scholarly journals The true picture of environmental DNA, a case study on harvested fishponds

2021 ◽  
Vol 4 ◽  
Author(s):  
Petr Blabolil ◽  
Tomáš Jůza ◽  
Vladislav Draštík ◽  
Jelena Knežević-Jarić ◽  
Romulo dos Santos ◽  
...  
Keyword(s):  
Cyprinus Carpio ◽  
Dominant Species ◽  
Field Experiments ◽  
Site Occupancy ◽  
Environmental Dna ◽  
Single Species ◽  
Abundant Species ◽  
Ctenopharyngodon Idella ◽  
Predatory Fish ◽  
Pseudorasbora Parva

The applications of environmental DNA (eDNA) metabarcoding are constantly increasing. Many validation studies have been performed in laboratories, however, field experiments are necessary to verify the robustness of eDNA based monitoring. In summer and autumn 2019 water samples in 39 sites and an inflow across three ponds of sizes of approximately 3 (A), 10 (B) and 29 (C) hectares in the Czech Republic were collected. 500 ml from each sample was filtered through 0.45 µl membrane filters and extracted using the Mu-DNA water protocol. Uniquely indexed vertebrate primers aligning mitochondrial 12S ribosomal RNA gene were utilised for eDNA amplification. PCR negative and positive controls were included to each sublibrary. Sequence reads were analysed using metaBEAT pipeline. The sequences were assigned to species level with exception Perca fluviatilis and Sander lucioperca which could not be differentiated, further referred as Perca+Sander and used as a single species. At the end of autumn, ponds were harvested and 319,833 fish of 27,054 kg of 22 species were captured. The most abundant species was Gymnocephalus cernua (on average 34.8%) followed by Cyprinus carpio and Pseudorasbora parva. Cyprinus carpio was also the dominant species in biomass (on average 90.7%), followed by the Ctenopharyngodon idella and Esox Lucius. The total number of sequences across 240 eDNA samples was 35,627,310. 21,540,396 sequences remained after bioinformatic filtering with an average read count per sample of 68,111. All samples detected 1–6 species, except for summer pond B where 64% were negative. In total, more species were detected in autumn than summer in pond A 12/10 and pond B 9/2 and the same in pond C 11/11. The only species detected in all campaigns was Cyprinus carpio with the highest average reads count of 28,961. Ctenopharyngodon idella, Rutilus rutilus, and Scardinius erythrophthalmus were detected in all campaigns except the summer pond B samples. The site occupancy values were variable between ponds and seasons with exception of ubiquitous Cyprinus carpio. The numbers of detected species in inflows were higher in autumn compared to summer in pond A (7/5) and B (9/4) and identical in pond C (6/6). The detected species in inflows were mostly the same as species detected in ponds. Gobio gobio was the only detected species in all campaigns. Lota lota was detected in eDNA in summer and autumn only in inflow to pond A. In pond B Perca+Sander and in pond C Pseudorasbora parva were detected in eDNA inflow in both periods and in harvest, but not in eDNA in ponds. The percentage of shared species detected by eDNA and at pond harvests was >50% in all ponds. During the pond harvest 1, 5 and 4 species were captured not detected in ponds´ eDNA compared to 3, 0, and 2 species detected only in ponds´ eDNA in ponds A, B and C, respectively. Significant positive relationships were observed between fish read counts/species site occupancy and fish abundance/biomass with exception of data from pond B in autumn. This study highlights the importance of field experiments and methods validation. Dominant species detection is relatively straightforward; however, detection of rare species is more challenging depending on species behaviour, habitat complexity. It further supports that eDNA should be applied in optimal conditions to achieve highest overall detection, which has important implications for applying this method to aid management and policy initiatives. This study was supported by projects MSM200961901, “The true picture of eDNA”, QK1920011 ”Methodology of predatory fish quantification in drinking-water reservoirs to optimize the management of aquatic ecosystems”, and by CAS within the program of the Strategy AV 21.

Effect of extremely severe winters on under-ice phytoplankton development in a mesotrophic lake (Eastern Poland)

2014 ◽  
Vol 43 (2) ◽  
Author(s):  
Władysława Wojciechowska ◽  
Tomasz Lenard
Keyword(s):  
Water Column ◽  
Dominant Species ◽  
Biomass Concentration ◽  
Thermal Conditions ◽  
Ice Cover ◽  
Abundant Species ◽  
Blue Green Algae ◽  
Cyanobacteria And Algae ◽  
Taxonomic Groups ◽  
The Vertical Distribution

AbstractThe research was carried out in a mesotrophic and dimictic lake during winters with ice cover. In the last forty years, the development of phytoplankton was analyzed in five extreme winter seasons. The studies of phytoplankton characteristics in the water column took into account values of biomass, concentration of chlorophyll-a and species composition, including dominant species. Differences in the vertical distribution of flagellate and non-flagellate species belonging to cyanobacteria and algae were analyzed in the gradient of light and thermal conditions. The phytoplankton biomass was low and vertically differentiated, with the lowest values at the deeper part of the water column. Flagellate species from the group of Cryptophyceae, Chrysophyceae and Dinophyceae were most abundant. Species biodiversity was low but every winter the dominant species represented different taxonomic groups. In some periods, larger non-motile phytoplankton species from green or blue-green algae dominated. The research proved that the development of phytoplankton under the ice cover was limited mainly by light and, to a lesser extent, by temperature.

scholarly journals Airborne environmental DNA metabarcoding detects more diversity, with less sampling effort, than a traditional plant community survey

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mark D. Johnson ◽  
Mohamed Fokar ◽  
Robert D. Cox ◽  
Matthew A. Barnes
Keyword(s):  
Plant Community ◽  
Plant Communities ◽  
Traditional Method ◽  
Environmental Dna ◽  
Single Species ◽  
Community Survey ◽  
Sampling Effort ◽  
Sampling Campaign ◽  
Dna Metabarcoding ◽  
Human Health Impacts

Abstract Background Airborne environmental DNA (eDNA) research is an emerging field that focuses on the detection of species from their genetic remnants in the air. The majority of studies into airborne eDNA of plants has until now either focused on single species detection, specifically only pollen, or human health impacts, with no previous studies surveying an entire plant community through metabarcoding. We therefore conducted an airborne eDNA metabarcoding survey and compared the results to a traditional plant community survey. Results Over the course of a year, we conducted two traditional transect-based visual plant surveys alongside an airborne eDNA sampling campaign on a short-grass rangeland. We found that airborne eDNA detected more species than the traditional surveying method, although the types of species detected varied based on the method used. Airborne eDNA detected more grasses and forbs with less showy flowers, while the traditional method detected fewer grasses but also detected rarer forbs with large showy flowers. Additionally, we found the airborne eDNA metabarcoding survey required less sampling effort in terms of the time needed to conduct a survey and was able to detect more invasive species than the traditional method. Conclusions Overall, we have demonstrated that airborne eDNA can act as a sensitive and efficient plant community surveying method. Airborne eDNA surveillance has the potential to revolutionize the way plant communities are monitored in general, track changes in plant communities due to climate change and disturbances, and assist with the monitoring of invasive and endangered species.

scholarly journals Checklist of Aquatic Oligochaetes Species in Tigris–Euphrates River basin

2014 ◽  
Vol 11 (3) ◽  
pp. 1397-1404 ◽  
Author(s):  
Baghdad Science Journal
Keyword(s):  
Single Species ◽  
Abundant Species ◽  
Tubifex Tubifex ◽  
Euphrates River ◽  
Tigris River ◽  
Limnodrilus Hoffmeisteri ◽  
Frequent Species ◽  
Aquatic Oligochaetes ◽  
Stylaria Lacustris ◽  
Tubificid Worms

A total of 60 species of aquatic oligochaetes were identified in different sites within Tigris-Euphrates basin / Iraq, including River Tigris, River Euphrates, Southern marshes ( Al-Haweiza , Al-Hammar and Al-Chebaiesh ) , Shutt Al-Germa, and Shatt Al-Arab. In River Euphrates 39 species were identified, 40 species from River Tigris and 32 species from Shatt-Al-Arab and southern marshes.The identified species were classified as four species of Family Aeolosomatidae, 54 species of Naididae ( 31 Naidinae , 8 Pristininae and 15 Tubificid worms), one species of each of Lumbriculidae ( Lumbriculus variegates ) and Lumbricidae ( Eiseiella tetraedra). Among Aeolosomatidae , Aelosoma aquaternarium, A. Liedyi, A. variegatum and A. hemprichi, in which, A. variegatum was the most frequent species, found in Euphrates river. Naidinae community were represented by five species of genus Chaetogaster, two species of each of Paranais, Slavina, & Stylaria, four species of Allonais , and seven species of each of Dero and Nais, in addition to Stephensoniana trivandrana, Specaria josinae and Ophidonais serpentina. Nais variabilis was the most abundant and frequent species in River Tigris while Stylaria lacustris & Ophidonais serpentina are abundant in River Euphrates . Species of Pristininae were representative by four species of genus Pristina and three species of genus pristinella, among them Priatina longiseta is the most abundant species.Tubificid worms, Branchuira sowerbyi and Limnodrilus hoffmeisteri were the most frequent and abundant species in the surface sediments of Iraqi waters. Beside L. hoffmeisteri , other five species of Limnodrilus, two species of Potomothrix, and a single species of Tubifex tubifex , Embolocephalus velutinus, Aulodrilus piguetia, Psammoryctides moravicus and Rhyacodrilus coccineus were recorded.

scholarly journals Factors affecting the herbage iodine content.

1974 ◽  
Vol 22 (3) ◽  
pp. 195-206 ◽  
Author(s):  
J. Hartmans
Keyword(s):  
Soil Type ◽  
Dry Matter ◽  
Field Experiments ◽  
Iodine Content ◽  
Single Species ◽  
Residual Effects ◽  
Grass Species ◽  
Yield Response ◽  
N Application ◽  
Factors Affecting

In pot and field experiments, N application somewhat increased the I content of the harvested crop, although I concentrations in the herbage decreased considerably (diluting effect of increased dry matter yields). Herbage I contents were not consistently affected by chemical fertilizers which produced no yield response. I contents were up to 13 times higher in dicotyledenous pasture species than in grasses. I contents varied between grass species and to less extent between varieties of a single species. Contrary to earlier New Zealand data, good quality grasses were lower in I content than medium-value and inferior grasses. Small I dressings were less effective than larger amounts in terms of percentage return in the harvested crop; residual effects in later cuts were always small. The effectiveness of I dressings depended on soil type and tended to be lowest on soils of low natural I content. ADDITIONAL ABSTRACT: Studies were with ryegrass in pots and pastures. N dressing increased I uptake by the crop but reduced the I content considerably because of the diluting effect of higher DM yields. Dressing with fertilizers which did increase yield did not affect herbage I content consistently. Dicotyledonous species in pasture had I contents up to 13 times that of grasses. The I content of grasses varied over a 2-fold range but variation was smaller in a given species. Good quality grasses had a lower I content than inferior grasses. Smaller I dressings gave a smaller percentage return in the crop than larger amounts; the efficiency depended on soil type and tended to be less for soils with the lowest natural I content. (Abstract retrieved from CAB Abstracts by CABI’s permission)

scholarly journals Acetylcholinesterase enzyme activity in carp brain and muscle after acute exposure to diafuran

2008 ◽  
Vol 65 (4) ◽  
pp. 340-345 ◽  
Author(s):  
Jaqueline Ineu Golombieski ◽  
Enio Marchesan ◽  
Edinalvo Rabaioli Camargo ◽  
Joseânia Salbego ◽  
Joele Schmitt Baumart ◽  
...  
Keyword(s):  
Common Carp ◽  
Cyprinus Carpio ◽  
Grass Carp ◽  
Ache Activity ◽  
Bighead Carp ◽  
Ctenopharyngodon Idella ◽  
Control Treatment ◽  
Aristichthys Nobilis ◽  
Early Biomarker ◽  
The Common

Sublethal adverse effects may result from exposure of aquatic organisms to insecticides at environmentally relevant concentrations. Fingerlings of the common carp (Cyprinus carpio, Linnaeus, 1758), grass carp (Ctenopharyngodon idella, Valenciennes, 1844), and bighead carp (Aristichthys nobilis, Richardson, 1845) were exposed to diafuran, an insecticide widely used during rice cultivation in Southern Brazil. The aim of this study was to verify the relationship between the lethal concentration (LC50) of diafuran and the acetylcholinesterase (AChE) activity in brain and muscle tissues of these species as a possible early biomarker of exposure to this insecticide. LC50 was determined for fish exposed to diafuran concentrations during 96 h (short term): common carp: control, 0.5, 1.0, 1.5, 2.0, 2.5 and 3.0 mg L-1; grass carp: control, 1.0, 2.0, 3.0 and 3.5 mg L-1 and, bighead carp: control, 0.5, 1.0, 1.5, 2.0, 3.0 and 4.0 mg L-1, as well as the determination of AChE at concentrations near LC50 for these species. LC50 values (nominal concentrations) were 1.81 mg L-1 for the common carp, 2.71 mg L-1 for the grass carp and, 2.37 mg L-1 for the bighead carp. All carps exposed to diafuran were lethargic (lower concentrations) or immobile. Diafuran inhibited the acetylcholinesterase activity in brain (~38%) and muscle (~50%) of all species. Muscle of bighead carp under control treatment showed higher specific AChE activity than brain (14.44 against 5.94 µmol min-1 g protein-1, respectively). Concentrations of diafuran used for rice cropping may affect Cyprinus carpio, Ctenopharyngodon idella and Aristichthys nobilis behaviors and the AChE activities in brain and muscle of these species may be an early biomarker of toxicity of this insecticide.

scholarly journals Fish assemblages in a tidal flat

2003 ◽  
Vol 46 (2) ◽  
pp. 233-242 ◽  
Author(s):  
Ana Lúcia Vendel ◽  
Sabine Granado Lopes ◽  
César Santos ◽  
Henry Louis Spach
Keyword(s):  
Cluster Analysis ◽  
Community Structure ◽  
Tidal Flat ◽  
Seasonal Changes ◽  
Dominant Species ◽  
Fish Assemblages ◽  
Seasonal Pattern ◽  
Abundant Species ◽  
Structure Index ◽  
Total Capture

Studies were carried out on fish assemblages in a tidal flat. Samples were obtained monthly at low tide of the half moon in the tidal flat of Paranaguá Bay, Brazil, with two seine nets, one with a 1 mm mesh, 30 m in length and 3 m in height and another with a 10 mm mesh, 65 m in length and 2 m in height. A total of 8,890 fish were captured, comprising 24 families and 53 species. The most abundant species were Harengula clupeola and Atherinella brasiliensis, which represented 63.4% of the total, capture. A seasonal tendency was observed in the abundance of fishes, with less fishes being captured during winter and part of spring. The number of species showed a seasonal pattern, with the gradual decrease through winter and a marked increase in summer. The community structure index indicated seasonal changes in the assemblage. The faunistic similarities between months separated the 12 months into four major groups. The seasonal pattern was apparent in the numerically dominant species and the Cluster Analysis revealed five main groups.

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