scholarly journals Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

2020 ◽  
Author(s):  
Andrea Polanco Fernández ◽  
Virginie Marques ◽  
Fabian Fopp ◽  
Jean‐Baptiste Juhel ◽  
Giomar Helena Borrero‐Pérez ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Reef Fishes ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Dna Metabarcoding ◽  
Tropical Reef

scholarly journals HUBUNGAN ANTARA KOMPOSISI IKAN TARGET DAN PRESENTASE TUTUPAN KARANG HIDUP DI KEPULAUAN KEI KECIL, MALUKU

2020 ◽  
Vol 26 (3) ◽  
pp. 147
Author(s):  
Ana Faricha ◽  
Isa Nagib Edrus ◽  
Rizkie Satriya Utama ◽  
Ahmad R. Dzumalex ◽  
Abdullah Salatalohi ◽  
...  
Keyword(s):  
Coral Reef ◽  
Reef Fishes ◽  
Average Density ◽  
Species Variation ◽  
Live Coral ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Ecological Values ◽  
Average Biomass ◽  
The Relationship

Ikan terumbu karang memiliki peranan penting baik secara ekonomi maupun ekologi, namun kondisi terumbu karang termasuk di perairan Indonesia yang menjadi habitat utama ikan karang mengalami degradasi. Penelitian ikan karang sudah banyak dilakukan, namun di Indonesia kondisi habitat ikan karang memiliki karakter yang berbeda-beda. Tujuan penelitian ini adalah untuk mengetahui hubungan antara komposisi ikan karang target dan tutupan karang hidup. Penelitian ini dilakukan pada bulan Oktober 2019 di Kepulauan Kei Kecil, Maluku. Metode yang digunakan adalah UVC (Underwater Visual Census) untuk data ikan karang dan UPT (Underwater Photo Transect) untuk mengkaji tutupan karang hidup. Hasil pengamatan menunjukkan bahwa terdapat 130 spesies ikan karang target yang mewakili 19 famili, dengan variasi jenis ikan target antar lokasi pengamatan berkisar antara 25-66 spesies. Kepadatan rata-rata ikan karang target sebesar 8.811 ± 4.107 Ind/ha, dan biomassa rata-rata 1.335 ± 899 Kg/ha. Komposisi ikan karang target yang memiliki kedekatan dengan tutupan karang hidup yaitu famili Siganidae, Serranidae, Lutjanidae, Holocentridae, dan Pomacentridae. Akan tetapi hubungan tersebut rendah, dan kemungkinan besar ada faktor lain yang mempengaruhi. Reef fishes have an important economic and ecological values. However, the coral reef of the globe including in the most of the Indonesian waters which is the vital habitat for reef fishes is degraded. Study on the reef fishes is an abundance, while the habitat characteristic of reef fishes in Indonesian waters has a differences. The aim of this study is to determine the relationship between the target reef fishes compositions and the percentage live coral covers. This study was carried out in October 2019 at the Kei Kecil islands, Maluku. The method used in this study is UVC (Underwater Visual Census) for collecting the reef fishes data, and the UPT (Underwater Photo Transect) for assessing the live coral coverage. The result shows that there are about 130 fishes, which representing 19 families, with species variation ranges from 25 to 66 species among the observation sites. The average density of target fishes was about 8.811 ± 4.107 Ind/ha, whereas the average biomass of target fishes was 1,335 ± 899 Kg/ha. The target reef fishes compositions that has relation with live coral covers is family Siganidae, Serranidae, Lutjanidae, Holocentridae, and Pomacentridae. However, this relationship is weak, and may influenced by other factors.

scholarly journals Beyond traditional biodiversity fish monitoring: environmental DNA metabarcoding and simultaneous underwater visual census detect different sets of a complex fish community at a marine biodiversity hotspot

2019 ◽  
Author(s):  
Tania Valdivia-Carrillo ◽  
Axayácatl Rocha-Olivares ◽  
Héctor Reyes-Bonilla ◽  
José Francisco Domínguez-Contreras ◽  
Adrian Munguia-Vega
Keyword(s):  
Gulf Of California ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Marine Ecology ◽  
Marine Biodiversity ◽  
Rocky Reef ◽  
Monitoring Methods ◽  
Visual Census ◽  
Traditional Methods ◽  
Underwater Visual Census

ABSTRACTSignificant advances in the study of marine fish communities have been achieved with traditional monitoring methods and recently with novel genetic approaches. eDNA metabarcoding is one of them and a powerful tool for the study of biodiversity still in continuous development. Its applicability in marine ecology and conservation studies may be gauged by comparing its results with those of traditional methods. In the present investigation, we compare results from the underwater visual census (UVC) with eDNA metabarcoding (eDNA) carried out simultaneously in 24 rocky reef sites along the Gulf of California. We developed a two-PCR library preparation protocol followed by high throughput sequencing aimed at teleost fish. Our results show that both methods had different detection capabilities, and each registered different sets of fish taxa from rocky reefs, with some overlap. In particular, eDNA identified taxa from pelagic, demersal, and estuarine habitats beyond the rocky reef itself, suggesting differences in detection mainly attributed to the transport and permanence time of the eDNA in the ocean. Overlap in the detection with both methods increased with taxonomic level. We argue that substantial gaps in sequence reference databases for teleost are at the root of major discrepancies. Our results also confirm that PCR-based eDNA metabarcoding of seawater samples does not reflect patterns in abundance and biomass of species estimated from traditional methods. We discuss how to reconcile the results of eDNA metabarcoding and traditional methods in marine hotspots.

Compensating for length biases in underwater visual census of fishes using stereo video measurements

2015 ◽  
Vol 66 (3) ◽  
pp. 286 ◽  
Author(s):  
Tom Davis ◽  
David Harasti ◽  
Stephen D. A. Smith
Keyword(s):  
Marine Protected Areas ◽  
Reef Fishes ◽  
Fish Length ◽  
Correction Factors ◽  
Visual Census ◽  
Underwater Visual Census ◽  
Observer Bias ◽  
Stereo Video ◽  
Non Destructive ◽  
Specific Correction

Underwater visual census (UVC) is a widely used technique for estimating species richness, abundance, and lengths of reef fishes. The technique has the advantage of being non-destructive, and can therefore be used for monitoring in marine protected areas. However, acquisition of robust data using UVC is reliant on the ability of individual divers to accurately identify fish, and estimate their lengths. Both of these variables can be affected by observer bias, which may also differ among observers. This study examines a technique with the potential to quantify and correct for observer bias in individual divers. We used simultaneous diver-operated stereo video and underwater visual census surveys, and compared the results to generate diver-specific correction factors. These correction factors were subsequently applied in additional estimates of fish length, with measurable improvement in the accuracy of the data.

Asosiasi ikan pada terumbu buatan di Teluk Tahuna Kabupaten Kepulauan Sangihe

2016 ◽  
Vol 2 (2) ◽  
Author(s):  
Wenseslaus Fransiscus Makawaehe ◽  
Lefrand Manoppo ◽  
Revols D.Ch. Pamikiran
Keyword(s):  
Visual Census ◽  
Underwater Visual Census ◽  
Scuba Divers

Minimnya pengetahuan tentang ekologi terumbu buatan merupakan inti masalah perdebatan penggunaannya dalam manajemen sumberdaya perikanan; dan membatasi aplikasi habitat buatan tersebut sebagai alat mitigasi pada berbagai kerusakan lingkungan. Pemahaman ekologi yang lebih baik akan menuntun pada pembuatan desain dan penggunaan struktur buatan secara lebih efektif dan efisien. Hal ini juga akan menjawab pertanyaan tentang manfaat konstruksi habitat buatan pada berbagai kondisi lingkungan. Asosiasi ikan di terumbu buatan bervariasi, namun perlu dilakukan perbandingan jenis ikan yang berasosiasi pada saat air pasang dan air surut. Oleh karena itu penelitian ini bertujuan untuk Membandingkan struktur asosiasi ikan di terumbu buatan pada saat air pasang naik dan pasang surut di perairan Teluk Tahuna. Penelitian ini dilakukan di perairan Teluk Tahuna, Kabupaten Kepulauan Sangihe pada bulan April–Juni 2015; yang didasarkan pada metode deskriptif. Asosiasi ikan di terumbu buatan diamati dengan teknik Underwater visual census (UVC) oleh dua orang SCUBA divers sebanyak 4 kali. Kelimpahan spesies ikan di terumbu buatan dianalisis dengan indeks keragaman dan indeks dominansi. Berdasarkan jumlah individu total ikan yang berasosiasi dengan terumbu buatan, maka nilai tertinggi terdapat pada bulan purnama saat pasang tertinggi (156 ekor), kemudian diikuti bulan kuartir pasang tertinggi (120 ekor), bulan purnama surut terendah (107 ekor) dan bulan kuartir surut terendah (103 ekor). Keanekaragaman spesies ikan, baik pada bulan kuartir maupun pada bulan purnama masih tergolong sedang dan dominansi spesies tergolong rendah

COMPARATIVE STUDY BETWEEN FISH COLLECTION BY NATIONAL CENSUS ON RIVER ENVIRONMENT AND ENVIRONMENTAL DNA METABARCODING

2018 ◽  
Vol 74 (5) ◽  
pp. I_415-I_420 ◽  
Author(s):  
Yoshihisa AKAMATSU ◽  
Takayoshi TSUZUKI ◽  
Ryota YOKOYAMA ◽  
Yayoi FUNAHASHI ◽  
Munehiro OHTA ◽  
...  
Keyword(s):  
Comparative Study ◽  
Environmental Dna ◽  
Dna Metabarcoding ◽  
Fish Collection

Environmental DNA for functional diversity

2018 ◽  
Author(s):  
Pierre Taberlet ◽  
Aurélie Bonin ◽  
Lucie Zinger ◽  
Eric Coissac
Keyword(s):  
Functional Groups ◽  
Functional Diversity ◽  
Environmental Dna ◽  
Soil Organisms ◽  
Meaningful Information ◽  
Dna Metabarcoding ◽  
Pros And Cons ◽  
Target Community

Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.

Sign in / Sign up

Export Citation Format

Share Document