A Review of Harmful Algal Bloom Prediction Models for Lakes and Reservoirs

Anthropogenic activity has led to eutrophication in water bodies across the world. This eutrophication promotes blooms, cyanobacteria being among the most notorious bloom organisms. Cyanobacterial blooms (more commonly referred to as harmful algal blooms (HABs)) can devastate an ecosystem. Cyanobacteria are resilient microorganisms that have adapted to survive under a variety of conditions, often outcompeting other phytoplankton. Some species of cyanobacteria produce toxins that ward off predators. These toxins can negatively affect the health of the aquatic life, but also can impact animals and humans that drink or come in contact with these noxious waters. Although cyanotoxin’s effects on humans are not as well researched as the growth, behavior, and ecological niche of cyanobacteria, their health impacts are of large concern. It is important that research to mitigate and understand cyanobacterial blooms and cyanotoxin production continues. This project supports continued research by addressing an approach to collect and summarize published articles that focus on techniques and models to predict cyanobacterial blooms with the goal of understanding what research has been done to promote future work. The following report summarizes 34 articles from 2003 to 2020 that each describe a mechanistic or data driven model developed to predict the occurrence of cyanobacterial blooms or the presence of cyanotoxins in lakes or reservoirs with similar climates to Utah. These articles showed a shift from more mechanistic approaches to more data driven approaches with time. This resulted in a more individualistic approach to modeling, meaning that models are often produced for a single lake or reservoir and are not easily comparable to other models for different systems

On the development of decision-making systems based on fuzzy models to assess water quality in rivers

There are many situations where a linguistic description of complex phenomena allows better assessments. It is well known that the assessment of water quality continues depending heavily upon subjective judgments and interpretation, despite the huge datasets available nowadays. In that sense, the aim of this study has been to introduce intelligent linguistic operations to analyze databases, and produce self interpretable water quality indicators, which tolerate both imprecision and linguistic uncertainty. Such imprecision typically reflects the ambiguity of human thinking when perceptions need to be expressed. Environmental management concepts such as: "water quality", "level of risk", or "ecological status" are ideally dealt with linguistic variables. In the present Thesis, the flexibility of computing with words offered by fuzzy logic has been considered in these management issues. Firstly, a multipurpose hierarchical water quality index has been designed with fuzzy reasoning. It integrates a wide set of indicators including: organic pollution, nutrients, pathogens, physicochemical macro-variables, and priority micro-contaminants. Likewise, the relative importance of the water quality indicators has been dealt with the analytic hierarchy process, a decision-aiding method. Secondly, a methodology based on a hybrid approach that combines fuzzy inference systems and artificial neural networks has been used to classify ecological status in surface waters according to the Water Framework Directive. This methodology has allowed dealing efficiently with the non-linearity and subjective nature of variables involved in this classification problem. The complexity of inference systems, the appropriate choice of linguistic rules, and the influence of the functions that transform numerical variables into linguistic variables have been studied. Thirdly, a concurrent neuro-fuzzy model based on screening ecological risk assessment has been developed. It has considered the presence of hazardous substances in rivers, and incorporates an innovative ranking and scoring system, based on a self-organizing map, to account for the likely ecological hazards posed by the presence of chemical substances in freshwater ecosystems. Hazard factors are combined with environmental concentrations within fuzzy inference systems to compute ecological risk potentials under linguistic uncertainty. The estimation of ecological risk potentials allows identifying those substances requiring stricter controls and further rigorous risk assessment. Likewise, the aggregation of ecological risk potentials, by means of empirical cumulative distribution functions, has allowed estimating changes in water quality over time. The neuro-fuzzy approach has been validated by comparison with biological monitoring. Finally, a hierarchical fuzzy inference system to deal with sediment based ecological risk assessment has been designed. The study was centered in sediments, since they produce complementary findings to water quality analysis, especially when temporal trends are required. Results from chemical and eco-toxicological analyses have been used as inputs to two parallel inference systems which assess levels of contamination and toxicity, respectively. Results from both inference engines are then treated in a third inference engine which provides a final risk characterization, where the risk is provided in linguistic terms, with their respective degrees of certitude. Inputs to the risk system have been the levels of potentially toxic substances, mainly metals and chlorinated organic compounds, and the toxicity measured with a screening test which uses the photo-luminescent bacteria Vibrio fischeri. The Ebro river basin has been selected as case study, although the methodologies here explained can easily be applied to other rivers. In conclusion, this study has broadly demonstrated that the design of water quality indexes, based on fuzzy logic, emerges as suitable and alternative tool to support decision makers involved in effective sustainable river basin management plans.Existen diversas situaciones en las cuales la descripción en términos lingüísticos de fenómenos complejos permite mejores resultados. A pesar de los volúmenes de información cuantitativa que se manejan actualmente, es bien sabido que la gestión de la calidad del agua todavía obedece a juicios subjetivos y de interpretación de los expertos. Por tanto, el reto en este trabajo ha sido la introducción de operaciones lógicas que computen con palabras durante el análisis de los datos, para la elaboración de indicadores auto-interpretables de calidad del agua, que toleren la imprecisión e incertidumbre lingüística. Esta imprecisión típicamente refleja la ambigüedad del pensamiento humano para expresar percepciones. De allí que las variables lingüísticas se presenten como muy atractivas para el manejo de conceptos de la gestión medioambiental, como es el caso de la "calidad del agua", el "nivel de riesgo" o el "estado ecológico". Por tanto, en la presente Tesis, la flexibilidad de la lógica difusa para computar con palabras se ha adaptado a diversos tópicos en la gestión de la calidad del agua. Primero, se desarrolló un índice jerárquico multipropósito de calidad del agua que se obtuvo mediante razonamiento difuso. El índice integra un extenso grupo de indicadores que incluyen: contaminación orgánica, nutrientes, patógenos, variables macroscópicas, así como sustancias prioritarias micro-contaminantes. La importancia relativa de los indicadores al interior del sistema de inferencia se estimó con un método de análisis de decisiones, llamado proceso jerárquico analítico. En una segunda fase, se utilizó una metodología híbrida que combina los sistemas de inferencia difusos y las redes neuronales artificiales, conocida como neuro-fuzzy, para el estudio de la clasificación del estado ecológico de los ríos, de acuerdo con los lineamientos de la Directiva Marco de Aguas. Esta metodología permitió un manejo adecuado de la no-linealidad y naturaleza subjetiva de las variables involucradas en este problema clasificatorio. Con ella, se estudió la complejidad de los sistemas de inferencia, la selección apropiada de reglas lingüísticas y la influencia de las funciones que transforman las variables numéricas en lingüísticas. En una tercera fase, se desarrolló un modelo conceptual neuro-fuzzy concurrente basado en la metodología de evaluación de riesgo ecológico preliminar. Este modelo consideró la presencia de sustancias peligrosas en los ríos, e incorporó un mapa auto-organizativo para clasificar las sustancias químicas, en términos de su peligrosidad hacia los ecosistemas acuáticos. Con este modelo se estimaron potenciales de riesgo ecológico por combinación de factores de peligrosidad y de concentraciones de las sustancias químicas en el agua. Debido a la alta imprecisión e incertidumbre lingüística, estos potenciales se obtuvieron mediante sistemas de inferencia difusos, y se integraron por medio de distribuciones empíricas acumuladas, con las cuales se pueden analizar cambios espacio-temporales en la calidad del agua. Finalmente, se diseñó un sistema jerárquico de inferencia difuso para la evaluación del riesgo ecológico en sedimentos de ribera. Este sistema estima los grados de contaminación, toxicidad y riesgo en los sedimentos en términos lingüísticos, con sus respectivos niveles de certeza. El sistema se alimenta con información proveniente de análisis químicos, que detectan la presencia de sustancias micro-contaminantes, y de ensayos eco-toxicológicos tipo "screening" que usan la bacteria Vibrio fischeri. Como caso de estudio se seleccionó la cuenca del río Ebro, aunque las metodologías aquí desarrolladas pueden aplicarse fácilmente a otros ríos. En conclusión, este trabajo demuestra ampliamente que el diseño y aplicación de indicadores de calidad de las aguas, basados en la metodología de la lógica difusa, constituyen una herramienta sencilla y útil para los tomadores de decisiones encargados de la gestión sostenible de las cuencas hidrográficas

Reducing the Memory Size of a Fuzzy Case-Based Reasoning System Applying Rough Set Techniques

Early work on case-based reasoning (CBR) reported in the literature shows the importance of soft computing techniques applied to different stages of the classical four-step CBR life cycle. This correspondence proposes a reduction technique based on rough sets theory capable of minimizing the case memory by analyzing the contribution of each case feature. Inspired by the application of the minimum description length principle, the method uses the granularity of the original data to compute the relevance of each attribute. The rough feature weighting and selection method is applied as a preprocessing step prior to the generation of a fuzzy rule system, which is employed in the revision phase of the proposed CBR system. Experiments using real oceanographic data show that the rough sets reduction method maintains the accuracy of the employed fuzzy rules, while reducing the computational effort needed in its generation and increasing the explanatory strength of the fuzzy rules

Proceedings Ocean Biodiversity Informatics: International Conference on Marine Biodiversity Data Management, Hamburg, Germany 29 November to 1 December, 2004

The International conference on Marine Biodiversity Data management ‘Ocean Biodiversity Informatics’ was held in Hamburg, Germany, from 29 November to 1 December 2004. Its objective was to offer a forum to marine biological data managers to discuss the state of the field, and to exchange ideas on how to further develop marine biological data systems. Many marine biologists are actively gathering knowledge, as they have been doing for a long time. What is new is that many of these scientists are willing to share their knowledge, including basic data, with others over the Internet. Our challenge now is to try and manage this trend, avoid confusing users with a multitude of contradicting sources of information, and make sure different data systems can be and are effectively integrated

Developing models for the data-based mechanistic approach to systems analysis:Increasing objectivity and reducing assumptions

Stochastic State-Space Time-Varying Random Walk models have been developed, allowing the existing Stochastic State Space models to operate directly on irregularly sampled time-series. These TVRW models have been successfully applied to two different classes of models benefiting each class in different ways. The first class of models - State Dependent Parameter (SDP) models and used to investigate the dominant dynamic modes of nonlinear dynamic systems and the non-linearities in these models affected by arbitrary State Variables. In SDP locally linearised models it is assumed that the parameters that describe system’s behaviour changes are dependent upon some aspect of the system (it’s ‘state’). Each parameter can be dependent on one or more states. To estimate the parameters that are changing at a rate related to that of it’s states, the estimation procedure is conducted in the state-space along the potentially multivariate trajectory of the states which drive the parameters. The introduction of the newly developed TVRW models significantly improves parameter estimation, particularly in data rich neighbourhoods of the state-space when the parameter is dependent on more than one state, and the ends of the data-series when the parameter is dependent on one state with few data points. The second class of models are known as Dynamic Harmonic Regression (DHR) models and are used to identify the dominant cycles and trends of time-series. DHR models the assumption is that a signal (such as a time-series) can be broken down into four (unobserved) components occupying different parts of the spectrum: trend, seasonal cycle, other cycles, and a high frequency irregular component. DHR is confined to uniformly sampled time-series. The introduction of the TVRW models allows DHR to operate on irregularly sampled time-series, with the added benefit of forecasting origin no longer being confined to starting at the end of the time-series but can now begin at any point in the future. Additionally, the forecasting sampling rate is no longer limited to the sampling rate of the time-series. Importantly, both classes of model were designed to follow the Data-Based Mechanistic (DBM) approach to modelling environmental systems, where the model structure and parameters are to be determined by the data (Data-Based) and then the subsequent models are to be validated based on their physical interpretation (Mechanistic). The aim is to remove the researcher’s preconceptions from model development in order to eliminate any bias, and then use the researcher’s knowledge to validate the models presented to them. Both classes of model lacked model structure identification procedures and so model structure was determined by the researcher, against the DBM approach. Two different model structure identification procedures, one for SDP and the other for DHR, were developed to bring both classes of models back within the DBM framework. These developments have been presented and tested here on both simulated data and real environmental data, demonstrating their importance, benefits and role in environmental modelling and exploratory data analysis

Ecological models at fish community and species level to support effective river restoration

RESUMEN Los peces nativos son indicadores de la salud de los ecosistemas acuáticos, y se han convertido en un elemento de calidad clave para evaluar el estado ecológico de los ríos. La comprensión de los factores que afectan a las especies nativas de peces es importante para la gestión y conservación de los ecosistemas acuáticos. El objetivo general de esta tesis es analizar las relaciones entre variables biológicas y de hábitat (incluyendo la conectividad) a través de una variedad de escalas espaciales en los ríos Mediterráneos, con el desarrollo de herramientas de modelación para apoyar la toma de decisiones en la restauración de ríos. Esta tesis se compone de cuatro artículos. El primero tiene como objetivos modelar la relación entre un conjunto de variables ambientales y la riqueza de especies nativas (NFSR), y evaluar la eficacia de potenciales acciones de restauración para mejorar la NFSR en la cuenca del río Júcar. Para ello se aplicó un enfoque de modelación de red neuronal artificial (ANN), utilizando en la fase de entrenamiento el algoritmo Levenberg-Marquardt. Se aplicó el método de las derivadas parciales para determinar la importancia relativa de las variables ambientales. Según los resultados, el modelo de ANN combina variables que describen la calidad de ribera, la calidad del agua y el hábitat físico, y ayudó a identificar los principales factores que condicionan el patrón de distribución de la NFSR en los ríos Mediterráneos. En la segunda parte del estudio, el modelo fue utilizado para evaluar la eficacia de dos acciones de restauración en el río Júcar: la eliminación de dos azudes abandonados, con el consiguiente incremento de la proporción de corrientes. Estas simulaciones indican que la riqueza aumenta con el incremento de la longitud libre de barreras artificiales y la proporción del mesohabitat de corriente, y demostró la utilidad de las ANN como una poderosa herramienta para apoyar la toma de decisiones en el manejo y restauración ecológica de los ríos Mediterráneos. El segundo artículo tiene como objetivo determinar la importancia relativa de los dos principales factores que controlan la reducción de la riqueza de peces (NFSR), es decir, las interacciones entre las especies acuáticas, variables del hábitat (incluyendo la conectividad fluvial) y biológicas (incluidas las especies invasoras) en los ríos Júcar, Cabriel y Turia. Con este fin, tres modelos de ANN fueron analizados: el primero fue construido solamente con variables biológicas, el segundo se construyó únicamente con variables de hábitat y el tercero con la combinación de estos dos grupos de variables. Los resultados muestran que las variables de hábitat son los ¿drivers¿ más importantes para la distribución de NFSR, y demuestran la importancia ecológica de los modelos desarrollados. Los resultados de este estudio destacan la necesidad de proponer medidas de mitigación relacionadas con la mejora del hábitat (incluyendo la variabilidad de caudales en el río) como medida para conservar y restaurar los ríos Mediterráneos. El tercer artículo busca comparar la fiabilidad y relevancia ecológica de dos modelos predictivos de NFSR, basados en redes neuronales artificiales (ANN) y random forests (RF). La relevancia de las variables seleccionadas por cada modelo se evaluó a partir del conocimiento ecológico y apoyado por otras investigaciones. Los dos modelos fueron desarrollados utilizando validación cruzada k-fold y su desempeño fue evaluado a través de tres índices: el coeficiente de determinación (R2 ), el error cuadrático medio (MSE) y el coeficiente de determinación ajustado (R2 adj). Según los resultados, RF obtuvo el mejor desempeño en entrenamiento. Pero, el procedimiento de validación cruzada reveló que ambas técnicas generaron resultados similares (R2 = 68% para RF y R2 = 66% para ANN). La comparación de diferentes métodos de machine learning es muy útil para el análisis crítico de los resultados obtenidos a través de los modelos. El cuarto artículo tiene como objetivo evaluar la capacidad de las ANN para identificar los factores que afectan a la densidad y la presencia/ausencia de Luciobarbus guiraonis en la demarcación hidrográfica del Júcar. Se utilizó una red neuronal artificial multicapa de tipo feedforward (ANN) para representar relaciones no lineales entre descriptores de L. guiraonis con variables biológicas y de hábitat. El poder predictivo de los modelos se evaluó con base en el índice Kappa (k), la proporción de casos correctamente clasificados (CCI) y el área bajo la curva (AUC) característica operativa del receptor (ROC). La presencia/ausencia de L. guiraonis fue bien predicha por el modelo ANN (CCI = 87%, AUC = 0.85 y k = 0.66). La predicción de la densidad fue moderada (CCI = 62%, AUC = 0.71 y k = 0.43). Las variables más importantes que describen la presencia/ausencia fueron: radiación solar, área de drenaje y la proporción de especies exóticas de peces con un peso relativo del 27.8%, 24.53% y 13.60% respectivamente. En el modelo de densidad, las variables más importantes fueron el coeficiente de variación de los caudales medios anuales con una importancia relativa del 50.5% y la proporción de especies exóticas de peces con el 24.4%. Los modelos proporcionan información importante acerca de la relación de L. guiraonis con variables bióticas y de hábitat, este nuevo conocimiento podría utilizarse para apoyar futuros estudios y para contribuir en la toma de decisiones para la conservación y manejo de especies en los en los ríos Júcar, Cabriel y Turia.Olaya Marín, EJ. (2013). Ecological models at fish community and species level to support effective river restoration [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/28853TESI

First, do no harm - Missing data treatment to support lake ecological condition assessment

Indicators of ecological condition status of water bodies associated with field measurements are often subject to data gaps. This obstacle can often lead to abandonment of assessment. Furthermore, it can lead to the use of methods, based merely on their availability. In response to these challenges, a systematic approach for expert-analyst interaction for missing data treatment is proposed. A combination of algorithms with hierarchical clustering of results is used. A particular emphasis is put on the preparation and interpretation of input data and the role of an expert in the workflow. The proposed approach enhances the decision-making process by improving communication and transparency throughout interactions between experts, analysts and decision makers. Future research should focus on assessing the scale of the ecological data drift phenomenon, which, based on the observed climate change, anthropological pressure and biodiversity loss, may impact the broad concept of indicator construction for lake water ecological assessmen

Determining the macroinvertebrate community indicators and relevant environmental predictors of the Hun-Tai River Basin (Northeast China): A study based on community patterning

[EN] It is essential to understand the patterning of biota and environmental influencing factors for proper rehabilitation and management at the river basin scale. The Hun-Tai River Basin was extensively sampled four times for macroinvertebrate community and environmental variables during one year. Self-Organizing Maps (SOMs) were used to reveal the aggregation patterns of the 355 samples. Three community types (i.e., clusters) were found (at the family level) based on the community composition, which showed a clearly gradient by combining them with the representative environmental variables: minimally impacted source area, intermediately anthropogenic impacted sites, and highly anthropogenic impacted downstream area, respectively. This gradient was corroborated by the decreasing trends in density and diversity of macroinvertebrates. Distance from source, total phosphorus and water temperature were identified as the most important variables that distinguished the delineated communities. In addition, the sampling season, substrate type, pH and the percentage of grassland were also identified as relevant variables. These results demonstrated that macroinvertebrates communities are structured in a hierarchical manner where geographic and water quality prevail over temporal (season) and habitat (substrate type) features at the basin scale. In addition, it implied that the local-scale environment variables affected macroinvertebrates under the longitudinal gradient of the geographical and anthropogenic pressure. More than one family was identified as the indicator for each type of community. Abundance contributed significantly for distinguishing the indicators, while Baetidae with higher density indicated minimally and intermediately impacted area and lower density indicated highly impacted area. Therefore, we suggested the use of abundance data in community patterning and classification, especially in the identification of the indicator taxa. (C) 2018 Elsevier B.V. All rights reserved.This work was supported by the National Natural Science Foundation of China (51779275, 41501204, 51479219) and the IWHR Research & Development Support Program (WE0145B532017).Zhang, M.; Muñoz Mas, R.; Martinez-Capel, F.; Qu, X.; Zhang, H.; Peng, W.; Liu, X. (2018). Determining the macroinvertebrate community indicators and relevant environmental predictors of the Hun-Tai River Basin (Northeast China): A study based on community patterning. The Science of The Total Environment. 634:749-759. https://doi.org/10.1016/j.scitotenv.2018.04.021S74975963

Bioindicator monitoring and modelling for informing river health management

Freshwaters are considered to be the most degraded ecosystems. In an attempt to monitor river health, macroinvertebrates and diatoms proved to be suitable for routine short- and long-term monitoring. However, making complex decisions for river health management based solely on the data generated by such monitoring efforts is challenging, mainly when data has limited predictive capacity. To overcome this, the thesis focuses on the integration of bioindicator monitoring and novel modelling techniques with the associated challenges to inform river health management. This thesis aimed firstly to document differences between two local catchments using ecological threshold models and then test the performance of two commonly used models. Results suggested three times higher total phosphorus (TP) thresholds in the Onkaparinga River catchment as compared to the River Torrens catchment. It was also found that thresholds for electrical conductivity (EC) specified by Hybrid Evolutionary Algorithms (HEA) exceeded those identified by Threshold Indicator Taxa Analysis (TITAN). Importantly, despite the observed differences in thresholds, results indicated that South Australian water quality guidelines for freshwater systems might be too high. Another study aimed to identify model-based bias in threshold identification, found that two commonly used methods, i.e. gradient forest (GF) and TITAN are robust in identifying change in species responses. Still, threshold identification differs depending on the analysis used and the nature of ecological data. Noting the differences in performance of the two methods on the same field and synthetic data, we recommend careful application of GF and TITAN, will improve their use for river health management. Another critical and neglected aspect of threshold identification is dependence on spatial scale. Data analysis from field monitoring of diatoms and water quality during autumn and spring for two years was further extended by merging with a broader data set from South Australian streams, to highlight spatial influences on thresholds. Consistent or lower thresholds were found across spatial scales when spatial resolution was increased from state to local scale. However, higher TP and EC thresholds were observed for the South East region than for the Adelaide and Mount Lofty Ranges. Thus we highlighted that thresholds derived at broad scales alone are unlikely to be appropriate for finer-scale assessment. Another study applied an integrated modelling approach using GF, Soil and Water Assessment Tool (SWAT) and HEA to predict river health for future climate and land use. This study quantified population dynamics of sensitive taxa identified by GF under SWAT simulated future scenarios of deforestation, reforestation, climate change, and 10% increased urbanisation, as projected by local authorities over the next 30 years. HEA, used to predict future abundances, suggested a nonlinear response of species within commonly used Ephemeroptera, Plecoptera and Trichoptera grouping and we recommend to redirect focus of such studies from community to species-level. In reforestation and climate change scenarios, SWAT results also suggested a shift in the unusual permanent flowing stream of Sixth Creek towards intermittency under climate change and reforestation scenarios. Overall, outcomes of this research provide an improved understanding of local catchment processes in the context of global-scale challenges of climate and land use changes.Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 202