Environmental DNA (eDNA) metabarcoding approaches to surveillance have great potential for advancing biodiversity monitoring and fisheries management. For eDNA metabarcoding, having a genetic reference sequence identified to fish species is vital to reduce detection errors. Detection errors will increase when there is no reference sequence for a species or when the reference sequence is the same between different species at the same sequenced region of DNA. These errors will be acute in high biodiversity systems like the Mekong River Basin, where many fish species have no reference sequences and many congeners have the same or very similar sequences. Recently developed tools allow for inspection of reference database coverage and the sequence similarity between species. These evaluation tools provide a useful pre-deployment approach to evaluate the breadth of fish species richness potentially detectable using eDNA metabarcoding. Here we combined established species lists for the Mekong River Basin, resulting in a list of 1345 fish species, evaluated the genetic library coverage across 23 peer-reviewed primer pairs, and measured the species specificity for one primer pair across four genera to demonstrate that coverage of genetic reference libraries is but one consideration before deploying an eDNA metabarcoding surveillance program. This analysis identifies many of the eDNA metabarcoding knowledge gaps with the aim of improving the reliability of eDNA metabarcoding applications in the Mekong River Basin. Genetic reference libraries perform best for common and commercially valuable Mekong fishes, while sequence coverage does not exist for many regional endemics, IUCN data deficient, and threatened fishes.

The Mekong River is one of the world’s largest rivers and has an annual captured fish production of about 2.3 million tonnes, equivalent to around 11 billion USD. Although the Mekong provides important ecological and socioeconomic benefits to millions of people, it is facing intensive change due to anthropogenic stressors. Therefore, it is necessary to understand the changes to the spatiotemporal fish communities to inform sustainable fisheries management. Here, we aimed to characterize patterns of the fish communities and identify the ecological status of each fish community using daily catch data from 2007 to 2018 at 25 monitoring sites in the Lower Mekong Basin (LMB). The collected data were classified by a self-organizing map into four main groups. Group 4 represented the lower Vietnam Mekong Delta (VMD), while groups 1, 2, and 3 were subdivided into subgroups 1a (upper LMB), 1b (upper and middle LMB), 2a (Mekong River below the Khone Falls and Sesan River), 2b (Mekong River below the Khone Falls and Sekong, Sesan and Srepok (3S) Rivers), 3a (Floodplain-Tonle Sap and Songkhram) and 3b (upper VMD). Among the 571 species recorded, 119 were identified as indicator species. Based on the abundance and biomass comparison curves, the fish community of 2b was in a healthier condition with a positive W-statistic value while the rest had a negative W-statistic value. The highest species richness and diversity were observed in 3a and 2b, so these subgroups deserve high management and conservation priority. Likewise, 1a should also be considered as a high priority area since it harbors several endangered and long-distant migratory fishes. It was also noticed that the fish communities of groups 3 and 4, located far from the hydropower dams, remained mostly unchanged compared to those of groups 1 and 2, close to the mainstream and tributary dams in the upper LMB and 3S Rivers.

Since fishery resources are regarded as an important source of income and food security, these resources need to be protected and conserved for sustainable use. To do this, the government of Cambodia has revised its policies, shifting management and responsibility to the local level. In response to government policy, Krala Peah village community fishery was established to manage resources within the area. The purpose of this study was to assess the outcome of community fishery management. Moreover, community fishery management was assessed through face-to-face interview and a participatory approach. The major findings of this study indicate that community fishery has led to a more equitable and efficient fishery within Krala Peah village. Although it has not led to improvements in fishing habitats and fish catch, it has reduced some factors that adversely affected sustainability. Furthermore, it has caused a reduction in illegal fishing, which was the main objective of the fishers.

The Mekong River faces increasing environmental threats. To understand fish community responses to these threats, we explored the links between functional diversity (FD) dynamics and environmental changes across four sites using trait-based methods and fish monitoring data for 347 species. We assessed functional richness (FRic) and divergence (FDiv) using standardized effect sizes to investigate the main assembly rules structuring fish communities and used generalized additive models to identify key environmental drivers. After dam construction, all four sites experienced significant changes in environmental conditions. Deterministic processes, particularly environmental filtering, dominated in structuring fish communities. The upstream Lao People's Democratic Republic site (LPB) influenced by deterministic and stochastic processes. The Cambodia sites in Stung Treng province (CST) and Tonle Sap (TLS) Lake primarily driven by deterministic process with a decline in FRic and FDiv. Conversely, the Viet Nam site (VCM) seemed primarily influenced by stochastic process with more subtle environmental effects, evidenced by an increase in FRic and FDiv over time. The upper sites (LPB, CST, and TLS) displayed a distinct seasonal pattern in FD indices, with values decreasing during the dry season and increasing during the wet season. Conversely, the lower site (VCM) exhibited the opposite. Water level emerged as the key driver across all sites, with temperature and total nitrogen as secondary drivers. Dam impacts and other anthropogenic factors not included in our analyses (e.g., unsustainable fishing and habitat degradation) probably contributed to the observed changes in FD at specific sites. These findings highlight potential strategies for conservation, offering national and regional practitioners an opportunity to develop and refine river management plans.