Environmental biomonitoring of reef fish community structure with eDNA metabarcoding in the Coral Triangle

Gelis, Ester Restiana Endang; Kamal, Mohammad Mukhlis; Subhan, Beginer; Bachtiar, Imam; Sani, Lalu M. Iqbal; Madduppa, Hawis

doi:10.1007/s10641-021-01118-3

Cited by 35 publications

(30 citation statements)

References 88 publications

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“…All samples were collected in May 2019. Environmental DNA samples were collected at each site using 4 L bottles on the water column by using Self-Contained Underwater Breathing Apparatus (SCUBA) (±5 meters below sea surface). All samples then were ltered using sterile lter paper (0.4 µm pore size,47 mm diameter) (Madduppa et al 2021;Gelis et al 2021) and peristaltic pump device (MASTERFLEX number 13-310-662) (Bakker et al 2017;). After the process was completed, the lter paper directly was cut into small pieces by sterilized scissors and placed them into a 2 ml cryotube containing 1.5 ml DNA shield (ZymoBIOMICS DNA/RNA shield).…”

Section: Study Site and Edna Seawater Collectionmentioning

confidence: 99%

“…The reads obtained from Illumina sequencing was initially analysed using the Multiplex Barcode Research and Visualization Environment (mBRAVE) online pipeline (www.mbrave.net) with OUT cluster data output (Gelis et al 2021;Leduc et al 2019;Ratnasingham and Hebert 2016). The steps carried out by MBRAVE were; removing forward and reverse primer sequence, trimming the 10 bp region at beginning of the reads, ltering the reads that meeting with these criteria to retain those with a length 200 bp.…”

Section: Bioinformatics Using Mbrave Pipelinementioning

confidence: 99%

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Environmental DNA biomonitoring revealed species diversity of Cnidarian and Poriferan across Jakarta Bay and Seribu Islands National Park

Maqbul

Fahrezi

Bakhri

et al. 2021

Preprint

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Indonesia, as a country having a unique sea lane known as the Indonesian Archipelagic Sea Lanes (ASLs), has become one of the busiest countries in the world with varied shipping activities. These actions have the ability to facilitate the transmission of species (bio-invasion). Until recently, the number of global introduced species has increased, with negative consequences for environment and the economy. Environmental DNA (eDNA) approaches for detecting the presence of invasive species are currently receiving a lot of interest as a broad approach method in ecological research. As a result, the study used the eDNA technique to compare the quantity and variety of introduced species from the Cnidaria and Porifera Phyla, as well as to characterize their invasiveness status and possible presence in the waters of Jakarta Bay. Based on data from the inside Zone of National Park (ZI) and Outside Zone of National Park (ZO), the biological community composition, richness, and diversity were assessed (ZO). The mBrave workflow generated a total of 14,275 reads from high-throughput sequencing of amplicons from two zones, with 8,917 reads in ZI and 5,358 reads in ZO. Blackfordia virginica , Cordylophora caspia , and Ectopleura crocea were among the imported species included in the invasive category, with E. crocea having the highest abundance and being detected in both zones, with a total of 1300 reads, consisting of 1253 reads in ZI and 47 reads in ZO. Based on the findings, the eDNA methodology can be used as a biomonitoring and conservation method for invasive species.

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Section: Study Site and Edna Seawater Collectionmentioning

confidence: 99%

Section: Bioinformatics Using Mbrave Pipelinementioning

confidence: 99%

Environmental DNA biomonitoring revealed species diversity of Cnidarian and Poriferan across Jakarta Bay and Seribu Islands National Park

Maqbul

Fahrezi

Bakhri

et al. 2021

Preprint

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“…Sampling was carried out in the waters of the Thousand Islands, precisely on Harapan and Untung Jawa islands,which was held in August 2019 (Figure 1). Seawater samples were taken directly at the bottom of the water at a depth of 8-9 meters with total volume of 4L per sample (Madduppa et al, 2021). The sampling method used is the same as that used by some researchers such aslocation (Miya et al, 2015;Andruszkiewicz et al, 2017).…”

Section: Edna Samplingmentioning

confidence: 99%

“…This limitation in the identification process of the Underwater Visual Census (UVC) method supports research to be carried out using more effective methods and analyses such as environmental DNA (eDNA), targeting all genetic material stored in the waters. Environmental DNA (eDNA) metabarcoding method is the on of the current alternative and effective bio-monitoring method for identifying reef fish species (DiBattista et al, 2017;Evans et al, 2017;Gelis et al, 2021;Wang et al, 2021). Thomsen et al (2012) stated that environmental DNA (eDNA) metabarcoding is a good method for identifying reef fish.…”

Section: Introductionmentioning

confidence: 99%

“…Thomsen et al (2012) stated that environmental DNA (eDNA) metabarcoding is a good method for identifying reef fish. Environmental DNA (eDNA) metabarcoding is an update method for estimating the richness and abundance of organisms such as fish and others that are difficult to identify and detect from the water column and sediments (Taberlet et al, 2012;Takahara et al, 2013;Gelis et al, 2021). Environmental DNA methods are also very effective for detecting the presence of organisms such as fish without isolating the target organisms (Lodge et al, 2012;Laramie et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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A CONTRAST PATTERN OF REEF FISH SPECIES DIVERSITY AND DISTRIBUTION USING ENVIRONMENTAL DNA (eDNA) METABARCODING IN LONGITUDINAL DISTANCE FROM JAKARTA BAY

Sani¹,

Benyamin²,

Husna³

et al. 2021

J. Ilmu dan Teknologi Kelautan Tropis

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The existence of reef fish is certainly closely related to the existence of reefs coral because the ecosystem is a habitat for reef fish. Coral reefs are ecosystems that are commonly found on small islands in the tropics including the Seribu Islands. The Seribu Islands are a group of 110 islands located off the coast of Jakarta and up to 80 kilometers north of the Java Sea. In this study, we examined the species distribution and diversity of reef fish species on two different distance location in Jakarta Bay using environmental DNA (eDNA) metabarcoding analysis from two sites which are Untung Jawa Island and Harapan Island. The 4L eDNA seawater samples were collected at a depth of 8-9 meters at each site and then analysis using specific primer (MiFish U) of 12S rRNA. Overall, the higher species richness was found on Harapan Island (52 species) followed by Untung Jawa Island (11 species). The Shannon-Wiener Index also showed Harapan Island has higher reef fish diversity based on three taxonomic level (family, genus, and species). There were only five mutual reef fish species found in the two locations, namely Atherinomorus aetholepis, Auxis thazard, Cephalopholis sexmaculata, Epinephelus chlorostigma, and Plectropomus areolatus. The results of these findings in this current study are in line with anthropogenic pressure different where Untung Jawa Island is the closer one to Jakarta Bay than the Harapan Island that located relatively far from Jakarta Bay.

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Diversity and spatiotemporal dynamics of fish communities in the Chongqing section of the upper Yangtze River based on eDNA metabarcoding

Shen,

Zhang,

Cheng

et al. 2023

Ecology and Evolution

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Fish diversity plays a critical role in maintaining the balance of water ecosystems, especially in the Chongqing section of the National Nature Reserve for Rare and Endemic Fishes in the upper Yangtze River, which serves as an important habitat for rare and endemic fish, as well as an important channel for the replenishment of fishery resources in the Three Gorges Reservoir. Under a 10‐year ban on fishing in the Yangtze River basin, we investigate fish diversity and seasonal variation in the Reserve by using environmental DNA (eDNA) metabarcoding. We found fishes belonging to 85 genera, 24 families, and 8 orders in the Reserve. A comparison of eDNA metabarcoding results with the diversity of a recent fish catch revealed that eDNA metabarcoding not only enables rapid and efficient fish monitoring but also has a high sensitivity. Furthermore, the study demonstrates that eDNA metabarcoding can be used as a tool for monitoring seasonal variations of fish composition in freshwater ecosystems. The alpha and beta diversity analysis both showed compositional differences in the fish community in accordance with seasonal variations. In addition, changes in eDNA relative sequence abundance and the detection of fish species at different sampling sites may reflect shifts in habitat use and distribution. Thus, we provide detailed seasonal data on fish diversity in the Chongqing section of the Reserve. This will contribute to conservation and to the understanding of fish diversity and community dynamics in the Chongqing section of the Reserve.

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Environmental biomonitoring of reef fish community structure with eDNA metabarcoding in the Coral Triangle

Cited by 35 publications

References 88 publications

Environmental DNA biomonitoring revealed species diversity of Cnidarian and Poriferan across Jakarta Bay and Seribu Islands National Park

Environmental DNA biomonitoring revealed species diversity of Cnidarian and Poriferan across Jakarta Bay and Seribu Islands National Park

A CONTRAST PATTERN OF REEF FISH SPECIES DIVERSITY AND DISTRIBUTION USING ENVIRONMENTAL DNA (eDNA) METABARCODING IN LONGITUDINAL DISTANCE FROM JAKARTA BAY

Diversity and spatiotemporal dynamics of fish communities in the Chongqing section of the upper Yangtze River based on eDNA metabarcoding

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