scholarly journals Using eDNA to biomonitor the fish community in a tropical oligotrophic lake

2018 ◽  
Author(s):  
Martha Valdez-Moreno ◽  
Natalia V. Ivanova ◽  
Manuel Elías-Gutiérrez ◽  
Stephanie L. Pedersen ◽  
Kyrylo Bessonov ◽  
...  
Keyword(s):  
Aquatic Ecosystems ◽  
Fish Community ◽  
Fish Fauna ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Coi Gene ◽  
Ion Torrent ◽  
Sequence Database ◽  
Ion Torrent Pgm ◽  
Invasive Fishes

AbstractEnvironmental DNA (eDNA) is an effective approach for detecting vertebrates and plants, especially in aquatic ecosystems, but prior studies have largely examined eDNA in cool temperate settings. By contrast, this study employs eDNA to survey the fish fauna in tropical Lake Bacalar (Mexico) with the additional goal of assessing the possible presence of invasive fishes, such as Amazon sailfin catfish. Sediment and water samples were collected from eight stations in Lake Bacalar on three occasions over a 4-month interval. Each sample was stored in the presence or absence of lysis buffer to compare eDNA recovery. Short fragments (184-187 bp) of the cytochrome c oxidase I (COI) gene were amplified using fusion primers and then sequenced on Ion Torrent PGM and S5 before their source species were determined using a custom reference sequence database constructed on BOLD. In total, eDNA sequences were recovered from 75 species of vertebrates including 47 fishes, 15 birds, 7 mammals, 5 reptiles, and 1 amphibian. Although all species are known from this region, 6 fish species represent new records for the study area, while 2 require verification. Sequences for five species (2 birds, 2 mammals, 1 reptile) were only detected from sediments, while sequences from 52 species were only recovered from water. Because DNA from the Amazon sailfin catfish was not detected, we used a mock eDNA experiment to confirm our methods were appropriate for its detection. We developed protocols that enabled the recovery of eDNA from tropical oligotrophic aquatic ecosystems, and confirmed their effectiveness in detecting diverse species of vertebrates including an invasive species of Amazon catfish.

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.

An SNP panel for the analysis of paternally inherited alleles in maternal plasma using ion Torrent PGM

2017 ◽  
Vol 132 (2) ◽  
pp. 343-352 ◽  
Author(s):  
Donggui Yang ◽  
Hao Liang ◽  
Shaobin Lin ◽  
Qing Li ◽  
Xiaoyan Ma ◽  
...  
Keyword(s):  
Maternal Plasma ◽  
Ion Torrent ◽  
Ion Torrent Pgm ◽  
Snp Panel

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines

2020 ◽  
Vol 43 (2) ◽  
Author(s):  
Gabriela Pereira Branco ◽  
Renan Valieris ◽  
Lucas Venezian Povoa ◽  
Luiza Ferreira de Araújo ◽  
Gustavo Ribeiro Fernandes ◽  
...  
Keyword(s):  
Cell Lines ◽  
Mirna Expression ◽  
Expression Profiles ◽  
Ion Torrent ◽  
Ion Torrent Pgm ◽  
Breast Cell Lines ◽  
Mirna Expression Profiles

scholarly journals Spatio-temporal variation in surf zone fish communities at Ilha do Cardoso State Park, São Paulo, Brazil

2017 ◽  
Vol 41 (2) ◽  
pp. 239-253
Author(s):  
Jana Menegassi del Favero ◽  
June Ferraz Dias
Keyword(s):  
Seasonal Changes ◽  
Fish Community ◽  
Surf Zone ◽  
High Tide ◽  
Fish Communities ◽  
Fish Fauna ◽  
Sao Paulo ◽  
Biological Data ◽  
Seasonal Effect ◽  
São Paulo

In order to analyze the time-space variation of the fish fauna in the surf zone fish communities at Ilha do Cardoso State Park, São Paulo, Brazil, four consecutive hauls were done over a year on three beaches with different degrees of exposure, at low and high tide. To evaluate the influence of each abiotic variable over the fish community, a Canonical Correspondence Analysis was conducted. We identified 7,286 individuals belonging to 20 families and 47 species, most specimens collected were juveniles. At low tide, the highest diversity and richness values were calculated while the highest dominance was obtained at high tide. As for the number of species collected at the three beaches, stood out for the lower values the cooler months, between June and September. Abiotic variables explained 41.3% of the variability of biological data, where 11.4% corresponds to the spatial variation. Meanwhile the temporal variables accounted for 31.9% of the variation in abundance, where 26.3% of the variance explained nycthemeral variation. Additionally two groups were clearly observed between months with low and high temperature. However in this variable, the tidal variation, excluding the seasonal effect, explained 6.2%, while seasonality, excluding tide effect, explained 26.3%. Although the main measurable seasonal changes were related to temperature, water temperature showed a low percentage of explanation in the fish fauna variability (2.7%). Finally, it is emphasized that the seasonal changes in surf zone fish community primarily reflect patterns of recruitment determined by the reproductive activity and coastal circulation.

scholarly journals Demersal fish community on the inner shelf of Ubatuba, southeastern Brazil

1998 ◽  
Vol 46 (2) ◽  
pp. 93-109 ◽  
Author(s):  
Gecely R. A. Rocha ◽  
Carmen L. D. B. Rossi-Wongtschowski
Keyword(s):  
Continental Shelf ◽  
Coastal Water ◽  
Fish Community ◽  
Species Abundance ◽  
Fish Fauna ◽  
Sampling Period ◽  
Demersal Fish ◽  
Southeastern Brazil ◽  
Otter Trawl ◽  
South Atlantic Central Water

Fluctuations in the distribution and abundance of demersal fishes collected by otter trawl on the continental shelf of Ubatuba were examined over a two-year sampling period, in an area up to 50 m depth. A total of 111 species were collected. Seasonal and annual fluctuations in species abundance were related to differences in the distribution of Coastal Water and South Atlantic Central Water masses. The demersal fish fauna in the area was divided into three ecologically distinct communities: Tropical Sciaenid, Subtropical Sciaenid, and Gerreid-Haemulid. The most important one is the Tropical Sciaenid Community, characterized by Ctenosciaena gracilicirrhus, Paralonchurus brasiliensis, and Cynoscion jamaicensis.

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