated GW specific conductance (SC) as a tracer along a 38 km reach of the Low...

Variability of river properties such as temperature, velocity, dissolved oxygen (DO) and light at small scales (centimeters to meters) can play an important role in the local exchanges of energy and mass. We hypothesize that significant transverse cross-sectional DO variation is observable within a river. Such variation may influence conventional s...

This work examines ammonia volatilization associated with agricultural irrigation employing recycled water. Effluent from a secondary wastewater treatment plant was applied using a center pivot irrigation system on a 12 ha agricultural site in Palmdale, California. Irrigation water was captured in shallow pans and ammonia concentrations were quanti...

This work examines the potential to predict the annual seed productivity of swamp timothy (Crypsis schoenoides) in two Central California managed wetlands by correlating spectral reflectance values and associated spectral vegetation indices (SVI) calculated from two sets of high resolution aerial images (May and June, 2006) to collected vegetation...

Nitrate is a key aquatic nitrogen species and an important indicator of anthropogenic impacts on water quality. Regulatory agencies through the world mandate nitrate monitoring in freshwater and coastal marine settings over large spatial scales. While remote sensing techniques are clearly advantageous in this context, and have proven useful in moni...

The San Joaquin River (SJR) restoration effort began in October 2009 with the onset of federally mandated continuous flow. A key objective of the effort is to restore and maintain fish populations in the main stem of the San Joaquin River, from below the Friant Dam to the confluence of the Merced River. In addition to the renewed flows, the restora...

Groundwater-surface water (GW-SW) discharge remains a challenging parameter to determine yet may be important to assessing nonpoint source pollutant inputs and their impacts on stream water quality and biogeochemical cycling. This work uses a series of periodic longitudinal surveys to collect high resolution water quality data longitudinally along...

Environmental cyber-observatory (ECO) planning and implementation has been ongoing for more than a decade now, and several major efforts have recently come online or will soon. Some investigators in the relevant research communities will use ECO data, traditionally by developing their own client-side services to acquire data and then manually creat...

Scientific metadata containing semantic descriptions of scientific data is expensive to capture and is typically not used across entire data analytic processes. We present an approach where semantic metadata is generated as scientific data is being prepared, and then subsequently used to configure models and to customize them to the data. The metad...

Soil salinization is a potentially negative side effect of irrigation with reclaimed water. While optimization schemes have been applied to soil salinity control, these have typically failed to take advantage of real-time sensor feedback. This study incorporates current soil observation technologies into the optimal feedback-control scheme known as...

The apparent electrical conductivity (σa) of soil is influenced by a complex combination of soil physical and chemical properties. For this reason, σa is proposed as an indicator of plant stress and potential community structure changes in an alkaline wetland setting. However, assessing soil σa is relatively laborious and difficult to accomplish ov...

With respect to the inevitable mis-registration and shadow effects on change detection analysis, we propose objectbased post-classification of the Multivariate Alteration Detection components (OB-MAD). Very high spatial resolution images of drained, managed wetland ponds were used to compare the proposed OB-MAD method with three commonly used class...

Metabolism estimates (gross primary production, GPP and community respiration, CR) obtained through the continuous monitoring of physicochemical properties in managed rivers may be used to evaluate the effects of various disturbances on ecosystem function. This work highlights the development of a GPP/CR observational network on the human-dominated...

This work examines the potential to predict the seed productivity of a key wetland plant species using spectral reflectance values and spectral vegetation indices. Specifically, the seed productivity of swamp timothy (Cripsis schenoides) was investigated in two wetland ponds, managed for waterfowl habitat, in California's San Joaquin Valley. Spectr...

The energy balance within a river reach is influenced significantly by the availability of light that can be used by primary and secondary producers. We are proposing a method to rapidly and inexpensively characterize the amount of available light within a river reach. We tested our approach within a 50 meter segment in the lower Merced River in Ca...

Stationary and distributed estimates of river metabolism developed during a 4-day period within a lowland section of the Merced River in California, allowed us to identify spatial and temporal variations in the estimates not related to the River Continuum Concept but to local factors. The estimates of whole-stream metabolism (Primary Production/Com...

Questions pertaining to stream restoration ecology, environmental flows, and hydrology may require higher resolution observation and simulation capabilities than are typical of hydrologic investigations. Multi-dimensional models can provide more insight into the coupled biogeochemical processes needed to fully understand these systems. Of course, s...

Soil contains vast ecosystems that play a key role in the Earth's water and nutrient cycles, but scientists cannot cur- rently collect the high-resolution data required to fully un- derstand them. In this paper, we present Suelo, an embed- ded networked sensing system designed for soil monitoring. An important challenge for Suelo is that many soil...

The capacity to adaptively manage irrigation and associated contaminant transport is desirable from the perspectives of water conservation, groundwater quality protection, and other concerns. This paper introduces the application of a feedback-control strategy known as Receding Horizon Control (RHC) to the problem of irrigation management. The RHC...

Environmental sensor networks offer a powerful combination of distributed sensing capacity, real‐time data visualization and analysis, and integration with adjacent networks and remote sensing data streams. These advances have become a reality as a combined result of the continuing miniaturization of electronics, the availability of large data stor...

Inorganic nitrogen (nitrate (NO3-) and ammonium (NH+)) from chemical fertilizer and livestock waste is a major source of pollution in groundwater, surface water and the air. While some sources of these chemicals, such as waste lagoons, are well-defined, their application as fertilizer has the potential to create distributed or non-point source poll...

The San Joaquin Valley, California is one of the most productive agricultural areas in the world. The application of fertilizer and manure to the land over decades has led to extensive nitrate contamination in Valley aquifer. Groundwater-surface water exchanges in the region have can result in significant nitrate fluxes into Valley rivers. This wor...

A small-scale field test of soil salinity control is demonstrated that fuses multisensor array data, state estimators, and optimization algorithms to autonomously maintain specified salt levels at a prescribed soil depth. Soil salinization is a problem associated with irrigation in arid and semi-arid environments; even more so when reclaimed water...

Net surface water-groundwater losses and gains may be estimated from flow gauges if they are adequately spaced such that flow differences are discernible. However, mapping of losses/gains on increasingly smaller scale river reaches is becoming important from the perspective of assessing non-point source pollution, ecological restoration efforts, an...

Soil organisms undertake every major ecosystem process, from primary production to decomposition to carbon sequestration, and those processes they catalyze have a bearing on the management of issues from agriculture to global climate change. Nonetheless, until recently, research to measure the dynamics of microscopic organisms living belowground ha...

This project has provided scientific support to a larger study of potential impacts to wetland moist soil plant habitat resulting from modification of seasonal wetland drawdown. Specific contributions have been the development of techniques for assessing wetland soil salinity using an electromagnetic sensing device and for developing accurate maps...

While it is true that miniaturization and Moore's law has enabled us to combine sensing, computation and wireless communication in integrated devices, and to embed networks of these devices in the physical world. We have found that it takes far more than embeddable devices to achieve the holy grail of "revealing the previously unobservable". Lookin...

Over-irrigation with reclaimed water may cause crop yield reduction and groundwater quality degradation. Continuous and automatic monitoring strategies are desirable as a means of guiding management schemes to avoid these problems. In this work, an optimal irrigation management scheme known as Receding Horizon Control (RHC) is proposed to balance w...

Spatially distributed hydraulic and water quality property characterization is important to understanding a broad range of river issues including confluence and discharge mixing phenomena, groundwater-surface water exchanges, and flow and temperature distributions in the context of habitat restoration efforts. Such characterization efforts often ne...

An integrated real-time distributed observing system could transform the understanding of the earth's water and related biogeochemical cycles across multiple spatial and temporal scales to enable improved forecasting and management of critical water processes affected by human activities.

This paper reports the first application of iterative experi mental design methodol- ogy for high spatiotemporal resolution characterization of river and lake aquatic systems per- formed using mobile robot sensing systems. Both applications involve dynamic phenomena spread over large spatial domain: 1) Characterization of contaminant concentration...

This work describes a novel design for a potentiometric microsensor for nitrate (NO 3 −) ion based on doped polypyrrole (PPy(NO 3 −)) films. First, 6–7 m diameter single carbon fiber filaments are coated with a thin (1–10 m) insulating layer of parylene C (poly(o-chloro-p-xylylene)). This preparatory step is followed by electrodeposition of a PPy(N...

Distributed, high-density spatiotemporal observations are proposed for answering many river related questions, including those pertaining to hydraulics and multi-dimensional river modeling, geomorphology, sediment transport and riparian habitat restoration. In spite of the recent advancements in technology, currently available systems have many con...

This work investigates the influence of soil type on electrodialytic remediation (EDR) of lead (Pb). In electrokinetic soil remediation, it is well known that pH is a key factor and that carbonate influences remediation efficiency negatively. This work provides results from laboratory-scale EDR experiments with ten representative industrially Pb-co...

Increasing demands on water supplies, along with concerns about non-point source pollution, and water quality-based ecological factors all point to the need for observing stream flow perturbations and pollutant discharges at higher resolution than has been practical until now. This work presents a rapidly deployable Networked Infomechanical System...

A mountain-to-valley virtual hydrologic observatory in Central California provides a focus for data and information in support of hydrologic research, a testbed for prototype measurement systems, and guidance for development of measurement and cyber infrastructure in an actual observatory. The multiple rivers and watersheds making up the 60,000 km2...

The presence of arsenic in the groundwater has led to the largest environmental poisoning in history; tens of millions of people in the Ganges Delta continue to drink groundwater that is dangerously contaminated with arsenic. A current working hypothesis is that arsenic is mobilized in the near surface environment where sediments are weathered by s...

Degradation of our nation's water resources is occurring at an unprecedented rate as a result of changes in the ways in which we interact with our environment. Unfortunately engineers, scientists, and policy makers have been hampered in their ability to respond to these rapid changes because we lack sufficient knowledge on the dynamics and spatial...

This project represents a key step toward developing an environmental observatory in the semiarid mountain- valley landscape of the far western United States. Two specific aims of this project are: (i) to formulate basin- scale measurement and modeling strategies to meet priority research issues, through analysis of existing operational and researc...

Rapidly deployable sensor networks are portable, reusable, and can take advantage of a human user in the field attending to the deployment. Unfortunately, even small disruptions or problems in collected data must be addressed quickly, as the overall quantity of data gathered is small relative to longterm deployments. In this paper we describe a pro...

Wireless sensor networks (WSNs) are a relatively new and rapidly developing technology; they have a wide range of applications including environmental monitoring, agriculture, and public health. Shared technology is a common usage model for technology adoption in developing countries. WSNs have great potential to be utilized as a shared resource du...

With increasing population and urban development, societies grow more and more concerned over balancing the need to maintain adequate water supplies with that of ensuring the quality of surface and groundwater resources. For example, multiple stressors such as overfishing, runoff of nutrients from agricultural fields and confined animal feeding lot...

This work focuses on improving pump-and-treat remediation by optimizing a two-stage operational scheme to reduce volumes extracted when confronted with nonequilibrium desorption, low-permeability units, and continuous contaminant sources such as non-aqueous phase liquids (NAPL). Q1 and Q2 are the initial short-term high pumping rate and later long-...

Increasing demands on water supplies, non-point source pollution, and water quality-based ecological concerns all point to the need for observing stream flow perturbations and pollutant discharges at higher resolution than was practical in the past. This work presents the results from a test of a rapidly deployable river observational approach cons...

Hydrologic and water quality observatories are being planned with a vision of enhancing our ability to better understand, forecast and adaptively manage both water quantity and quality. To adequately cover these spatially and temporally variable systems, distributed, embedded sensor networks must be designed with the proper mix (multimodality) of s...

This work describes the development and fabrication of stable potentiometric solid state sensors for the perchlorate ion (ClO4−) based on doped poly(3,4-ethylenedioxythiophene) (PEDOT) films. PEDOT, one of the most promising conducting polymers, is extremely stable in its oxidized state. Using PEDOT(ClO4−) films as sensing material in ion selective...

This work describes the development and testing of a sensitive and selective potentiometric nitrate microsensor based on doped polypyrrole films. Utilizing 6–7 μm carbon fibers as a substrate for pyrrole electropolymerization allowed fabrication of flexible, miniature and inexpensive sensors for in situ monitoring of nitrate. The sensors have a rap...

This work describes the integration of data acquisition (DAQ) hardware and software for the purpose of acquiring not only data but real-time transport model parameter estimates in the context of subsurface flow and transport problems. Integrated DAQ parameter estimation systems can be used to reduce data storage requirements, trigger event recognit...

Nitrate ion is an important environmental and human health analyte and thus its detection and quantification is considered essential. This article summarizes a simple procedure for preparing and testing a nitrate ion-selective electrode based on doped polypyrrole films. Everyday pencil leads were used as a substrate for the electrochemical depositi...

A coupled systems approach is presented for the simulation of fluid flow and solute transport within a heterogeneous vadose zone-groundwater environment. Separate model domains were developed for the vadose and saturated zones. The numerical model used is FEMWATER, a three-dimensional finite element model for simulating flow and transport in variab...

This work describes the development of flexible, miniature and inexpensive nitrate sensors by electropolymerizing pyrrole onto carbon fiber substrates, using nitrate as a dopant. Carbon microfibers were found to be an excellent substitute to expensive conductive materials, such as glassy carbon or platinum. The electrodes with a 3-5 micron layer of...

An issue associated with agricultural irrigation using reclaimed wastewater is the potential threat to underlying groundwater quality. A prime example is nitrate, which serves as a fertilizing agent but has the potential to leach into groundwater. In order to balance water reuse and groundwater protection, intelligent irrigation management and moni...

The environmental behavior of fuel oxygenates (other than methyl tert-butyl ether [MTBE]) is poorly understood because few data have been systematically collected and analyzed. This study evaluated the potential for groundwater resource contamination by fuel hydrocarbons (FHCs) and oxygenates (e.g., tert-butyl alcohol [TBA], tertamyl methyl ether [...

The use of reclaimed wastewater for irrigation in agriculture can be a significant source of nutrients, in particular nitrogen species, but its use raises concern for groundwater, riparian, and water quality. A 'smart' technology would have the ability to measure wastewater nutrients as they enter the irrigation system, monitor their transport in s...

The design and execution of a phase II field pilot test at a site in Southern California were presented. The phase II test succeeded in transferring additional energy to the soil (relative to the phase I test completed over the same time scale) by introducing burner waste gases through a perforated exhaust tube and by reinjection of excess waste ga...

This paper investigates the dissolution characteristics of ternary nonaqueous phase liquid (NAPL) mixtures with the goal of comparing the relative contributions of multicomponent (intra-NAPL) diffusion, film transfer and thermodynamic nonideality. These contributions are compared at the pore scale and intermediate scale (several centimeters downstr...

This work examines the potential role of embedded, networked sensing (ENS) protocols in monitoring the fate and transport of contaminants in the subsurface. The ultimate goal is to deploy a large dense array of chemical sensors for the purpose of identifying key transport parameters that are spatially distributed (e.g., porous media dispersivity) a...