Molecular studies on marine fish diversity in Java and Bali, Indonesia

Abstract

Marine ecosystem reflects a substantial contribution to genetic biodiversity than the freshwater and terrestrial ecosystem. The economic benefit is also generated from the marine ecosystem with the presence of aquatic biota that is used in fisheries and management of this valuable resources. Furthermore, numerous products are also capable of producing other derivatives those are more beneficial for the human being (e.g., for food and medicine) and for industrial purposes. Fish diversity in the specific marine ecosystem can be reflected in the health condition of the marine ecosystem, thus requiring the regular in monitoring and observation. Indonesia is the center of marine biodiversity which espouses with the extraordinary wealth of coral reef ecosystem. The previous study recorded 2,057 species in the marine ecosystem of Indonesia; then the latest of the FishBase database had been recorded 3,611 species, which confirms that Indonesia is the wealthiest country for coral reef fisheries. Traditionally, for estimating marine biodiversity has some limitations in a particular area, which uses bottom trawls and rotenone poisoning. Then, the lack of local taxonomist may stymie morphological-based species identification, which ubiquitous faces in developing countries. The previous study, combining between conventional survey and geographical information system (GIS) techniques, have been performed to comprehend fish distribution and spatial analysis. Presently, a sophisticated method had been developed to monitor biodiversity in aquatic ecosystems through environmental DNA metabarcoding analysis. The extraction and analysis of genetic materials obtained directly from the environment by collecting these living particles as an alternative approach to monitor and analyze marine fish and performed as time and cost-effective survey method can be applied as the alternative method in biodiversity assessment. The accuracy on detection of some endangered species, invasive species, and marine fish distribution was performed by environmental DNA metabarcoding had been performed by numerous researchers. In this research, environmental DNA metabarcoding has been conducted by marine water sample from Java and Bali Island, Indonesia, by the MiFish pipeline. The environmental DNA analysis in four sampling locations revealed 333 species in 405 representative haplotype (99-100% identity) and 52 putative species (95-98% identity). Alpha biodiversity in Bali, both south and north part, have higher than Java sampling site. The Shannon-Wiener Index and Margalef Index in north Bali are highest. In this study we found the fish species under the order Perciformes are dominat, we identified 295 haplotypes (72.84%) under this order, followed by Clupeiformes 29 haplotypes (7.16%) and Tetaraodontiformes 19 haplotypes (4.69%). The Perciformes most diverse order than others, with 44 families had been identified by eDNA metabarcoding analysis. The coral reefs, seagrass and mangrove ecosystem in both north Bali and south Bali was supported marine biodiversity on the Bali Island. That result revealed that the surrounding Lovina beach in the northern part has higher biodiversity. In conclusion, tropical marine fish around the Bali strait provides an overview of the effectiveness and sensitiveness of the method of environmental DNA metabarcoding in collecting primary data about the fish biodiversity of the given area. The next-generation sequencing (NGS) based tropical marine analysis fish will allow us to apply biodiversity information beside improvement of the GenBank database, especially in cryptic species for coral-reef fish species. Therefore, proper monitoring and regular survey should be taken, which may increase the number of marine fish detection along this region. Biodiversity study in this region is very crucial for the policy makers in sustainable marine water resources management.