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Interactions among hydrogeomorphology, vegetation, and nutrient biogeochemistry in floodplain ecosystems

Hydrogeomorphic, vegetative, and biogeochemical processes interact in floodplains resulting in great complexity that provides opportunities to better understand linkages among physical and biological processes in ecosystems. Floodplains and their associated river systems are structured by four dimensional gradients of hydrogeomorphology: longitudinal, lateral, vertical, and temporal components. These four dimensions create dynamic hydrologic and geomorphologic mosaics that have a large imprint on the vegetation and nutrient biogeochemistry of floodplains. Plant physiology, population dynamics, community structure, and productivity are all very responsive to floodplain hydrogeomorphology. The strength of this relationship between vegetation and hydrogeomorphology is evident in the use of vegetation as an indicator of hydrogeomorphic processes. However, vegetation also influences hydrogeomorphology by modifying hydraulics and sediment entrainment and deposition that typically stabilize geomorphic patterns. Nitrogen and phosphorus biogeochemistry commonly influence plant productivity and community composition, although productivity is not limited by nutrient availability in all floodplains. Conversely, vegetation influences nutrient biogeochemistry through direct uptake and storage as well as production of organic matter that regulates microbial biogeochemical processes. The biogeochemistries of nitrogen and phosphorus cycling are very sensitive to spatial and temporal variation in hydrogeomorphology, in particular floodplain wetness and sedimentation. The least studied interaction is the direct effect of biogeochemistry on hydrogeomorphology, but the control of nutrient availability over organic matter decomposition and thus soil permeability and elevation is likely important. Biogeochemistry also has the more documented but indirect control of hydrogeomorphology through regulation of plant biomass. In summary, the defining characteristics of floodplain ecosystems are determined by the many interactions among physical and biological processes. Conservation and restoration of the valuable ecosystem services that floodplains provide depends on improved understanding and predictive models of interactive system controls and behavior.

Book chapter↗

Retention of NO3/- in an upland stream environment: A mass balance approach

Models of the effects of atmospheric N deposition in forested watersheds have not adequately accounted for the effects of aquatic and near-stream processes on the concentrations and loads of NO3/- in surface waters. This study compared the relative effects of aquatic and near-stream processes with those from the terrestrial ecosystem on the retention and transport of NO3/- in two contrasting stream reaches of the Neversink River, a forested watershed in the Catskill Mountains of New York that receives among the highest load of atmospheric N deposition in the northeastern United States. Stream water samples were collected every two hours and ground-water and tributary samples were collected daily at base flow conditions during four 48-hour periods from April to October 1992, and NO3/- mass balances were calculated for each site. Results indicated diurnal variations in stream NO3/- concentrations in both reaches during all four sampling periods; this is consistent with uptake of NO3/- by photoautotrophs during daylight hours. Mass-balance results revealed significant stream reach losses of NO3/- at both sites during all sampling periods. The diurnal variations in NO3/- concentrations and the retention of NO3/- relative to terrestrial contributions to the stream reaches were greater downstream than upstream because physical factors such as the head gradients of inflowing ground water and the organic matter content of sediment are more favorable to uptake and denitrification downstream. The mass retention of NO3/- increased as the mean 48-hr stream discharge increased at each site, indicating that the responsible processes are dependent on NO3/- supply. Low stream temperatures during the April sampling period, however, probably reduced the rate of retention processes, resulting in smaller losses of NO3/- than predicted from stream discharge alone. Water samples collected from the stream, the hyporheic zone, and the alluvial ground water at sites in both reaches indicated that the net effect of hyporheic processes on downstream NO3/- transport ranged from conservative mixing to complete removal by denitrification. The relative effects of biological uptake and denitrification as retention mechanisms could not be quantified, but the results indicate that both processes are significant. These results generally confirm that aquatic and near-stream processes cause significant losses of NO3/- in the Neversink River, and that the losses by these processes at downstream locations can exceed the NO3/- contributions to the stream from the terrestrial environment during summer and fall base-flow conditions. Failure to consider these aquatic and near-stream processes in models of watershed response to atmospheric N deposition could result in underestimates of the amount of NO3/- leaching from forested ecosystems and to an inability to unequivocally relate geographic differences in NO3/- concentrations of stream waters to corresponding differences in terrestrial processes.

Biogeochemistry↗

Regional geologic setting of Late Cenozoic lacustrine diatomite deposits, Great Basin and surrounding region: Overview and plans for investigation

Freshwater diatomite deposits are present in all of the Western United States, including the Great Basin and surrounding regions. These deposits are important domestic sources of diatomite, and a better understanding of their formation and geologic settings may aid diatomite exploration and land-use management. Diatomite deposits in the Great Basin are the products of two stages: (1) formation in Late Cenozoic lacustrine basins and (2) preservation after formation. Processes that favored long-lived diatom activity and diatomite formation range in decreasing scale from global to local. The most important global process was climate, which became increasingly cool and dry from 15 Ma to the present. Regional processes included tectonic setting and volcanism, which varied considerably both spatially and temporally in the Great Basin region. Local processes included basin formation, sedimentation, hydrology, and rates of processes, including diatom growth and accumulation; basin morphology and nutrient and silica sources were important for robust activity of different diatom genera. Only optimum combinations of these processes led to the formation of large diatomite deposits, and less than optimum combinations resulted in lakebeds that contained little to no diatomite. Postdepositional processes can destroy, conceal, or preserve a diatomite deposit. These processes, which most commonly are local in scale, include uplift, with related erosion and changes in hydrology; burial beneath sedimentary deposits or volcanic flows and tuffs; and alteration during diagenesis and hydrothermal activity. Some sedimentary basins that may have contained diatomite deposits have largely been destroyed or significantly modified, whereas others, such as those in western Nevada, have been sufficiently preserved along with their contained diatomite deposits. Future research on freshwater diatomite deposits in the Western United States and Great Basin region should concentrate on the regional and local processes that led to the formation and preservation of the deposits. Major questions that need to be answered include (1) why were some basins favorable for diatomite formation, whereas others were not; (2) what post-depositional conditions are needed for diatomite preservation; and (3) what were the optimum process combinations that led to the formation and preservation of economic diatomite deposits?

Great Basin↗

Framework developed for geomorphic mapping of Fern Ridge Lake, Oregon, 2023

The construction and operation of large reservoirs in the Willamette River Basin, Oregon, influences important cultural, biological, and other natural or economic resources in affected river corridors. The present-day landforms and cover within the reservoirs have been shaped by a variety of processes, including the pre-dam valley setting and geomorphic processes related to dam operations. Maps of reservoir geomorphic process domains, landforms, and cover provide a foundation for understanding how erosion and deposition processes in or near the reservoirs may affect cultural resources. Detailed geomorphic mapping of Fern Ridge Lake in 2023 provides a basis for evaluating geomorphic processes and patterns of sediment transfer within the reservoir. These processes are related to geomorphic and hydroclimatic conditions as well as annual lake level fluctuation for seasonal flood-control operations. This geomorphic mapping also provides an inventory of existing landforms from which to evaluate the spatial and temporal geomorphic change over time. Digital maps based on high-resolution digital surface models and orthophotographs acquired during low-pool conditions in 2023 extend over an area of about 30 square kilometers (km) upstream of the Fern Ridge Dam. The mapping framework has 3 main components consisting of several subtypes: 5 process domains, 18 landforms, and 7 cover categories. The overarching classification structure is tied to the process domains, which correspond to dissimilar regions of the reservoir that have distinct landforms and broadly similar suites of geomorphic processes. This document describes the geomorphic mapping framework for the reservoir at Fern Ridge Lake and provides mapping unit descriptions including delineation criteria, hypothesized formation processes inferred from remote-sensing and field observations and the literature, and relevance during drawdown operations.

Oregon↗

UCODE_2005 and six other computer codes for universal sensitivity analysis, calibration, and uncertainty evaluation constructed using the JUPITER API

This report documents the computer codes UCODE_2005 and six post-processors. Together the codes can be used with existing process models to perform sensitivity analysis, data needs assessment, calibration, prediction, and uncertainty analysis. Any process model or set of models can be used; the only requirements are that models have numerical (ASCII or text only) input and output files, that the numbers in these files have sufficient significant digits, that all required models can be run from a single batch file or script, and that simulated values are continuous functions of the parameter values. Process models can include pre-processors and post-processors as well as one or more models related to the processes of interest (physical, chemical, and so on), making UCODE_2005 extremely powerful. An estimated parameter can be a quantity that appears in the input files of the process model(s), or a quantity used in an equation that produces a value that appears in the input files. In the latter situation, the equation is user-defined. UCODE_2005 can compare observations and simulated equivalents. The simulated equivalents can be any simulated value written in the process-model output files or can be calculated from simulated values with user-defined equations. The quantities can be model results, or dependent variables. For example, for ground-water models they can be heads, flows, concentrations, and so on. Prior, or direct, information on estimated parameters also can be considered. Statistics are calculated to quantify the comparison of observations and simulated equivalents, including a weighted least-squares objective function. In addition, UCODE_2005 can be used fruitfully in model calibration through its sensitivity analysis capabilities and its ability to estimate parameter values that result in the best possible fit to the observations. Parameters are estimated using nonlinear regression: a weighted least-squares objective function is minimized with respect to the parameter values using a modified Gauss-Newton method or a double-dogleg technique. Sensitivities needed for the method can be read from files produced by process models that can calculate sensitivities, such as MODFLOW-2000, or can be calculated by UCODE_2005 using a more general, but less accurate, forward- or central-difference perturbation technique. Problems resulting from inaccurate sensitivities and solutions related to the perturbation techniques are discussed in the report. Statistics are calculated and printed for use in (1) diagnosing inadequate data and identifying parameters that probably cannot be estimated; (2) evaluating estimated parameter values; and (3) evaluating how well the model represents the simulated processes. Results from UCODE_2005 and codes RESIDUAL_ANALYSIS and RESIDUAL_ANALYSIS_ADV can be used to evaluate how accurately the model represents the processes it simulates. Results from LINEAR_UNCERTAINTY can be used to quantify the uncertainty of model simulated values if the model is sufficiently linear. Results from MODEL_LINEARITY and MODEL_LINEARITY_ADV can be used to evaluate model linearity and, thereby, the accuracy of the LINEAR_UNCERTAINTY results. UCODE_2005 can also be used to calculate nonlinear confidence and predictions intervals, which quantify the uncertainty of model simulated values when the model is not linear. CORFAC_PLUS can be used to produce factors that allow intervals to account for model intrinsic nonlinearity and small-scale variations in system characteristics that are not explicitly accounted for in the model or the observation weighting. The six post-processing programs are independent of UCODE_2005 and can use the results of other programs that produce the required data-exchange files. UCODE_2005 and the other six codes are intended for use on any computer operating system. The programs consist of algorithms programmed in Fortran 90/95, which efficiently performs numerical calculations. The model runs required to obtain perturbation sensitivities can be performed using multiple processors. The programs are constructed in a modular fashion using JUPITER API conventions and modules. For example, the data-exchange files and input blocks are JUPITER API conventions and many of those used by UCODE_2005 are read or written by JUPITER API modules. UCODE-2005 includes capabilities likely to be required by many applications (programs) constructed using the JUPITER API, and can be used as a starting point for such programs.

Techniques and Methods↗

Multi-decadal simulation of marsh topography evolution under sea level rise and episodic sediment loads

Coastal marsh within Mediterranean climate zones is exposed to episodic watershed runoff and sediment loads that occur during storm events. Simulating future marsh accretion under sea level rise calls for attention to: (a) physical processes acting over the time scale of storm events and (b) biophysical processes acting over time scales longer than storm events. Using the upper Newport Bay in Southern California as a case study, we examine the influence of event-scale processes on simulated change in marsh topography by comparing: (a) a biophysical model that integrates with an annual time step and neglects event-scale processes (BP-Annual), (b) a physical model that resolves event-scale processes but neglects biophysical interactions (P-Event), and (c) a biophysical model that resolves event-scale physical processes and biophysical processes at annual and longer time scales (BP-Event). A calibrated BP-Event model shows that large (>20-year return period) episodic storm events are major drivers of marsh accretion, depositing up to 30 cm of sediment in one event. Greater deposition is predicted near fluvial sources and tidal channels and less on marshes further from fluvial sources and tidal channels. In contrast, the BP-Annual model poorly resolves spatial structure in marsh accretion as a consequence of neglecting event-scale processes. Furthermore, the P-Event model significantly overestimates marsh accretion as a consequence of neglecting marsh surface compaction driven by annual scale biophysical processes. Differences between BP-Event and BP-Annual models translate up to 20 cm per century in marsh surface elevation.

California↗

Data files from “CWB Free-Field Strong-Motion Data from the 21 September Chi-Chi, Taiwan, Earthquake”

The Central Weather Bureau (CWB) of Taiwan completed a deployment of 1200 modern digital strong-motion instruments in 1996 at free-field sites and in buildings and bridges. Consequently, a very extensive set of strong-motion records were obtained for the M W = 7.6 Chi-Chi earthquake in 1999, including over 60 near-field records within 20 km of the fault ruptures. For documentation purposes, we included all relevant data files on the attached CD-ROM from our article, “CWB Free-Field Strong-Motion Data from the 21 September Chi-Chi, Taiwan, Earthquake” in this issue. We presented the data in four different ways to make the data more user friendly: (1) the original recorded data by accelerograph type; (2) the processed data in ASCII text format; (3) the processed data in SUDS format; and (4) the processed data in SAC format. (1)-(3) are exactly the same as in Lee et al. ( 2001 ), except the files are zipped (or compressed). (4) is provided for users using the SAC software on a Unix computer, and it also contains waveform plots of the data in PDF files for ease of viewing. The attached CD contains the full report of Lee et al. ( 2001 ) in 25 PDF files for viewing or printing. This full report described the data set and the data processing performed in details. It also contains plots of all processed data with an index map showing the fault, mainshock location, and the station location. We also provided a readme.txt on the CDROM to augment this Short Note with further explanations. We classify the recorded data files into four quality groups. Since the recorded strong-motion data are based on a triggering algorithm, a main concern is the amount of pre-event data and whether or not the record is long enough to cover the entire duration of the ground shaking at that station. In addition, we are concerned whether or not the record has defects (e.g., spikes, or a component was not recorded), and whether or not the record has absolute timing. In general, QA-class records are the best and can be used for any studies. QB-class records are the next best, except most of them do not have absolute timing. QC-class records cover the principal strong motions but may not have adequate pre-event data and/or post strong-motion data. QD-class records have some defects; they are included here for completeness and should not be used for most studies. Since most A800 accelerographs have a colocated A900 or A900A accelerograph, the user should use the A900 or A900A data files whenever possible. There are a readme file and six subdirectories containing the data files described in our article on the attached CDROM, under the directory of \LeeWHK: (1) readme.txt: an ASCII text file of this Short Note and additional explanations. (2) DOCfiles (subdirectory): documentary files in PDF format for viewing, and some files in ASCII text format for use in data processing. User should view or print the Reportxx.pdf files which describe the Chi-Chi strong-motion data set in details (xx is a number from 01 through 25). (3) Software (subdirectory): containing computer programs from the accelerograph manufacturers for viewing and converting the original recorded data; they are grouped by manufacturer. (4) ORGfiles (subdirectory): the original recorded data files grouped by accelerograph types; these files are for archival purposes only. (5) SUDfiles (subdirectory): the processed strong-motion data files in PC-SUDS format, and are grouped by quality class. (6) ASCfiles (subdirectory): the processed strong-motion data files are in ASCII text format and are grouped by quality class. (7) SACfiles (subdirectory): the processed strong-motion data files are in SAC format and are grouped by quality class. Within each quality class, the data are given by station. Each station has two files—xxx.pdf for viewing the three-component strong-motion data, and xxx_SAC.zip, a WINZIP file containing three SAC data files corresponding to the three components of the recorded acceleration. We use “xxx” here to denote the station name.

Bulletin of the Seismological Society of America↗

Stable isotope systematics of sulfate minerals

Stable isotope studies of sulfate minerals are especially useful for unraveling the geochemical history of geological systems. All sulfate minerals can yield sulfur and oxygen isotope data. Hydrous sulfate minerals, such as gypsum, also yield oxygen and hydrogen isotope data for the water of hydration, and more complex sulfate minerals, such as alunite and jarosite also yield oxygen and hydrogen isotope data from hydroxyl sites. Applications of stable isotope data can be divided into two broad categories: geothermometry and tracer studies. The equilibrium partitioning of stable isotopes between two substances, such as the isotopes of sulfur between barite and pyrite, is a function of temperature. Studies can also use stable isotopes as a tracer to fingerprint various sources of hydrogen, oxygen, and sulfur, and to identify physical and chemical processes such as evaporation of water, mixing of waters, and reduction of sulfate to sulfide. Studies of sulfate minerals range from low-temperature surficial processes associated with the evaporation of seawater to form evaporite deposits to high-temperature magmatic-hydrothermal processes associated with the formation of base-and precious-metal deposits. Studies have been conducted on scales from submicroscopic chemical processes associated with the weathering of pyrite to global processes affecting the sulfur budget of the oceans. Sulfate isotope studies provide important information to investigations of energy and mineral resources, environmental geochemistry, paleoclimates, oceanography (past and present), sedimentary, igneous, and metamorphic processes, Earth systems, geomicrobiology, and hydrology. One of the most important aspects of understanding and interpreting the stable isotope characteristics of sulfate minerals is the complex interplay between equilibrium and kinetic chemical and isotopic processes. With few exceptions, sulfate minerals are precipitated from water or have extensively interacted with water at some time in their history. Because of this nearly ubiquitous association with water, the kinetics of isotopic exchange reactions among dissolved species and solids are fundamental in dictating the isotopic composition of sulfate minerals. In general, the heavier isotope of sulfur is enriched in the higher oxidation state, such that under equilibrium conditions, sulfate minerals (e.g. barite, anhydrite) are expected to be enriched in the heavy isotope relative to disulfide minerals (e.g. pyrite, marcasite), which in turn are expected to be enriched relative to monosulfide minerals (e.g. pyrrhotite, sphalerite, galena) ( Sakai 1968 , Bachinski 1969 ). The kinetics of isotopic exchange among minerals with sulfur at the same oxidation state, such as sphalerite, and galena, are such that equilibrium is commonly observed. In contrast, isotopic equilibrium for exchange reactions between minerals of different oxidation states depends on factors such as the pH, time and temperature of reaction, the direction of reaction, fluid composition, and the presence or absence of catalysts ( Ohmoto and Lasaga 1982 ). The kinetics of oxygen isotope exchange between dissolved sulfate and water are extremely sluggish. Extrapolation of the high-temperature (100 to 300°C) isotopic exchange kinetic data of Chiba and Sakai (1985) to ambient temperatures suggests that it would take several billions of years for dissolved sulfate and seawater to reach oxygen isotopic equilibrium. In contrast, the residence time of sulfate in the oceans is only 7.9 million years ( Holland 1978 ). However, at higher temperatures (>200°C), oxygen isotopic exchange is sufficiently rapid to permit application of sulfate isotope geothermometry to geothermal systems and hydrothermal mineral deposits. In general, equilibrium prevails at low pH and high temperatures, whereas kinetic factors preclude equilibrium at low temperatures even at low pH. Thus, the sluggish kinetics of sulfur and oxygen isotope exchange reaction at low temperatures impair the use of these isotopes to understand the conditions of formation of sulfate minerals in these environments. However, because of these slow kinetics, the oxygen and sulfur isotopic compositions of sulfate minerals may preserve a record of the sources and processes that initially produced the dissolved sulfate, because the isotope ratios may not re-equilibrate during fluid transport and mineral precipitation. The first part of this chapter is designed to provide the reader with a basic understanding of the principles that form the foundations of stable isotope geochemistry. Next, an overview of analytical methods used to determine the stable isotope composition of sulfate minerals is presented. This overview is followed by a discussion of geochemical processes that determine the stable isotope characteristics of sulfate minerals and related compounds. The chapter then concludes with an examination of the stable isotope systematics of sulfate minerals in a variety of geochemical environments.

Reviews in Mineralogy and Geochemistry↗

On the nature of persistence in dendrochronologic records with implications for hydrology

Hydrologic processes are generally held to be persistent and not secularly independent. Impetus for this view was given by Hurst in his work which dealt with properties of the rescaled range of many types of long geophysical records, in particular dendrochronologic records, in addition to hydrologic records. Mandelbrot introduced an infinite memory stationary process, the fractional Gaussian noise process (F), as an explanation for Hurst's observations. This is in contrast to other explanations which have been predicated on the implicit non-stationarity of the process underlying the construction of the records. In this work, we introduce a stationary finite memory process which arises naturally from a physical concept and show that it can accommodate the persistence structures observed for dendrochronological records more successfully than an F or any other of a family of related processes examined herein. Further, some question arises as to the empirical plausibility of an F process. Dendrochronologic records are used because they are widely held to be surrogates for records of average hydrologic phenomena and the length of these records allows one to explore questions of stochastic process structure which cannot be explored with great validity in the case of generally much shorter hydrologic records.

Journal of Hydrology↗

Rock-weathering rates as functions of time

The scarcity of documented numerical relations between rock weathering and time has led to a common assumption that rates of weathering are linear. This assumption has been strengthened by studies that have calculated long-term average rates. However, little theoretical or empirical evidence exists to support linear rates for most chemical-weathering processes, with the exception of congruent dissolution processes. The few previous studies of rock-weathering rates that contain quantitative documentation of the relation between chemical weathering and time suggest that the rates of most weathering processes decrease with time. Recent studies of weathering rinds on basaltic and andesitic stones in glacial deposits in the western United States also clearly demonstrate that rock-weathering processes slow with time. Some weathering processes appear to conform to exponential functions of time, such as the square-root time function for hydration of volcanic glass, which conforms to the theoretical predictions of diffusion kinetics. However, weathering of mineralogically heterogeneous rocks involves complex physical and chemical processes that generally can be expressed only empirically, commonly by way of logarithmic time functions. Incongruent dissolution and other weathering processes produce residues, which are commonly used as measures of weathering. These residues appear to slow movement of water to unaltered material and impede chemical transport away from it. If weathering residues impede weathering processes then rates of weathering and rates of residue production are inversely proportional to some function of the residue thickness. This results in simple mathematical analogs for weathering that imply nonlinear time functions. The rate of weathering becomes constant only when an equilibrium thickness of the residue is reached. Because weathering residues are relatively stable chemically, and because physical removal of residues below the ground surface is slight, many weathering features require considerable time to reach constant rates of change. For weathering rinds on volcanic stones in the western United States, this time is at least 0.5 my.

Quaternary Research↗

Parallelization of a hydrological model using the message passing interface

With the increasing knowledge about the natural processes, hydrological models such as the Soil and Water Assessment Tool (SWAT) are becoming larger and more complex with increasing computation time. Additionally, other procedures such as model calibration, which may require thousands of model iterations, can increase running time and thus further reduce rapid modeling and analysis. Using the widely-applied SWAT as an example, this study demonstrates how to parallelize a serial hydrological model in a Windows® environment using a parallel programing technology—Message Passing Interface (MPI). With a case study, we derived the optimal values for the two parameters (the number of processes and the corresponding percentage of work to be distributed to the master process) of the parallel SWAT (P-SWAT) on an ordinary personal computer and a work station. Our study indicates that model execution time can be reduced by 42%–70% (or a speedup of 1.74–3.36) using multiple processes (two to five) with a proper task-distribution scheme (between the master and slave processes). Although the computation time cost becomes lower with an increasing number of processes (from two to five), this enhancement becomes less due to the accompanied increase in demand for message passing procedures between the master and all slave processes. Our case study demonstrates that the P-SWAT with a five-process run may reach the maximum speedup, and the performance can be quite stable (fairly independent of a project size). Overall, the P-SWAT can help reduce the computation time substantially for an individual model run, manual and automatic calibration procedures, and optimization of best management practices. In particular, the parallelization method we used and the scheme for deriving the optimal parameters in this study can be valuable and easily applied to other hydrological or environmental models.

Environmental Modelling and Software↗

Digital mapping of the Mars Pathfinder landing site: Design, acquisition, and derivation of cartographic products for science applications

The Imager for Mars Pathfinder (IMP) acquired more than 16,000 images and provided panoramic views of the surface of Mars at the Mars Pathfinder landing site in Ares Vallis. This paper describes the stereoscopic, multispectral IMP imaging sequences and focuses on their use for digital mapping of the landing site and for deriving cartographic products to support science applications of these data. Two‐dimensional cartographic processing of IMP data, as performed via techniques and specialized software developed for ISIS (the U.S. Geological Survey image processing software package), is emphasized. Cartographic processing of IMP data includes ingestion, radiometric correction, establishment of geometric control, coregistration of multiple bands, reprojection, and mosaicking. Photogrammetric processing, an integral part of this cartographic work which utilizes the three‐dimensional character of the IMP data, supplements standard processing with geometric control and topographic information [ Kirk et al. , this issue]. Both cartographic and photogrammetric processing are required for producing seamless image mosaics and for coregistering the multispectral IMP data. Final, controlled IMP cartographic products include spectral cubes, panoramic (360° azimuthal coverage) and planimetric (top view) maps, and topographic data, to be archived on four CD‐ROM volumes. Uncontrolled and semicontrolled versions of these products were used to support geologic characterization of the landing site during the nominal and extended missions. Controlled products have allowed determination of the topography of the landing site and environs out to ∼60 m, and these data have been used to unravel the history of large‐ and small‐scale geologic processes which shaped the observed landing site. We conclude by summarizing several lessons learned from cartographic processing of IMP data.

Journal of Geophysical Research E: Planets↗

A systematic literature review of forecasting and predictive models of harmful algal blooms in flowing waters

Occurrences of harmful algal blooms (HABs) in rivers challenge the belief that rivers are not susceptible to HABs because of their short residence times and fluctuating hydrology. Here we present a systematic literature review of predictive and forecasting models for HABs in flowing waters, including rivers, flowing in-stream reservoirs (e.g., run-of-river reservoirs and lock-and-dam systems) and tidal or estuarine systems with riverine processes. The review aimed to understand current and historical modeling approaches for predicting and forecasting river HABs, without restricting to specific taxa, such as cyanobacteria, or modeling endpoints. The review included 162 articles published over nearly 50 years, covering more than 80 rivers worldwide. Eutrophic, non-wadable rivers with in-stream obstruction were commonly modeled, though diverse environmental characteristics were reported. Most articles used algal biomass or chlorophyll as modeling endpoints, with a quarter using novel or unique endpoints. Algal toxins motivated model development in 23% of the articles, however just 5% used algal toxins as an endpoint. Only 6% of the articles modeled benthic HABs; the rest focused on pelagic HABs. There was no standard model used for modeling river HABs. Process-based models were more common (59%) than data-driven approaches (37%), with model formulations ranging from simple to complex, which contrasts with a lake-focused literature review of HAB models that found data-driven models were more common. Models in river settings shared similar input variables as those previously identified for lakes, such as water temperature, nutrients, and light availability. However, streamflow and other transport metrics took prominence in river models compared to lake models. Algal cell physiology (such as growth, predation, and motility) was routinely included as input data or as mathematical formulations in process-based models and these processes were frequently identified as an important predictor by the articles’ authors. Conversely, data-driven models rarely included these processes, instead using predictors related to environmental conditions, such as nutrients, water quality, water temperature, and streamflow. These important proxy predictors have apparent success with modeling overall algal biomass (irrespective of taxa) whereas other factors, such as those related to algal physiology and other biological processes, are likely responsible for more subtle shifts in community composition. These differences highlight the influence of data availability, especially for processes that are difficult, time-consuming, or expensive to measure, on model development and model outcomes, raising questions about the selection of modeling inputs and endpoints. Challenges to advancing river HAB modeling include the lack of site-specific model inputs representing key processes (e.g., photosynthetic parameters and predation rates), overlooked riverine environments like the benthos and side/back-channel areas, lack of information on environmental settings, and poorly reported model performance metrics. This review emphasizes opportunities for advancing river HAB modeling by learning from well-honed estuarine models, supporting current forecasting and operationalization efforts, and developing common datasets for river HAB model development and evaluation.

BioRxiv↗

Know what you don't know: Embracing state uncertainty in disease-structured multistate models

Hidden Markov models (HMMs) are broadly applicable hierarchical models that derive their utility from separating state processes from observation processes yielding the data. Multistate models such as mark–recapture and dynamic multistate occupancy models are HMMs frequently used in ecology. In their early formulations, states, such as pathogen infection status, were assumed to be perfectly observed without ambiguity. However, state uncertainty is a pervasive feature of many ecological studies, and multievent models were developed to explicitly account for it. We developed a novel extended multievent mark–recapture model that incorporates state uncertainty at multiple levels of detection. Using a disease-structured example, both false negative and false positive state assignment errors are modelled at two levels of state assignment—the pathogen sampling process and the diagnostic process that samples are subjected to. We additionally describe methods to jointly model infection intensity to integrate heterogeneity in ecological parameters, such as mortality and infection dynamics, and the pathogen detection processes. We provide code to simulate and analyse datasets with various underlying ecological processes and fit our model to a mark–recapture dataset of Mixophyes fleayi (Fleay's barred frog) infected with the amphibian chytrid fungus ( Batrachochytrium dendrobatidis , Bd ). In our case study, we found evidence for various state assignment errors: the sampling protocol performed poorly in detecting Bd , pathogen detection was highly dependent on infection intensity and false positives were non-negligible. Incorporating state uncertainty yielded significantly higher estimates of infection prevalence and 4–5 times lower rates of infection state transitions compared to those obtained from a traditional multistate model. Our results highlight that incorporating state assignment errors improves inference on the ecological process, especially when sensitivity and specificity of the state assignment processes are low. The general model structure can be applied to other HMMs, providing a foundation for modelling state uncertainty in related models. For disease-structured multistate models, we recommend conducting robust design surveys and collecting samples during each capture event to facilitate incorporating pathogen detection errors.

Methods in Ecology and Evolution↗

Landsat-4 and Landsat-5 thematic mapper band 6 historical performance and calibration

Launched in 1982 and 1984 respectively, the Landsat-4 and -5 Thematic Mappers (TM) are the backbone of an extensive archive of moderate resolution Earth imagery. However, these sensors and their data products were not subjected to the type of intensive monitoring that has been part of the Landsat-7 system since its launch in 1999. With Landsat-4's 11 year and Landsat-5's 20+ year data record, there is a need to understand the historical behavior of the instruments in order to verify the scientific integrity of the archive and processed products. Performance indicators of the Landsat-4 and -5 thermal bands have recently been extracted from a processing system database allowing for a more complete study of thermal band characteristics and calibration than was previously possible. The database records responses to the internal calibration system, instrument temperatures and applied gains and offsets for each band for every scene processed through the National Landsat Archive Production System (NLAPS). Analysis of this database has allowed for greater understanding of the calibration and improvement in the processing system. This paper will cover the trends in the Landsat-4 and -5 thermal bands, the effect of the changes seen in the trends, and how these trends affect the use of the thermal data.

Conference Paper↗

Preliminary photointerpretation map of landslide and other surficial deposits of the Mount Hamilton quadrangle and parts of the Mount Boardman and San Jose quadrangles, Alameda and Santa Clara Counties, California

The nine San Francisco Bay region counties lie within a geologically active, young, and dynamic part of the central and northern Coast Ranges of California. Significant movements of the earth's crust are occurring here at the present time, posing numerous problems to urbanization, including some of special concern. Geological processes such as fault movements, earthquakes, land subsidence, landsliding, slow downslope movement of bedrock and surficial materials, coastal and stream erosion, flooding, and sedimentation are all potentially hazardous. Because of these factors, an understanding of the operation of physical processes in the bay region is desirable for harmonious, efficient, and safe land-use planning, particularly now, with greatly expanded pressures for urban growth. This map presents preliminary information about one aspect of the physical environment necessary to sound land-use planning--the nature and distribution of surficial deposits. Because surficial deposits are common and well developed in much of the bay region, it is useful to know how and why they have formed, as well as what properties they possess. When maps like this are used in combination with other types of environmental information, such as data on soils, bedrock geology, slopes, vegetation, climatic variation, seismic response, and hydrology, it should be easier to arrive at sound decisions regarding the physical aspects of land use. The U.S. Geological Survey is studying many of these factors in the bay region and hopes to provide the community with much of the required information as part of its San Francisco Bay Region Study in cooperation with the Department of Housing and Urban Development. The representation of surficial deposits on this map reflects the way in which a geologist, working exclusively with aerial photographs, interpreted the origin of various elements of the present landscape. The deposits shown here have not been examined in the field. However, by viewing overlapping vertical aerial photographs through a stereoscope, the geologist sees a three-dimensional relief model of the ground surface and can study and interpret the origins of landforms with considerable ease. In fact, for mapping surficial deposits, particularly in reconnaissance-type studies, photointerpretation has advantages over both ground observations and laboratory studies of surficial materials. Of course, better information can be provided when all aspects of the study are integrated. These preliminary photointerpretation maps are only the first stage in a detailed study of surficial deposits in the bay region, but they should provide land-use planners with immediately useful information about the regional distribution of landslide and other surficial deposits. This map indicates the dominant surficial processes that have probably been operative by showing the distribution of different types of surficial deposits. Processes such as weathering, erosion, sedimentation, and the slow as well as rapid downslope movement of earth materials have constantly reshaped the land surface in the past and will continue to in the future, although at varying rates. The processes are interrelated to varying degrees. For example, crustal uplift of the Coast Ranges will lead to increased erosion and downcutting by streams that in turn generally results in increased deposition of sediments in river valleys, lakes, and shoreline areas. Older flood planes and river deposits may be eroded, leaving elevated terrace deposits. In addition, downcutting by streams may cause adjacent slopes to become unstable, thereby increasing the possibility of slope failures. Man's activities can alter natural physical processes in many ways. Simple acts such as overwatering a lawn or placing a septic tank drainfield in ground that is marginally stable may weaken the bedrock and surficial materials enough to induce landsliding. Relatively stable areas may be made unstable as a result of construction activities that involve cutting or oversteepening of natural slopes. Engineers, builders, conservationists, and others concerned with land use must evaluate the potential effects of all types of development, and maps that show the nature and distribution of surficial deposits should provide much of the basic information they need. This map, then, shows the cumulative effects of various processes that have yielded surficial deposits up to the time the photographs used for photointerpretation were taken. It does not indicate directly areas where processes will be most active, nor does it show the rate at which they will operate. However, knowledge of the history of geologic events is a key to understanding and predicting the evolution of an area, even where man's activities significantly change the character of the land. Almost all new landslides, for example, occur in areas with a history of landslide activity.

California↗

Surficial sediment character of the Louisiana offshore continental shelf region: A GIS compilation

The Louisiana coastal zone, comprising the Mississippi River delta plain stretching nearly 400 km from Sabine Pass at the Texas border east to the Chandeleur Islands at the Mississippi border, represents one of North America’s most important coastal ecosystems in terms of natural resources, human infrastructure, and cultural heritage. At the same time, this region has the highest rates of coastal erosion and wetland loss in the Nation due to a complex combination of natural processes and anthropogenic actions over the past century. Comparison of historical maps dating back to 1855 and recent aerial photography show the Louisiana coast undergoing net erosion at highly variable rates. Rates have increased significantly during the past several decades. Earlier published statewide average shoreline erosion rates were >6 m/yr; rates have increased recently to >10 m/yr. The increase is attributable to collective action of storms, rapid subsidence, and pervasive man-made alterations of the rivers and the coast. In response to the dramatic landloss, regional-scale restoration plans are being developed by a partnership of federal and state agencies for the delta plain that have the objectives of maintaining the barrier islands, reducing wetland loss, and enhancing the natural sediment delivery processes. There is growing awareness that the sustainability of coastal Louisiana's natural resources and human infrastructure depends on the successful restoration of natural geologic processes. Critical to the long term success of restoration is scientific understanding of the geologic history and processes of the coastal zone region, including interactions between the rivers, wetlands, coast, and inner shelf. A variety of geophysical studies and mapping of Late Quaternary sedimentary framework and coastal processes by U.S. Geological Survey and other scientists during the past 50 years document that the Louisiana delta plain is the product of a complex history of cyclic delta switching by the Mississippi River and its distributaries over the past ~10,000 years that resulted in laterally overlapping deltaic depocenters. The interactions among riverine, coastal, and inner shelf processes have been superimposed on the Holocene transgression resulting in distinctive landforms and sedimentary sequences. Four Holocene shelf-phase delta complexes have been identified using seismic reflection data and vibracores. Each delta complex is bounded by transgressive surfaces. Following each cycle of deposition and abandonment, the delta lobes undergo regional subsidence and marine reworking that forms transgressive coastal systems and barrier islands. Ultimately, the distal end of each of the abandoned delta lobes is marked by submerged marine sand bodies representing drowned barriers. These sand bodies (e.g. Ship Shoal, Outer Shoal, Trinity Shoal, Tiger Shoal, St. Bernard Shoal) offer the largest volumes and highest quality sand for beach nourishment and shoreline and wetlands restoration. These four large sand shoals on inner continental shelf, representing the reworked remnants of former prograded deltaic headlands that existed on the continental shelf at lower sea level, were generated in the retreat path of the Mississippi River delta plain during the Holocene transgression. Penland and others (1989) have shown these sand bodies represent former shoreline positions associated with lower still stands in sea level. Short periods of rapid relative sea-level rise led to the transgressive submergence of the shorelines which today can be recognized at the -10 m to -20 m isobaths on the Louisiana continental shelf. Trinity Shoal and Ship Shoal represent the -10 m middle-to-late Holocene shoreline trend, whereas Outer Shoal and the St. Bernard Shoals define the -20 m early Holocene shoreline trend (Penland and others, 1989). Collectively, these sand shoals constitute a large volume of high quality sandy sediment potentially suitable for barrier island nourishment and coastal restoration. The USGS has actively supported coastal and wetlands geologic research for the past two decades in partnership with universities (e.g., Louisiana State University, University of New Orleans), state agencies (e.g. Louisiana Geological Survey, Louisiana Department of Natural Resources), and private organizations (Williams and others, 1992a,b; Williams and Cichon, 1993; List and others, 1994). These studies have focused on regional-scale mapping of coastal and wetland change and developing a better understanding of the processes that cause coastal erosion and wetlands loss, particularly the rapid deterioration of Louisiana's barrier islands, estuaries, and wetlands environments. With a better understanding of these processes, the ability to model and predict erosion and wetlands loss will improve. More accurate predictions will, in turn, allow for proper management of coastal resources. Improved predictions will also allow for better assessments of the utility of different restoration alternatives.

Louisiana↗

Effects of wastewater effluent discharge and treatment facility upgrades on environmental and biological conditions of Indian Creek, Johnson County, Kansas, June 2004 through June 2013

Indian Creek is one of the most urban drainage basins in Johnson County, Kansas, and environmental and biological conditions of the creek are affected by contaminants from point and other urban sources. The Johnson County Douglas L. Smith Middle Basin (hereafter referred to as the “Middle Basin”) and Tomahawk Creek Wastewater Treatment Facilities (WWTFs) discharge to Indian Creek. In summer 2010, upgrades were completed to increase capacity and include biological nutrient removal at the Middle Basin facility. There have been no recent infrastructure changes at the Tomahawk Creek facility; however, during 2009, chemically enhanced primary treatment was added to the treatment process for better process settling before disinfection and discharge with the added effect of enhanced phosphorus removal. The U.S. Geological Survey, in cooperation with Johnson County Wastewater, assessed the effects of wastewater effluent on environmental and biological conditions of Indian Creek by comparing two upstream sites to four sites located downstream from the WWTFs using data collected during June 2004 through June 2013. Environmental conditions were evaluated using previously and newly collected discrete and continuous data and were compared with an assessment of biological community composition and ecosystem function along the upstream-downstream gradient. This study improves the understanding of the effects of wastewater effluent on stream-water and streambed sediment quality, biological community composition, and ecosystem function in urban areas. After the addition of biological nutrient removal to the Middle Basin WWTF in 2010, annual mean total nitrogen concentrations in effluent decreased by 46 percent, but still exceeded the National Pollutant Discharge Elimination System (NPDES) wastewater effluent permit concentration goal of 8.0 milligrams per liter (mg/L); however, the NPDES wastewater effluent permit total phosphorus concentration goal of 1.5 mg/L or less was achieved at the Middle Basin WWTF. At the Tomahawk Creek WWTF, after the addition of chemically enhanced primary treatment in 2009, effluent discharges also had total phosphorus concentrations below 1.5 mg/L. After the addition of biological nutrient removal, annual total nitrogen and phosphorus loads from the Middle Basin WWTF decreased by 42 and 54 percent, respectively, even though effluent volume increased by 11 percent. Annual total phosphorus loads from the Tomahawk Creek WWTF after the addition of chemically enhanced primary treatment decreased by 54 percent despite a 33-percent increase in effluent volume. Total nitrogen and phosphorus from the WWTFs contributed between 30 and nearly 100 percent to annual nutrient loads in Indian Creek depending on streamflow conditions. In-stream total nitrogen primarily came from wastewater effluent except during years with the highest streamflows. Most of the in-stream total phosphorus typically came from effluent during dry years and from other urban sources during wet years. During 2010 through 2013, annual mean discharge from the Middle Basin WWTF was about 75 percent of permitted design capacity. Annual nutrient loads likely will increase when the facility is operated at permitted design capacity; however, estimated maximum annual nutrient loads from the Middle Basin WWTF were 27 to 38 percent lower than before capacity upgrades and the addition of biological nutrient removal to treatment processes. Thus, the addition of biological nutrient removal to the Middle Basin wastewater treatment process should reduce overall nutrient loads from the facility even when the facility is operated at permitted design capacity. The effects of wastewater effluent on the water quality of Indian Creek were most evident during below-normal and normal streamflows (about 75 percent of the time) when wastewater effluent represented about 24 percent or more of total streamflow. Wastewater effluent had the most substantial effect on nutrient concentrations in Indian Creek. Total and inorganic nutrient concentrations at the downstream sites during below-normal and normal streamflows were 10 to 100 times higher than at the upstream sites, even after changes in treatment practices at the WWTFs. Median total phosphorus concentrations during below-normal and normal streamflows at a downstream site were 43 percent lower following improvements in wastewater treatment processes. Similar decreases in total nitrogen were not observed, likely because total nitrogen concentrations only decreased in Middle Basin effluent and wastewater contributed a higher percentage to streamflows when nutrient samples were collected during the after-upgrade period. The wastewater effluent discharges to Indian Creek caused changes in stream-water quality that may affect biological community structure and ecosystem processes, including higher concentrations of bioavailable nutrients (nitrate and orthophosphorus) and warmer water temperatures during winter months. Other urban sources of contaminants also caused changes in stream-water quality that may affect biological community structure and ecosystem processes, including higher turbidities downstream from construction areas and higher specific conductance and chloride concentrations during winter months. Chloride concentrations exceeded acute and chronic exposure criteria at all Indian Creek study sites, regardless of wastewater influence, for weeks or months during winter. Streambed sediment chemistry was affected by wastewater (elevated nutrient and organic wastewater-indicator compound concentrations) and other contaminants from urban sources (elevated polyaromatic hydrocarbon concentrations). Overall habitat conditions were suboptimal or marginal at all sites; general decline in habitat conditions along the upstream-downstream gradient likely was caused by the cumulative effects of urbanization with increasing drainage basin size. Wastewater effluent likely affected algal periphyton biomass and community composition, primary production, and community respiration in Indian Creek. Functional stream health, evaluated using a preliminary framework based on primary production and community respiration, was mildly or severely impaired at most downstream sites relative to an urban upstream Indian Creek site. The mechanistic cause of the changes in these biological variables are unclear, though elevated nutrient concentrations were positively correlated with algal biomass, primary production, and community respiration. Macroinvertebrate communities indicated impairment at all sites, and Kansas Department of Health and Environment aquatic life support scores indicated conditions nonsupporting of aquatic life, regardless of wastewater influences. Urban influences, other than wastewater effluent discharge, likely control macroinvertebrate community structure in Indian Creek. Changes in treatment processes at the Middle Basin and Tomahawk Creek WWTFs improved wastewater effluent quality and decreased nutrient loads, but wastewater effluent discharges still had negative effects on the environmental and biological conditions at downstream Indian Creek sites. Wastewater effluent discharge into Indian Creek likely contributed to changes in measures of ecosystem structure (streamflow, water and streambed-sediment chemistry, algal biomass, and algal periphyton community composition) and function (primary production and community respiration) along the upstream-downstream gradient. Wastewater effluent discharges maintained streamflows and increased nutrient concentrations, algal biomass, primary production, and community respiration at the downstream sites. Functional stream health was severely impaired downstream from the Middle Basin WWTF and mildly impaired downstream from the Tomahawk WWTF relative to the urban upstream site. As distance from the Middle Basin WWTF increased, nutrient concentrations, algal biomass, primary production, and community respiration decreased, and functional stream health was no longer impaired 9.5 kilometers downstream from the discharge relative to the urban upstream site. Therefore, although wastewater effluent caused persistent changes in environmental and biological conditions and functional stream health at sites located immediately downstream from WWTF effluent discharges, some recovery to conditions more similar to the urban upstream site occurred within a relatively short distance.

Kansas↗