scholarly journals GENETIC IDENTIFICATION OF AQUATIC INVERTEBRATES OF KAZAKHSTAN AS INDICATORS OF ORGANIC POLLUTANTS

2018 ◽  
pp. 139-148
Author(s):  
Alexandr Anatoljevich Volkov ◽  
Larisa Anatoljevna Kovaljova ◽  
Tatjana Timofeevna Troshina ◽  
Zhanara Omirbekovna Mazhibaeva ◽  
Dmitrij Valerjevich Pilin ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Trees ◽  
Aquatic Invertebrates ◽  
Species Abundance ◽  
Ecological Status ◽  
Taxonomic Status ◽  
Organic Pollution ◽  
Water Bodies ◽  
Genetic Identification ◽  
Morphological Identity

The article deals with carrying out DNA barcoding of aquatic invertebrates of Kazakhstan to identify their taxonomic status as organic pollution indicators. 33 species of the Balkhash-Alakol basin and the Zhayik river were analyzed. 21 species correlate (95-100%) with previously published sequences of invertebrates with well-known classifications in the GenBank and BOLD databases. The taxonomic discrepancy in morphometric and genetic parameters in certain species has been revealed. The discrepancy may be caused by the morphological identity in chironomids at a larval stage. The phylogenetic trees of the investigated species within the families Chironomidae and Moinidae have been indicated. Chironomids are represented by ten clades of different types of genetic polymorphism of DNA gene. Genetic links of Moinidae are detected in four groups including a cryptic species from Lake Alakol. It has been stated that in distribution of cryptic taxons in Moina family factors of salinity and depth of the lake are important, as well as differences in depth. Molecular DNA-barcoding of invertebrates of Kazakhstan should be continued with covering a greater number of species and several replications, with qualified primary fixation of subjects of research and a sufficient number of samples. Authenticity of composition defining, species abundance, species characteristics of aquatic invertebrates from the water bodies of poorly explored arid regions is necessary for using them as indicators of the ecological status of water bodies.

scholarly journals Benthic Diatoms in River Biomonitoring—Present and Future Perspectives within the Water Framework Directive

Water ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 478
Author(s):  
Andreas Masouras ◽  
Ioannis Karaouzas ◽  
Elias Dimitriou ◽  
George Tsirtsis ◽  
Evangelia Smeti
Keyword(s):  
Water Framework Directive ◽  
Ecological Status ◽  
Organic Pollution ◽  
Water Bodies ◽  
Benthic Diatoms ◽  
Quality Indices ◽  
Eu Member States ◽  
Advantages And Disadvantages ◽  
Different Types ◽  
Quality Assessments

The European Water Framework Directive 2000/60/EC (WFD) has been implemented over the past 20 years, using physicochemical, biological and hydromorphological elements to assess the ecological status of surface waters. Benthic diatoms (i.e., phytobenthos) are one of the most common biological quality elements (BQEs) used in surface water monitoring and are particularly successful in detecting eutrophication, organic pollution and acidification. Herein, we reviewed their implementation in river biomonitoring for the purposes of the WFD, highlighting their advantages and disadvantages over other BQEs, and we discuss recent advances that could be applied in future biomonitoring. Until now, phytobenthos have been intercalibrated by the vast majority (26 out of 28) of EU Member States (MS) in 54% of the total water bodies assessed and was the most commonly used BQE after benthic invertebrates (85% of water bodies), followed by fish (53%), macrophytes (27%) and phytoplankton (4%). To meet the WFD demands, numerous taxonomy-based quality indices have been developed among MS, presenting, however, uncertainties possibly related to species biogeography. Recent development of different types of quality indices (trait-based, DNA sequencing and predictive modeling) could provide more accurate results in biomonitoring, but should be validated and intercalibrated among MS before their wide application in water quality assessments.

scholarly journals High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

2021 ◽  
Vol 4 ◽  
Author(s):  
Régis Vivien ◽  
Laure Apothéloz-Perret-Gentil ◽  
Jan Pawlowski ◽  
Inge Werner ◽  
Michel Lafont ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
Genetic Identification ◽  
Dna Barcodes ◽  
Biological Quality ◽  
Dna Metabarcoding ◽  
Morphological Approach

Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.

To the flora of сonjugates (Streptophyta, Conjugatophyceae) of the Valdai District area of the National Park «Valdaiskiy» (Novgorod Region, Russia)

2014 ◽  
Vol 48 ◽  
pp. 81-88
Author(s):  
A. F. Luknitskaya
Keyword(s):  
Species Distribution ◽  
National Park ◽  
Species Abundance ◽  
Water Bodies ◽  
Number Of Species ◽  
First Time

76 species, 3 varieties and 1 form from 21 genera of Streptophyta, Conjugatophyceae (Actinotaenium, Bambusina, Closterium, Cosmarium, Cylindrocystis, Euastrum, Gonatozygon, Haplotaenium, Micrasterias, Mougeotia, Netrium, Penium, Planotaenium, Pleurotaenium, Raphidiastrum, Spirogyra, Spirotaenia, Staurastrum, Staurodesmus, Tetmemorus, Xanthidium) were found in the basins of the Valdai District area of the National Park «Valdaiskiy» (Novgorod Region, Russia). The list of species is annotated with data on the species distribution in 55 collecting sites of 29 water bodies of the national park, and species abundance in collected samples according to Luknitskaya (2009). Among above mentioned genera, the genus Cosmarium is represented by the greatest number of species (20). Staurastrum chaetoceros has been found for the first time for the Novgorod Region.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals Assessment of the Impact of Small Hydropower Plants on the Ecological Status Indicators of Water Bodies: A Case Study in Lithuania

Water ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 433
Author(s):  
Laima Česonienė ◽  
Midona Dapkienė ◽  
Petras Punys
Keyword(s):  
Water Quality ◽  
Benthic Macroinvertebrates ◽  
Suspended Solids ◽  
Ecological Status ◽  
Fish Abundance ◽  
Water Bodies ◽  
Small Hydropower ◽  
Hydropower Plants ◽  
Physico Chemical ◽  
The Impact

Hydropower plants produce renewable and sustainable energy but affect the river’s physico-chemical characteristics and change the abundance and composition of the aquatic organisms. The impact of large HPPs on the ecological conditions of surface water bodies have been extensively studied, but less attention has been paid to environmental impact studies of small hydropower plants (SHPs). The impact of hydropeaking on both the river flow regime and ecosystems has been well-studied for peaking mode plants, mainly medium to large-sized ones. However, for small hydroelectric power plants, and especially for those in lowland rivers, the available information on water quality, benthic macroinvertebrates communities and fish abundance, and biomass is not sufficient. Ten small hydropower plants were selected, and the ecological status of water bodies was assessed in different parts of Lithuania. The studies were performed at the riverbed upstream from the SHPs, where the hydrological regime has not changed, and downstream from the SHPs. It was found that the small hydropower plants do not affect the physico-chemical values of the water quality indicators. This study demonstrated that the total number of benthic macroinvertebrates taxa (TS) is influenced by the concentration of nitrogen and suspended solids, the water flow, the river area, and the current speed; the number of EPT (Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies)) taxa is influenced by the concentration of nitrogen and suspended solids. The studied indicators do not have a significant impact on biomass. The SHPs affect the fish abundance and biomass. The Lithuanian fish index (LFI) is influenced by the average depth and area of the river. Some SHPs operating in lowland areas may yield somewhat significant hydrograph ramping but more detailed investigation is needed to support the significance of this impact on the biological indices.

scholarly journals Influence of Anthropogenic Loads on Surface Water Status: A Case Study in Lithuania

2021 ◽  
Vol 13 (8) ◽  
pp. 4341
Author(s):  
Laima Česonienė ◽  
Daiva Šileikienė ◽  
Vitas Marozas ◽  
Laura Čiteikė
Keyword(s):  
Total Nitrogen ◽  
Water Status ◽  
Arable Land ◽  
Ecological Status ◽  
Water Bodies ◽  
Agricultural Pollution ◽  
Good Ecological Status ◽  
Water Catchment ◽  
Lake Basins

Twenty-six water bodies and 10 ponds were selected for this research. Anthropogenic loads were assessed according to pollution sources in individual water catchment basins. It was determined that 50% of the tested water bodies had Ntotal values that did not correspond to the good and very good ecological status classes, and 20% of the tested water bodies had Ptotal values that did not correspond to the good and very good ecological status classes. The lake basins and ponds received the largest amounts of pollution from agricultural sources with total nitrogen at 1554.13 t/year and phosphorus at 1.94 t/year, and from meadows and pastures with total nitrogen at 9.50 t/year and phosphorus at 0.20 t/year. The highest annual load of total nitrogen for lake basins on average per year was from agricultural pollution from arable land (98.85%), and the highest total phosphorus load was also from agricultural pollution from arable land (60%).

Duplex DNA barcoding allows accurate species determination of morphologically similar limpets (Patella spp.) from non-destructive sampling

2016 ◽  
Vol 97 (7) ◽  
pp. 1479-1482 ◽  
Author(s):  
Thomas J. Ashton ◽  
Meriem Kayoueche-Reeve ◽  
Andrew J. Blight ◽  
Jon Moore ◽  
David M. Paterson
Keyword(s):  
Dna Barcoding ◽  
Species Abundance ◽  
Microscopic Analysis ◽  
Cost Effective ◽  
Field Studies ◽  
Similar Species ◽  
Species Determination ◽  
Destructive Sampling ◽  
Species Specific ◽  
Non Destructive

Accurate discrimination of two morphologically similar species of Patella limpets has been facilitated by using qPCR amplification of species-specific mitochondrial genomic regions. Cost-effective and non-destructive sampling is achieved using a mucus swab and simple sample lysis and dilution to create a PCR template. Results show 100% concurrence with dissection and microscopic analysis, and the technique has been employed successfully in field studies. The use of highly sensitive DNA barcoding techniques such as this hold great potential for improving previously challenging field assessments of species abundance.

scholarly journals Physicochemical Characteristics of the Okomu Wetland, Edo State, Nigeria

2020 ◽  
Vol 4 (2) ◽  
pp. 398-410
Author(s):  
A.E. Ogbeibu ◽  
S.I Ehiorobo
Keyword(s):  
Physicochemical Parameters ◽  
Forest Canopy ◽  
Oxygen Demand ◽  
Water Quality Assessment ◽  
Organic Pollution ◽  
Physicochemical Characteristics ◽  
Water Bodies ◽  
Temporary Ponds ◽  
Forested Wetland ◽  
Sampling Protocols

Water quality assessment was carried out within the 202 km2 Okomu National Park located within the 1,082km2Okomu Forest Reserve between January 2017 and December 2018. Water sampling was carried in ten compartments of approximately 1.6km2 each, covering Ponds, Stream and River, based on easy accessibility. No such study has been carried out for the Okomu Wetlands in the past three decades. Sampling protocols, laboratory analysis and quality control/quality assurance measures followed standard procedures. All physicochemical parameters showed significant (P < 0.001) spatial variations. The maximum and minimum values obtained for physicochemical parameters of the Okomu Wetland are 23.6 and 38.0°C air temperature; 21.0 – 38°C water temperature; 0.15 – 1.02m water level; 16.7 – 150.7mg/l total dissolved Solids (TDS); 0.5 – 18.8mg/l total suspended Solids (TSS); 0.2 – 14.8mg/l turbidity; 40. 0 – 307.4µS/cm electrical conductivity (EC); 4.4 – 6.7 pH; 0.02 – 0.14mg/l salinity; 0.7 – 5.5mg/l dissolve oxygen (DO); 0.5 – 3.8mg/l biochemical oxygen demand (BOD); 1.5 – 120.2mg/l chemical oxygen demand (COD); 23.8 – 593.6mg/l bicarbonates (HCO3); 69.9 – 245.3mg/l Chlorine (Cl); 0.02 – 0.59mg/l nitrite (NO2); 0.11 – 2.34mg/l nitrate (NO3); 0.04 – 2.11mg/l ammonium-nitrogen (NH4N); 0.05 – 2.96mg/l sulphate (SO4); 0.09 – 9.2mg/l phosphorus (P); 0.20 – 2.72mg/l sodium (Na), 0.03 – 1.32mg/l potassium (K); 0.88 – 5.88mg/l calcium (Ca); 0.13 – 3.1mg/l magnesium (Mg); 5.8 – 18.9mg/l iron (Fe); 0.04 – 1.1mg/l manganese (Mn); 0.02 – 0.09mg/l copper (Cu); 0.93 – 6.0mg/l zinc (Zn); 0.01 – 2.9mg/l lead (Pb); 0.01 – 0.18mg/l cadmium (Cd); 0.06 – 4.0mg/l chromium (Cr); 0.01 – 0.15mg/l nickel (Ni); 0.01 – 11mg/l vanadium (V). Air and water temperatures were mostly influenced by forest canopy cover. pH levels indicate that the water bodies within the forested wetland are slightly acidic. Higher DO values were recorded in the Arhakhuan Stream and Okomu River (Agekpukpu and Iron bridge) than in the temporary ponds. BOD levels of greater than 1mg/l were observed which is indicative of slight levels of organic pollution. Higher concentrations of TDS, TSS, turbidity, EC, Colour, HCO3, NH4N, NO2, NO3, P, Na, K, Ca Mg and heavy metals were recorded in the temporary ponds than in the Stream and River. Research on water bodies within wetlands should be carried out routinely in order to monitor changes in the water conditions that could occur overtime whether natural or anthropogenic. This becomes even more pertinent in the light of glaring impacts of climate change and increasing environmental modifications.

scholarly journals Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4499 ◽  
Author(s):  
Aisha Tahir ◽  
Fatma Hussain ◽  
Nisar Ahmed ◽  
Abdolbaset Ghorbani ◽  
Amer Jamil
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Species Level ◽  
Practical Implementation ◽  
Medicinal Species ◽  
Level Identification ◽  
Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

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