scholarly journals Characterizing Industrial and Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data

Foods ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1425
Author(s):  
Demian A. Willette ◽  
Gabriela Navarrete-Forero ◽  
Zachary Gold ◽  
Apollo Marco D. Lizano ◽  
Leonardo Gonzalez-Smith ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Artisanal Fishing ◽  
Species Identity ◽  
Early Step ◽  
Tissue Samples ◽  
Fishing Vessels ◽  
Versatile Tool ◽  
Monitoring And Surveillance ◽  
Fish Species Composition ◽  
Catch Composition

The decline in wild-caught fisheries paired with increasing global seafood demand is pushing the need for seafood sustainability to the forefront of national and regional priorities. Validation of species identity is a crucial early step, yet conventional monitoring and surveillance tools are limited in their effectiveness because they are extremely time-consuming and require expertise in fish identification. DNA barcoding methods are a versatile tool for the genetic monitoring of wildlife products; however, they are also limited by requiring individual tissue samples from target specimens which may not always be possible given the speed and scale of seafood operations. To circumvent the need to individually sample organisms, we pilot an approach that uses forensic environmental DNA (eDNA) metabarcoding to profile fish species composition from the meltwater in fish holds on industrial and artisanal fishing vessels in Ecuador. Fish identified genetically as present were compared to target species reported by each vessel’s crew. Additionally, we contrasted the geographic range of identified species against the satellite-based fishing route data of industrial vessels to determine if identified species could be reasonably expected in the catch.

scholarly journals Prediction of delayed mortality using vitality scores and reflexes, as well as catch, processing, and post-release conditions: evidence from discarded flatfish in the Western Baltic trawl fishery

2018 ◽  
Vol 76 (1) ◽  
pp. 330-341 ◽  
Author(s):  
S B M Kraak ◽  
A Velasco ◽  
U Fröse ◽  
U Krumme
Keyword(s):  
Scientific Evidence ◽  
Handling Time ◽  
Fishing Ground ◽  
High Survival ◽  
Trawl Fishery ◽  
Fishing Vessels ◽  
Reflex Action ◽  
Delayed Mortality ◽  
Catch Composition ◽  
The Eu

Abstract The EU discard ban and its high-survival exemption exposed our lack of scientific evidence on discard survival in the fisheries. Discard survival is known to be highly variable and influenced by numerous factors, including conditions during the catch, on-board the fishing vessels, and post-discard. Therefore, obtaining unambiguous results in discard survival experiments is challenging. We conducted the first systematic year-round discard survival study of flatfish in the Western Baltic Sea on-board a commercial stern trawler under realistic fishing conditions (13 monthly hauls from May 2015 to May 2016) to test whether delayed mortality can be predicted by vitality scores and reflex action mortality predictor (RAMP) scores in combination with variable conditions during catch, processing, and post-release. The factors vessel type, gear, haul duration, fishing ground, depth, handling time, and processing procedures were kept constant as much as possible. On-board, live individual flatfish were tested for vitality and the presence of reflexes for RAMP, then “discarded” and kept in cages on the bottom of the seafloor for about a week after which the delayed mortality was determined. The proportions of “discarded” plaice, flounder, and dab that were dead after being kept in the cages ranged from 5% to 100%, 0% to 96%, and 33% to 100%, respectively. Higher mortalities occurred in summer-autumn when air and water temperatures were higher, catches smaller, and catches contained smaller proportions of roundfish. Relationships between RAMP scores and mortality probabilities varied substantially across the monthly trials. Indeed, in addition to RAMP or vitality scores and individual reflexes, the factors air and water temperature and catch weight and catch composition were significant in logistic GLMs explaining delayed mortality. Cross-validations indicated that delayed mortality could be predicted by these models with a reasonable accuracy. Nevertheless, the presence of possible confounding effects calls for caution in inferring causality and extrapolating the conclusions on predictability.

scholarly journals COMPETITION FOR SPACE BETWEEN FISHING AND EXPLORATORY OIL DRILLING, OBSERVED FROM A DRILLING PLATFORM IN THE ESPIRITO SANTO BASIN, SOUTHEASTERN BRAZIL

2015 ◽  
Vol 63 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Alessandra Coutinho Thomé da Silva ◽  
Jean Louis Valentin ◽  
Marcelo Vianna
Keyword(s):  
Southeastern Brazil ◽  
Brazilian Coast ◽  
Factorial Correspondence Analysis ◽  
Artisanal Fishing ◽  
Oil Drilling ◽  
Espírito Santo ◽  
Fishing Vessels ◽  
Competition For Space ◽  
High Incidence ◽  
Espirito Santo

Fishing and oil drilling compete for space in some regions off the Brazilian coast. Fish congregate around drilling platforms, which attracts fishing vessels that may illegally breach the 500 m safety perimeter. The objective of this study was to identify the fleets that frequent the safety zone of a platform and their behavior and to determine if there was a seasonal relationship in this interaction, during two exploration campaigns, in different periods, carried out on the "Ocean Star" platform in the Espírito Santo Basin. The results indicated a high incidence of artisanal fishing vessels inside the prohibited area, and of uncooperative behavior on the part of the boat crews. The statistical method of Factorial Correspondence Analysis distinguished vessels that were using pelagic longlines to fish for dolphinfish, registered in the state of Espírito Santo and longer than 11 m, which operated during the summer campaign. Vessels fishing for scombrids, which were less than 11 m long and registered outside Espírito Santo, were prominent in the autumn-winter campaign. In conclusion, the data showed that the fleets involved in each exploratory campaign were different, but to determine the real reason why the boats insist on frequenting the area close to the platform further study is necessary.

Understanding recruitment patterns of historically strong juvenile year classes in redfish (Sebastes spp.): the importance of species identity, population structure, and juvenile migration

2015 ◽  
Vol 72 (5) ◽  
pp. 774-784 ◽  
Author(s):  
Alexandra E. Valentin ◽  
Don Power ◽  
Jean-Marie Sévigny
Keyword(s):  
Population Structure ◽  
Species Composition ◽  
Spatial Dispersion ◽  
Adult Population ◽  
Distinct Population ◽  
Species Identity ◽  
Tissue Samples ◽  
Grand Banks ◽  
Spatiotemporal Trends ◽  
Sebastes Mentella

Genetic analyses were undertaken on archived otoliths from juveniles representing historically strong year classes of northwest Atlantic redfish (Sebastes spp.) and on tissue samples from adults of known species and population of origin. The results indicated that the species composition of a year class is key information for understanding recruitment dynamics, with redfish species having distinct population-associated patterns of spatial dispersion. In the Gulf of St. Lawrence – Laurentian Channel area (GSL–LCH), the last strong year class (which supported the fishery for more than 30 years) belonged to Sebastes mentella and originated from the area. In contrast, four year classes that appeared abundant at young ages in research surveys in GSL–LCH but contributed only marginally to the adult population and the fishery of the region belonged to Sebastes fasciatus and carried the genetic signature of the adult population from the slope of the Newfoundland Grand Banks. Ocean currents and spatiotemporal trends in abundance-at-length suggest that the latter population uses the Gulf of St. Lawrence as a nursery area, with larvae and early juveniles drifting toward the Gulf of St. Lawrence and older juveniles migrating back to the slope of the Grand Banks after about 5–6 years. It is suggested that juvenile migration behaviour is a postsettlement process that plays an important role in redfish recruitment dynamics and carries both demographic and evolutionary implications.

scholarly journals Bacteria are everywhere, even in your COI data: Τhe art of getting to know the unknown unknowns and shine light on the dark matter!

2021 ◽  
Vol 4 ◽  
Author(s):  
Haris Zafeiropoulos ◽  
Laura Gargan ◽  
Christina Pavloudi ◽  
Evangelos Pafilis ◽  
Jens Carlsson
Keyword(s):  
Dark Matter ◽  
Phylogenetic Tree ◽  
Sequence Data ◽  
Marker Gene ◽  
Environmental Dna ◽  
Tree Of Life ◽  
Taxonomic Assignment ◽  
Species Identity ◽  
Consensus Sequences ◽  
Coi Sequences

Environmental DNA (eDNA) metabarcoding has been commonly used in recent years (Jeunen et al. 2019) for the identification of the species composition of environmental samples. By making use of genetic markers anchored in conserved gene regions, universally present acrooss the species of large taxonomy groups, eDNA metabarcoding exploits both extra- and intra-cellular DNA fragments for biodiversity assessment. However, there is not a truly “universal” marker gene that is capable of amplifying all species across different taxa (Kress et al. 2015). The mitochondrial cytochrome C oxidase subunit I gene (COI) has many of the desirable properties of a “universal" marker and has been widely used for assessing species identity in Eukaryotes, especially metazoans (Andjar et al. 2018). However, a great number of COI Operational Taxonomic Units (OTUs) or/and Amplicon Sequence Variants (ASVs) retrieved from such studies do not match reference sequences and are often referred to as “dark matter” (Deagle et al. 2014). The aim of this study was to discover the origins and identities of these COI dark matter sequences. We built a reference phylogenetic tree that included as many COI-sequence-related information across the tree of life as possible. An overview of the steps followed is presented in Fig. 1a. Briefly, the Midori reference 2 database was used to retrieve eukaryotes sequences (183,330 species). In addition, the API of the BOLD database was used as source for the corresponding Bacteria (559 genera) and Archaea (41 genera) sequences. Consensus sequences at the family level were constructed from each of these three initial COI datasets. The COI-oriented reference phylogenetic tree of life was then built by using 1,240 consensus sequences with more than 80% of those coming from eukaryotic taxa. Phylogeny-based taxonomic assignment was then used to place query sequences. The a) total number of sequences, b) sequences assigned to Eukaryotes and c) unassigned subsets of OTUs, from marine and freshwater samples, retrieved during in-house metabarcoding experiments, were placed in the reference tree (Fig. 1b). It is clear that a large proportion of sequences targeting the COI region of Eukaryotes actually represents bacterial branches in the phylogenetic tree (Fig. 1b). We conclude that COI metabarcoding studies targeting Eukaryotes may come with a great bias derived from amplification and sequencing of bacterial taxa, depending on the primer pair used. However, for the time being, publicly available bacterial COI sequences are far too few to represent the bacterial variability; thus, a reliable taxonomic identification of them is not possible. We suggest that bacterial COI sequences should be included in the reference databases used for the taxonomy assignment of OTUs/ASVs in COI-based eukaryote metabarcoding studies to allow for bacterial sequences that were amplified to be excluded enabling researchers to exclude non-target sequences. Further, the approach presented here allows researchers to better understand the unknown unknowns and shed light on the dark matter of their metabarcoding sequence data.

scholarly journals PERILAKU SOSIAL BERINVESTASI DAN PROSPEK PENGEMBANGAN PERIKANAN RAKYAT DI WPP 714

2017 ◽  
Vol 8 (2) ◽  
pp. 111
Author(s):  
Armen Zulham
Keyword(s):  
Cold Storage ◽  
Artisanal Fisheries ◽  
Commercial Fisheries ◽  
Artisanal Fishing ◽  
Fishing Vessels ◽  
Managerial Training ◽  
Management Area ◽  
The Government ◽  
Electrical Supply

Tulisan ini mempelajari perikanan rakyat pada WPP 714 yang berlokasi di Kota Kendari dan di Kota Tual. Data tentang nelayan perikanan rakyat yang digunakan merupakan data hasil survey yang dikumpulkan pada Bulan Mei 2015 dan bulan Oktober 2015. Basis analisis adalah kelompok alat tangkap Pancing, Jaring dan Perangkap. Jumlah responden pada setiap pengambilan data per lokasi masing-masing 100 responden. Hasil analisis menunjukkan: investasi nelayan perikanan rakyat merupakan induced investment karena memanfaatkan dana sendiri. Pada lokasi tertentu telah memaanfaatkan jasa bank dan pedagang. Armada perikanan rakyat pada dua lokasi itu mampu mensubtitusi peran perikanan komersial, jika berbagai infrastruktur (autonomous investment) seperti: Pabrik Es, Cold Storage, pasokan listrik serta sarana transportasi distribusi ikan, pasokan BBM disiapkan oleh pemerintah. Keberhasilan membangun dan memfungsikan infrastruktur dapat mempercepat transformasi armada perikanan rakyat menuju perikanan komersial. Tulisan ini merekomendasikan transformasi armada perikanan rakyat menjadi armada komersial harus segera dilakukan dengan mengganti PTM dan PMT menjadi armada KM dengan tonase kapal >=20 GT. Transformasi harus dikuti dengan pelatihan manajerial bisnis dan didukung oleh skema pembiayaan yang mudah diakses dengan bunga rendah.This paper studied about artisanal fisheries in Fisheries Management Area of Indonesian Republic (FMAs) 714 located in Kendari City and Tual City. Data in this paper are obtained from survey conducted in May and October 2015. The analysis is based on the group of fishing equipments: line, net, and trap. Total numbers of respondents are 100 on each location. It is found that the fishing investment of artisanal fisheries can be called as induced investment, because it used a personal funding. In some particular locations they used bank and merchant services. Artisanal fishing vessel on both locations are able to substitute the role of commercial fisheries. This could only occur with the presence of various infrastructures (autonomous investement) such as ice factory, cold storage, electrical supply, fish transportation and distribution equipment, and fuel supply fasilities, prepared by the government. The other things are prepared and accessible of the capital support scheme. The success in building and functioning infrastructures mentioned above could accelerate transformation of the artisanal fisheries towards commercial fisheries. This paper recommends the transformation to be immediately implemented by substituting non powered fishing vessels and out board fishing vessels to inboard powered fishing vessels with tonnage >=20 GT. This transformation should be followed by business managerial training and be supported by accessible funding scheme with low interest.

scholarly journals Pilot Study on Fish Species Composition Using Environmental DNA in Marine Sediment

2021 ◽  
Vol 44 (4) ◽  
pp. 79-84
Author(s):  
Tomohiro SHIRAGAKI ◽  
Taku INOUE ◽  
Hideki FUKUDA ◽  
Masayuki USHIO ◽  
Miki KUSAKA ◽  
...  
Keyword(s):  
Pilot Study ◽  
Species Composition ◽  
Fish Species ◽  
Marine Sediment ◽  
Environmental Dna ◽  
Fish Species Composition

scholarly journals DNA barcoding reveals the diversity of sharks in Guyana coastal markets

2017 ◽  
Vol 15 (4) ◽  
Author(s):  
Matthew A. Kolmann ◽  
Ahmed A. Elbassiouny ◽  
Elford A. Liverpool ◽  
Nathan R. Lovejoy
Keyword(s):  
Dna Barcoding ◽  
Accurate Determination ◽  
Total Sample ◽  
Artisanal Fishing ◽  
Species Identity ◽  
Sustainable Fisheries ◽  
International Union ◽  
Accurate Identification ◽  
Fundamental Challenge

ABSTRACT A fundamental challenge for both sustainable fisheries and biodiversity protection in the Neotropics is the accurate determination of species identity. The biodiversity of the coastal sharks of Guyana is poorly understood, but these species are subject to both artisanal fishing as well as harvesting by industrialized offshore fleets. To determine what species of sharks are frequently caught and consumed along the coastline of Guyana, we used DNA barcoding to identify market specimens. We sequenced the mitochondrial co1 gene for 132 samples collected from six markets, and compared our sequences to those available in the Barcode of Life Database (BOLD) and GenBank. Nearly 30% of the total sample diversity was represented by two species of Hammerhead Sharks (Sphyrna mokarran and S. lewini), both listed as Endangered by the International Union for Conservation of Nature (IUCN). Other significant portions of the samples included Sharpnose Sharks (23% - Rhizoprionodon spp.), considered Vulnerable in Brazilian waters due to unregulated gillnet fisheries, and the Smalltail Shark (17% - Carcharhinus porosus). We found that barcoding provides efficient and accurate identification of market specimens in Guyana, making this study the first in over thirty years to address Guyana’s coastal shark biodiversity.

scholarly journals Metabarcoding of environmental samples suggest wide distribution of eelgrass (Zostera marina) pathogens in the north Pacific

2021 ◽  
Vol 5 ◽  
Author(s):  
Damian M. Menning ◽  
Hunter A. Gravley ◽  
Melissa N. Cady ◽  
Daniel Pepin ◽  
Sandy Wyllie-Echeverria ◽  
...  
Keyword(s):  
Zostera Marina ◽  
North Pacific ◽  
Species Complex ◽  
Environmental Dna ◽  
Wide Distribution ◽  
Biodiversity Data ◽  
Tissue Samples ◽  
Seagrass Meadows ◽  
The North ◽  
The North Pacific

Seagrass meadows provide important ecological services to the marine environment but are declining worldwide. Although eelgrass meadows in the north Pacific are thought to be relatively healthy, few studies have assessed the presence of known disease pathogens in these meadows. In a pilot study to test the efficacy of the methods and to provide foundational disease biodiversity data in the north Pacific, we leveraged metabarcoding of environmental DNA extracted from water, sediment, and eelgrass tissue samples collected from five widely distributed eelgrass meadows in Alaska and one in Japan and uncovered wide prevalence of two classes of pathogenic organisms – Labyrinthula zosterae and other associated strains of Labyrinthula, and the Phytophthora/Halophytophthora blight species complex – known to have caused decline in eelgrass (Zostera marina) elsewhere in the species’ global distribution. Although the distribution of these disease organisms is not well understood in the north Pacific, we uncovered the presence of at least one eelgrass pathogen at every locality sampled.

scholarly journals FISHERIES AND ENVIRONMENTAL IMPACTS IN THE GREAT JAKARTA BAY ECOSYSTEM

2018 ◽  
Vol 23 (2) ◽  
pp. 69
Author(s):  
Hari Eko Irianto ◽  
Sri Turni Hartati ◽  
Lilis Sadiyah
Keyword(s):  
Histological Study ◽  
Artificial Reef ◽  
Fish Population ◽  
Marine Conservation ◽  
Perna Viridis ◽  
Conservation Area ◽  
Portunus Pelagicus ◽  
Tissue Samples ◽  
Fishing Gears ◽  
Catch Composition

The Great Jakarta Bay Ecosystem (GJBE) supports the economic growth for the surrounding community, including fisheries sector. This large ecosystem is consisted of two coastal ecosystems, i.e. Jakarta Bay and Thousands islands. There are only traditional fisheries operating either in Jakarta Bay or Thousand islands. Some economically important fisheries include shrimp, demersal and small pelagic fisheries, which are caught using different fishing gears, either active or passive fishing gears. There are some serious concerns related to the fish resources and habitat degradations in the GJBE, which in turn can cause the decrease in fish population and fish species diversity, respectively. CPUE and catch composition of the fixed lift nets, sero and fixed gillnet fisheries were obtained from the observations in 2006 and 2014. In addition, to determine the level of pollution, tissue samples were collected for green mussel (Perna viridis), blue swimming crab (Portunus pelagicus) and white-spotted spinefoot (Siganus canaliculatus) in 2009. The CPUE trend and catch composition showed that overfishing might have been occurring in the Jakarta Bay. The histological study on gill tissues of the three species shows that the Jakarta Bay has been polluted. Several efforts have been done to address the problems, including sea farming, habitat rehabilitation (artificial reef and mangrove restoration), marine conservation area and fish shelter, restocking and sea ranching.

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