On the eDNA Trail of the Mekong Giant Catfish

eDNA Sampling

It’s surprisingly difficult to find some of the world’s biggest fish. Despite their behemoth size, many of the largest freshwater fish species are critically endangered, meaning there are few of them left to find. Such is the case of the Mekong Giant Catfish (Pangasianodon gigas), the world’s largest freshwater fish, which can grow up to nearly 10 feet long and weigh 650 pounds. Trying to track down this elusive giant in an expansive setting like the Mekong River Basin is a daunting task, coupled with the fact that many traditional fish sampling methods, such as using nets or electrofishing, could injure or kill these rare fish. That’s where environmental DNA (eDNA) techniques can come to the rescue. Methods using eDNA can detect trace amounts of genetic material that a fish or other animal leaves behind in the river, whether from skin cells, mucus, urine, or other sources. A team of researchers from the French laboratory SPYGEN, Griffith University in Australia, and the World Wide Fund for Nature (WWF) in Laos has successfully demonstrated the use of eDNA for detecting giant catfish in the vast Mekong River (Bellemain 2016). These findings suggest new approaches for the study and conservation of rare aquatic species.

There are many benefits and challenges to using eDNA in freshwater ecosystems. Studying eDNA from water samples is a non-destructive way to sample for many species at once, including very rare species. However, DNA breaks down rapidly in the environment, leaving a short window of opportunity to detect it, and such studies can’t confirm if the species is alive or dead. Still, the approach holds appeal for settings where finding a rare fish is like searching for a needle in a hay stack. To test for eDNA, water samples are collected, filtered, and probed with special genetic tools called primers that latch on to and amplify DNA from a particular species of interest. The study of giant catfish in the Mekong is the first to apply eDNA tools to detect a single species of interest in a large and diverse tropical river that is filled with hundreds of other fish species.

Mekong Catfish Sign

The team validated the eDNA technique at a reservoir in Thailand that serves as a hatchery for Mekong giant catfish. Successfully detecting Mekong giant catfish DNA in water where the fish were definitely present helped confirm the tool was sensitive to this species. The team then set out to collect water samples to search for giant catfish along the Lower Mekong River, traveling to six locations in Laos, Thailand, and Cambodia. They chose their sampling locations based on historical catch records of Mekong giant catfish, as well as the ecological knowledge of local fishermen. Mekong giant catfish are known to seek refuge in deep pools in the river during the dry season when the water level is lower. The scientists therefore collected water samples at deep pools during the end of the dry season (April and May). Using a tool called an immersion cylinder that can collect water from specific depths, they sampled at the bottom of the river, in the middle of the water column, and at the water’s surface at each site.

After analyzing their samples in the laboratory, the team documented a single positive detection of giant catfish DNA at one site, on the border between northern Thailand and Laos, in an area that local people believe the fish uses for spawning. The scientists conclude that the scant results highlight the rarity of the species, and the multiple conditions that must be met to obtain a positive eDNA detection. The study authors write that eDNA is a useful tool for conducting baseline biodiversity surveys in rivers, and for identifying key locations that can be more intensively sampled with other methods, or designated as protected areas. The many threats to the survival of the giant catfish underscore the need for innovative approaches to conservation in the Mekong basin, such as this one.

Project Launch: Wonders of the Mekong

Kids holding fish along river bank in cambodia

The Mekong River sustains life for millions of people and is remarkable for the diversity of its wildlife; however, the river is also threatened by the rising pace of development and faces many complex challenges. These challenges have inspired a group of experts to come together through a new initiative called Wonders of the Mekong, which seeks to understand and communicate the value of the Mekong River.

confluence of tonel sap river and mekong river

Launched in Phnom Penh, Cambodia, on 7 February 2017, the project is a partnership between the University Nevada Reno’s Global Water Center and the Inland Fisheries Research and Development Institute of Cambodia (IFReDI), with funding from U.S. Agency for International Development (USAID). Other collaborators include FISHBIO, the University of Sydney, and Utah State University. This interdisciplinary team will study the economic, environmental, and cultural importance of the Mekong to describe the tangible and intangible benefits of this rich ecosystem.

The project also hopes to foster discussions around aligning development goals with conservation, and how the Mekong region can adapt to a changing climate. We are excited to regularly feature stories from this project through the Mekong Fish Network website. You can watch a video introducing the project here, and can follow the project on Facebook, Twitter, and Instagram for more updates.

Same River, Different Catch: Findings from Lao Fishermen

Measuring Fish Length

Neighboring rural villages nestled on the banks of the Mekong River in Laos seem to blend together as you pass by, and it may be easy to assume that these communities share similar fishing practices. However, FISHBIO found this is not always the case through a fisheries study that involved the participation of fishermen themselves. Small-scale fisheries, such as those in Laos, are often dispersed in hard-to-access rural locations, and may require non-traditional approaches to fisheries monitoring. Participatory research methods directly involve fishers in the process, build on their local ecological knowledge, and are generally a cost-effective approach in these situations. FISHBIO recently completed a final report on a pilot project we conducted to test participatory fisher survey protocols in two neighboring villages on the Mekong River in Sangthong District near the Lao capital of Vientiane. This project trained local fishers to gather data on their catch, which is essential for developing effective conservation and management strategies. The project also focused on collecting baseline information on Jullien’s Golden Carp (Probarbus jullieni) and thicklipped barb (Probarbus labeamajor), two commercially valuable fish listed as “endangered” on the IUCN Red List.

The pilot study spanned a three-month period in the Lao dry season between October 2013 and January 2014. FISHBIO staff led the study with assistance from District and Provincial Agriculture and Forestry Offices, and with funding from The Mohamed bin Zayed Species Conservation Fund and FISHBIO. The villages of Ban Sakai and Ban Ang Noi along the Mekong River were selected based on reports of nearby spawning habitat for Probarbus fishes. Many fishers in this area target spawning Probarbus because they fetch a high price across the river in Thailand. Five fishers selected as fisher technicians in each village were trained to collect data on their own catch. For this pilot effort, we focused on fishing practices that are predominately performed by male fishers in the mainstream rivers; however, it’s important to note that women also play an important role in Lao fisheries.

The results of the study indicate that fishers in the two villages used different gear types, which made sense because the river habitats fished by the two villages differed considerably, despite their proximity. In Ban Sakai, there is a deep pool and rapids near the village, and the most common gear type was a bottom longline weighted down with rocks. In Ban Ang Noi, the river is shallow and sandy, which can cause disconnected off-channel pools to form in the dry season, and the most common gear type were nets (usually gill nets). The average daily catch per fisher ranged between 0.52 and 1.67 kg per day, which is higher than the average of 0.32 kg per day per fisher reported by the Mekong River Commission’s log book program, a similar participatory monitoring program in the region (Halls et al. 2013).

Fig1_Ban Ang Noi Species CompFigure 1. Species composition by number of individuals in the catch in Ban Ang Noi.

Fishers reported catching more than 54 species (40 genera), and the composition of the catch differed between villages. Catch in Ang Noi was dominated by small individuals of the cyprinid Amblyrhynchichthys truncatus, which made up 89% of the catch by number of individual fish and 25% of the fish catch by weight (kg) during the study in this village. In contrast, this species only made up about 3% of the fish captured in Sakai, where various Bagarius catfish species were the dominant fish at 43% of the catch. Probarbus, our fish species of interest, were infrequently reported, making up only 0.43% (n = 19) and 0.41% (n=3) of the catch by number of individuals in Ang Noi and Sakai, respectively. However, it is notable that Probarbus made up 18% of fish catch by weight in Ang Noi. The largest individual recorded in the study was a Probarbus labeamajor that weighed over 16 kg, although the species can grow up to 70 kg (Baird 2006).

Fig2_ Ban SakaiFigure 2. Species composition by number of individuals in the catch in Ban Sakai and Ban Ang Noi.

During the closing workshop for this project, participating fishers expressed concerns about having enough fish for future generations. A fisher with more than 40 years of experience on the Mekong River reported he has only used gill nets for the past 10 years. Before then, he did not catch Probarbus and used traditional fishing gear, such as bamboo traps and hook and line. Similarly, Baird (2006) reports that before the early 1970s, Probarbus were generally abundant in Southern Laos, and large-mesh nylon gill nets were rare. However, Probarbus are now an important target fish in a gill-net fishery, and catch has been declining, suggesting declines in Probarbus in Laos may be associated with modernization of fishing gears. The communities are especially troubled by the lack of enforcement to address illegal fishing gears (electrofishing gear and dynamite), and are interested in establishing, enforcing, and monitoring fish conservation zones to better manage their community-based fisheries. The first step toward improved management would be developing co-management committees and fisheries regulations. The information presented in this report can serve as a starting point for developing local fisheries co-management, which is a key part of FISHBIO’s work in Lao PDR. Watch a new video about the project here.

The Greater Mekong Forum

Forum Group Photo

The Greater Mekong Forum on Water, Food and Energy is the largest meeting that focuses on the costs and benefits of balancing water, food, and energy necessary for sustained growth around the Mekong region. The Forum was held in November 2016 in Thailand, and saw attendance from more than 360 participants representing 30 different nationalities and 185 different organizations. This reflected quite an increase in participation compared to 2015 when only 139 participants attended. The Consultative Group for International Agricultural Research (CGIAR) Program on Water, Land and Ecosystems (WLE) hosted the forum with support from the Department of Foreign Affairs and Trade (DFAT) of the Australian government and the International Water Management Institute (IWMI) in Thailand. The Forum consisted of 35 sessions organized under six themes that included governance, resettlement, food and development, monitoring for management, a changing environment, and energy solutions.

Invertebrate Activity

This Forum allowed for researchers and technical experts to share their experiences, and provided a good opportunity for FISHBIO Laos and The Asia Foundation to give a presentation on monitoring macroinvertebrates to assess river health. Before giving the talk, the presenters played a macroinvertebrate picture game with attendees so they could  learn how to identify species of macroinvertebrates, such as insect larvae or molluscs, and how to assign each species a score related to river water quality condition.

Forum panel

At the end of the workshop, an evaluation survey was conducted to learn whether the participants found the knowledge and experiences shared during the forum to be useful. The evaluation results show that participants thought water quality monitoring using macroinvertebrates to assess river health was a very informative method that could be applied in different habitats where there are the streams, rivers, and even wetlands.  It was very exciting day for participants to meet many people and build their networks with technical  experts from many different counties.

Innovative Solutions for Fish Passage

Pak Peung Fishway

Water infrastructure is being developed at an increasing rate in the Lower Mekong Basin (LMB), and fish passage technology may help alleviate some of the impacts on fish populations, thereby sustaining food security. The “Lower Mekong Fish Passage Conference: Applying Innovation to Secure Fisheries Productivity” held in Vientiane, Lao PDR, in November was hosted by the Living Aquatic Resources Research Centre (LARReC) in Lao PDR, and supported by the Australian Centre for International Agricultural Research and the U.S. Agency for International Development. This conference built on a previous fish passage conference hosted by the Lao government in 2013, and it brought together experts in river development, fish passage, and fisheries ecology experts from around the world, along with local government agencies and provincial and district leaders. The objective was to share current research and discuss opportunities for sustaining fish populations and healthy aquatic ecosystems during this period of dramatic economic development.

To set the stage on the first day of the conference, and speakers discussed the overall importance of fisheries in the LMB. In 2015, the economic value of the LMB fisheries was estimated at 17 billion USD, explained Dr. So Nam of the Mekong River Commission during the plenary talks. In Lao PDR alone, fisheries contributed 13% of the national gross domestic product. Dr. Nanna Roos of the University of Copenhagen described how fish can be pivotal in addressing childhood malnutrition in LMB. Fish can be considered a ‘superfood’ because of their long chain fatty acids, vitamins and minerals, and if children can secure good nutrition during the first three years of life, then they will benefit more from the nutrition than in any other period. Dr. Caroline Garaway from the University College London described how fisheries play an important and diverse role in the livelihoods of people in the Lower Mekong Basin, so it is important to consider how development may cause uncertainty in people’s lives, and to look for ways to support sustainable livelihoods. Dr. Ian Cowx, University of Hull, explained how it is possible to communicate the importance of fish conservation and fisheries livelihoods by talking in terms of ecosystem services. Later in the day, FISHBIO researchers followed up on this topic by presenting on the importance of ecosystem services of wetlands in Cambodia and Vietnam, with a particular focus on an ongoing project funded by SUMERNET.

Presentations in the second day examined fish passage projects in the Lower Mekong Basin and provided technical details on fish passage successes and challenges. Participants toured the fishway at Pak Peung wetland in Pak San and heard from researchers and district officials involved in the design and implementation of the project. This demonstrated an example of a successful fishway designed specifically for Mekong fish species. The final day of the conference focused on hydropower research in the LMB, including lessons learned and developer’s perspectives. Dr. Toby Coe of Fishtek Consulting and Guillaume Morier-Genoud of Poyry gave presentations on the design and development of the fish passage facilities at the Xayaburi Dam, the first dam on the mainstem of the Mekong outside of China. The fish passage facilities at the dam include a massive 500-m long, 18-m wide vertical-slot fish passage that leads to two vertical fish locks, which will lift fish the rest of the way to the top of the dam. As this is the first fish passage of its size in the region, the presenters as well as audience members stressed the need for an extensive monitoring program to determine the effectiveness of these facilities. In the afternoon, Karl Pomorin (KarlTek Pty Ltd.) and Dr. Lee Baumgartner (Charles Sturt University) gave presentations on PIT tag technology and how it could be used in the region. The presenters explained how they have already tested the feasibility of tagging local species and have plans to install PIT tag antennas in the fishway at Pak Peung wetland to collect data on fish passage into and out of the wetland. We are grateful to the conference hosts for planning this valuable conference and look forward to future opportunities to exchange knowledge about fisheries in the basin.