scholarly journals Lateral and longitudinal fish eDNA distribution in dynamic riverine habitats

2020 ◽  
Author(s):  
Bettina Thalinger ◽  
Dominik Kirschner ◽  
Yannick Pütz ◽  
Christian Moritz ◽  
Richard Schwarzenberger ◽  
...  
Keyword(s):  
Fish Species ◽  
Environmental Dna ◽  
Fold Increase ◽  
Species Traits ◽  
Diurnal Changes ◽  
Sampling Schemes ◽  
Hydrological Conditions ◽  
Cyprinid Species ◽  
The Status ◽  
Species Specific

AbstractAssessing the status and distribution of fish populations in rivers is essential for management and conservation efforts in these dynamic habitats. Currently, methods detecting environmental DNA (eDNA) are being established as an alternative and/or complementary approach to the traditional monitoring of fish species. In lotic systems, a sound understanding of hydrological conditions and their influence on the local target detection probability and DNA quantity is key for the interpretation of eDNA-based results. However, the effect of seasonal and diurnal changes in discharge and the comparability of semi-quantitative results between species remain hardly addressed. We conducted a cage experiment with four fish species (three salmonid and one cyprinid species) in a glacier-fed, fish-free river in Tyrol (Austria) during summer, fall, and winter discharge situations (i.e. 25-fold increase from winter to summer). Each season, water samples were obtained on three consecutive days at 13 locations downstream of the cages including lateral sampling every 1-2 m across the wetted width. Fish eDNA was quantified by species-specific endpoint PCR followed by capillary electrophoresis. Close to the cages, lateral eDNA distribution was heterogenous and mirrored cage placement within the stream. In addition to the diluting effect of increased discharge, longitudinal signal changes within the first 20 m were weakest at high discharge. For downstream locations with laterally homogenous eDNA distribution, the signals decreased significantly with increasing distance and discharge. Generally, the eDNA of the larger-bodied salmonid species was less frequently detected, and signal strengths were lower compared to the cyprinid species. This study exemplifies the importance of hydrological conditions for the interpretation of eDNA-based data across seasons. To control for heterogenous eDNA distribution and enable comparisons over time, sampling schemes in lotic habitats need to incorporate hydrological conditions and species traits.

scholarly journals GoFish: A Streamlined Environmental DNA Presence/Absence Assay for Marine Vertebrates

2018 ◽  
Author(s):  
Mark Y. Stoeckle ◽  
Mithun Das Mishu ◽  
Zachary Charlop-Powers
Keyword(s):  
New York ◽  
Fish Species ◽  
River Estuary ◽  
Environmental Dna ◽  
Hudson River ◽  
Illumina Miseq ◽  
Turnaround Time ◽  
Seasonal Abundance ◽  
Thermal Cycler ◽  
Species Specific

AbstractHere we describe GoFish, a streamlined environmental DNA (eDNA) presence/absence assay. The assay amplifies a 12S segment with broad-range vertebrate primers, followed by nested PCR with M13-tailed, species-specific primers. Sanger sequencing confirms positives detected by gel electrophoresis. We first obtained 12S sequences from 77 fish specimens representing 36 northwestern Atlantic taxa not well documented in GenBank. Using the newly obtained and published 12S records, we designed GoFish assays for 11 bony fish species common in the lower Hudson River estuary and tested seasonal abundance and habitat preference at two sites. Additional assays detected nine cartilaginous fish species and a marine mammal, bottlenose dolphin, in southern New York Bight. GoFish sensitivity was equivalent to Illumina MiSeq metabarcoding. Unlike quantitative PCR (qPCR), GoFish does not require tissues of target and related species for assay development and a basic thermal cycler is sufficient. Unlike Illumina metabarcoding, indexing and batching samples are unnecessary and advanced bioinformatics expertise is not needed. The assay can be carried out from water collection to result in three days. The main limitations so far are species with shared target sequences and inconsistent amplification of rarer eDNAs. We think this approach will be a useful addition to current eDNA methods when analyzing presence/absence of known species, when turnaround time is important, and in educational settings.

scholarly journals The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

2021 ◽  
Vol 9 ◽  
Author(s):  
Bettina Thalinger ◽  
Andreas Rieder ◽  
Anna Teuffenbach ◽  
Yannick Pütz ◽  
Thorsten Schwerte ◽  
...  
Keyword(s):  
Water Samples ◽  
Energy Use ◽  
Environmental Dna ◽  
Species Traits ◽  
Digital Pcr ◽  
Intermittent Flow ◽  
Species Identity ◽  
Surrounding Water ◽  
Species Specific ◽  
And Behavior

The quantitative measurement of environmental DNA (eDNA) from field-collected water samples is gaining importance for the monitoring of fish communities and populations. The interpretation of these signal strengths depends, among other factors, on the amount of target eDNA shed into the water. However, shedding rates are presumably associated with species-specific traits such as physiology and behavior. Although such differences between juvenile and adult fish have been previously detected, the general impact of movement and energy use in a resting state on eDNA release into the surrounding water remains hardly addressed. In an aquarium experiment, we compared eDNA shedding between seven fish species occurring in European freshwaters. The investigated salmonids, cyprinids, and sculpin exhibit distinct adaptions to microhabitats, diets, and either solitary or schooling behavior. The fish were housed in aquaria with constant water flow and their activity was measured by snapshots taken every 30 s. Water samples for eDNA analysis were taken every 3 h and energy use was determined in an intermittent flow respirometer. After controlling for the effect of fish mass, our results demonstrate a positive correlation between target eDNA quantities as measured with digital PCR, fish activity, and energy use, as well as species-specific differences. For cyprinids, the model based on data from individual fish was only partly transferable to groups, which showed lower activity and higher energy use. Our findings highlight the importance of fish physiology and behavior for the comparative interpretation of taxon-specific eDNA quantities. Species traits should therefore be incorporated into eDNA-based monitoring and conservation efforts.

scholarly journals Simultaneous absolute quantification and sequencing of fish environmental DNA in a mesocosm by quantitative sequencing technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tatsuhiko Hoshino ◽  
Ryohei Nakao ◽  
Hideyuki Doi ◽  
Toshifumi Minamoto
Keyword(s):  
Fish Species ◽  
High Throughput Sequencing ◽  
Correlation Coefficients ◽  
Environmental Dna ◽  
Digital Pcr ◽  
Absolute Quantification ◽  
Taqman Probe ◽  
Individual Species ◽  
Natural Environments ◽  
Target Sequence

AbstractThe combination of high-throughput sequencing technology and environmental DNA (eDNA) analysis has the potential to be a powerful tool for comprehensive, non-invasive monitoring of species in the environment. To understand the correlation between the abundance of eDNA and that of species in natural environments, we have to obtain quantitative eDNA data, usually via individual assays for each species. The recently developed quantitative sequencing (qSeq) technique enables simultaneous phylogenetic identification and quantification of individual species by counting random tags added to the 5′ end of the target sequence during the first DNA synthesis. Here, we applied qSeq to eDNA analysis to test its effectiveness in biodiversity monitoring. eDNA was extracted from water samples taken over 4 days from aquaria containing five fish species (Hemigrammocypris neglectus, Candidia temminckii, Oryzias latipes, Rhinogobius flumineus, and Misgurnus anguillicaudatus), and quantified by qSeq and microfluidic digital PCR (dPCR) using a TaqMan probe. The eDNA abundance quantified by qSeq was consistent with that quantified by dPCR for each fish species at each sampling time. The correlation coefficients between qSeq and dPCR were 0.643, 0.859, and 0.786 for H. neglectus, O. latipes, and M. anguillicaudatus, respectively, indicating that qSeq accurately quantifies fish eDNA.

scholarly journals Advancing improvement in riverine water quality caused a non-native fish species invasion and native fish fauna recovery

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Łukasz Głowacki ◽  
Andrzej Kruk ◽  
Tadeusz Penczak
Keyword(s):  
Water Quality ◽  
Fish Species ◽  
Native Species ◽  
Interference Competition ◽  
Fish Fauna ◽  
Species Traits ◽  
Native Fish ◽  
Biological Degradation ◽  
Species Invasion ◽  
Prussian Carp

AbstractThe knowledge of biotic and abiotic drivers that put non-native invasive fishes at a disadvantage to native ones is necessary for suppressing invasions, but the knowledge is scarce, particularly when abiotic changes are fast. In this study, we increased this knowledge by an analysis of the biomass of most harmful Prussian carp Carassius gibelio in a river reviving from biological degradation. The species' invasion followed by the invasion's reversal occurred over only two decades and were documented by frequent monitoring of fish biomass and water quality. An initial moderate improvement in water quality was an environmental filter that enabled Prussian carp’s invasion but prevented the expansion of other species. A later substantial improvement stimulated native species’ colonization of the river, and made one rheophil, ide Leuciscus idus, a significant Prussian carp’s replacer. The redundancy analysis (RDA) of the dependence of changes in the biomass of fish species on water quality factors indicated that Prussian carp and ide responded in a significantly opposite way to changes in water quality in the river over the study period. However, the dependence of Prussian carp biomass on ide biomass, as indicated by regression analysis and analysis of species traits, suggests that the ecomorphological similarity of both species might have produced interference competition that contributed to Prussian carp’s decline.

​Discrimination of Five Gobid Species (Family: Gobiidae) based on Otolith Morphometry

2021 ◽  
Author(s):  
Vikas Pathak ◽  
Rinchen N. Bhutia ◽  
Shashi Bhushan ◽  
Geetanjali Deshmukhe ◽  
A.K. Jaiswar
Keyword(s):  
Fish Species ◽  
Discriminant Function Analysis ◽  
Function Analysis ◽  
Allometric Growth ◽  
Fish Size ◽  
Sagittal Otolith ◽  
Shape Indices ◽  
Glossogobius Giuris ◽  
Species Specific ◽  
Boleophthalmus Dussumieri

Background: The fishes of family Gobiidae are one of the least studied fishes, especially for otolith structure. The otoliths were possess species specific features. Hence, traits of sagittal otolith of gobid species studied. Methods: Five gobid species Odontamblyopus roseus (Valenciennes, 1837), Trypauchen vagina (Bloch and Schneider, 1801), Glossogobius giuris (Hamilton, 1822), Parachaeturichthys polynema (Bleeker, 1853) and Boleophthalmus dussumieri (Valenciennes, 1837) were investigated by three methods including morphological, shape indices and step wise discriminant function analysis (SDFA). Result: Interrelationship between shape indices investigated, at 95% level of confidence (P less than 0.05), revealed that perimeter of P. polynema and area of T. vagina have isometric growth with their length (b = 3.0071, 2.90, respectively) and otolith area of B. dussumieri have positive allometric growth (b = 4.23077). SDFA, based on otolith morphometry, discriminated species up with 97.18% accuracy. Hence, the results of present investigation can be used for discrimination of the species and as a tool in predicting fish size from the otoliths and in calculating the biomass of these less studied fish species.

scholarly journals Individual Serum Triiodothyronine and Thyroxine Levels in Seven Freshwater Fish Species

2021 ◽  
Vol 23 (1) ◽  
pp. 59-66
Author(s):  
Alexander Atanasoff ◽  
Dimitrinka Zapryanova ◽  
Cigdem Urku ◽  
Galin Nikolov
Keyword(s):  
Serum Concentration ◽  
Thyroid Hormones ◽  
Fresh Water ◽  
Fish Species ◽  
Reference Intervals ◽  
Specific Reference ◽  
Fresh Water Fish ◽  
Water Fish ◽  
Total Thyroxine ◽  
Species Specific

Abstract The thyroid hormones (THs) play an important role in the regulation of the rate of metabolism, affect the growth and function of different systems in the organism. The aim of this study was to assess serum concentration of total triiodothyronine (T3), total thyroxine (T4) as well as T3/T4 ratio in serum from healthy fresh water fish from Salmonidae, Acipenseridae, Cyprinidae, and Clariidae families to determine species-specific reference intervals. Mean concentrations of T3 and T4 levels varied significantly among fish. Finally, the test results show clear differences in the serum concentration of the T3 and T4 and give new insight into the thyroid hormones reference values in some commercial fresh water fish species.

scholarly journals Development of species-specific Cichla species eDNA primers for alien invasive species (AIS) monitoring in Malaysia

2021 ◽  
Vol 4 ◽  
Author(s):  
O. Nurul Fizatul Nabilah ◽  
A. R. Ramizah ◽  
A. B. Adibah ◽  
S. Syazwan ◽  
A.G. Intan Faraha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Environmental Dna ◽  
Coi Gene ◽  
Alien Invasive Species ◽  
Survey Method ◽  
Specific Primers ◽  
Invasive Fishes ◽  
Specific Amplification ◽  
Species Specific ◽  
High Level

Peacock bass or the cichlids are known locally as top predator fishes which are invasive in Malaysia freshwater system. Detection probabilities for these fishes are typically low, especially using conventional capture-survey method due to the fish’s behaviour of hiding beneath the water’s surface. Hence, the environmental DNA (eDNA) monitoring is a relatively new approach that can be used to assess the distribution of these invasive fishes. Here, we report the strategy to develop small fragment (280- 400 bp) specific-specific primers for three selected invasive Cichla species namely, C. ocellaris, C. monoculus, and C. kelberi based on mitochondrial DNA (mtDNA) sequences. Current research showed that the developed species-specific primers from cytochrome oxidase I (COI) gene has high resolution at species level. Species-specific amplification tests also proved the specificity of the developed primers, securing the high- level species identification potential which may help in controlling the spread of alien invasive fish species.

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