How does environmental DNA in two different depths reveal the existence of Bali Sardine in Bali Strait-Indonesia?

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About This Project

Regions of Bali Strait, Indonesia, have often experienced a dominant catch of Sardinella lemuru in the last decades [1,2,3], which benefits the economy & ecology aspects. However, where it went during the rising La Nina intensity in the climate change era [4] with morphological sample scarcity, this study proposes new sampling to increase eDNA recovery of S.lemuru by increasing the previous standard filtered water [11,12,18] to 3-10 L triplicate in 3 & 15 m depth without adding high field cost.

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What is the context of this research?

Bali Sardine (Sardinella lemuru) in the Bali Strait with a production volume proportion reaching 91.47% [2,6] from 1976-2006. However, due to increased sea surface temperatures, S.lemuru experienced a shortage in La Nina [3,4,10]. As a result, its status is categorized as near-threatened on the IUCN Red List and gains more significant concern regarding its sensitivity due to overfishing and environmental changes. The scarcity abundance of S.lemuru, especially in La Nina years, results in difficulties in DNA analysis, which requires morphological samples. Therefore, environmental DNA can be analyzed in depth for DNA sequences of S.lemuru to indicate their existence in seawater [11,12]. This information can be developed into a monitoring and sustainable management baseline.

What is the significance of this project?

Without proper management in Bali Strait, S.lemuru populations will be more pressured and may disappear. We are implementing eDNA as a complementary tool to map the distribution & diversity of marine species in Indonesia [10,11]. However, S.lemuru detection is poorly known with eDNA in one of its habitats [12,13]. The eDNA sampling strategies are required to ensure their distribution, regardless of their observations of morphological size [14] & catch production [3], which fluctuates temporally [4,15,16,17], even though their scarcity happened [2]. We hypothesize that recovering the eDNA of S.lemuru at a higher rate will be achieved by increasing filtered water, varying depths, & spatial distance [11,18]. This project result will be used for expanded monsoonal season monitoring & beyond.

What are the goals of the project?

Our main goal is to find S.lemuru, which is reported to have catch scarcity, so imports are needed for fish canning. We have already surveyed sites with abundant S.lemuru & sites with a declining but persistent population. We will survey 3 sites: one potential fishing site, one less potential (whether true decline or lack of fishing effort), & one site where S.lemuru scarcity was reported in 2012 [5,14,15]. Based on their vertical migration, we will filter seawater from 3-10 L triplicate at 3 & 15 m depth. Each water sample also offers other fish (i.e., substitute & invasive fish), meaning their unique DNA is revealed by eDNA. So, S.lemuru is an umbrella species symbolizing cheap & nutritious for local communities. We will publish findings & inform future decision-makers for monitoring.


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Field equipment, such as water pumps with weight bucket, CastAway-CTD for depth detection, peristaltic pumps, & 4.9 mm filter holders for eDNA filtration, has been supported by previous research collaborations between Federico M. Lauro, Sabine Matallana-Surget, & Aida Sartimbul groups through the National Research Foundation, the Prime Minister's Office (SG), & Natural Environment Council (UK) under the NERC-SEAP-2020 grant call, "Understanding the Impact of Plastic Pollution on Marine Ecosystem in Southeast Asia." Although high costs were covered for field equipment, we need extra funds to purchase field materials & eDNA sampling kits, rent a car and boat to access the site (304.3 km from Brawijaya University), & Illumina sequencers for eDNA analysis in a specialized lab. The technical methodology publication will be provided for long-term monitoring, mainly to verify the former fishing sites [5,15]. So, making recommendations is needed to provide the best eDNA sampling for S.lemuru.

Endorsed by

The project will be helpful in the detection of economic fish in Indonesia, like Sardinella lemuru, especially in mapping how this species is distributed and ecological impacts from fisheries locations in Indonesia, such as in Bali Straits. In addition, this research has been beneficial in revealing the distribution of this species at different depths to know how useful eDNA is in monitoring this species in the future.
This project show how eDNA will be beneficial for fisheries study in Indonesia.
It sounds like an exciting research idea to conduct, and I believe it would be beneficial into many aspects; it is not only for scientific communities, but also for many other stack holders.

Project Timeline

Field work was started from 2023-March 2024 to observe monthly fish landing, including S.lemuru and water quality in Bali Strait. The fieldwork period for eDNA will be from late June until the beginning of July 2024, during which we will trip to 3 sites at 2 depths. After trips, we will analyze the eDNA filter at a specialized eDNA laboratory, e.g., Oceanogen-Indonesia. This will result in a multispecies fish, including S.lemuru. Data analysis & writing will run from Oct 2024-Jan 2025.

Mar 29, 2024

Project Launched

Apr 15, 2024

Project Launched

May 27, 2024

Start Logistical Preparation

Jun 24, 2024

Travel to Muncar-Banyuwangi, West Part of Bali Strait, where S.lemuru fishing grounds have been recorded

Jul 01, 2024

Post pictures from field trips in this lab note platform

Meet the Team

Victor Adi Winata
Victor Adi Winata
M.Sc Student


Brawijaya University, Fisheries and Marine Science, Aquaculture Department
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Team Bio

My supervisor Aida Sartimbul, Ph.D is the regional leader of the national collaborative research on eDNA biomonitoring to investigate S.lemuru & fish diversity in the small island & coastal waters in Indonesia. Her expertise is inevitable. She accomplished milestones for S.lemuru research projects for years. Aida's connections enable us to run this project smoothly & efficiently.

My other supervisor Feni Iranawati, Ph.D, supports me scientifically & shares her experiences in fish genetics.

Victor Adi Winata

After completing my Bachelor's in Marine Science at Brawijaya University, Indonesia, I strongly desired to deepen my knowledge of environmental DNA (eDNA) to trace the Bali Sardine because of the significant dwindling and overfishing in the past decades in Bali Strait, Indonesia. I also estimate the fish diversity in Southern East Java & Bali Strait, which will be presented at the 2nd UN Ocean Decade Regional Conference. Since 2022, I have been pursuing a master's degree in Aquaculture, specializing in environment, at Brawijaya University to continue with my passion and work with Bali Sardine.

I am experienced with the fish genetics population with nuclear DNA & eDNA targeted for marine fish diversity via high-throughput sequencing. My previous research project specialization in the phylogenetic and population genetic study of Bali Sardine, based on the mitochondrial DNA, which was published (i.e., genetic connectivity of S.lemuru & Molecular and phylogenetic analysis of S.lemuru). The skills I honed during my previous project have equipped me immensely for my upcoming work with eDNA because of the challenge of obtaining S.lemuru morphological samples during the La Nina in the Bali Strait, & estimating fish diversity, including substitute & invasive fish.

During my graduate studies, I lead a fieldwork project as a representative field coordinator to collect microplastic biofilm microbes & eDNA sampling of bacterial communities in two depths in Bali Strait. I found that transcending research fields and borders to learn and exchange from diverse experts in Southeast Asia & the UK is most stimulating and critical to promoting collaborative projects in coastal environments with innovative molecular techniques in Southeast Asia in the face of global challenges, e.g., microplastics. During my time as a laboratory assistant since 2022, I have started to unravel jellyfish species, plankton communities, & pathogen bacteria with eDNA.

Lab Notes

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Additional Information

Any additional funding obtained beyond our goal through the eDNA grant innovation challenges and crowdfunding in the experiment platform will facilitate a fourth site of eDNA sampling conducted at the end of July in Southern East Java-Indonesia, including their eDNA sequencing. This fourth site was selected to confirm the consistency of the existence of S.lemuru because of the surprisingly high catch of S.lemuru during an intense El Nino event in 2019, followed by a high abundance of its food availability [17,19,20].

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