eDNA Customer Publications

Environmental DNA (eDNA)metabarcoding has become an alternative method used for biodiversity monitoring of an ecosystem. The eDNA metabarcoding has advantages compared to the conventional method because it is non–invasive, quick, and requires less cost. However, the effectiveness of the eDNA method is highly dependent on the coverage of the DNA barcode reference and primerpair. A study using the eDNA method was conducted for fish biodiversity monitoring in Singkarak Lake.Two–liter water samples were collected using sterile bottle samples at each sampling site (five sites). The universal primers (Fish FI and Fish R1) used for Next–generation sequencing (GRIDION, Nanopore, Oxford Technologies). The study detected 152 fish species using eDNA metabarcoding. Ten species out of the 30 originally reported in Singkarak Lake were detected using eDNA metabarcoding. The low percentage of fish detected is thought to be due to several factors;incomplete/unavailability of freshwater fish DNA barcodes in Indonesia registered in the database repository, inappropriate primer pair selection, low DNA quality, and the absence of target species DNA in collected water samples. The results demonstrated the significance of correctly registering DNA barcodesto the database and appropriate primer pair selection to identify eDNA metabarcoding. This study provides recommendations using eDNA metabarcoding for monitoring in future work.

The Next Generation Sequences (NGS)is one of the establishedmetabarcodingmethodsfor analyzing microbial communities. Investigation of the cyanobacterial community in eutrophic freshwater habitats is important, especially for those known as toxic–released cyanobacteria. Thisstudy aimedto analyze the structure communityof cyanobacteria in Agung and Sunter Barat Lakesin North Jakarta, DKI Jakarta Provinceusing the NGS method. The physico–chemical parameters were also measured. Sampling plots were selected by purposive sampling method.The result of the study successfully analyzed the bacterial community structure and portrayed the dominancy of the cyanobacterialpopulation on the twolakes. Several cyanobacteria genera previously reported in 2008 research were found, including Arthrospiraand Planktothrix. The diversityindex in Agung Lake (4.7) was higher than in Sunter Barat Lake (3.7). Two dominant populations were found, which were Raphidiopsis(in Agung Lake) and Planktothrix(in Sunter Barat Lake).Both generahave been acknowledged as toxin–releasing cyanobacteria,whichcould be harmful tothe water–biotic community as well as humanhealth.The presence of potentially toxic cyanobacteria in the recreation area of Agung Lake should be taken into consideration for biomonitoring management.

nvasive species are alien species that enter the ecosystem and can adapt to the ecosystem quickly. So, the presence of invasive fish can threaten endemic diversity inthese ecosystems. This study aims to detect the presence and distribution of invasive fish in the Progo River, Yogyakarta, Indonesia, through the environmental DNA (eDNA) method. Water samples were taken at three observation points in the upstream area of the river (site 1), the middle of the river (site 2), and downstream of the river (site 3). The water samples were filtered using 0.45 μm MF–Milipore installed on the filtration pump and extracted using the ZymoBIOMICS DNA Miniprep Kit. Sequencing used nanopore sequencing. The primers used were FishF2 and FishR2. The sequencing results were analyzed using the mBRAVE software, which was then classified as an invasive species based on government regulations and journals. The results showed that 188 OTUs were detected in the upstream area (site 1), 227 OTUs in the middle area (site 2) and 154 OTUs downstream. Lagocephalusand Sciaenopswere found in the upstream area (site 1). In the middle area of the river (site 2), Gambusiaand Lepomiswere found, while in the lower reaches of the river (site 3), Gambusiaand Sciaenopswere found. With the detection of these invasive species, appropriate management and conservation efforts must be carried out immediately to protectendemic species in the Progo River.