Slender naiad (Najas flexilis) habitat quality assessment

N. flexilis is a rare aquatic plant species of European conservation importance. The species is believed to be under increasing threat in its Scottish stronghold. However, the factors that affect the health of N. flexilis populations in Scotland are not fully understood, such as why does the species disappear, and where and why it fares well in some sites. In addition, more needs to be known about what actions can be taken to ensure that the habitat quality needed to support populations of N. flexilis is either maintained or restored. This report highlights that much of the sensitivity of N. flexilis to the known threats of eutrophication, competition with other plants and the mild acidification of circumneutral lakes can be related to its physiology as an obligate user of CO2; N. flexilis plants being unable to metabolise bicarbonate for photosynthesis

Nitrogen and phosphorus limitation and the management of small productive lakes

Many inland waters are enriched with nutrients, causing deleterious effects to their ecology and the benefits they provide for society, but their effective management first requires identification of the nutrient(s) that limit algal production. Concentrations of nutrients and chlorophyll a (Chl-a) were used to assess nutrient limitation seasonally at 17 meres over 2 time periods: historic (2005–2009; 1995–1998 at one site) and contemporary (2014–2018). Different approaches were used to assess nutrient limitation because they reflect different aspects of nutrient availability and their conversion into biomass. In the historic period, 3 meres were phosphorus (P) limited, 3 nitrogen (N) limited, 5 co-limited; the remaining 6 meres were not nutrient limited. For this period, ecological status assessed using phytoplankton Chl-a was only at good or high ecological status (sensu the Water Framework Directive) at 2 sites. The contemporary period was slightly improved, with 4 sites at good status. At the sites that failed to meet good ecological status, the required reduction in P concentration was least in P-limited sites and, conversely, the reduction in N was least in N-limited sites, suggesting that remediation by nutrient reduction would be most efficient if it was targeted using site-specific information. Even in primarily P-limited sites, once input of P has been reduced, further ecological benefit of reducing N at targeted sites should be explored

WISER deliverable D3.1-4: guidance document on sampling, analysis and counting standards for phytoplankton in lakes

Sampling, analysis and counting of phytoplankton has been undertaken in European lakes for more than 100 years (Apstein 1892, Lauterborn 1896, Lemmermann 1903, Woloszynska 1912, Nygaard 1949). Since this early period of pioneers, there has been progress in the methods used to sample, fix, store and analyse phytoplankton. The aim of the deliverable D3.1-4 is to select, harmonize and recommend the most optimal method as a basis for lake assessment. We do not report and review the huge number of European national methods or other published manuals for phytoplankton sampling and analysis that are available. An agreement on a proper sampling procedure is not trivial for lake phytoplankton. In the early 20th century, sampling was carried out using plankton nets. An unconcentrated sample without any pre-screening is required for quantitative phytoplankton analysis, for which various water samplers were developed. Sampling of distinct water depths or an integral sample of the euphotic zone affects the choice of the sampler and sampling procedure. The widely accepted method to quantify algal numbers together with species determination was developed by Utermöhl (1958), who proposed the counting technique using sediment chambers and inverse microscopy. This is the basis for the recently agreed CEN standard “Water quality - Guidance standard on the enumeration of phytoplankton using inverted microscopy (Utermöhl technique)” (CEN 15204, 2006). This CEN standard does not cover the sampling procedure or the calculation of biovolumes for phytoplankton species, although Rott (1981), Hillebrand et al (1999) and Pohlmann & Friedrich (2001) have contributed advice on how to calculate taxa biovolumes effectively. Willén (1976) suggested a simplified counting method, when counting 60 individuals of each species. For the Scandinavian region an agreed phytoplankton sampling and counting manual was compiled, which has been in use for about 20 years (Olrik et al. 1998, Blomqvist & Herlitz 1998). It is very unfortunate that no European guidance on sampling of phytoplankton in lakes was agreed before the phytoplankton assessment methods for the EU-WFD were developed and intercalibrated by Member States. In 2008 an initiative by the European Commission (Mandate M424) for two draft CEN standards on sampling in freshwaters and on calculation of phytoplankton biovolume was unfortunately delayed by administrative difficulties. Recently a grant agreement was signed between the Commission and DIN (German Institute for Standardization) in January 2012 to develop these standards. We believe this WISER guidance document can usefully contribute to these up-coming standards

Automated colonoscopy withdrawal phase duration estimation using cecum detection and surgical tasks classification

Colorectal cancer is the third most common type of cancer with almost two million new cases worldwide. They develop from neoplastic polyps, most commonly adenomas, which can be removed during colonoscopy to prevent colorectal cancer from occurring. Unfortunately, up to a quarter of polyps are missed during colonoscopies. Studies have shown that polyp detection during a procedure correlates with the time spent searching for polyps, called the withdrawal time. The different phases of the procedure (cleaning, therapeutic, and exploration phases) make it difficult to precisely measure the withdrawal time, which should only include the exploration phase. Separating this from the other phases requires manual time measurement during the procedure which is rarely performed. In this study, we propose a method to automatically detect the cecum, which is the start of the withdrawal phase, and to classify the different phases of the colonoscopy, which allows precise estimation of the final withdrawal time. This is achieved using a Resnet for both detection and classification trained with two public datasets and a private dataset composed of 96 full procedures. Out of 19 testing procedures, 18 have their withdrawal time correctly estimated, with a mean error of 5.52 seconds per minute per procedure

Slender naiad (Najas flexilis) habitat quality assessment – site prioritisation.

This report is the result of the second phase of the slender naiad (Najas flexilis) habitat quality assessment project

Hyperspectral remote sensing of cyanobacterial pigments as indicators for cell populations and toxins in eutrophic lakes

The growth of mass populations of toxin-producing cyanobacteria is a serious concern for the ecological status of inland waterbodies and for human and animal health. In this study we examined the performance of four semi-analytical algorithms for the retrieval of chlorophyll a (Chl a) and phycocyanin (C-PC) from data acquired by the Compact Airborne Spectrographic Imager-2 (CASI-2) and the Airborne Imaging Spectrometer for Applications (AISA) Eagle sensor. The retrieval accuracies of the semi-analytical models were compared to those returned by optimally calibrated empirical band-ratio algorithms. The best-performing algorithm for the retrieval of Chl a was an empirical band-ratio model based on a quadratic function of the ratio of re!ectance at 710 and 670 nm (R2=0.832; RMSE=29.8%). However, this model only provided a marginally better retrieval than the best semi-analytical algorithm. The best-performing model for the retrieval of C-PC was a semi-analytical nested band-ratio model (R2=0.984; RMSE=3.98 mg m−3). The concentrations of C-PC retrieved using the semi-analytical model were correlated with cyanobacterial cell numbers (R2=0.380) and the particulate and total (particulate plus dissolved) pools of microcystins (R2=0.858 and 0.896 respectively). Importantly, both the empirical and semi-analytical algorithms were able to retrieve the concentration of C-PC at cyanobacterial cell concentrations below current warning thresholds for cyanobacteria in waterbodies. This demonstrates the potential of remote sensing to contribute to early-warning detection and monitoring of cyanobacterial blooms for human health protection at regional and global scales

Capacity challenges in water quality monitoring: understanding the role of human development

Monitoring the qualitative status of freshwaters is an important goal of the international community, as stated in the Sustainable Development Goal (SDGs) indicator 6.3.2 on good ambient water quality. Monitoring data are, however, lacking in many countries, allegedly because of capacity challenges of less-developed countries. So far, however, the relationship between human development and capacity challenges for water quality monitoring have not been analysed systematically. This hinders the implementation of fine-tuned capacity development programmes for water quality monitoring. Against this background, this study takes a global perspective in analysing the link between human development and the capacity challenges countries face in their national water quality monitoring programmes. The analysis is based on the latest data on the human development index and an international online survey amongst experts from science and practice. Results provide evidence of a negative relationship between human development and the capacity challenges to meet SDG 6.3.2 monitoring requirements. This negative relationship increases along the course of the monitoring process, from defining the enabling environment, choosing parameters for the collection of field data, to the analytics and analysis of five commonly used parameters (DO, EC, pH, TP and TN). Our assessment can be used to help practitioners improve technical capacity development activities and to identify and target investment in capacity development for monitoring

Ecological resilience in lakes and the conjunction fallacy

There is a pressing need to apply stability and resilience theory to environmental management to restore degraded ecosystems effectively and to mitigate the effects of impending environmental change. Lakes represent excellent model case studies in this respect and have been used widely to demonstrate theories of ecological stability and resilience that are needed to underpin preventative management approaches. However, we argue that this approach is not yet fully developed because the pursuit of empirical evidence to underpin such theoretically grounded management continues in the absence of an objective probability framework. This has blurred the lines between intuitive logic (based on the elementary principles of probability) and extensional logic (based on assumption and belief) in this field

Storm impacts on phytoplankton community dynamics in lakes

In many regions across the globe, extreme weather events such as storms have increased in frequency, intensity, and duration due to climate change. Ecological theory predicts that such extreme events should have large impacts on ecosystem structure and function. High winds and precipitation associated with storms can affect lakes via short‐term runoff events from watersheds and physical mixing of the water column. In addition, lakes connected to rivers and streams will also experience flushing due to high flow rates. Although we have a well‐developed understanding of how wind and precipitation events can alter lake physical processes and some aspects of biogeochemical cycling, our mechanistic understanding of the emergent responses of phytoplankton communities is poor. Here we provide a comprehensive synthesis that identifies how storms interact with lake and watershed attributes and their antecedent conditions to generate changes in lake physical and chemical environments. Such changes can restructure phytoplankton communities and their dynamics, as well as result in altered ecological function (e.g., carbon, nutrient and energy cycling) in the short‐ and long‐term. We summarize the current understanding of storm‐induced phytoplankton dynamics, identify knowledge gaps with a systematic review of the literature, and suggest future research directions across a gradient of lake types and environmental conditions

Effective management of ecological resilience – are we there yet?

1. Ecological resilience is developing into a credible paradigm for policy development and environmental management for preserving natural capital in a rapidly changing world. However, resilience emerges from complex interactions, limiting the translation of theory into practice. 2. Main limitations include the following: (i) difficulty in quantification and detection of changes in ecological resilience, (ii) a lack of empirical evidence to support preventative or proactive management and (iii) difficulties in managing processes operating across socio-ecological systems that vary in space and time. 3. We highlight recent research with the potential to address these limitations including new and/or improved indicators of resilience and tools to assess scale as a driver of resilience. 4. Synthesis and applications. Effective resilience-based management must be adaptive in nature. To support this, we propose an operational model using resilience-based iterative management actions operating across scales