scholarly journals Response of diatom assemblages to the disruption of the running water continuum in urban areas, and its consequences on bioassessment

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12457
Author(s):  
Ewelina Szczepocka ◽  
Paulina Nowicka-Krawczyk ◽  
Rafał M. Olszyński ◽  
Joanna Żelazna-Wieczorek
Keyword(s):  
Urban Areas ◽  
Aquatic Ecosystems ◽  
Ecological Status ◽  
Data Matrix ◽  
Biological Assessment ◽  
Assessment Procedure ◽  
Correct Result ◽  
Diatom Assemblages ◽  
Stream Channels ◽  
Running Water

Transformation of river and stream channels disrupts their natural ecological cycles and interrupts the continuum of their ecosystems. Changes in natural hydromorphological conditions transform lotic communities into those atypical of flowing waters, resulting in bioassessment procedures yielding incorrect results. This study shows how hydromorphological transformations of ecosystems affect the ecological status bioassessment results by disturbing diatom communities typical for rivers. Moreover, the article presents a new biological assessment procedure for urban transformed rivers including the verification of the community structure based on autecology and quantity of species. The ecological status of the ecosystem was assessed using benthic diatom assemblages and supported with results of hydrochemical analysis. The structure of the assemblages and their relationships between individual sampling sites were clarified by shade plot and multivariate data analyses. The analysis of dominant species vitality at sampling sites and their autecology gave the foundation for modification of taxa data matrix and recalculation the diatom indices. Biological assessment showed that one of the artificial ponds constructed at the stream channel was characterized by good ecological status, and its presence strongly affected the state of the downstream ecosystem following the development of a unique assemblage of diatoms that prefer oligosaprobic and oligotrophic waters. The presence of these species was also noted in the downstream sections, but most of the cells were dead. As the indicator values of these taxa are high, their presence artificially increased the ecological status of the stream, resulting in the hydrochemical assessment not being in line with the bioassessment. Therefore, a new procedure was adopted in which non-characteristic taxa for the downstream sections were excluded from analysis. This approach corrected the results of bioassessment characterizing the ecological status of the stream as poor along its entire course, with the exception of this unique pond. For hydromorphologically transformed streams and rivers with disturbed channel continuity, the correct result of an incorrect diatom-based bioassessment may be retrieved after excluding species unusual for the type of ecosystem from the studied assemblages, i.e., the species which are unable to reproduce in that area and are only carried into it by the water flow. Assessment of the ecological status of aquatic ecosystems based on biotic factors is an essential tool of aquatic ecosystems monitoring in many countries. This type of assessment requires a multifaceted approach, in particular, to identify factors that may disrupt this assessment. Standardization of biomonitoring methods is an important step in correct assessment; thus, the findings of this paper will be useful in routine biomonitoring around the world.

scholarly journals Diversity of Aquatic Ecosystems in Urban Areas - Public Expectations

2015 ◽  
Vol 16 (1) ◽  
pp. 125-134
Author(s):  
Joanna Sender ◽  
Weronika Maślanko
Keyword(s):  
Urban Areas ◽  
Aquatic Ecosystems ◽  
Public Awareness ◽  
Ecological Status ◽  
Urban Ecosystems ◽  
Poor Quality ◽  
Natural Lakes ◽  
Ancient Times ◽  
Bodies Of Water ◽  
River Valleys

Abstract In urban ecosystems, typically created by humans, it is very difficult to balance the needs of all its inhabitants. Significance of nature in the cities has been perceived since the ancient times. In the city there are many problems associated with the lack or sometimes excess of water, as well as poor quality. In times of water resources decline and their progressive degradation, each aquatic ecosystem should be investigated because of its values. Among the aquatic ecosystems occurring in the cities, there are: river valleys, natural lakes, water reservoirs, as well as small bodies of water. The aim of this study is to raise public awareness about the role of aquatic ecosystems in cities with different sizes and with a varying number of inhabitants. All respondents in each type of city felt the need of water presence in their surroundings and treated it as a necessary part of the proper functioning, as well as a place for rest and recreation. However, lack of management and a poor ecological status of them were noticed

Diatom biomonitoring – scientific foundations, commonly discussed issues and frequently made errors

2018 ◽  
Vol 47 (3) ◽  
pp. 313-325 ◽  
Author(s):  
Ewelina Szczepocka ◽  
Joanna Żelazna-Wieczorek
Keyword(s):  
Water Quality ◽  
Surface Water ◽  
Aquatic Ecosystems ◽  
Objective Assessment ◽  
Ecological Status ◽  
Biological Assessment ◽  
Basic Tool ◽  
Diatom Indices ◽  
The World ◽  
Made In

Abstract Contemporary assessment of the ecological status of aquatic ecosystems is based on various groups of organisms, including diatoms. Biological assessment, implemented by the Water Framework Directive, has been applied worldwide for more than 15 years. Currently, the most basic “tool” used in biomonitoring are diatom indices, which are routinely applied in Europe and other countries around the world. In Poland, the diatom indices have been used for over 5 years, which is a period of time allowing to summarize and evaluate the effectiveness of these methods in the assessment of aquatic ecosystems. The purpose of this work was to analyse the use of diatom indices in the biomonitoring of surface water by collecting data on the possibilities and limitations of using diatom indices for the objective assessment of water quality. Attention was paid to mistakes made in the course of biological assessment performed with the use of diatom phytobenthos, which have a significant impact on the obtained results. The paper also contains suggestions for introducing several important changes in biological monitoring, which will improve its quality and efficiency in assessing the ecological status of various aquatic ecosystems.

scholarly journals SPECIES IDENTIFICATION FOR AQUATIC BIOMONITORING USING DEEP RESIDUAL CNN AND TRANSFER LEARNING

2021 ◽  
Vol 20 (1) ◽  
pp. 001
Author(s):  
Aleksandar Milosavljević ◽  
Đurađ Milošević ◽  
Bratislav Predić
Keyword(s):  
Species Identification ◽  
Transfer Learning ◽  
Aquatic Insects ◽  
Aquatic Ecosystems ◽  
Data Augmentation ◽  
Ecological Status ◽  
Multiple Images ◽  
Public Datasets ◽  
Learning Data ◽  
Small Dataset

Aquatic insects and other benthic macroinvertebrates are mostly used as bioindicators of the ecological status of freshwaters. However, an expensive and time-consuming process of species identification represents one of the key obstacles for reliable biomonitoring of aquatic ecosystems. In this paper, we proposed a deep learning (DL) based method for species identification that we evaluated on several available public datasets (FIN-Benthic, STONEFLY9, and EPT29) along with our Chironomidae dataset (CHIRO10). The proposed method relies on three DL techniques used to improve robustness when training is done on a relatively small dataset: transfer learning, data augmentation, and feature dropout. We applied transfer learning by employing ResNet-50 deep convolutional neural network (CNN) pretrained on ImageNet 2012 dataset. The results show significant improvement compared to original contributions and confirms that there is a considerable gain when there are multiple images per specimen.

scholarly journals The use of eDNA and DNA metabarcoding in monitoring the ecological condition of Norwegian lakes

2021 ◽  
Vol 4 ◽  
Author(s):  
Sara Atienza Casas ◽  
Markus Majaneva ◽  
Thomas Jensen ◽  
Marie Davey ◽  
Frode Fossøy ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ecological Status ◽  
Ecological Condition ◽  
Molecular Techniques ◽  
Taxonomic Resolution ◽  
Potential Cost ◽  
Running Water ◽  
National Monitoring ◽  
Monitoring Programs ◽  
Dna Metabarcoding

Biodiversity assessments using molecular identification of organisms through high-throughput sequencing techniques have been a game changer in ecosystem monitoring, providing increased taxonomic resolution, more objective identifications, potential cost reductions, and reduced processing times. The use of DNA metabarcoding of bulk samples and environmental DNA (eDNA) is now widespread but is not yet universally implemented in national monitoring programs. While bulk sample metabarcoding involves extraction of DNA from organisms in a sample, eDNA analysis involves obtaining DNA directly from environmental samples, which can include microorganisms, meiofauna-size taxa and macrofauna traces such as larval stages, skin and hair cells, gametes, faeces and free DNA bound to particles. In Norway, freshwater biomonitoring in compliance with the EU Water Framework Directive (WFD) is conducted on several administrative levels, including national monitoring programs for running water, small and large lakes. These programs typically focus on a fraction of the actual biodiversity present in the monitored habitats (Weigand 2019). DNA metabarcoding of both bulk samples and eDNA samples are relevant tools for future freshwater biomonitoring in Norway. The aim of this PhD project is to develop assessment protocols based on DNA-metabarcoding and eDNA of benthic invertebrates, microcrustaceans and fish that can be used as standard biomonitoring tools to assess the ecological condition of lakes. The main topics addressed will be: - Development of protocols throughout the eDNA-metabarcoding workflow (i.e. sampling, filtration, preservation, extraction, amplification and sequencing) suitable to execute biodiversity assessments and determine the ecological status of lakes. - Comparison of the results obtained using molecular tools and traditional morphology-based approaches in order to assess the feasibility of such techniques to be incorporated as standard biomonitoring tools, such as the ones implemented under the provisions of the WFD. - Evaluate the effect of improved taxonomic resolution from molecular techniques on determining the ecological status of lakes, both by broadening the number of taxa analyzed and by identifying more taxa to species level. - Assess the feasibility of using eDNA extracted from water samples, taken at different depths and fish densities, to measure fish abundance/biomass as a proxy to calculate the ecological quality indices regulated in the WFD. - Analyze the coverage and resolution provided by reference libraries for certain taxa, such as crustacea, in order to assess the reliability and precision of taxonomic assignments.

scholarly journals The Fellowship of the Ring Test: DNAqua-Net WG2 initiative to compare diatom metabarcoding protocols used in routine freshwater biomonitoring for standardisation

2021 ◽  
Vol 4 ◽  
Author(s):  
Valentin Vasselon ◽  
Éva Ács ◽  
Salomé Almeida ◽  
Karl Andree ◽  
Laure Apothéloz-Perret-Gentil ◽  
...  
Keyword(s):  
Dna Extraction ◽  
High Throughput ◽  
Aquatic Ecosystems ◽  
Quality Index ◽  
Ecological Status ◽  
Pcr Amplification ◽  
Ring Test ◽  
Dna Metabarcoding ◽  
Ecological Status Assessment ◽  
Status Assessment

During the past decade genetic approaches have been developed to monitor biodiversity in aquatic ecosystems. These enable access to taxonomic and genetic information from biological communities using DNA from environmental samples (e.g. water, biofilm, soil) and methods based on high-throughput sequencing technologies, such as DNA metabarcoding. Within the context of the Water Framework Directive (WFD), such approaches could be applied to assess Biological Quality Elements (BQE). These are used as indicators of the ecological status of aquatic ecosystems as part of national monitoring programs of the european network of 110,000 surface water monitoring sites with 79.5% rivers and 11% lake sites (Charles et al. 2020). A high-throughput method has the potential to increase our spatio-temporal monitoring capacity and to accelerate the transfer of information to water managers with the aim to increase protection of aquatic ecosystems. Good progress has been made with developing DNA metabarcoding approaches for benthic diatom assemblages. Technological innovation and protocol optimization have allowed robust taxonomic (species) and genetic (OTU, ESV) information to be obtained from which diatom quality indices can be calculated to infer ecological status to rivers and lakes. Diatom DNA metabarcoding has been successfully applied for biomonitoring at the scale of national river monitoring networks in several countries around the world and can now be considered technically ready for routine application (e.g. Apothéloz-Perret-Gentil et al. 2017, Bailet et al. 2019, Mortágua et al. 2019, Vasselon et al. 2019, Kelly et al. 2020, Pérez-Burillo et al. 2020, Pissaridou et al. 2021). However, protocols and methods used by each laboratory still vary between and within countries, limiting their operational transferability and the ability to compare results. Thus, routine use of DNA metabarcoding for diatom biomonitoring requires standardization of all steps of the metabarcoding procedure, from the sampling to the final ecological status assessment in order to define good practices and standards. Following previous initiatives which resulted in a CEN technical report for biofilm sampling and preservation (CEN 2018), a set of experiments was initiated during the DNAqua-Net WG2 diatom workshop (Cyprus, 2019) to focus on DNA extraction and PCR amplification steps in order to evaluate: i) the transferability and reproducibility of a protocol between different laboratories; ii) the variability introduced by different protocols currently applied by the scientific community. 19 participants from 14 countries performed DNA extraction and PCR amplification in parallel, using i) the same fixed protocol and ii) their own protocol. Experiments were performed by each participant on a set of standardized DNA and biofilm samples (river, lake, mock community). In order to specifically test the variability of DNA extraction and PCR amplification steps, all other steps of the metabarcoding process were fixed and the preparation of the Miseq sequencing was performed by only one laboratory. The variability within and between participants will be evaluated on DNA extracts quantity, taxonomic (genus, species) and genetic richness, community structure comparison and diatom quality index scores (IPS). We will also evaluate the variability introduced by different DNA extraction and PCR amplification protocols on diatom quality index scores and the final ecological status assessment. The results from this collaborative work will not serve to define “one protocol to rule them all”, but will provide valuable information to define guidelines and minimum requirements that should be considered when performing diatom metabarcoding for biomonitoring.

scholarly journals Exposure Indices of Extreme Wind-Driven Rain Events for Built Heritage

Atmosphere ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 163 ◽  
Author(s):  
Scott Allan Orr ◽  
May Cassar
Keyword(s):  
Cultural Heritage ◽  
Exposure Assessment ◽  
Urban Areas ◽  
Prolonged Exposure ◽  
Extreme Weather Events ◽  
Assessment Procedure ◽  
Statistical Confidence ◽  
Potential Impact ◽  
Rain Events ◽  
Two Stages

Building performance and material change of cultural heritage in urban areas are negatively impacted by wind-driven rain (WDR). The frequency and intensity of WDR exposure are modified by climate change. Current approaches to exposure assessment emphasise prolonged exposure. Here, we propose indices to represent the exposure of cultural heritage to extreme WDR events. The indices are derived in two stages: (1) time-binning of long-term exposure, and (2) statistical representation of the occurrence of infrequent but intense events by fitting to the Generalised Extreme Value (GEV) distribution. A comparison to an existing exposure assessment procedure demonstrates that the proposed indices better represent shorter, more intense, and more consistent WDR events. Indices developed for seasons had greater statistical confidence than those developed for annual exposure. One index is contextualised within a model of a gutter on a terraced building: this converts the index from a measure of exposure to potential impact. This evaluation demonstrated the importance of maintenance to reduce the potential impact of WDR events. This work has direct and indirect implications for developing robust assessment procedures for cultural heritage exposure to extreme weather events.

scholarly journals Ecological assessment of the River Nile around Gizert El-Warrak by Phytoplankton and macroinvertebrates assemblages

2018 ◽  
Author(s):  
Kadria M.A. Mahmoud ◽  
Sara S.M. Sayed ◽  
Mohamed R. Habib
Keyword(s):  
Diversity Index ◽  
Ecological Status ◽  
Organic Pollution ◽  
Ecological Assessment ◽  
Biological Assessment ◽  
Biotic Index ◽  
Trophic State Index ◽  
River Nile ◽  
Summary Statement ◽  
State Index

AbstractBiological assessment is considered a useful tool for assessing the ecological status of the aquatic ecosystems. Therefore, the goal of the present study was to use phytoplankton and macroinvertebrates as biological tools for ecological assessment of the River Nile around Gizert El-Warrak. A total of 33 phytoplankton species identified in the studied stations; these include 16 species of Chlorophyta, 5 species of Cyanophyta and 12 species of Bacillariophyta. All investigated stations characterized by high organic pollution according to Palmer′s index. Trophic state index showed a hyper-eutrophic status in stations S1, S2, S4, S6 and S8 and an eutrophic status in stations S3, S5 and S7.Gastropoda and Oligochaeta were the most dominant of macroinvertebrates taxa recorded 50.8 and 24.6%, respectively. Diversity Index (H′) ranged (1.14 – 2) which indicated that the structure of macroinvertebrates habitat was poor. Also, Evenness Index (J) ranged (0.016 – 0.043) which indicated that individuals were not distributed equally. The values of biotic index depending on macroinvertebrates categories showed that the River Nile’s water quality is fairly poor with significant organic pollution.Summary statementBioassessment based on non-taxonomic measurements of algae and biotic indices of macroinvertebrates may be considered as vital methods that reflect disturbances in aquatic systems for both short-term and long-term.

scholarly journals Ranga bioindykacji w ekotoksykologii wód

2012 ◽  
Vol 10 (2) ◽  
pp. 33-52 ◽  
Author(s):  
Urszula Sadowska
Keyword(s):  
Surface Water ◽  
Biological Monitoring ◽  
Aquatic Ecosystems ◽  
Ecological Status ◽  
Standard Test ◽  
Monitoring Systems ◽  
Long Time ◽  
Test Organisms ◽  
Bioindication Methods

Bioindication methods are applied in ecotoxicological studies which in turn are widely used in the biological monitoring of surface water. Bioindication has been applied for a long time and so far it has created multiple classificationsbased on diagnosis groups of organisms. Bioindicators play a signi]cant role in bioindication; they are species used to monitor the health of the environment or ecosystem. Some of them are standard test organisms used in ecotoxicologyin the so-called bioassays, which provide a great deal of information about the type and in^uence of pollution. These studies are vital nowadays, as compounds have been found to be the greatest threat to aquatic ecosystems. In relation to ecotoxicology, research allows us to determine bioconcentration, bioaccumulation and biomagni]cation factors, and to assess the ecological status of water used in many different indexes so as to determine such relevant parameters as saprobic, biological bio-diversity and biotic indexes. Poland is preparing for the extension of monitoring systems that take into account all the necessary elements of the environment, even the sediments. It is required by the Water Frame Directive.

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