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Contributions to Peer Reviewed Literature

Recent EPA staff contributions to peer-reviewed literature that have bearing on nutrient criteria development are compiled below. Select the author's name to obtain a list of their nutrient relevant articles and abstract/summaries.

  • Naomi Detenbeck, Ph.D., Ecologist, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Office of Research and Development, U.S. Environmental Protection Agency

    Fetscher, E., M. Sutula, A. Sengupta, and N.E. Detenbeck. 2014. Linking Nutrients to Alterations in Aquatic Life in California Wadeable Streams. EPA/600/R-14/043. U.S. Environmental Protection Agency, Washington, DC.

    Summary: This report estimates the natural background and ambient concentrations of primary producer abundance indicators in California wadeable streams, identifies thresholds of adverse effects of nutrient-stimulated primary producer abundance on benthic macroinvertebrate and algal community structure in CA wadeable streams, and evaluates existing nutrient-algal response models for CA wadeable streams (Tetra Tech 2006), with recommendations for improvements. This information will be included in an assessment of the science forming the basis of recommendations for stream nutrient criteria for the state of California.

    Sutula, M., L. Green, G. Cicchetti, N. Detenbeck, and P. Fong 2014. Thresholds of adverse effects of macroalgal abundance and sediment organic matter on benthic habitat quality in estuarine intertidal flats. Estuaries and Coasts 37(6):1532-1548.

    Abstract: Confidence in the use of macroalgae as an indicator of estuarine eutrophication is limited by the lack of quantitative data on the thresholds of its adverse effects on benthic habitat quality. In the present study, we utilized sediment profile imagery (SPI) to identify thresholds of adverse effects of macroalgal biomass, sediment organic carbon (%OC) and sediment nitrogen (%N) concentrations on the apparent Redox Potential Discontinuity (aRPD), the depth that marks the boundary between oxic near-surface sediment and the underlying suboxic or anoxic sediment. At 16 sites in eight California estuaries, SPI, macroalgal biomass, sediment percent fines, %OC, and %N were analyzed at 20 locations along an intertidal transect. Classification and Regression Tree (CART) analysis was used to identify step thresholds associated with a transition from "reference" or natural background levels of macroalgae, defined as that range in which no effect on aRPD was detected. Ranges of 3–15 g dw macroalgae m−2, 0.4–0.7%OC and 0.05–0.07%N were identified as transition zones from reference conditions across these estuaries. Piecewise regression analysis was used to identify exhaustion thresholds, defined as a region along the stress–response curve where severe adverse effects occur; levels of 175 g dw macroalgae m−2, 1.1%OC and 0.1%N were identified as thresholds associated with a shallowing of aRPD to near zero depths. As an indicator of ecosystem condition, shallow aRPD has been related to reduced volume and quality for benthic infauna and alteration in community structure. These effects have been linked to reduced availability of forage for fish, birds and other invertebrates, as well as to undesirable changes in biogeochemical cycling.

    Smucker, N., N.E. Detenbeck, and A. Morrison. 2013. Diatom responses to watershed development and potential moderating effects of near-stream forest and wetland cover. Freshwater Science 32(1):230-249.

    Abstract: Watershed development alters hydrology and delivers anthropogenic stressors to streams via pathways affected by impervious cover. We characterized relationships of diatom communities and metrics with upstream watershed % impervious cover (IC) and with riparian % forest and wetland cover in 120-m buffers along each side of upstream networks. Threshold Indicator Taxa ANalysis (TITAN) identified potential threshold responses of diatom communities at 0.6 and 2.9%IC. Boosted regression trees (BRTs) indicated potential thresholds between 0.7 and 4.5%IC at which relative abundances of low-nutrient diatoms decreased and those of high-nutrient, prostrate, and motile diatoms increased. These individual thresholds indicated that multiple stressors or magnitudes of stressors related to increasing watershed %IC differentially affected relative abundances of taxa, and these differential effects probably contributed to a more gradual, but still substantial, change in overall community structure. BRTs showed that near-stream buffers with >65% and ideally >80% forest and wetland cover were associated with a 13 to 34% reduction in the effects of watershed % IC on diatom metrics and community structure and with a 61 to 68% reduction in the effects of watershed % pasture on motile and high-P diatom relative abundances. Watershed %IC and riparian % forest and wetland cover probably affect hydrologic, nutrient, and sediment regimes, which then affect diatom community physiognomy and taxa sensitive to nutrients and conductivity. Our results emphasize the importance of implementing mindful development and protective measures, especially in watersheds near watershed %IC thresholds. Effects of development potentially could be reduced by restoring and conserving near-stream forests and wetlands, but management and restoration strategies that extend beyond near-stream buffers are needed.

    Smucker, N., M. Becker, N. Detenbeck, and A. Morrison. 2013. Using algal metrics and biomass to evaluate multiple ways of defining concentration-based nutrient criteria in streams and their ecological relevance. Ecological Indicators 32:51-61.

    Abstract: We examined the utility of nutrient criteria derived solely from total phosphorus (TP) concentrations in streams (regression models and percentile distributions) and evaluated their ecological relevance to diatom and algal biomass responses. We used a variety of statistics to characterize ecological responses and to develop concentration-based nutrient criteria (derived from ecological effects) for streams in Connecticut, USA, where urbanization is the primary cause of watershed alteration. Mean background TP concentration in the absence of anthropogenic land cover was predicted to be 0.017 mg/l, which was similar to the 25th percentile of all study sites. Increased TP concentrations were significantly correlated with altered diatom community structure, decreased percent low P diatoms and diatoms sensitive to impervious cover, and increased percent high P diatoms, diatoms that increase with greater impervious cover, and chlorophyll a (P < 0.01). Variance partitioning models showed that shared effects of anthropogenic land cover and chemistry (i.e., chemistry affected by land cover) represented the majority of explained variation in diatom metrics and chlorophyll a. Bootstrapped regression trees, threshold indicator taxa analysis, and boosted regression trees identified TP concentrations at which strong responses of diatom metrics and communities occurred, but these values varied among analyses. When considering ecological responses, scientifically defensible and ecologically relevant TP criteria were identified at (1) 0.020 mg/l for designating highest quality streams and restoration targets, above which sensitive taxa steeply declined, tolerant taxa increased, and community structure changed, (2) 0.040 mg/l, at which community level change points began to occur and sensitive diatoms were greatly reduced, (3) 0.065 mg/l, above which most sensitive diatoms were lost and tolerant diatoms steeply increased to their maxima, and (4) 0.082 mg/l, which appeared to be a saturated threshold, beyond which substantially altered community structure was sustained. These criteria can inform anti-degradation policies for high quality streams, discharge permit decisions, and future strategies for watershed development and management. Our results indicated that management practices and decisions at the watershed scale will likely be important for improving degraded streams and conserving high quality streams. Results also emphasized the importance of incorporating ecological responses and considering the body of evidence from multiple conceptual approaches and statistical analyses for developing nutrient criteria, because solely relying on one approach could lead to misdirected decisions and resources.
  • Scot Hagerthey, Ph.D., Supervisory Biologist, U.S. Environmental Protection Agency, Office of Water

    Hagerthey, S.E., M. Kobza, M.I. Cook, S. Newman, and B.J. Bellinger. 2014. Aquatic fauna responses to an induced regime shift in the phosphorus-impacted Everglades. Freshwater Biology 59(7):1389-1405.

    Summary:

    1. Wetland eutrophication increases the susceptibility of native communities to invasion by opportunistic plant species, which then commonly form monotypic stands. Wetland aquatic fauna are negatively affected by associated changes of eutrophication in the physiochemical environment, habitat structural complexity, and ecological interactions. In addition to reducing external nutrient loads, it is predicted that efforts that reduce the resilience of the altered ecosystem are required to accelerate ecosystem recovery.
    2. We assessed the small fish and decapod crustacean responses to a three-year ecosystem scale experiment that tested the effectiveness of chemical treatment and controlled burning as a management strategy to accelerate the recovery of eutrophic Everglades marsh. The management strategy resulted in the removal, on average, of 91% and 81% of the emergent macrophyte cover in two regions differing in enrichment effects. The resulting open-water habitats were characterized by higher dissolved oxygen concentrations, greater periphyton and submersed aquatic vegetation, and increased structural complexity.
    3. The average combined density and biomass of small fish and decapod crustaceans did not differ significantly between dense emergent vegetation and created openings but regional and water year differences occurred. More importantly, community composition did differ between treatments with the crayfish Procambarus fallax dominating in dense vegetation and small fish Gambusia holbrooki, Jordanella floridae, and Poecilia latipinna and grass shrimp Palaemonetes paludosus dominating in open water.
    4. We compared the whole body carbon (C), nitrogen (N), and phosphorus (P) contents (%) and C:N:P stoichiometry among small fish and decapod crustaceans. Fish had greater whole body C and P contents (low C:P) compared to the two crustaceans. While the management action did not alter the quantity (mg carbon m-2) or energy (kcal m-2) of fauna, the resultant shift in composition was coincident with an increase in the nutrient quality (mg P m-2 and low C:P) of fauna.
    5. Faunal community composition of the created open-water habitats in the eutrophic Everglades was similar to the oligotrophic Everglades; however, density and biomass were significantly lower for the oligotrophic regi. Moreover, intra-specific comparisons showed that small fish and decapod crustaceans from the oligotrophic region were smaller and had lower whole body phosphorus contents than organisms from eutrophic regions. Thus, suggesting that phosphorus limitation in the Everglades extends beyond autotrophs to include consumers.
    6. The high densonity of emergent macrophytes typically formed in eutrophic wetlands creates a physical barrier to predators, limiting the trophic transfer of energy. The combination of burning and chemical treatment not only maintained the abundance and biomass of aquatic fauna, but produced a compositional shift towards higher quality prey for wading birds and predatory fishes. We recognize that contrasting nature between the created openings in the eutrophic and oligotrophic Everglades highlights major structural and functional differences in natural sloughs versus enriched created “sloughs”, but we suggest that active management efforts to accelerate the recovery of P impacted regions could provide temporary benefits to Everglades wildlife by improving access to abundant, high quality prey.

    Bellinger, B.J., S.E. Hagerthey, S. Newman, and M.I. Cook. 2012. Detrital flocculent and surface soil microbial biomarker responses to active management in the nutrient impacted Florida Everglades. Microbial Ecology 64(4):893-908.

    Abstract: Production of toxic secondary metabolites by cyanobacteria, collectively referred to as cyanotoxins, has been well described for eutrophied water bodies around the world. However, cohesive cyanobacterial mats also comprise a significant amount of biomass in subtropical oligotrophic wetlands. As these habitats generally do not support much secondary production, cyanotoxins, coupled with other physiological attributes of cyanobacteria, may be contributing to the minimized consumer biomass. Periphyton from the Florida Everglades have a diverse and abundant cyanobacterial assemblage whose species produce toxic metabolites; therefore, by screening periphyton representative of the greater Everglades ecosystem, six different cyanotoxins and one toxin (domoic acid) produced by diatoms were identified, ranging in content from 3×10-9 to 1.3×10-6 (g • g-1), with saxitoxin, microcystin, and anatoxin-a being the most common. While content of toxins were generally low, when coupled with the tremendous periphyton biomass (3-3000 g • m-2), a significant amount of cyanotoxins may be present. While the direct effects of the toxins identified here on the local grazing community need to be determined, the screening process utilized proved effective in showing the broad potential of periphyton to produce a variety of toxins.

    Hagerthey, S.E., S. Newman, and S. Xui. 2012. Periphyton-based transfer functions to assess ecological imbalance and management of a subtropical ombrotrophic peatland. Freshwater Biology 57(9):1947-1965.

    Summary

    1. To assess the biological status and response of aquatic resources to management actions, managers and decision makers require accurate and precise metrics. This is especially true for some parts of the Florida Everglades where multiple stressors (e.g., hydrologic alterations and eutrophication) have resulted in a highly degraded and fragmented ecosystem. Biological assessments are required that directly allow for the evaluation of historical and current status and responses to implantation of large-scale restoration projects.
    2. Utilizing periphyton composition and water quality data obtained from long-term (15 years) monitoring programs, we developed, calibrated, and verified periphyton-based numerical models (transfer functions) that could be used to simultaneously assess multiple stressors affecting the Everglades peatland (e.g., salinity, nitrogen, and phosphorus). Periphyton is an ideal indicator because responses to stressors are rapid and predictable and possess valued ecological attributes.
    3. Weighted averaging partial least squares regression was used to develop models to infer water quality concentrations from 456 samples comprised of 319 periphyton taxa. Measured versus periphyton inferred concentrations were strongly related for log transformed salinity (r2jackknife=0.81; RMSEP 0.15 mg/L) and log transformed TP (r2jackknife=0.70; RMSEP 0.18 mg/L) but weakly related for TKN (r2jackknife=0.46; RMSEP 0.12 mg/L). Validation results using an independent 455 sample dataset were similar (log(salinity) r2=0.78, log(TP) r2=0.65, and log(TKN) r2=0.38).
    4. Water Conservation Area 1 (WCA-1), a large ombrotrophic subtropical peatland impacted by multiple water quality stressors that has undergone major changes in water management, was used as a case study. The models were applied to a long-term periphyton dataset to reconstruct water quality trends in relation to restoration efforts to reduce nutrient loading to the Everglades. The combination of biologically inferred TP and salinity were used to identify the ecological status of periphyton assemblages. Periphyton assemblages were ecologically imbalanced with respect to salinity and TP. Salinity imbalance varied spatially and temporally whereas TP was spatially restricted. Imbalances caused by water management were due to salinity more so than TP.
    5. The transfer functions developed for the Everglades are trait-based quantitative numerical methods and are ideal because the abundances of species are modeled numerically in relation to a stressor. The resulting inferred value is a numerical representation of the stressor’s effect on biological condition that can be compared against the management of the stressor independent of other factors. The benefits are that biological lags or hysteresis events can easily be identified and environmental conditions can be estimated when measurements are lacking. Reporting biological assessments in terms of well-defined water quality metrics (e.g., numeric criterion) increased the communicative ability of the assessment. The use of multiple metrics to assess ecological imbalance increased the ability to identify probable causes.

    Hagerthey, S.E., B. Bellinger, K. Wheeler, M. Gantar, and E. Gaiser. 2011. Everglades periphyton: A biogeochemical perspective. Critical Reviews in Environmental Science and Technology 41(6):309-343.

    Abstract: Periphyton is an important component of the Everglades biogeochemical cycle but remains poorly understood. From a biogeochemical perspective, periphyton is a dense aggregation of diverse microorganisms (autotrophic and heterotrophic) and particles (mineral and detrital) imbedded within an extracellular matrix. Here we synthesize Everglades periphyton biogeochemistry and diversity at the ecosystem and community scales. The primary regulator of biogeochemical processes (material flux, transformation, and storage) is photosynthesis which controls oxidation-reduction potentials and heterotrophic metabolism. Eutrophication and hydrologic alterations have resulted in fundamental periphyton biogeochemical differences. Elucidation of these processes is required to predict and interpret responses to ecosystem restoration.

    Gaiser, E., P.V. McCormick, S.E. Hagerthey, and A. Gottlieb. 2011. Landscape patterns of periphyton in the Florida Everglades. Critical Reviews in Environmental Science and Technology 41(6):92-120.

    Abstract: Periphyton is an abundant and ubiquitous feature of the Florida Everglades, often forming thick mats that blanket shallow sediments and submersed plants. They are considered to be primary ecosystem engineers in the Everglades by forming and stabilizing soils, controlling concentrations of nutrients and gases, and supplying food and structure for other organisms. Distribution patterns are related to underlying physicochemical gradients as well as those hydrologic changes imposed by water management. Because communities respond rapidly to environmental change, their use has been advocated to provide indication of system degradation or restoration. We review studies on the distribution of periphyton in the Everglades, highlighting major findings relevant to water management, and also areas where additional exploration is necessary.

    Hagerthey, S.E., J.J. Cole, and D. Kilbane. 2010. Aquatic metabolism in the Everglades: The dominance of water column heterotrophy. Limnology and Oceanography 55(2):653-666.

    Abstract: Using high frequency measurements of free water dissolved oxygen (O2), we assessed gross primary production (GPP), respiration (R), and net aquatic production (NAP) in the shallow water Everglades peatland between 1996 and 2005. We distinguish NAP from net ecosystem production (NEP) since the boundary for shallow aquatic ecosystems may include aboveground GPP of wetland biota. Metabolism was estimated for 68 sites distributed among nine habitats and yielded 1085 5-day deployments or 5425 site-days. Habitats differed in vegetation composition, trophic status, and hydrology. System-wide O2 averaged 3.8±2.2 mg L-1 (mean±SD), or 49±30% of atmospheric saturation. GPP, R, and NAP averaged 103±76, 220±79, and -117±65 mmol O2 m-2 d-1, respectively. Metabolism was greater during the summer-wet season when greater irradiance, temperature, and material flux stimulate primary production and decomposition. Paradoxically, GPP was inversely related to total phosphorus (TP) with oligotrophic (TP<7 µg/L) open-water habitats dominated by periphyton having the highest and eutrophic (TP>35 µg/L) habitats with dense emergent macrophytes the lowest rates. R was greatest for moderately enriched (TP=15 µg/L) open-water habitats with floating macrophytes. The prevalence of net heterotrophy, 96% of the 1085 NAP estimates, reveals the importance of aboveground biota in regulating aquatic metabolism and O2 dynamics in shallow ecosystems. R is not only regulated by the influx of aboveground autochthonous carbon but also by aquatic GPP. Carbon turnover is greater in habitats where O2 production by aquatic vegetation enables aerobic respiration. Conversely, water column GPP is suppressed by dense emergent macrophytes, which limits O2 availability, favors anaerobic respiration, and reduces carbon turnover.
  • James S. Latimer, Ph.D., Research Scientist, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Office of Research and Development, U.S. Environmental Protection Agency

    Latimer, J.S., M.A. Tedesco, R.L. Swanson, C. Yarish, P. Stacey, and C. Garza. 2014. Long Island Sound: Prospects for the Urban Sea. Springer Series on Environmental Management. New York, New York.

    Summary: Long Island Sound: Prospects for the Urban Sea is the first synthesis of the science of Long Island Sound in more than thirty-five years. Described by Daniel Webster as the American Mediterranean, four centuries of human habitation, use, and abuse have created a trajectory of change being duplicated in estuaries throughout the country. Now subject to coordinated restoration efforts, the fate of Long Island Sound is a harbinger of the fate of coastal waters and economies everywhere.

    Six technical chapters summarize our knowledge about the human history, geology, physical oceanography, geochemistry, pollutant history, and biology and ecology of Long Island Sound. The last chapter identifies the linkages between science and environmental management, drawing extensively from hard-learned lessons on identifying threats and implementing strategies to confront them. This synthesis will be of interest to anyone engaged in the conservation and restoration of coastal ecosystems: scientists, students, managers, planners, and environmentalists.

    Latimer, J.S. and S.A. Rego. 2010. Empirical relationship between eelgrass extent and predicted watershed-derived nitrogen loading for shallow New England estuaries. Estuarine Coastal and Shelf Science 90(4):231-240.

    Abstract: Seagrasses provide important ecological services that directly or indirectly benefit human well-being and the environment. Excess nitrogen inputs are a major cause of eelgrass loss in the marine environment. Here we describe the results of a study aimed at quantifying the extent of eelgrass as a function of predicted watershed-derived nitrogen loading for small-to-medium-sized shallow estuaries in New England. Findings confirm that reduced extent of eelgrass corresponds to increased loading of nitrogen to this class of estuary. At lower levels of nitrogen loading (≤50 Kg ha−1 yr−1), eelgrass extent is variable and is likely controlled by other ecosystem factors unrelated to water quality. At higher loading rates, eelgrass coverage decreases markedly, with essentially no eelgrass at loading levels ≥100 Kg ha−1 yr−1.

    Latimer, J.S. and M.A. Charpentier. 2010. Nitrogen inputs to seventy-four southern New England estuaries: application of a watershed nitrogen loading model. Estuarine Coastal and Shelf Science 89(2):125-136.

    Abstract: Excess nitrogen inputs to estuaries have been linked to deteriorating water quality and habitat conditions which in turn have direct and indirect impacts on aquatic organisms. This paper describes the application of a previously verified watershed loading model to estimate total nitrogen loading rates and relative source contributions to 74 small-medium sized embayment-type estuaries in southern New England. The study estuaries exhibited a gradient in nitrogen inputs of a factor of over 7000. On an areal basis, the range represented a gradient of approximately a factor of 140. Therefore, all other factors being equal, the study design is sufficient to evaluate ecological effects conceptually tied to excess nitrogen along a nitrogen gradient. In addition to providing total loading inputs rates to the study estuaries, the model provides an estimate of the relative contribution of the nitrogen sources from each watershed to each associated estuary. Cumulative results of this analysis reveal the following source ranking (means): direct atmospheric deposition (37%), ≈wastewater (36%), >indirect atmospheric deposition (16%), and >fertilizer (12%). However, for any particular estuary the relative magnitudes of these source types vary dramatically. Together with scientific evidence on symptoms of eutrophication, the results of this paper can be used to develop empirical pressure-state models to determine critical nitrogen loading limits for the protection of estuarine water quality.
  • Blake A. Schaeffer, Ph.D., Assistant Laboratory Director, Safe and Sustainable Water Resources, National Exposure Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency

    Lunetta, R.S., B.A. Schaeffer, R.P. Stumpf, D. Keith, S.A. Jacobs, and M.S. Murphy. 2015. Evaluation of cyanobacteria cell count detection derived from MERIS imagery across the eastern USA. Remote Sensing of Environment 157(24-34).

    Abstract: Inland waters across the United States (US) are at potential risk for increased outbreaks of toxic cyanobacteria blooms events resulting from elevated water temperatures and extreme hydrologic events attributable to climate change and increased nutrient loadings associated with intensive agricultural practices. Current monitoring efforts are limited in scope due to resource limitations, analytical complexity, and data integration efforts. The goals of this study were to validate an algorithm for satellite imagery that could potentially be used to monitor surface cyanobacteria events in near real-time to provide a compressive monitoring capability for freshwater lakes (> 100 ha). The algorithm incorporated narrow spectral bands specific to the European Space Agency’s (ESA’s) MEdium Resolution Imaging Spectrometer (MERIS) instrument that were optimally oriented at phytoplankton pigment absorption features including phycocyanin at 620 nm. A validation of derived cyanobacteria cell counts was performed using available in situ data assembled from existing monitoring programs across eight states in the eastern US over a 39-month period (2009–2012). Results indicated that MERIS provided robust estimates for low (10,000–109,000 cells/mL) and very high (> 1,000,000 cells/mL) cell enumeration ranges (approximately 90% and 83%, respectively). However, the results for two intermediate ranges (110,000–299,000 and 300,000–1,000,000 cells/mL) were substandard, at approximately 28% and 40%, respectively. The confusion associated with intermediate cyanobacteria cell count ranges was largely attributed to the lack of available taxonomic data and distinction of natural counting units for the in situ measurements that would have facilitated conversions between cell counts and cell volumes. The results of this study document the potential for using MERIS-derived cyanobacteria cell count estimates to monitor freshwater lakes (> 100 ha) across the eastern US.

    Keith, D.J., B.A. Schaeffer, R.S. Lunetta, R.W. Gould Jr., K. Rocha, and D.J. Cobb. 2014. Remote sensing of selected water-quality indicators with the hyperspectral imager for the coastal ocean (HICO) sensor. International Journal of Remote Sensing 35(9):2927-2962.

    Abstract: The Hyperspectral Imager for the Coastal Ocean (HICO) offers the coastal environmental monitoring community an unprecedented opportunity to observe changes in coastal and estuarine water quality across a range of spatial scales not feasible with traditional field-based monitoring or existing ocean colour satellites. HICO, an Office of Naval Research-sponsored programme, is the first space-based maritime hyperspectral imaging instrument designed specifically for the coastal ocean. HICO has been operating since September 2009 from the Japanese Experiment Module – Exposed Facility on the International Space Station (ISS). The high pixel resolution (approximately 95 m at nadir) and hyperspectral imaging capability offer a unique opportunity for characterizing a wide range of water colour constituents that could be used to assess environmental condition. In this study, we transform atmospherically corrected ISS/HICO hyperspectral imagery and derive environmental response variables routinely used for evaluating the environmental condition of coastal ecosystem resources. Using atmospherically corrected HICO imagery and a comprehensive field validation programme, three regionally specific algorithms were developed to estimate basic water-quality properties traditionally measured by monitoring agencies. Results indicated that a three-band chlorophyll a algorithm performed best (R2 = 0.62) when compared with in situ measurement data collected 2–4 hours of HICO acquisitions. Coloured dissolved organic matter (CDOM) (R2 = 0.93) and turbidity (R2 = 0.67) were also highly correlated. The distributions of these water-quality indicators were mapped for four estuaries along the northwest coast of Florida from April 2010 to May 2012. However, before the HICO sensor can be transitioned from proof-of-concept to operational status and its data applied to benefit decisions made by coastal managers, problems with vicarious calibration of the sensor need to be resolved and standardized protocols are required for atmospheric correction. Ideally, the sensor should be placed on a polar orbiting platform for greater spatial and temporal coverage as well as for image synchronization with field validation efforts.

    Mishra, D.R., B.A. Schaeffer, and D. Keith. 2014. Performance evaluation of normalized difference chlorophyll index in coastal waters using HICO data. GIScience and Remote Sensing 15(2):175-198.

    Abstract: The Hyperspectral Imager for the Coastal Ocean (HICO) was used to derive chlorophyll-a (chl-a) based on the normalized difference chlorophyll index (NDCI) in two Gulf of Mexico coastal estuaries. Chl-a data were acquired from discrete in situ water sample analysis and above-water hyperspectral surface acquisition system (HyperSAS) remote sensing reflectance in Pensacola Bay (PB) and Choctawhatchee Bay (CB). NDCI algorithm calibrations and validations were completed on HICO data. Linear and best-fit (polynomial) calibrations performed strongly with R2 of 0.90 and 0.96, respectively. The best validation of NDCI resulted with an R2 of 0.74 and root-mean-square error (RMSE) of 1.64 µg/L. A strong spatial correspondence was observed between NDCI and chl-a, with higher NDCI associated with higher chl-a and these areas were primarily located in the northern PB and eastern CB at the river mouths. NDCI could be effectively used as a qualitative chl-a monitoring tool with a reduced need for site-specific calibration.

    Barnes, B.B., C. Hu, J.P. Cannizzaro, S.E. Craig, P. Hallock, D.L. Jones, J.C. Lehrter, N. Melod, B.A. Schaeffer, and R. Zepp. 2013. Estimation of diffuse attenuation of ultraviolet light in optically shallow Florida Keys waters from MODIS measurements. Remote Sensing of Environment 140:519-532.

    Abstract: Diffuse attenuation of solar light (Kd, m−1) determines the percentage of light penetrating the water column and available for benthic organisms. Therefore, Kd can be used as an index of water quality for coastal ecosystems that are dependent on photosynthesis, such as the coral reef environments of the Florida Reef Tract. Ultraviolet (UV) light reaching corals can lead to reductions in photosynthetic capacity as well as DNA damage. Unfortunately, field measurements of Kd(UV) lack sufficient spatial and temporal coverage to derive statistically meaningful patterns, and it has been notoriously difficult to derive Kd in optically shallow waters from remote sensing due to bottom contamination. Here we describe an approach to derive Kd(UV) in optically shallow waters of the Florida Keys using variations in the spectral shape of MODIS-derived surface reflectance. The approach used a principal component analysis and stepwise multiple regression to parsimoniously select modes of variance in MODISderived reflectance data that best explained variance in concurrent in situ Kd(UV) measurements. The resulting models for Kd(UV) retrievals in waters 1–30 m deep showed strong positive relationships between derived and measured parameters [e.g., for Kd(305) ranging from 0.28 to 3.27 m−1 ; N = 29; R2 = 0.94]. The predictive capabilities of these models were further tested, also showing acceptable performance [for Kd(305), R2 = 0.92; bias = −0.02 m−1; URMS = 23%]. The same approach worked reasonably well in deriving the absorption coefficient of colored dissolved organic matter (CDOM) in UV wavelengths [ag(UV), m−1], as Kd(UV) is dominated by ag(UV). Application of the approach to MODIS data showed different spatial and temporal Kd(305) patterns than the Kd(488) patterns derived from a recently validated semi-analytical approach, suggesting that different mechanisms are controlling Kd in the UV and in the visible. Given the importance of water clarity and light availability to shallow-water flora and fauna, the new Kd(UV) and ag(UV) data products provide unprecedented information for assessing and monitoring of coral reef health, and could further assist ongoing regional protection efforts.

    Barnes, B.B., C. Hu, B.A. Schaeffer, Z. Lee, and D.A. Palandro. 2013. MODIS derived spatiotemporal water clarity patterns in optically shallow Florida Keys waters: A new approach to remove bottom contamination. Remote Sensing of Environment 134:377-391.

    Abstract: Retrievals of water quality parameters from satellite measurements over optically shallow waters have been problematic due to bottom contamination of the signals. As a result, large errors are associated with derived water column properties. These deficiencies greatly reduce the ability to use satellites to assess the shallow water environments around coral reefs and seagrass beds. Here, a modified version of an existing algorithm is used to derive multispectral diffuse attenuation coefficient (Kd) from MODIS/Aqua measurements over optically shallow waters in the Florida Keys. Results were validated against concurrent in situ data (Kd(488) from 0.02 to 0.20 m−1, N = 22, R2 = 0.68, Mean Ratio = 0.93, unbiased RMS = 31%), and showed significant improvement over current products when compared to the same in situ data (N = 13, R2 = 0.37, Mean Ratio = 1.61, unbiased RMS = 50%). The modified algorithm was then applied to time series of MODIS/Aqua data over the Florida Keys (in particular, the Florida Keys Reef Tract), whereby spatial and temporal patterns of water clarity between 2002 and 2011 were elucidated. Climatologies, time series, anomaly images, and empirical orthogonal function analysis showed primarily nearshore–offshore gradients in water clarity and its variability, with peaks in both at the major channels draining Florida Bay. ANOVA revealed significant differences in Kd(488) according to distance from shore and geographic region. Excluding the Dry Tortugas, which had the lowest climatological Kd(488), water was clearest at the northern extent of the Reef Tract, and Kd(488) significantly decreased sequentially for every region along the tract. Tests over other shallow-water tropical waters such as the Belize Barrier Reef also suggested general applicability of the algorithm. As water clarity and light availability on the ocean bottom are key environmental parameters in determining the health of shallow-water plants and animals, the validated new products provide unprecedented information for assessing and monitoring of coral reef and seagrass health, and could further assist ongoing regional zoning efforts.

    Zhao, J., B. Barnes, N. Melob, D. English, B. Lapointe, F. Muller-Kargera, B. Schaeffer, and C. Hu. 2013. Assessment of satellite-derived diffuse attenuation coefficients and euphotic depths in south Florida coastal waters. Remote Sensing of Environment 131:38-50.

    Abstract: Optical data collected in coastal waters off South Florida and in the Caribbean Sea between January 2009 and December 2010 were used to evaluate products derived with three bio-optical inversion algorithms applied to MODIS/Aqua, MODIS/Terra, and SeaWiFS satellite observations. The products included the diffuse attenuation coefficient at 490 nm (Kd_490) and for the visible range (Kd_PAR), and euphotic depth (Zeu, corresponding to 1% of the surface incident photosynthetically available radiation or PAR). Above-water hyperspectral reflectance data collected over optically shallow waters of the Florida Keys between June 1997 and August 2011 were used to help understand algorithm performance over optically shallow waters. The in situ data covered a variety of water types in South Florida and the Caribbean Sea, ranging from deep clear waters, turbid coastal waters, and optically shallow waters (Kd_490 range of ~0.03–1.29 m−1 ). An algorithm based on Inherent Optical Properties (IOPs) showed the best performance (RMSDb13% and R2 ~1.0 for MODIS/Aqua and SeaWiFS). Two algorithms based on empirical regressions performed well for offshore clear waters, but underestimated Kd_490 and Kd_PAR in coastal waters due to high turbidity or shallow bottom contamination. Similar results were obtained when only in situ data were used to evaluate algorithm performance. The excellent agreement between satellite-derived remote sensing reflectance (Rrs) and in situ Rrs suggested that the different product uncertainties resulted primarily from algorithm inversion as opposed to atmospheric correction. A simple empirical model was developed to derive Zeu from Kd_490 for satellite measurements of nearshore waters. MODIS/Aqua gave the best results in general relative to in situ observations. Our findings lay the basis for synoptic time-series studies of water quality in coastal ecosystems, yet more work is required to minimize the bottom interference in the Florida Keys optically shallow waters.

    Schaeffer, B.A., J.D. Hagy, and R.P. Stumpf. 2013. An approach to developing numeric water quality criteria for coastal waters: Transitioning from SeaWiFS to MODIS and MERIS. Journal of Applied Remote Sensing 7(073544):1-18.

    Abstract: States can adopt numeric water quality criteria into their water quality standards to protect the designated uses of their coastal waters from eutrophication impacts. The first objective of this study was to provide an approach for developing numeric water quality criteria for coastal waters based on archived SeaWiFS ocean color satellite data. The second objective was to develop an approach for transferring water quality criteria assessments to newer ocean color satellites, such as MODIS and MERIS. Measures of SeaWiFS, MODIS, and MERIS chlorophyll-a (ChlRS-a, mgm−3) were resolved across Florida’s coastal waters between 1998 and 2009. Annual geometric means of SeaWiFS ChlRS-a were evaluated to determine a quantitative reference baseline from the 90th percentile of the annual geometric means. A method for transferring to multiple ocean color sensors was implemented with SeaWiFS as the reference instrument. The ChlRS-a annual geometric means for each coastal segment from MODIS and MERIS were regressed against SeaWiFS to provide a similar response among all three satellites. Standardization factors for each coastal segment were calculated based on the differences between 90th percentile from SeaWiFS to MODIS and SeaWiFS to MERIS. This transfer approach was allowed for future assessments, typically with <7% difference in the calculated criteria.

    Schaeffer, B.A., K.G. Schaeffer, D. Keith, R.S. Lunetta, R. Conmy, and R.W. Gould. 2013. Barriers to adopting satellite remote sensing for water quality management. International Journal of Remote Sensing 34(21):7534-7544.

    Abstract: Sustainable practices require a long-term commitment to creating solutions to environmental, social, and economic issues. The most direct way to ensure that management practices achieve sustainability is to monitor the environment. Remote sensing technology has the potential to accelerate the engagement of communities and managers in the implementation and performance of best management practices. Over the last few decades, satellite technology has allowed measurements on a global scale over long time periods, and is now proving useful in coastal waters, estuaries, lakes, and reservoirs, which are relevant to water quality managers. Comprehensive water quality climate data records have the potential to provide rapid water quality assessments, thus providing new and enhanced decision analysis methodologies and improved temporal/spatial diagnostics. To best realize the full application potential of these emerging technologies an open and effective dialogue is needed between scientists, policy makers, environmental managers, and stakeholders at the federal, state, and local levels. Results from an internal US Environmental Protection Agency qualitative survey were used to determine perceptions regarding the use of satellite remote sensing for monitoring water quality. The goal of the survey was to begin understanding why management decisions do not typically rely on satellite-derived water quality products.

    Schaeffer, B.A., J.C. Kurtz, and M.K. Hein. 2012. Phytoplankton community composition in nearshore coastal waters of Louisiana. Marine Pollution Bulletin 64:1705-1712.

    Abstract: Phytoplankton community compositions within near-shore coastal and estuarine waters of Louisiana were characterized by group diversity, evenness, relative abundance and biovolume. Sixty-six taxa were identified in addition to eight potentially harmful algal genera including Gymnodinium sp. Phytoplankton group diversity was lowest at Vermillion Bay in February 2008, but otherwise ranged between 2.16 and 3.40. Phytoplankton evenness was also lowest at Vermillion Bay in February 2008, but otherwise ranged between 0.54 and 0.77. Dissolved oxygen increased with increased biovolume (R2 = 0.85, p < 0.001) and biovolume decreased with increased light attenuation (R2 = 0.34, p = 0.007), which supported the importance of light in regulating oxygen dynamics. Diatoms were dominant in relative abundance and biovolume at almost all stations and all cruises. Brunt–Väisälä frequency was used as a measure of water column stratification and was negatively correlated (p = 0.02) to diatom relative percent total abundance.

    Schaeffer, B.A., J.D. Hagy, J.C. Lehrter, R.N. Conmy, and R.P. Stumpf. 2012. An approach to developing numeric water quality criteria for coastal waters using the SeaWiFS satellite data record. Environmental Science and Technology 46:916-922.

    Abstract: Human activities on land increase nutrient loads to coastal waters, which can increase phytoplankton production and biomass and associated ecological impacts. Numeric nutrient water quality standards are needed to protect coastal waters from eutrophication impacts. The Environmental Protection Agency determined that numeric nutrient criteria were necessary to protect designated uses of Florida’s waters. The objective of this study was to evaluate a reference condition approach for developing numeric water quality criteria for coastal waters, using data from Florida. Florida’s coastal waters have not been monitored comprehensively via field sampling to support numeric criteria development. However, satellite remote sensing had the potential to provide adequate data. Spatial and temporal measures of SeaWiFS OC4 chlorophyll-a (Chl(RS)-a, mg m(-3)) were resolved across Florida’s coastal waters between 1997 and 2010 and compared with in situ measurements. Statistical distributions of Chl(RS)-a were evaluated to determine a quantitative reference baseline. A binomial approach was implemented to consider how new data could be assessed against the criteria. The proposed satellite remote sensing approach to derive numeric criteria may be generally applicable to other coastal waters.

    Schaeffer, B.A., G.A. Sinclair, J.C. Lehter, M.C. Murrella, J.C. Kurtz, R.W. Gould, and D.F. Yates. 2011. An analysis of diffuse attenuation in the northern Gulf of Mexico hypoxic zone using the SeaWiFS satellite data record. Remote Sensing of Environment 115:3748-3757.

    Abstract: The Sea-viewing Wide Field-of-View Sensor (SeaWiFS) derived diffuse light attenuation along the Louisiana continental shelf (LCS) was examined at monthly scales from 1998 to 2007 to characterize temporal and spatial patterns, and responsible physical forcing conditions. The SeaWiFS diffuse light attenuation ranged from 0.10 to 2.64 m−1. Stepwise multiple linear regression analysis suggested that spatial and temporal patterns in diffuse light attenuation were influenced by wind speed, nutrient loading, and river discharge from the Mississippi and Atchafalaya River Basin. SeaWiFS daily integrated surface photosynthetically active radiation (PAR, 400–700 nm) and diffuse light attenuation were used to calculate the absolute PAR and percentage of surface PAR that reached the sediment water interface (SWI) on the LCS. Large portions of the LCS were euphotic to the SWI especially during April and May. This finding implied that significant primary production was possible beneath the pycnocline during spring and early summer. In addition, this study was the first to demonstrate that the euphotic depth was correlated to the depth at which the water column turned hypoxic on the LCS. The development of hypoxic waters may be influenced by decreased light availability below the pycnocline in addition to aforementioned physical forcing.

    Schaeffer, B.A., R.N. Conmy, J. Aukampa, G. Cravena, and E.J. Ferer. 2011. Organic and inorganic matter in Louisiana coastal waters at Vermilion, Atchafalaya, Terrebonne, Barataria, and Mississippi locations. Marine Pollution Bulletin 62:415-422.

    Abstract: Chromophoric dissolved organic matter (CDOM) spectral absorption, dissolved organic carbon (DOC) concentration, and the particulate fraction of inorganic (PIM) and organic matter (POM) were measured in Louisiana coastal waters at Vermilion, Atchafalaya, Terrebonne, Barataria, and Mississippi River locations, in 2007–2008. The range of CDOM was 0.092 m−1 at Barataria in June 2008 to 11.225 m−1 at Mississippi in February 2008. An indicator of organic matter quality was predicted by the spectral slope of absorption coefficients from 350 to 412 nm which was between 0.0087 m−1 at Mississippi in May 2008 and 0.0261 m−1 at Barataria in June 2008. CDOM was the dominant component of light attenuation at Terrebonne and Barataria. Detritus and CDOM were the primary components of light attenuation at Vermilion, Atchafalaya, and Mississippi. DOC ranged between 65 and 1235 μM. PIM ranged between 1.1 and 426.3 mg L−1 and POM was between 0.3 and 49.6 mg L−1.
  • Lester Yuan, Ph.D., Office of Science and Technology, U.S. Environmental Protection Agency

    Yuan, L.L., A.I. Pollard. 2015. Deriving nutrient targets to prevent excessive cyanobacterial densities in U.S. lakes and reservoirs. Freshwater Biology. June 2015.

    Summary:
    1. High densities of cyanobacteria can interfere with the use of lakes and reservoirs for recreation and as sources for drinking water, and one approach for reducing the amount of cyanobacteria is to reduce nutrient concentrations in the waterbody.
    2. An approach is described for deriving numeric targets for concentrations of total phosphorus (TP) and total nitrogen (TN) that are associated with a pre-specified probability of cyanobacterial biovolume that exceeds the recommended World Health Organization thresholds for recreation in the water. The analysis consisted of two phases. First, a divisive tree algorithm was used to identify groups of lakes in which the relationship between nutrients and cyanobacterial biovolume was similar. Second, hierarchical Bayesian models were used to estimate relationships between cyanobacterial biovolume, TP and TN, while partitioning the observed variance in biovolume into components associated with sampling variability, temporal variability, and among-lake differences.
    3. The final model accounted for 91% of the variance in cyanobacterial biovolume among different lakes and was used to identify nutrient concentrations that maintain a low probability of excessively high cyanobacterial biovolumes.
    4. When no classes of lakes were specified and the relationship between cyanobacterial biovolume and nutrient concentrations was modelled using a national data set, mean targets of 87 and 1100 μg L−1 were derived for TP and TN, respectively, to maintain cyanobacterial biovolume below moderate risk levels as defined by the World Health Organization. After classification, mean nutrient targets in lakes that were found to be most susceptible to high biovolumes of cyanobacteria (i.e. deep lakes) were 61 and 800 μg L−1 for TP and TN, while higher nutrient thresholds were observed for other classes of lakes.

    Yuan, L.L., A.I. Pollard. 2014. Classifying Lakes to Improve Precision of Nutrient-Chlorophyll Relationships. Freshwater Science 33 (4):1184-1194.

    Abstract: Accurate and precise estimates of relationships between stressors and environmental responses can inform management decisions most usefully when models can be easily interpreted. Here, we describe an approach for classifying lakes and reservoirs that can improve estimates of the relationships between total P (TP) and chlorophyll a (chl a) concentration, while preserving a model that can be readily interpreted by environmental managers and stakeholders. We selected classification variables statistically with a classification and regression tree in which relationships between TP and chl a were the terminal nodes of the tree. We developed a set of classification trees from bootstrapped replicates of the calibration data to explore a broader range of possible trees. We chose a final tree based on its predictive performance with a validation data set. The total N:TP mass ratio was the classification variable selected most frequently from a broad array of biological, chemical, and physical candidate classification variables. Relationships between TP and chl a in the resulting lake classes provided predictions that were substantially more accurate than predictions computed using nutrient ecoregions based on aggregations of Omernik Level III ecoregions, but predictions from a random forest model that averaged an ensemble of trees were even more accurate. Thus, the classification approach presented here sacrifices a small amount of predictive accuracy to retain a tree structure that is readily interpretable.

    Yuan, L.L., A.I. Pollard. 2014. Classifying Lakes to Quantify Relationships Between Epilimnetic Chlorophyll a and Hypoxia. Environmental Management. December 2014.

    Abstract: Excess nutrient loading increases algal abundance which can cause hypoxia in many lakes and reservoirs. We used a divisive partitioning approach to analyze dissolved oxygen profile data collected across the continental United States to increase the precision of estimated relationships between chlorophyll a (chl a) concentrations and the extent of hypoxia in the water column. Chl a concentrations predicted the extent of hypoxia most accurately in lakes that were stratified at the time of sampling with a maximum temperature gradient of at least 1.2 °C/m. Lake elevation, Secchi depth, and lake geometry ratio further refined the specification of groups of lakes with different relationships between chl a and the extent of hypoxia. The statistical relationships between chl a and the extent of hypoxia that were estimated can be used directly for setting management thresholds for chl a in particular types of lakes.

    Yuan, L.L., A.I. Pollard, S. Pather, J.L. Oliver, and L. D'Anglada. 2014. Managing microcystin: identifying national-scale thresholds for total nitrogen and chlorophyll a. Freshwater Biology 59(9):1970-1981.

    Summary:
    1. The occurrence of high cyanotoxin concentrations can severely impair the use of a waterbody for drinking water and recreational purposes. Cyanotoxins are likely to occur under specific environmental conditions, and so identifying these conditions can facilitate management of the waterbody to reduce the likelihood of high cyanotoxin concentrations.
    2. We analyzed data collected from lakes across the contiguous United States to identify environmental variables that are strongly associated with occurrence of high concentrations of a common cyanotoxin, microcystin (MC).
    3. Since many different environmental variables covary and are associated with high MC, we used least absolute shrinkage and selection operator (LASSO) regression to identify a few variables that provided accurate predictions of high MC (≥1 μg L−1).
    4. Our analysis indicated that total nitrogen (TN) and chlorophyll a (chl a) concentrations yielded a parsimonious model that accurately predicted the occurrence of high MC. Based on this model, we identified management thresholds for TN and chl a that would maintain the probability of high MC at or below 10 and 5%.

    Gerritsen, J., L.L. Yuan, P. Shaw-Allen, and D. Farrar. Chapter 11: Regional Observational Studies: Assembling and Exploring Data; Gerritsen, J., L.L. Yuan, P. Shaw-Allen, and S.M. Cormier. Chapter 12: Regional Observational Studies: Deriving Evidence; and Farrar, D., L.C. Alexander, L.L. Yuan, and J. Gerritsen. Chapter 13: Regional Observational Studies: Addressing Confounding In Norton, S.B., S.M. Cormier, and G.W. Suter II. 2014. Ecological Causal Assessment. CRC Press.

    Summary:
    Chapter 11: This chapter expands the discussion of data acquisition and exploratory data analysis to obsevrational studies beyond the specific study site. These initial activities are important for identifying the strengths and limitations of the data for deriving evidence (discussed in the next chapter).
    Chapter 12: This chapter reviews several approaches for deriving evidence from regional observational studies. Observational studies have the advantage of reflecting realistic exposure conditions, but analyses may be hampered by high natural variability and the influence of confounding factors.
    Chapter 13: Observational studies have the advantage of realistic exposure conditions. However, estimating the effect of an individual stressor in the presence of covarying stressors and natural gradients is challenging because the observed effect can be the result of one or more confounding variables. This chapter discusses methods for identifying confounding variables and mitigating their influence on models used to develop evidence from observational data sets.

    Yuan, L.L.. 2013. Using correlation of daily flows to identify index gauges for ungauged streams. Water Resources Research 49(1):604-613.

    Abstract: Predictions of daily flows in ungauged streams frequently rely on index gauges, where the timing of the daily flow at the index gauge is assumed to be similar to that in the ungauged stream. When some limited flow measurements are available at the ungauged sites, the strength of correlation between these flows and candidate index gauges can inform the selection of the index gauges. Here the use of the correlation of daily flows to select index gauges is systematically evaluated using a large flow data set from the Ohio River Valley, USA. Then, a novel method is introduced for predicting the strength with which daily flows at different gauges are correlated with daily flow at a completely ungauged site, using the physical characteristics of the ungauged site. The index gauges can then be selected based on these predicted correlations. The analysis indicates that this new method provides a means of identifying index sites that will yield a desired level of accuracy in flow predictions at ungauged locations. The ungauged sites at which sufficient index gauges are not available are also identified, and flow predictions are not calculated for these sites. Using this new method improves the overall accuracy of predicted flows, relative to existing methods.

    Allan, D.J., L.L. Yuan, P. Black, T. Stockton, P.E. Davies, R.H. Magierowski, and S.M. Read. 2012. Investigating the relationships between environmental stressors and stream condition using Bayesian belief networks. Freshwater Biology 57(s1):58-73.

    Summary:
    1. Stream reaches found to be impaired by physical, chemical or biological assessment generally are associated with greater extent of urban and agricultural land uses, and lesser amount of undeveloped lands. However, because stream condition commonly is influenced by multiple stressors as well as underlying natural gradients, it can be difficult to establish mechanistic relationships between altered land use and impaired stream condition.
    2. This study explores the use of Bayesian belief networks (BBNs) to model presumed causal relationships between stressors and response variables. A BBN depicts the chain of causal relationships resulting in some outcome such as environmental impairment and can make use of evidence from expert judgment as well as observational and experimental data.
    3. Three case studies illustrate the flexibility of BBN models. Expert elicitation in a workshop setting was employed to model the effects of sedimentation on benthic invertebrates. A second example used empirical data to explore the influence of natural and anthropogenic gradients on stream habitat in a highly agricultural watershed. The third application drew on several forms of evidence to develop a decision support tool linking grazing and forestry practices to stream reach condition.
    4. Although data limitations challenge model development and our ability to narrow the range of possible outcomes, model formulation forces participants to conceptualise causal mechanisms and consider how to resolve data shortfalls. With sufficient effort and resources, models with greater evidentiary strength from observational and experimental data may become practical tools to guide management decisions.
    5. Such models may be used to explore possible outcomes associated with a range of scenarios, thus benefiting management decision-making, and to improve insight into likely causal relationships.

    Pollard, A.I., and L.L. Yuan. 2010. Assessing the consistency of response metrics of the invertebrate benthos: a comparison of trait- and identity-based measures. Freshwater Biology 55(7):1420-1429.

    Summary:
    1. The use of species traits to interpret biological changes in invertebrate assemblages across environmental gradients has been suggested as a method to improve discrimination over existing species composition methods. One reason for greater potential discrimination and predictive ability is the assumed universality of traits across a range of spatial and temporal scales. We explore this assumption by comparing the consistency of stressor–response relationships of a trait characteristic (percent clinging taxa) and a common taxonomy-based metric [percent Ephemeroptera, Plecoptera and Trichoptera (EPT)] over a stressor gradient of increasing benthic fine sediment.
    2. We use invertebrate assemblage and environmental data from three large-scale surveys that cover the western United States, eastern United States and the Mid-Atlantic Highlands of the US. These three datasets allow us to compare stressor–response relationships in terms of geographic position (west versus east) and spatial scale (entire east versus a sub-region of the east). We compare the slopes and intercepts of the two measures of assemblage response.
    3. Trait characteristics exhibited more consistent stressor–response relationships than identity characteristics. Stressor–response relationships generated for clinging invertebrate richness had statistically similar slopes over sediment gradients, regardless of spatial scale or geographic location. In contrast, slopes were significantly different for relationships generated with EPT richness over sediment gradients.
    4. Results of this study support the hypothesis that trait-based measures have a more consistent response to a stressor gradient than identity-based assemblage measures. Choosing consistent measures of community response will facilitate comparisons among assemblages across large spatial scales.

    Yuan, L.L. 2010. Estimating the effects of excess nutrients on stream invertebrates from observational data. Ecological Applications 20:110-125.

    Abstract: Increased nutrient concentrations in streams and rivers have altered biological structure and function. Manipulative studies have provided insights into different mechanisms by which changes in nutrient concentrations influence aquatic biota, but these studies are limited in spatial scope and in their quantification of nutrient effects on aggregate measures of the invertebrate assemblage. Observational data provide a complementary source of information to manipulative studies, but these data must be analyzed such that the potential effects of spurious correlations are minimized. Propensity scores, a technique developed to analyze human health observational data, are applied here to estimate the effects of increased nutrients on the total taxon richness of stream invertebrates in a large observational data set collected from the western United States. The analysis indicates that increases in nutrient concentration are strongly associated with and cause decreases in invertebrate richness in large, but wadeable, open-canopied streams. These decreases in invertebrate richness were not mediated by periphyton biomass, a commonly proposed mechanism by which nutrients influence invertebrates. In smaller, closed-canopied streams, increases in nutrients were associated with small increases in total richness that were not statistically significant. Using propensity scores can greatly improve the accuracy of insights drawn from observational data by minimizing the potential that factors other than the factor of interest may confound the results.

    Yuan, L.L., A.I. Pollard, and D.M. Carlisle. 2009. Using propensity scores to estimate the effects of insecticides on stream invertebrates from observational data. Environmental Toxicology and Chemistry 28(7):1518-1527.

    Abstract: Analyses of observational data can provide insights into relationships between environmental conditions and biological responses across a broader range of natural conditions than experimental studies, potentially complementing insights gained from experiments. However, observational data must be analyzed carefully to minimize the likelihood that confounding variables bias observed relationships. Propensity scores provide a robust approach for controlling for the effects of measured confounding variables when analyzing observational data. Here, we use propensity scores to estimate changes in mean invertebrate taxon richness in streams that have experienced insecticide concentrations that exceed aquatic life use benchmark concentrations. A simple comparison of richness in sites exposed to elevated insecticides with those that were not exposed suggests that exposed sites had on average 6.8 fewer taxa compared to unexposed sites. The presence of potential confounding variables makes it difficult to assert a causal relationship from this simple comparison. After controlling for confounding factors using propensity scores, the difference in richness between exposed and unexposed sites was reduced to 4.1 taxa, a difference that was still statistically significant. Because the propensity score analysis controlled for the effects of a wide variety of possible confounding variables, we infer that the change in richness observed in the propensity score analysis was likely caused by insecticide exposure.

    Norton, S.B., S.M. Cormier, G.W. Suter II, K. Schofield, L.L. Yuan, P. Shaw-Allen, and C.R. Ziegler. Chapter 17: CADDIS: The Causal Analysis/Diagnosis Decision Information System In Marcomini, A., G.W. Suter II, and A. Critto. 2009. Decision Support Systems for Risk-Based Management of Contaminated Sites.

    Abstract: Biological monitoring and assessment methods have become indispensable tools for evaluating the condition of aquatic and terrestrial ecosystems. When an undesirable biological condition is observed (e.g., a depauperate fish assemblage), its cause (e.g., toxic substances, excess fine sediments, or nutrients) must be determined in order to design appropriate remedial management actions. Causal analysis challenges environmental scientists to bring together, analyze, and synthesize a broad variety of information from monitoring studies, models, and experiments to determine the probable cause of ecological effects. Decision-support systems can play an important role in improving the efficiency, quality and transparency of causal analyses.

    CADDIS is an on-line decision framework for identifying the stressors responsible for undesirable biological conditions in aquatic systems. CADDIS was developed in response to requirements under the U.S. Clean Water Act to develop plans for restoring impaired aquatic systems. CADDIS is based on U.S. EPA’s 2000 Stressor Identification Guidance document, and draws from multiple types of eco-epidemiological evidence. A major update in 2007 added summaries of commonly encountered causes of biological impairment: metals, sediments, nutrients, flow alteration, temperature, ionic strength, low dissolved oxygen, and toxic chemicals. These reviews are designed to help practitioners choose which causes to consider, based on sources, site information, and observed biological effects. A series of conceptual models illustrates connections between sources, stressors and effects. Another major new section provides advice and tools for analyzing data and interpreting results as causal evidence; these tools help quantify associations between any cause and any biological impairment using innovative methods such as species-sensitivity distributions, biological inferences, conditional probability analysis, and quantile regression analysis.

    An essential part of the development strategy for CADDIS has been the use of case studies to test the process and tools in different regions, and with different causal factors. Case studies have been conducted in streams on the urbanized east coast and the agriculturally-dominated mid-west to the arid west, and have considered causes including low dissolved oxygen, increased temperature, toxic substances, altered food resources and fine sediments. Lessons learned from the case studies include the importance of a structure for organizing the large variety of evidence that is often available, the need for well-matched reference sites for comparison, the benefits of iterative and directed data collection, and the frequency of surprising results. The case studies illustrate the promise of CADDIS: by building on the foundation of biological monitoring, we can provide a powerful means for improving the health of our aquatic systems.

    Paulsen, S.G., C.P. Hawkins, J. Van Sickle, L.L. Yuan, and S.M. Holdsworth. 2008. An invitation to apply national survey data to ecological research. Journal of the North American Benthological Society 27(4):1017-1018.

    Abstract: The data from the Wadeable Streams Assessment (WSA) cover 1392 stream sites from across the conterminous US. Beyond the summary information available in the WSA and the papers in this special issue, the raw data for the biological, chemical, physical-habitat, and watershed land cover are available to the research community for more in-depth assessments or for application in ecological research. We encourage the ecological research community to make use of these rich data sets.

    Hawkins, C.P., S.G. Paulsen, J. Van Sickle, and L.L. Yuan. 2008. Regional assessments of stream ecological condition: scientific challenges associated with the USA’s national Wadeable Stream Assessment. Journal of the North American Benthological Society 27(4):805-807.

    Abstract: In this special issue of J-NABS, we have compiled a series of papers that describe some of the major scientific challenges that were encountered during the national Wadeable Streams Assessment (WSA) and some of the lessons learned subsequent to the assessment. Our goal in producing this series was to use the WSA as a case study to illustrate the variety of scientific challenges that can arise when planning and implementing regional assessments, describe how those challenges were addressed for the WSA, describe some important spin-offs that emerged as a consequence of the WSA, and identify remaining knowledge or data gaps that will require attention in future regional assessments. We hope these papers will stimulate thinking about how to improve future assessments in the U.S. and elsewhere.

    Yuan, L.L., C.P. Hawkins, and J. Van Sickle. 2008. Effects of regionalization decisions on an O/E index for the US national assessment. Journal of the North American Benthological Society 27(4):892-905.

    Abstract: We examined the effects of different regionalization schemes on the performance of River InVertebrate Prediction and Classification System (RIVPACS)-type predictive models in assessing the biological conditions of streams of the US for the National Wadeable Streams Assessment (WSA). Three regionalization schemes were considered: a single national predictive model (MOD1), separate predictive models for each of the 9 WSA aggregated Omernik level III ecoregions (MOD9), and 3 predictive models roughly corresponding to the western US, the Appalachian Mountains, and the Central and Coastal Plains (MOD3). The goal of the WSA was to assess stream condition at the national scale and at the scale of WSA aggregated ecoregions, so we compared the performance of the ratio of the observed number of taxa to the expected number of taxa (O/E) index estimated using different regionalization schemes at both of these spatial scales. We assessed model performance with a randomized resampling procedure, in which we set aside 10% of the reference sites, calibrated the model with the remaining sites, and applied the model to the set-aside sites. Performance statistics for the set-aside reference sites were accumulated over 10 iterations. When summarized at the national scale, mean model predictions of O/E for set-aside reference sites from the 3 different regionalization schemes were all reasonably close to 1. When summarized by the 9 aggregated ecoregions, MOD1 and MOD3 predictions of O/E differed systematically from 1 in certain aggregated ecoregions. Over all 9 ecoregions, the magnitude of these differences was significantly greater than observed with MOD9 predictions. Results from our analysis suggest that O/E values at test sites should be interpreted with respect to mean and SD of O/E of reference sites from the same region to minimize the effects of systematic biases in the predictions. RIVPACS-type predictive models also should be calibrated at a spatial scale similar to the scale at which summary statistics are reported.

    Paulsen, S.G., A. Mayio, D.V. Peck, J.L. Stoddard, E. Tarquinio, S.M. Holdsworth, J. Van Sickle, L.L. Yuan, C.P. Hawkins, A.T. Herlihy, P.R. Kaufmann, M.T. Barbour, D.P. Larsen, and A.R. Olsen. 2008. Condition of stream ecosystems in the US: an overview of the first national assessment. Journal of the North American Benthological Society 27(4):812-821.

    Abstract: The Wadeable Streams Assessment (WSA) provided the first statistically sound summary of the ecological condition of streams and small rivers in the US. Information provided in the assessment filled an important gap in meeting the requirements of the US Clean Water Act. The purpose of the WSA was to: 1) report on the ecological condition of all wadeable, perennial streams and rivers within the conterminous US, 2) describe the biological condition of these systems with direct measures of aquatic life, and 3) identify and rank the relative importance of chemical and physical stressors affecting stream and river condition. The assessment included perennial wadeable streams and rivers that accounted for 95% of the length of flowing waters in the US. The US Environmental Protection Agency, states, and tribes collected chemical, physical, and biological data at 1392 randomly selected sites. Nationally, 42% of the length of US streams was in poor condition compared to best available reference sites in their ecoregions, 25% was in fair condition, and 28% was in good condition. Results were reported for 3 major regions: Eastern Highlands, Plains and Lowlands, and West. In the West, 45% of the length of wadeable flowing waters was in good condition. In the Eastern Highlands, only 18% of the length of wadeable streams and rivers was in good condition and 52% was in poor condition. In the Plains and Lowlands, almost 30% of the length of wadeable streams and rivers was in good condition and 40% was in poor condition. The most widespread stressors observed nationally and in each of the 3 major regions were N, P, riparian disturbance, and streambed sediments. Excess nutrients and excess streambed sediments had the highest impact on biological condition; streams scoring poor for these stressors were at 2 to 3× higher risk of having poor biological condition than were streams that scored in the good range for the same stressors.

    Herlihy, A.T., S.G. Paulsen, J. Van Sickle, J.L. Stoddard, C.P. Hawkins, and L.L. Yuan. 2008. Striving for consistency in a national assessment: the challenges of applying a reference-condition approach at a continental scale. Journal of the North American Benthological Society 27(4):860-877.

    Abstract: One of the biggest challenges when conducting a continental-scale assessment of streams is setting appropriate expectations for the assessed sites. The challenge occurs for 2 reasons: 1) tremendous natural environmental heterogeneity exists within a continental landscape and 2) reference sites vary in quality both across and within major regions of the continent. We describe the process used to set expectations for the multimetric index of biotic integrity (MIBI) and observed/expected (O/E) indices generated from predictive models used to assess stream condition for the US Wadeable Streams Assessment (WSA). The assessment was based on a reference-site approach, in which the least-disturbed sites in each region of the US were used to establish benchmarks for assessing the condition of macroinvertebrate assemblages at other sites. Reference sites were compiled by filtering WSA sample sites for disturbance using a series of abiotic variables. Additional reference sites were needed and were obtained from other state, university, and federal monitoring programs. This pool of potential reference sites was then assessed for uniformity in site quality and comparability of macroinvertebrate sample data. Ultimately, 1625 sites were used to set reference expectations for the WSA. Reference-site data were used to help define 9 large ecoregions that minimized the naturally occurring variation in macroinvertebrate assemblages associated with continental-wide differences in biogeography. These ecoregions were used as a basis for developing MIBI and O/E indices and for reporting results. A least-disturbed definition of reference condition was used nationally, but we suspect that the quality of the best extant sites in ecoregions, such as the Northern Plains and Temperate Plains, was lower than that of sites in other ecoregions. For the MIBI assessment, we used a simple modeling approach to adjust scores in ecoregions where gradients in reference-site quality could be demonstrated conclusively. The WSA provided an unparalleled opportunity to push the limits of our conceptual and technical understanding of how to best apply a reference-condition approach to a real-world need. Our hope is that we have learned enough from this exercise to improve the technical quality of the next round of national assessments.

    Stevenson, R.J., B.H. Hill, A.T. Herlihy, L.L. Yuan, and S.B. Norton. 2008. Algae–P relationships, thresholds, and frequency distributions guide nutrient criterion development. Algae 27(3):783-799.

    Abstract: We used complementary information collected using different conceptual approaches to develop recommendations for a stream nutrient criterion based on responses of algal assemblages to anthropogenic P enrichment. Benthic algal attributes, water chemistry, physical habitat, and human activities in watersheds were measured in streams of the Mid-Atlantic Highlands region as part of the Environmental Monitoring and Assessment Program of the US Environmental Protection Agency. Diatom species composition differed greatly between low- and high-pH reference streams; therefore, analyses for criterion development were limited to a subset of 149 well-buffered streams to control for natural variability among streams caused by pH. Regression models showed that TP concentrations were ∼10 μg/L in streams with low levels of human activities in watersheds and that TP increased with % agriculture and urban land uses in watersheds. The 75th percentile at reference sites was 12 μg TP/L. Chlorophyll a and ash-free dry mass increased and acid and alkaline phosphatase activities decreased with increasing TP concentration. The number of diatom taxa, evenness, proportion of expected native taxa, and number of high-P taxa increased with TP concentration in streams. In contrast, the number of low-P native taxa and % low-P individuals decreased with increasing TP. Lowess regression and regression tree analysis indicated nonlinear relationships for many diversity indices and attributes of taxonomic composition with respect to TP. Thresholds in these responses occurred between 10 and 20 μg/L and helped justify recommending a P criterion between 10 and 12 μg TP/L to protect high-quality biological conditions in streams of the Mid-Atlantic Highlands.

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