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Metabarcoding of Fish Larvae in the Merbok River Reveals Species Diversity and Distribution Along its Mangrove Environment.

ABSTRACT: The Merbok River (north-west of Peninsular Malaysia) is a mangrove estuary that provides habitat for over 100 species of fish, which are economically and ecologically important. Threats such as habitat loss and overfishing are becoming a great concern for fisheries conservation and management. The identification of larval fish in this estuarine system is important to complement information on the adults. This is because the data could inform the spawning behaviour, reproductive biology, selection of nursery grounds and migration route of fish. Such information is invaluable for fisheries and aquatic environmental monitoring, and thus for their conservation and management. However, identifying fish larvae is a challenging task based only on morphology and even traditional DNA barcoding. To address this, DNA metabarcoding was utilised to detect the diversity of fish in the Merbok River. To complete the study, the fish larvae were collected at six sampling sites of the river. The extracted larval DNA was amplified for the Cytochrome Oxidase subunit 1 (COI) and 12S ribosomal RNA (12S rRNA) genes based on the metabarcoding approach using shotgun sequencing on the next-generation sequencing (NGS) Illumina MiSeq platform. Eighty-nine species from 65 genera and 41 families were detected, with Oryzias javanicus, Oryzias dancena, Lutjanus argentimaculatus and Lutjanus malabaricus among the most common species. The lower diversity observed from previous morphological studies is suggested to be mainly due to seasonal variation over the sampling period between the two methods and limited 12S rRNA sequences in current databases. The metabarcode data and a validation Sanger sequencing step using 15 species-specific primer pairs detected three species in common: Oryzias javanicus, Decapterus maruadsi and Pennahia macrocephalus. Several discrepancies observed between the two molecular approaches could be attributed to contaminants during sampling and DNA extraction, which could mask the presence of target species, especially when DNA from the contaminants is more abundant than the target organisms. In conclusion, this rapid and cost-effective identification method using DNA metabarcoding allowed the detection of numerous fish species from bulk larval samples in the Merbok River. This method can be applied to other sites and other organisms of interest.

SUBMITTER: Alshari NFMAH

PROVIDER: S-EPMC9169113 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The study of changes in species richness and composition along rivers has focused on large spatial scales. It has been ignored that in different sections of the river (high mountain area, middle zone, and mouth of the river) the specific environmental conditions can generate different longitudinal patterns of the species richness and composition. In this study, we determine whether species richness and composition of the riparian plant communities change along a mountain river and whether these changes are related to environmental variables. We expect an increase in species richness and turnover along the river, that the upstream communities would be a subset of the downstream communities, and that such would be related to edaphic and hydrologic conditions. To test this, we sampled three strata of the riparian vegetation (upper: individuals with <1 cm of ND, middle: individuals with >1 cm of ND, low: individuals with >1 m tall) in a set of 15 sites that we place along a mountain river. Additionally, we recorded topographic, hydrological, morphological, and soil variables. We performed correlation analyzes to determine whether changes in species richness and turnover were related to increased distance to the origin of the river. Also, we obtained the nestedness and evaluated the importance of environmental variables with GLM, LASSO regression, and CCA. With the increase in distance, the species richness decreases in the upper stratum, but not in the middle and the low stratum (although the highest values were observed near the origin of the river), the turnover increase in all strata and the upstream communities were not a subset of the downstream communities. The changes in species richness and composition were related to topographic (altitude), hydrological (flow), and edaphic (conductivity and pH) variables. Our results indicate that at small spatial scales the patterns of richness and composition differ from what has been found at larger spatial scales and that these patterns are associated with environmental changes in the strong altitude gradients of mountain rivers.

Project description:The primary objective of this study was to examine the status of woody species composition and diversity along the Walga River of Wonchi, Southwestern Ethiopia. Fifty quadrats of 10 m x 50 m were laid at 500 m interval through systematic sampling method along the river line. Vegetation height (≥2.5 m) and DBH (≥2.5 cm) of only tree species were measured and altitude, ecological disturbances such as, grazing intensity and human impacts were included as main environmental variables at each of the sampled plots. The data was analyzed using different R statistical packages. Ninety-nine woody vascular plant species belonged to 81 genera and 45 familieswere recorded in Walga riparian vegetation. Only 10% of specieswere endemic to the Flora area. Asteraceae and Fabaceae had the highest number of species. Majority of the species (52.5%) were shrubs. Four major plant community types were identified: Euclea divinorum-Maytenus arbutifolia (1), Pterolobium stellatum- Calpurnia aurea (2), Brucea antidysenterica-Prunus africana (3), Erica arborea-Hagenia abyssinica (4). Species richness, true diversity and importance values were highestin community type 2(the lowest altitude ranges between 1976-2212 m a.s.l.) while evenness was highestin community type 3(mid altitude ranges between 2359-2676 m a.s.l.). Both community typeswere comprised of 56% of all recorded species and all endemic taxa except two. The highest percentage of species in lower frequency classes indicates a higher degree of floristic heterogeneity. There was a strong negative correlation (r = -0.65, p<0.001) between species richness and altitude with 42% of the variation in species richness per plot being explained by altitude. Our findings suggest that human disturbances and excessive livestock grazing are the main threats in community types1 and 2. We conclude that identifying major plant community types and underlying environmental conditions may help to manage and conserve forest resources in the area.

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Metabarcoding of Fish Larvae in the Merbok River Reveals Species Diversity and Distribution Along its Mangrove Environment.

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