scholarly journals Applicability of diatom metabarcoding in the ecological status assessment of Hungarian lotic and soda pan habitats

2021 ◽  
Vol 4 ◽  
Author(s):  
Mónika Duleba ◽  
Angéla Földi ◽  
Adrienn Micsinai ◽  
Anita Mohr ◽  
Rita Sipos ◽  
...  
Keyword(s):  
Ecological Status ◽  
Benthic Diatom ◽  
Reference Database ◽  
Sensitivity Index ◽  
Running Waters ◽  
Diatom Assemblages ◽  
Diatom Index ◽  
Rivers And Streams ◽  
Ecological Status Assessment ◽  
Status Assessment

Diatoms, eukaryotic algae with silica cell wall have been proved to be reliable bioindicators and are applied in ecological status assessment of aquatic ecosystems using indices calculated from pollution sensitivity and indicator values of species. Traditional method of identification of diatom species is based on morphological features of frustule that requires in-depth taxonomical knowledge and expertise. Metabarcoding that combines barcodes and high-throughput sequencing offers a promising alternative. In this pilot study we tested the applicability of metabarcoding of benthic diatom assemblages for ecological status assessment of water bodies in Hungary comparing its performance to that of morphology-based identification of species. Samples from 78 rivers and streams arranged along a trophic gradient and 14 soda pans representing unique types of habitats were investigated. Sequences of the barcode region of rbcL gene suggested by Vasselon et al. (2017) were acquired revealing 1135 diatom amplicon sequence variants (ASVs) of which 54% could be assigned at species level using Diat.barcode (Rimet et al. 2019) as reference database. Morphological investigation detected more species and intraspecific taxa in the lotic and lentic samples (413 and 78, respectively) than metabarcoding (190 and 75). Correspondence between taxa detected based on morphology and DNA sequences was relatively low (on average 24% in lotic and 26% in lentic samples) but considerably increased (on average 66% and 56%, respectively) when taking into account only the taxa reaching higher than 5% relative abundance in microscopy counting. The differences mainly derived from that a considerable portion (59% and 32%, respectively) of the morphologically identified taxa were not recorded in the reference database. Community structure of samples from both running and standing waters based on microscopy and DNA sequence analysis showed significant correlation as revealed using Mantel test. For rivers and streams diatom index IPS (Specific Pollution Sensitivity Index, (Coste in Cemagref, 1982) for soda pans indices H (Ziemann et al., 2001) and IBD (Indice Biologique Diatomées, Lenoir and Coste, 1996) were calculated from the results of the two aspects. Strong correlation was found between morphology- and sequence-based indices and in about half of the samples, the ecological status class obtained with the two methods coincided. Our results suggest that metabarcoding inheres a great opportunity and could be successfully applied in benthic diatom-based ecological status assessment of Hungarian waters after the reference database is supplemented with taxa frequently occurring in these habitats. References Cemagref, 1982. Etude des méthodes biologiques quantitativesd’appréciation de la qualité des eaux, Rapport Division Qualité des Eaux Lyon. Agence financière de Bassin Rhône-Méditerranée-Corse, Pierre-Bénite, France. Lenoir, A., Coste, M., 1996. Development of a practical diatom index of overall water quality applicable to the French National Water Board Network. Presented at the International symposium, Volksbildungsheim Grilhof Vill, AUT, 17-19 September 1995, Universität Innsbruck, pp. 29–43. Rimet, F., Gusev, E., Kahlert, M., Kelly, M.G., Kulikovskiy, M., Maltsev, Y., Mann, D.G., Pfannkuchen, M., Trobajo, R., Vasselon, V., Zimmermann, J., Bouchez, A., 2019. Diat.barcode, an open-access curated barcode library for diatoms. Sci. Rep. 9, 15116. Vasselon, V., Rimet, F., Tapolczai, K., Bouchez, A., 2017. Assessing ecological status with diatoms DNA metabarcoding: Scaling-up on a WFD monitoring network (Mayotte island, France). Ecol. Indic. 82, 1–12. Ziemann, H., Kies, L., Schulz, C.-J., 2001. Desalinization of running waters: III. Changes in the structure of diatom assemblages caused by a decreasing salt load and changing ion spectra in the river Wipper (Thuringia, Germany). Limnologica 31, 257–280.

scholarly journals Diatom diversity and water quality of a suburban stream: a case study of the Rzeszów city in SE Poland

2016 ◽  
Vol 41 (1) ◽  
pp. 19-34 ◽  
Author(s):  
Teresa Noga ◽  
Jadwiga Stanek-Tarkowska ◽  
Urszula Kloc ◽  
Natalia Kochman-Kędziora ◽  
Mateusz Rybak ◽  
...  
Keyword(s):  
Water Quality ◽  
Ecological Status ◽  
Sensitivity Index ◽  
Diatom Assemblages ◽  
Diatom Index ◽  
Se Poland ◽  
Physicochemical Factors ◽  
Index Index ◽  
The City

Abstract The aim of this work was to investigate the diversity of diatom assemblages developed in the Przyrwa stream, to assess water quality based on benthic diatoms and to make an attempt at the identification of physicochemical factors having the greatest impact on the differentiation of diatom assemblages. Studies were conducted in 2011-2012 on the Przyrwa stream, a left-side tributary of the Wisłok River flowing through the city of Rzeszów and with its spring section located on the borders of the city. A total of 259 diatom taxa were identified in the Przyrwa stream during three studied seasons. At all investigated sites, the most abundant population consisted of Ulnaria ulna (Nitzsch) Compère, Cocconeis pediculus Ehrenb., Achnanthidium minutissimum (Kütz.) Czarnecki var. minutissimum, Navicula gregaria Donkin, Planothidium frequentissimum (Lange-Bert.) Lange-Bert., P. lanceolatum (Brébisson) Lange-Bert., Navicula lanceolata (C. Agardh) Ehrenb., Amphora pediculus (Kütz.) Grunow, Eolimna minima, (Grunow) Lange-Bert., Melosira varians C. Agardh and Cyclotella meneghiniana Kütz. Based on IPS (Specific Pollution Sensitivity Index) and GDI (Generic Diatom Index) indices, the ecological status of the Przyrwa stream was assessed as moderate to poor (mostly III-IV class of water quality), while the TDI (Trophic Diatom Index) index indicated a poor to bad ecological status (mainly IV-V class of water quality).

Demonstration of the Bzura River restoration using diatom indices

Biologia ◽  
2011 ◽  
Vol 66 (3) ◽  
Author(s):  
Barbara Rakowska ◽  
Ewelina Szczepocka
Keyword(s):  
Water Quality ◽  
Benthic Diatom ◽  
Biological Assessment ◽  
Sensitivity Index ◽  
Running Waters ◽  
Class Iii ◽  
Gradual Improvement ◽  
Diatom Index ◽  
Diatom Indices ◽  
The Impact

AbstractThe quality of running waters is reflected in the composition of benthic diatom assemblages. The biological assessment of changes in the composition, and thus of changes in water quality, was carried out in the lowland mid-sized Bzura River, Central Poland, over the period of 30 years. The benthic diatom material consisted of samples collected in two investigation periods, in 1972 and in 2003–2004. The methods applied were three diatom indices, IPS — Specific Pollution Sensitivity Index, GDI — Genetic Diatom Index and TDI —Trophic Diatom Index, and the OMNIDIA computer program, which are commonly used in Europe. The aim of the study was demonstrating the process of restoration that occurred in the river. The Bzura was included to the most polluted ones in Poland till 1996. Since 1998 a gradual improvement in water quality has been observed, which is caused by a number of biological-technical measures, mostly a proper organization of sewage management in most cites located on the river. In 1972 the IPS classified Bzura water into Water Quality Class IV-V, while in 2003–2004 it reached much higher values, i.e. Class III–IV. On the basis of the GDI Class III was determined in the whole river in 2003–2004, while its values indicated Class III–IV in 1972. The trophic index, TDI attributed Bzura water to the eutrophic to hypereutrophic zone in 2003–2004, and to one degree better water, i.e. from the mesoeutrophic to eutrophic zone, in 1972.From the carried out research it follows that the IPS is the best index, which may be commonly applied to assess saprobic pollution of running waters in Poland. It indicated an improvement in water that occurred in the Bzura over 30 years and took into account the impact of pollution sources and tributaries in given river sections.

scholarly journals Do benthic diatom assemblages reflect abiotic typology: a case study of Croatian streams and rivers

2017 ◽  
Vol 76 (1) ◽  
pp. 80-90
Author(s):  
Koraljka Kralj Borojević ◽  
Marija Gligora Udovič ◽  
Petar Žutinić ◽  
Gábor Várbíró ◽  
Anđelka Plenković-Moraj
Keyword(s):  
Indicator Species ◽  
Ecological Status ◽  
Benthic Diatoms ◽  
Specific Reference ◽  
Running Waters ◽  
Self Organizing Map ◽  
Diatom Assemblages ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Rivers And Streams

Abstract Benthic diatoms are widely used in Europe and worldwide to access ecological status of running waters. One of key goals of Water Framework Directive is to classify rivers and streams using biological quality elements and type specific reference conditions. According to system B which incorporates additional abiotic descriptors, there are 24 water types in Croatia. For biological analyses 92 rivers and streams with 140 sampling points were chosen and sampled for benthic diatoms and water chemistry simultaneously. Self organizing map (SOM) analysis was used to define biotypes from species composition and abundance of benthic diatoms. Grouping of samples in SOM resulted in 10 distinctive groups. Based on their geographical position and site characteristics, groups represent sites with similar properties (as waterbed, catchment size, altitude, size of stream) belonging to different ecoregions in Croatia. Analysis of variance revealed statistically significant differences (p<0.05) among SOM groups concerning ammonia, nitrates and total phosphorus. Indicator species analysis (IndVal) singled out species that were significantly characteristic (p<0.05) for SOM and abiotic types. Compared to abiotic groups, in which 7 out of 24 have no indicator species, all SOM groups have one or several characteristic diatom species, thus indicating diatom assemblages as valuable site descriptors. Canonical analysis of principal coordinates analysis also indicated that SOM grouping of samples is statistically reliable. Grouping of similar sites, although placed into different abiotic types, makes SOM groups with its corresponding representative species an easy tool for water quality assessment and description of reference assemblage.

scholarly journals Applicability of diatom metabarcoding in the ecological status assessment of Hungarian lotic and soda pan habitats

2021 ◽  
Vol 130 ◽  
pp. 108105
Author(s):  
Mónika Duleba ◽  
Angéla Földi ◽  
Adrienn Micsinai ◽  
Gábor Várbíró ◽  
Anita Mohr ◽  
...  
Keyword(s):  
Ecological Status ◽  
Ecological Status Assessment ◽  
Status Assessment ◽  
Soda Pan

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.

Sign in / Sign up

Export Citation Format

Share Document