scholarly journals The composition of fish species shows little seasonal variation in eDNA based survey at urban streams

2021 ◽  
Vol 4 ◽  
Author(s):  
Yujin Kang ◽  
Youngkeun Song
Keyword(s):  
Invasive Species ◽  
Fish Species ◽  
Survey Methods ◽  
Environmental Dna ◽  
Urban Streams ◽  
Community Structures ◽  
Survey Period ◽  
Monsoon Period ◽  
Significant Difference ◽  
Tachysurus Fulvidraco

Biodiversity in the city is becoming important as cities are expanded. Thus, the cost-efficient and accurate methodology for the investigation of biota has been consistently demanded. Environmental DNA (eDNA) is one of the emerging tools to supplement traditional survey methods and improve the efficiency of the survey. Summer (from July to August) is the monsoon period in South Korea, so it is excluded from the survey period because of the unstable aquatic environment, the safety of investigators, and accessibility to study sites. On the other hand, spring and autumn (from March to October), excluding the flooding season, are considered suitable times for the survey. This study compared fish composition and distribution by season in summer and autumn using eDNA to identify the change of fish composition and determine the suitability of the eDNA survey for seasonal fish investigation at urban streams. The number of eDNA reads, fish composition, and their community structures was changed according to the season. The total eDNA read was 2.3 times more in October (1,419,062) than in July (3,202,626). In addition, compared to the summer when 13 families and 33 species were detected, 13 families and 35 species were detected in fall. A total of 13 families and 32 species were detected in common. Three species (Acheilognathus rhombeus, Tachysurus fulvidraco, Pungtungia herzi) more were identified, and one (Hemiculter leucisculus) was not detected in October. The result described that the distribution rate of fish species has changed in the study area. Especially, the appearance of invasive species increased from 14 to 20 sites and the habitat range of invasive species was extended in October than July. However, there was no significant difference in richness and diversity except for abundance among fish community structures. This result revealed that eDNA survey methods can identify changes in the composition and distribution of fish by season. Furthermore, based on the little fluctuation in the species appearing according to the season, the study suggested that eDNA can be used to complement traditional survey methods by conducting fish surveys regardless of the survey period.

scholarly journals MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

2015 ◽  
Vol 2 (7) ◽  
pp. 150088 ◽  
Author(s):  
M. Miya ◽  
Y. Sato ◽  
T. Fukunaga ◽  
T. Sado ◽  
J. Y. Poulsen ◽  
...  
Keyword(s):  
Fish Species ◽  
Survey Methods ◽  
Hypervariable Region ◽  
Environmental Dna ◽  
Pcr Primers ◽  
12S Rrna ◽  
Rrna Gene ◽  
Sufficient Information ◽  
Diverse Range ◽  
Spatial And Temporal Scales

We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.

scholarly journals Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout

2020 ◽  
Vol 8 ◽  
Author(s):  
Akio Imamura ◽  
Kana Hayami ◽  
Masayuki Sakata ◽  
Toshifumi Minamoto
Keyword(s):  
Invasive Species ◽  
Species Richness ◽  
Rainbow Trout ◽  
Fish Species ◽  
Seasonal Changes ◽  
Fish Community ◽  
Environmental Dna ◽  
Native Fish ◽  
Native Salmonids ◽  
Hokkaido Island

In freshwater ecosystems, invasive salmonid fishes can have a significant impact on native fish species. Detecting the invasion and its negative effects is critical for the conservation of native fish communities. We examined the species composition and seasonal changes in the freshwater fish community, including salmonids, on the Kamikawa Plain, Hokkaido Island, Japan, using environmental DNA (eDNA) metabarcoding. We detected 23 fish species in 176 samples collected from 16 sites over 12 months (October 2018 – August 2019). Between 11 and 20 species were detected at each site, including five native salmonids (Oncorhynchus masou, Oncorhynchus keta, Parahucho perryi, Salvelinus leucomaenis leucomaenis and Salvelinus malma krascheninnikova). The invasive alien rainbow trout Oncorhynchus mykiss was detected at all 16 sites and it was the most commonly detected salmonid. Although we found no obvious competitive exclusion of native salmonids by rainbow trout in the study area, the invasive species occurred more often and at more sites than any of the natives. We also determined the occurrence and seasonal changes in the fish community, classified as native salmonids, invasive rainbow trout, Cypriniformes and other benthic fishes. There were fewer species overall in winter, but the sites with higher species richness in winter were on the lower reaches of the river. In addition, we detected domestic invaders, such as the topmouth gudgeon, Pseudorasbora parva, although they were less prevalent than rainbow trout. These results show the effectiveness of eDNA metabarcoding, which can be used for surveying species richness at an ecosystem scale. In particular, the detection of the early stages of establishment and spread of invasive species can be achieved by eDNA monitoring.

scholarly journals Environmental DNA and Specific Primers for Detecting the Invasive Species Ectopleura crocea (Hydrozoa: Anthoathecata) in Seawater Samples

2020 ◽  
Vol 12 (6) ◽  
pp. 2360 ◽  
Author(s):  
Philjae Kim ◽  
Tae Joong Yoon ◽  
Sook Shin
Keyword(s):  
Invasive Species ◽  
Survey Methods ◽  
Environmental Dna ◽  
Visual Assessment ◽  
Molecular Techniques ◽  
Mitochondrial Cytochrome ◽  
Specific Primer ◽  
Specific Primers ◽  
Seawater Samples ◽  
Species Specific

In marine environments, environmental DNA (eDNA) can be effectively detected and possibly quantified when combined with molecular techniques, as demonstrated by several recent studies. In this study, we developed a species-specific primer set and a probe to detect the distribution and biomass of an invasive hydrozoan in South Korea, Ectopleura crocea. These molecular markers were designed to amplify a 187 bp region based on mitochondrial cytochrome c oxidase subunit I (COI) of E. crocea and were tested on seawater samples from 35 Korean harbors in 2017. Of the 35 sites we investigated, only nine harbors returned positive detections when using traditional survey methods, while surveys based on the use of eDNA techniques detected E. crocea DNA in all seawater samples. These results suggest that eDNA surveys based on molecular techniques are more effective at identifying species distribution and estimating biomass than traditional surveys based on visual assessment of morphology.

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 Quantification of Environmental DNA (eDNA) shedding and decay rates for three commercially harvested fish species and comparison between eDNA detection and trawl catches

2021 ◽  
Author(s):  
Anish Kirtane ◽  
Daniel Wieczorek ◽  
Thomas Noji ◽  
Liza Baskin ◽  
Claire Ober ◽  
...  
Keyword(s):  
Fish Species ◽  
Environmental Dna ◽  
Decay Rates ◽  
Trawl Catches

Proximate composition of male and female African catfish (Clarias gariepinus) and tilapia (Tilapia zilli) in Jega river, Kebbi state, Nigeria

2020 ◽  
Vol 01 (02) ◽  
pp. 28-35
Author(s):  
W. M. Namaga ◽  
B. Yahaya ◽  
M. A. Salam
Keyword(s):  
Protein Content ◽  
Fish Species ◽  
Lipid Content ◽  
Proximate Composition ◽  
Clarias Gariepinus ◽  
Fibre Content ◽  
African Catfish ◽  
Male And Female ◽  
Juvenile Female ◽  
Significant Difference

Fish is highly nutritious, tasty, and easily digestible. It is much sought after by a broad cross-section of the world’s population, particularly in developing countries as it provides the cheapest protein source. Nigeria is blessed with numerous inland freshwater rivers and lakes scattered all over the country. This freshwater habitat consists of many species of fish that have successfully dominated all niches over time and have for many reasons remained unstudied. The situation concealed a lot of scientific information particularly on food security and safety to the inmates and the country at large. Jega River which transcended many States in the North-Western part of Nigeria to open into the river Niger is one of such rivers largely uncared for, study-wise. African catfish (Clarias gariepinus) and Tilapia (Tilapia zillii) have been wisely selected for the present proximate composition studies. The juveniles of these fishes were purchased from local fishermen in Mariner Waje landing site of the river which flows by Jega town, a local government area in Kebbi State, Nigeria. For the study, the methodology approved by the Association of Official Analytical Chemists (AOAC) was used to determine the proximate composition of the fishes. The highest percentage crude protein content of 49.18 ± 0.30% was observed in juvenile female C. gariepinus; while the lowest protein content of 39.22± 0.50% was observed in juvenile male T. zilli. The highest percentage lipid content of 11.75± 1.50% was observed in juvenile female tilapia; while the lowest percentage lipid content of 6.25± 0.29% was observed in male African catfish. The highest percentage fibre content of 4.00 ± 0.29% was observed in male and female C. gariepinus, while the lowest percentage fibre content of 0.75± 0.29% was observed in male tilapia. There were variations (p< 0.05) when the protein and lipid contents of both the species were compared with each other. There was also a significant difference (p< 0.05) when the carbohydrate contents were compared between the fish species, but there was no significant difference (p > 0.05) when the fibre content was compared within the species. The analyses showed that both the male and female fish species studied had high protein contents.

scholarly journals Using redundant primer sets to detect multiple native Alaskan fish species from environmental DNA

2018 ◽  
Vol 12 (1) ◽  
pp. 109-123 ◽  
Author(s):  
Damian Menning ◽  
Trey Simmons ◽  
Sandra Talbot
Keyword(s):  
Fish Species ◽  
Environmental Dna ◽  
Primer Sets ◽  
Native Alaskan

scholarly journals Effect of land-use types on the ecomorphological structure of fish assemblage in distinct mesohabitats of neotropical streams

2021 ◽  
Vol 21 (3) ◽  
Author(s):  
Leonardo Antunes Pessoa ◽  
Matheus Tenório Baumgartner ◽  
Marcelo Percilio Santana Junior ◽  
João Paulo Alves Pagotto ◽  
Luiz Gustavo Antunes Pessoa ◽  
...  
Keyword(s):  
Land Use ◽  
Urban Environment ◽  
Fish Species ◽  
Fish Assemblage ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Canopy Cover ◽  
Distinct Species ◽  
Urban Streams ◽  
Land Use Types

Abstract The use and occupation of land by human population substantially influence environmental variables and fish assemblage in streams. However, there is little knowledge on how these changes affect the ecomorphological structure of fish assemblage in mesohabitats. Therefore, we aim to assess whether the land-use types affect the ecomorphological structure of fish assemblage in distinct mesohabitats. Environmental and ichthyofaunistic data were collected in three mesohabitats (rifles, runs, and pools) of five rural and five urban streams. Twenty-one ecomorphological indices were obtained from the mean of linear morphological measurements and areas of the fishes. Subsequently, the Euclidean distance was calculated, based on the ecomorphological indices, between each pair of species, to measure the ecomorphological distances for the mesohabitats of the rural and urban streams. The results show that the urban environment is more harmful to streams than the rural one, due to changes in the environmental variables and decrease in species richness. The main environmental changes found in urban streams were the decrease in canopy cover by riparian vegetation and dissolved oxygen, and the increase in electrical conductivity and bed silting. Also, there was a significant decrease in the morphological similarity between fish species in the mesohabitats of urban streams compared to rural ones. Therefore, we can conclude that the urban environment leads to the loss of morphologically similar fish species in the mesohabitats, with only a few functionally distinct species remaining.

scholarly journals Use of environmental DNA (eDNA) in streams to detect feral swine (Sus scrofa)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8287
Author(s):  
Amberly N. Hauger ◽  
Karmen M. Hollis-Etter ◽  
Dwayne R. Etter ◽  
Gary J. Roloff ◽  
Andrew R. Mahon
Keyword(s):  
Invasive Species ◽  
Water Temperature ◽  
Linear Model ◽  
Detection Probability ◽  
Generalized Linear Model ◽  
Environmental Dna ◽  
The United States ◽  
Stream Data ◽  
Feral Swine ◽  
Animal Populations

Invasive feral swine can damage ecosystems, disrupt plant and animal populations, and transmit diseases. Monitoring of feral swine populations requires expensive and labor-intensive techniques such as aerial surveys, field surveys for sign, trail cameras, and verifying landowner reports. Environmental DNA (eDNA) provides an alternative method for locating feral swine. To aid in detection of this harmful invasive species, a novel assay was developed incorporating molecular methods. From August 2017 to April 2018, water samples and stream data were collected along 400 m transects in two different stream types where swine DNA was artificially introduced to investigate potential factors affecting detection. A generalized linear model (family binomial) was used to characterize environmental conditions affecting swine DNA detection; detection was the dependent variable and stream measurements included stream type, distance downstream, water temperature, velocity, turbidity, discharge, and pH as independent variables. Parameters from the generalized linear model were deemed significant if 95% confidence intervals did not overlap 0. Detection probability for swine DNA negatively related to water temperature (β =  − 0.21, 95% CI [−0.35 to −0.09]), with the highest detection probability (0.80) at 0 °C and lowest detection probability (0.05) at 17.9 °C water temperature. Results indicate that sampling for swine eDNA in free-flowing stream systems should occur at lower water temperatures to maximize detection probability. This study provides a foundation for further development of field and sampling techniques for utilizing eDNA as a viable alternative to monitoring a terrestrial invasive species in northern regions of the United States.

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