Biomonitoring of intermittent rivers and ephemeral streams in Europe: current practice and priorities to enhance ecological status assessments

Intermittent rivers and ephemeral streams (IRES) are common across Europe and dominate some Mediterranean river networks. In all climate zones, IRES support high biodiversity and provide ecosystem services. As dynamic ecosystems that transition between flowing, pool, and dry states, IRES are typically poorly represented in biomonitoring programmes implemented to characterize EU Water Framework Directive ecological status. We report the results of a survey completed by representatives from 20 European countries to identify current challenges to IRES status assessment, examples of best practice, and priorities for future research. We identify five major barriers to effective ecological status classification in IRES: 1. the exclusion of IRES from Water Framework Directive biomonitoring based on their small catchment size; 2. the lack of river typologies that distinguish between contrasting IRES; 3. difficulties in defining the ‘reference conditions’ that represent unimpacted dynamic ecosystems; 4. classification of IRES ecological status based on lotic communities sampled using methods developed for perennial rivers; and 5. a reliance on taxonomic characterization of local communities. Despite these challenges, we recognize examples of innovative practice that can inform modification of current biomonitoring activity to promote effective IRES status classification. Priorities for future research include reconceptualization of the reference condition approach to accommodate spatiotemporal fluctuations in community composition, and modification of indices of ecosystem health to recognize both taxon-specific sensitivities to intermittence and dispersal abilities, within a landscape context

Benthic algae assessments in the EU and the US: Striving for consistency in the face of great ecological diversity

Freshwaters face multiple environmental problems including eutrophication, acidification, salinization, and climate-change, all of which can lead to impairment of ecosystem structure and function. Furthermore, these stressors often act in combination. Benthic algal-based assessments to quantify impairment are used in both the EU and US. In this review, we use case studies, experience, and the literature to compare concepts, approaches, and methods between the EU and US to offer an updated picture of benthic algal-based assessments. Both the US and EU are composed of numerous constituent states having considerable flexibility to adopt individual methods. The goal of this work is to synthesize the various approaches that are used across the EU and US. Specifically, we compare and contrast benthic algal assessment performed in response to core legislation – the Water Framework Directive in the EU and the Clean Water Act in the US, with a particular focus on the steps taken to ensure consistency at different stages of the process. This includes consideration of approaches to sampling design and field methods, taxonomic resolution and laboratory harmonization, metric selection and choice of algal groups, assessment of stressors and stressor/response relationships. A number of commonalities emerged during this process, particularly the focus on diatoms over other algal groups. However, there are also a number of key differences, including more widespread use of multimetric indices in the US compared with the EU. Finally, we consider emerging opportunities, including the potential for using metagenomic approaches for bioassessment in the future

Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive

Assessment of ecological status for the European Water Framework Directive (WFD) is based on “Biological Quality Elements” (BQEs), namely phytoplankton, benthic flora, benthic invertebrates and fish. Morphological identification of these organisms is a time-consuming and expensive procedure. Here, we assess the options for complementing and, perhaps, replacing morphological identification with procedures using eDNA, metabarcoding or similar approaches. We rate the applicability of DNA-based identification for the individual BQEs and water categories (rivers, lakes, transitional and coastal waters) against eleven criteria, summarised under the headlines representativeness (for example suitability of current sampling methods for DNA-based identification, errors from DNA-based species detection), sensitivity (for example capability to detect sensitive taxa, unassigned reads), precision of DNA-based identification (knowledge about uncertainty), comparability with conventional approaches (for example sensitivity of metrics to differences in DNA-based identification), cost effectiveness and environmental impact. Overall, suitability of DNA-based identification is particularly high for fish, as eDNA is a well-suited sampling approach which can replace expensive and potentially harmful methods such as gill-netting, trawling or electrofishing. Furthermore, there are attempts to replace absolute by relative abundance in metric calculations. For invertebrates and phytobenthos, the main challenges include the modification of indices and completing barcode libraries. For phytoplankton, the barcode libraries are even more problematic, due to the high taxonomic diversity in plankton samples. If current assessment concepts are kept, DNA-based identification is least appropriate for macrophytes (rivers, lakes) and angiosperms/macroalgae (transitional and coastal waters), which are surveyed rather than sampled. We discuss general implications of implementing DNA-based identification into standard ecological assessment, in particular considering any adaptations to the WFD that may be required to facilitate the transition to molecular data

The influence of land use on water quality and diatom community structures in urban and agriculturally stressed rivers

Epilithic diatom communities offer a holistic and integrated approach for assessing water quality as they remain in one place for a number of months and reflect an ecological memory of water quality over a period of time. The objective of this study is to use diatom assemblages to distinguish between particular land types and associated water quality impacts that are linked to these land-use patterns. Water quality and diatom community data were collected from sites in the Crocodile and Magalies Rivers (Gauteng and North West Province, South Africa) associated with agricultural, urban and natural (reference) adjacent land use respectively. The data collected were subjected to multivariate statistical techniques to analyse spatial and temporal patterns in water quality (principal component analysis) and diatom community structures (non-metric multidimensional scaling) to elucidate hypothesised differences in community structure per land-use type. Five diatom response indices (Generic Diatom Index, Specific Pollution Sensitivity Index, Biological Diatom Index, Eutrophication/Pollution Index and Percentage Pollution Tolerant Valves) incorporated in the OMNIDIA software were implemented to assess the integrity of diatom communities per land-use type. Principle component ordination of water quality describes 56.6% of the variation in data observed, and indicates the separation of reference sites from test sites for low and high flow conditions combined. It was, however, not possible to distinguish between the agricultural and urban land-use sites using PCA based on water quality data. One-way ANOSIM showed a significant difference ( p 0.05) between groups made up of sites exhibiting the same land-use patterns. Diatom indices showed that agricultural sites were in a slightly more modified ecological state than urban sites overall. Based on the species similarity (SIMPER analyses), reference sites showed strong associations with Achnanthes minutissima, Gomphonema venusta and Cocconeis placentula var. euglypta, whilst urban sites were associated with Diatoma vulgaris, Navicula tripunctata and Amphorapediculus. Agriculture could be separated into high- and low-intensity practices based on species composition. Sites where high-intensity agriculture took place were dominated by motile species of the genus Nitzschia, and low-intensity agriculture was indicated by motile species of the genus Navicula. Urban sites contained a combination of species that were tolerant of spikes in water quality

Use of indigenous riverine invertebrates in applied toxicology and water resource-quality management

The National Water Policy (DWAF, 1997). and the National Water Act (No 36 of 1998)(NWA) provide the legal and management context for the application of results. The law and the policy are founded on the concepts of equity (fairness of access to water and water services) and sustainability (the opportunity to optimally use water resources now and into the future)(NWA, l (l)(xviii)(b)). The concept of sustainability is based on the understanding that on earth water comes packaged in aquatic ecosystems, and that the product, water, is intimately related to and affected by the structure and functioning of these ecosys-tems.(Aquatic ecosystems include rivers, lakes, wetlands, aquifers and estuaries. Impoundments act as artificial lakes connected to river sys-tems.) A key recognition during the development of the policy and the NWA was that" the environment" does not compete with users for re-sources-the environment (in this case aquatic ecosystems) is the re-source. Therefore a key poiicy of DWAF is that vi resource protection in order to achieve sustainable resource use. Resource protection is achieved through the implementation of resource directed measures (RDM) and source directed controls (SDC)

An evaluation of SASS (South African scoring system) as a tool for the rapid bioassessment of water quality

Bibliography: pages 139-150.The South African Scoring System (SASS) is a rapid bioassessment technique based on one component of riverine biotas, the benthic macroinvertebrates. Each taxon is assigned a tolerance/sensitivity score, which are summed to provide a Total Score. The Average Score per Taxon (ASPT) is calculated by dividing this Total Score by the number of taxa. This study was undertaken to evaluate the SASS technique as a tool for the assessment of water quality. Three study-sites, which differed in water quality, in the south-western Cape were selected for a detailed investigation into sample variability and replication of two methods of biological assessment, namely quantitative box-sampling and SASS. The ability of each method to differentiate between these sites was determined. The more general application of SASS in the south-western Cape was examined at forty nine sites and potential problems associated with SASS, namely biotope availability, temporal variability and longitudinal changes were investigated. A minimum of twelve and four quantitative samples is needed to ensure collection of 95% or 75% of benthic macroinvertebrate taxa respectively. Sampling within a single biotope component, such as a "riffle" or "run" would reduce the number of samples needed. A minimum of four and two SASS samples is needed to ensure collection of 95% or 75% of the taxa respectively. This technique is however designed such that only one sample is taken per site. The Total Score that one sample would produce as a percentage of the Total Score from 20 samples, were 28% , 59% and 45% for Sites 1, 2 and 3 respectively. Total Score increases with increasing sampling effort, whilst ASPT is relatively unaffected by sampling effort. ASPT should therefore be used in interpretation of scores. Variability, as determined by both quantitative sampling and rapid bioassessment, was greatest at the least impacted site. Such sites should be more intensively sampled, either by increasing the number of box- samples taken, or by increasing the time period for SASS sampling

Ecological assessment of a temperate river system using biomonitoring techniques: a case study of the Bloukrans River system, South Africa

Escalating pressures from growing human populations and environmental impacts increasingly imperil freshwater ecosystems. The Bloukrans River, which drains an urbanised and agricultural catchment in the Eastern Cape province of South Africa, is no exception. Detailed knowledge of the structure and function of the aquatic ecosystems is required in order to create models and matrices that predict, guide assessment and direct intervention on ecological integrity and water quality management in these systems. The main objectives of this research were to: examine the effects of urbanization on the benthic macroinvertebrate functional feeding guild structure among different stream orders; determine if benthic diatoms can be used as effective and reliable indicators of ionic composition and conductivity in different stream order categories and finally; to evaluate the applicability of the South African Diatom Index (SADI) and other indices in the Eastern Cape region of South Africa. Field studies were carried out to explore temporal patterns in community structure (macroinvertebrates and diatoms) and ecosystem function related to land-use patterns, instream habitat availability, and water quality parameters in the Bloukrans River system across four study periods: February (summer) and July (winter) 2016 and February (summer) and May/July (winter) 2018. The study was conducted along a gradient of impacts from less impacted agricultural headwaters to highly impacted urban sites located immediately downstream of the city of Makhanda. Macroinvertebrates were separated into functional feeding groups (FFGs) (i.e. collector-gatherer, collector-filterer, scraper, shredder, and predator) which were then used to assess the effects of selected physico-chemical variables and riparian zone condition on FFG organization. Collector-gatherers were the most abundant in the Bloukrans River and represented 71.3 % of the macroinvertebrate assemblages. Stream order 1species such as Nitzschia palea, Gomphonema parvulum, Tryblionella apiculata, Diploneis vulgaris and Staurosira elliptica. Multivariate analysis (Canonical correspondence analysis (CCA)) indicated that differences in diatom community assemblages were best explained by calcium, magnesium, pH, phosphate, nitrate, dissolved oxygen, sediment nitrate, conductivity and salinity. These results indicate that diatoms can be used as bioindicators for monitoring highly impacted river systems and to also further examine pollution gradients and impacts of specific/point pollution sources. In order to further test the application of diatom indices, nine sites with contrasting water quality were sampled along the length river system in February, May and July 2018. Diatom-based indices incorporated in OMNIDIA software were applied to assess the integrity of the water quality as indicated by diatom communities. For comparative purposes, several foreign indices (e.g. the trophic diatom index (TDI), the percentage pollution-tolerant valves (%PTV), biological diatom index (BDI)) and the South African Diatom Index (SADI) were used in the study. From the results, the Percentage Pollution-Tolerant Valves (%PTV) of most urban sites in the Bloukrans River was above the 20% limit indicating the presence of organic pollutants. Although the foreign diatom indices were applicable in the study, the SADI had significant correlations with most water quality variables (p < 0.05) compared to other indices such as Watanabe Index (WAT), Biological Index of Water Quality Trophic Index (BIWQ) and Trophic Index (TI)). These results support wider use of the SADI as an indicator of water quality conditions in South African river systems. Finally, the observed variations in diatom community structure and composition as a result of changes in water quality were broadly in agreement with the results of macroinvertebrate FFG structure indicating that the two biological indicators can, and should, be used as complementary techniques in the biomonitoring of rivers and streams in South Africa

Biological variation in temporary streams: understanding river patches at different scales for monitoring and management applications

Biota and ecological processes are highly complex and vary at every scale. This underscores the importance of employing a multi-scale design to adequately understand these processes and complex relationships in riverine ecosystems. In addition, there is a strong need to develop appropriately scaled indicators of river ecosystem health that include this biotic complexity in a manageable fashion. Unfortunately, currently available indicators are either too complex or do not adequately capture the highly variable changes to the ecosystem. Patches are good templates for various ecological processes and because they are considered to be stable over the spatial and temporal scales, they can be used as functional filters of important processes in streams. The aim of this thesis is to employ patch theory and multi-scale approach to develop structural and functional indicators of the ecosystem health at the patch level and evaluate in which of the scales these indicators are of the highest relevance for the patch. The system at which these indicators were tested consists of headwater intermittent streams within a Mediterranean catchment. Three scales were considered: reach scale, stream scale and catchment scale. According to the results patch as a source of variation was not well explained by the structural measures of benthic communities at catchment scale. This was related to the effect of occurrence of a strong environmental filter (mainly altitude and its association with conductivity and temperature), which limited distribution of biota and constrained the occurrences of certain species at the smaller scales. Also, these filters were demonstrated to act indirectly through patterns in habitat formation and availability. Patch investigated at the reach scale provided slightly more predictable unit of species organization, nonetheless, still benthic communities of some of the patch types overlapped. Instead, the most consistent measures of ecosystem health that could be applied to studying patches were the metabolism measurements at the reach scale and the isotopic signatures at the stream scale. Next step forward would be to establish reference values for these two approaches for undisturbed systems, and subsequently to incorporate these measures into biomonitoring guidelines. Following disturbance, patches have been shown to be the most appropriate unit used when evaluating biotic recovery. As such, this study represents an important step towards development of better biomonitoring tools as well as evaluation of the restoration effort

Diatoms (an ecoregional indicator of nutrients, organic mater and micropollutants pollution)

Les diatomées sont des microalgues ubiquistes d'une diversité exceptionnelle. Cela en fait de bons indicateurs de la qualité des écosystèmes aquatiques et sont utilisées depuis plus de 50 ans. Depuis l'année 2000, la Directive Cadre Européenne sur l'Eau impose leur utilisation pour évaluer la qualité écologique des cours d'eau. Un cadre typologique doit être utilisé afin de comparer des rivières comparables entre elles, c'est-à-dire des rivières de mêmes régions bioclimatiques, coulant sur les mêmes substrats géologiques et à des altitudes comparables. Différentes classifications écorégionales ont été définies sur la base de ces paramètres. Nous avons montré qu'à une échelle couvrant 4 pays (Espagne, France, Italie, Suisse) et à une régionale (Nord-est de la France), les écorégions et la géologie sont déterminantes pour expliquer les communautés. Les paramètres caractérisant la pollution sont moins importants. Contrairement à certains auteurs, nous n'avons pas observé d'homogénéisation des communautés lorsque le niveau de pollution augmente. D'autre part nous n'avons pas observé de communautés restreintes géographiquement : cela permettrait de rassembler des écorégions distinctes géographiquement mais présentant les mêmes caractéristiques physiques. Les diatomées présentent une diversité spécifique très importante qui peut être un frein à leur utilisation en routine. Nous avons montré qu'en augmentant la précision de détermination (de la subdivision à l'espèce), les performances d'évaluation de la pollution augmentait mais beaucoup moins que le nombre de taxons. Les performances d'évaluation entre le genre et l'espèce sont d'ailleurs proches, alors qu'il y a dix fois plus d'espèce que de genres. Nous avons montré aussi que des métriques simplificatrices (formes de vie, guildes écologiques) permettaient d'évaluer aussi bien le niveau en nutriment que des indices diatomiques basés sur les espèces. Ces métriques apportent des informations supplémentaires en termes de structure de biofilm qui ne sont accessible aux données en espèce. Enfin, la pollution des rivières par les micropolluants devient une préoccupation sociétale croissante. Nous avons émis l'hypothèse que les diatomées pouvaient être de bons candidats pour évaluer la pression en herbicides. Quatre expérimentations de 2 mois ont été réalisées en mésocosmes lotiques. Nous avons montré que les diatomées vivant entourées de matrices polysaccharidiques épaisses étaient plus résistantes aux pesticides dissous. Au contraire les diatomées présentant une surface cellulaire de contact importante avec l'eau étaient défavorisées. Ce type de métrique pourrait être utilisé in situ à plus large échelle. Nous concluons sur l'intérêt d'intégrer ces métriques à la bioindication par les diatomées. Mais également nous soulignons l'importance de croiser la phylogénie et l'écologie pour mieux comprendre quelles pressions environnementales ont forcées les diatomées à s'adapter. Si ces pressions peuvent être reliées à des pressions anthropiques, la bioindication par les diatomées en sera améliorée.Diatoms are ubiquitous microalgae of an extreme diversity. This made them good indicators of aquatic ecosystems quality and they are used since 50 years for this purpose. Since year 2000, the European Water Framework Directive requires their use to assess the ecological quality of watercourses. A typological framework has to be used in order to compare comparable rivers between each other, that is, rivers of the same bioclimatic regions, flowing on the same geological substrate at similar altitudes. Various ecoregional classifications were defined on the basis of these parameters. We showed at a scale covering 4 countries (Spain, France, Italy and Switzerland) and at a regional scale (north-east France) that ecoregions and geology are determinant to explain communities. Parameters characterizing pollution were less important. Unlike some authors, we did not observe any homogenization of the communities when pollution level was increasing. Moreover, we did not observe geographically restricted communities: this would enable to aggregate ecoregions geographically distinct but presenting the same physical characteristics. Diatoms display a very important specific diversity which can be a problem for their routine use. We showed that when increasing determination precision (from sub-division to species), pollution assessment performances were increasing but much less than the number of taxa. Assessment performances between genus and species are similar anyway, whereas there are ten time more species than genera. We also showed that using simplifying metrics (life-forms, ecological guilds) enable assessing nutrient level as well as diatom indices based on species. These metrics bring additional information about biofilms structure that is not available with species data. At last, micropollutants pollution in rivers is of increasing concern to citizens. We hypothesized that diatoms could be good candidates to assess herbicide pressure. Four experiments lasting 2 months were conducted in lotic mesocosms. We showed that diatoms surrounded by thick exopolysaccharid matrices were more resistant to dissolved pesticides. On the over hand, diatoms presenting an important cell surface contact with water were disadvantaged. This kind of metric could be used in situ at a larger scale. We conclude on the interest to integrate such metrics to diatom bioassessment. But we also strength the importance to cross phylogeny and ecology to better understand which environmental pressure forced diatoms adapt. If these pressures can be related to anthropogenic pressures, diatom bioassessment will be improved.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF