scholarly journals Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples

PLoS ONE ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. e41732 ◽  
Author(s):  
Philip Francis Thomsen ◽  
Jos Kielgast ◽  
Lars Lønsmann Iversen ◽  
Peter Rask Møller ◽  
Morten Rasmussen ◽  
...  
Keyword(s):  
Marine Fish ◽  
Fish Fauna ◽  
Environmental Dna ◽  
Seawater Samples

scholarly journals Enviromental DNA (eDNA) reveals potential for interoceanic fish invasions across the Panama Canal

2021 ◽  
Author(s):  
Lennart Schreiber ◽  
Gustavo Castellanos-Galindo ◽  
Mark Torchin ◽  
Karina Chavarria ◽  
Silke Laakmann ◽  
...  
Keyword(s):  
Marine Fish ◽  
New Records ◽  
Fish Fauna ◽  
Environmental Dna ◽  
Diversity Indices ◽  
Molecular Data ◽  
Panama Canal ◽  
Marine Fish Species ◽  
Cytochrome Oxidase Subunit ◽  
The Pacific

Interoceanic canals can facilitate biological invasions as they connect the world’s oceans and dissolve dispersal barriers between bioregions. As a consequence, multiple opportunities for biotic exchange arise and the resulting establishment of migrant species often causes adverse ecological and economic impacts. The Panama Canal is a key region for biotic exchange as it connects the Pacific and Atlantic Oceans in Central America. In this study, we used two complementary methods (environmental DNA (eDNA) and gillnetting) to survey fish communities in this unique waterway. Using COI (cytochrome oxidase subunit I) metabarcoding, we detected a total of 142 taxa, including evidence for the presence of sixteen Atlantic and eight Pacific marine fish inside different sections of the Canal. Of these, ten are potentially new records of marine taxa detected in the freshwater segment of the Canal. Molecular data did not capture all species caught with gillnets, but generally provided a more complete image of the fish fauna. Diversity indices based on eDNA surveys revealed significant differences across different sections of the Canal reflecting in part the prevailing environmental conditions. The observed increase in the presence of marine fish species in the Canal indicates a growing potential for interoceanic exchange of fishes across the Isthmus. Monitoring using eDNA is a rapid and efficient way to assess potential changes in the fishes of this important waterway.

scholarly journals Environmental DNA (eDNA) reveals potential for interoceanic fish invasions across the Panama Canal

2021 ◽  
Author(s):  
Lennart Schreiber ◽  
Gustavo Castellanos-Galindo ◽  
Mark Torchin ◽  
Karina Chavarria ◽  
Silke Laakmann ◽  
...  
Keyword(s):  
Marine Fish ◽  
New Records ◽  
Fish Fauna ◽  
Environmental Dna ◽  
Diversity Indices ◽  
Molecular Data ◽  
Panama Canal ◽  
Marine Fish Species ◽  
Cytochrome Oxidase Subunit ◽  
The Pacific

Interoceanic canals can facilitate biological invasions as they connect the world’s oceans and dissolve dispersal barriers between bioregions. As a consequence, multiple opportunities for biotic exchange arise and the resulting establishment of migrant species often causes adverse ecological and economic impacts. The Panama Canal is a key region for biotic exchange as it connects the Pacific and Atlantic Oceans in Central America. In this study, we used two complementary methods (environmental DNA (eDNA) and gillnetting) to survey fish communities in this unique waterway. Using COI (cytochrome oxidase subunit I) metabarcoding, we detected a total of 142 taxa, including evidence for the presence of sixteen Atlantic and eight Pacific marine fish inside different sections of the Canal. Of these, ten are potentially new records of marine taxa detected in the freshwater segment of the Canal. Molecular data did not capture all species caught with gillnets, but generally provided a more complete image of the fish fauna. Diversity indices based on eDNA surveys revealed significant differences across different sections of the Canal reflecting in part the prevailing environmental conditions. The observed increase in the presence of marine fish species in the Canal indicates a growing potential for interoceanic exchange of fishes across the Isthmus. Monitoring using eDNA is a rapid and efficient way to assess potential changes in the fishes of this important waterway.

scholarly journals Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia

2019 ◽  
Vol 20 (12) ◽  
Author(s):  
Sapto Andriyono ◽  
MD. JOBAIDUL ALAM ◽  
HYUN-WOO KIM
Keyword(s):  
Marine Fish ◽  
Molecular Identification ◽  
Environmental Dna ◽  
Fish Diversity ◽  
Morphological Identification ◽  
Fish Samples ◽  
Identification Of Species ◽  
Seawater Samples ◽  
Next Generation Sequencing Ngs ◽  
Diversity Study

Abstract. Andriyono S, Jobaidul Alam Md, Kim HW. 2019. Environmental DNA (eDNA) metabarcoding: Diversity study around the Pondok Dadap fish landing station, Malang, Indonesia. Biodiversitas 20: 3772-3781. Molecular identification of species is now fast growing and currently widely applied method in the diversity estimation of aquatic biota; even though morphological identification is still carried out. The molecular approach is beneficial complementing on regular surveys, e.g. use of nets, traps, fishing rods, and even with poisons. In this study, the eDNA metabarcoding was applied to water samples around the Pondok Dadap fish landing station, Indonesia to determine the diversity of fish around the waters and also to identify marine fish landed in this area. Molecular identification was carried out on fish samples obtained from the fish market improved GenBank database on COI and ITS. While, seawater samples were carried out by using the next-generation sequencing (NGS) platform to obtain the eDNA metabarcoding data for the first time. Molecular identification obtained 34 species (68 sequences of COI and ITS regions) belonging to 28 genera, 18 families, 4 orders, while the eDNA metabarcoding approach identified 53 marine fish species by using the MiFish pipeline representing 38 genera, 27 families, and 7 orders. From the present study, we can able to estimated fish diversity by eDNA metabarcoding, and this finding will be helpful for baseline data preparation for future effective management of resources in this area.

scholarly journals Particle Size Distribution of Environmental DNA from the Nuclei of Marine Fish

2019 ◽  
Vol 53 (16) ◽  
pp. 9947-9956 ◽  
Author(s):  
Toshiaki Jo ◽  
Mio Arimoto ◽  
Hiroaki Murakami ◽  
Reiji Masuda ◽  
Toshifumi Minamoto
Keyword(s):  
Particle Size ◽  
Particle Size Distribution ◽  
Size Distribution ◽  
Marine Fish ◽  
Environmental Dna

scholarly journals Larval anisakid infections of some tropical fish species from north-west Australia

2003 ◽  
Vol 77 (4) ◽  
pp. 363-365 ◽  
Author(s):  
R.G. Doupé ◽  
A.J. Lymbery ◽  
S. Wong ◽  
R.P. Hobbs
Keyword(s):  
Marine Fish ◽  
Fish Species ◽  
Fish Fauna ◽  
Tropical Fish ◽  
Preliminary Survey ◽  
North West ◽  
High Prevalence ◽  
Potential Impact

AbstractDespite the commercial and zoonotic importance of larval anisakid infestations of teleosts, their distribution among Australia's diverse marine fish fauna is poorly understood. A preliminary survey of Australia's tropical north-west revealed a generally high prevalence of larval anisakids representing four genera (Anisakis, Terranova, Thynnascaris and Raphidascaris) among only seven fish species. The potential impact of high larval anisakid infections on both the health of recreational fishermen and aquaculture environments is discussed.

scholarly journals Survival and detection of bivalve transmissible neoplasia from the soft-shell clam Mya arenaria (MarBTN) in seawater

2021 ◽  
Author(s):  
Rachael M Giersch ◽  
Samuel FM Hart ◽  
Satyatejas G Reddy ◽  
Marisa A Yonemitsu ◽  
María J Orellana Rosales ◽  
...  
Keyword(s):  
Infectious Agent ◽  
Environmental Dna ◽  
Mya Arenaria ◽  
Physical Contact ◽  
Soft Shell Clam ◽  
Highly Sensitive ◽  
Route Of Transmission ◽  
Soft Shell ◽  
Salinity Levels ◽  
Seawater Samples

Many pathogens can cause cancer, but cancer itself does not normally act as an infectious agent. However, transmissible cancers have been found in a few cases in nature: in Tasmanian devils, dogs, and several bivalve species. The transmissible cancers in dogs and devils are known to spread through direct physical contact, but the exact route of transmission of bivalve transmissible neoplasia (BTN) has not yet been confirmed. It has been hypothesized that cancer cells could be released by diseased animals and spread through the water column to infect/engraft into other animals. To test the feasibility of this proposed mechanism of transmission, we tested the ability of BTN cells from the soft-shell clam (Mya arenaria BTN, or MarBTN) to survive in artificial seawater. We found that BTN cells are highly sensitive to salinity, with acute toxicity at salinity levels lower than those found in their environment. BTN cells also survive longer at lower temperatures, with >48% of cells surviving a week in seawater at temperatures from 4°C to 16°C, and 49% surviving for more than two weeks at 4°C. With one clam donor, living cells were observed for more than eight weeks at 4°C. We also used qPCR of environmental DNA (eDNA) to detect the presence of BTN-specific DNA in the environment. We observed release of BTN-specific DNA into the water of aquaria from tanks with highly BTN-positive clams, and we detected BTN-specific DNA in seawater samples collected from BTN-endemic areas, although the level detected was much lower. Overall, these data show that BTN cells can survive well in seawater, and they are released into the water by diseased animals, supporting the hypothesis that BTN is spread from animal-to-animal by cells through seawater.

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 Seasonal variation in the relative importance of assembly processes in marine fish communities as determined by environmental DNA analyses

2021 ◽  
Author(s):  
Naoto Shinohara ◽  
Yuki Hongo ◽  
Momoko Ichinokawa ◽  
Shota Nishijima ◽  
Shuhei Sawayama ◽  
...  
Keyword(s):  
Marine Fish ◽  
Seasonal Changes ◽  
Variation Partitioning ◽  
Environmental Filtering ◽  
Fish Communities ◽  
Environmental Dna ◽  
Compositional Variation ◽  
Short Time Scale ◽  
Relative Importance ◽  
Spatial Processes

Compositional variation among local communities is a result of environmental (e.g., environmental filtering) and spatial (e.g., dispersal limitation) processes. Growing evidence suggests that their relative importance varies temporally, but little is known about the short-time scale dynamics, that is, seasonality. Using marine fish communities in a Japanese bay as a model system, we tested the hypothesis that seasonal changes in the environment induce a shift in the relative importance of environmental and spatial processes. We used one-year monthly monitoring data obtained using environmental DNA and conducted a variation partitioning analysis to decompose the two processes. The relative importance of environmental and spatial processes was comparable averaged over the year but changed seasonally. During summer, when lower dissolved oxygen concentrations may adversely affect organisms, species composition was more explained by space despite larger environmental heterogeneity than in other seasons. This suggests that environmental processes weakened during the season with extremely severe environments, likely due to the random loss of individuals. We conclude that the assembly processes of communities of mobile organisms, such as fishes, can shift even within a year in response to seasonal changes in environmental severity. The results also indicate the applicability of eDNA techniques for community assembly studies.

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