Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool

The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning.

First documentation on herpetofauna diversity in Gunung Belumut Amenity Forest, Peninsular Malaysia: Implications for conservation in an Environmentally Sensitive Area (ESA)

Malaysia is blessed with lush tropical rainforests that harbour an exceptional diversity of amphibians and reptiles. However, compared to other animal groups, amphibians and reptiles have received limited attention in research, despite their ecological significance. With amphibians and reptile species having been declining rapidly due to anthropogenic activities, there is a pressing need to conserve these species and their habitats. Environmentally Sensitive Areas (ESAs) are designated regions that are beneficial due to their critical role in providing essential ecosystem services and serving as repositories of biodiversity. Nonetheless, the classification of ESAs in Malaysia lacks biological elements and only focuses on physical attributes. To enhance the current ESA classification framework by integrating biological components, there is an urgent need to obtain information on diversity and habitat in Malaysia. Therefore, the objectives of this study were twofold: to determine the diversity of amphibians and reptiles in Gunung Belumut Amenity Forest and to conduct a comparative analysis between the herpetofauna assemblages in Gunung Belumut with other forest reserves in Peninsular Malaysia. The survey was carried out between March and June 2022, with additional sampling conducted in February 2023. The Visual Encounter Survey (VES) and pitfall trap methods were employed to survey the herpetofauna species, focusing on both aquatic and terrestrial habitats within the study area. A total of 210 individuals representing 38 species of herpetofauna were recorded, comprising 18 amphibian and 20 reptile species. Amongst the observed species, Limnonectesblythii was the most frequently encountered amphibian, with 59 individuals observed, while the dominant reptile species was Cyrtodactylusconsobrinus, represented by eight individuals. This pioneering study serves as a vital baseline documentation of the amphibian and reptile assemblages in Gunung Belumut Amenity Forest. It provides valuable information for identifying extant herpetofauna species, including those of potential conservation concern or rarity. These findings contribute to ongoing conservation efforts dedicated to the preservation of herpetofauna within the region. By understanding the diversity and distribution patterns of amphibians and reptiles in Gunung Belumut, effective conservation strategies can be developed to protect these species and their habitats.

Understorey bird assemblages in selected environmentally sensitive areas (ESA) of Selangor, Peninsular Malaysia

Environmentally Sensitive Areas (ESA) refer to areas that are of critical importance in terms of ecosystem services such as goods, services and life-support systems, such as water purification, pest control and erosion regulation. In addition, they also refer to areas that harbour the wealth of the nation's biodiversity. However, the classification of ESA in Malaysia is incomprehensible and lacks weightage on biological elements as the current classification is more centred on physical attributes. In order to enhance the existing classification of ESA by introducing biological elements, biological data are urgently required, especially for forest reserves and protected habitat. Hence, we conducted understorey birds surveys in three ESA rank II permanent forest reserves, located in northern Selangor as baseline information to strengthen the ESA classification. The surveys were carried out using mist-netting in three 400 m × 200 m plots. Alpha diversity indices were calculated and showed a significant difference in terms of diversity, composition and biomass of understorey birds between investigated sites. Analysis of similarity (ANOSIM) showed that bird assemblages from forest reserves designated as ESA rank II in Selangor, based on disturbances levels, have weakly diverged and SIMPER analysis has identified six species that contributed to 60% of the differences amongst the bird assemblages. The finding provides the first insight into understorey birds of the study sites and the importance of conserving and preserving ESA of permanent forest reserves, especially the small and fragmented forests.