Metabarcoding of fish eDNA in the Java Sea

Mangrove ecosystems support a diverse array of animal species and also deliver pivotal ecosystem services to humans, such as coastal protection. However, these vital habitats are in global decline, leading to coastal degradation. To address this, a mangrove restoration project in Demak, Java, Indonesia, introduces the use of semi-permeable coastal protective barriers made of bamboo pilings to safeguard the shore zone and hinterland. Introduction of such hard substrate in the marine environment can attract a range of species and it is important to monitor changes in biodiversity from a restoration point of view. Here, we used environmental DNA metabarcoding to assess changes in fish biodiversity following the introduction of bamboo pilings. Our results show slight but significant changes in species richness and fish community composition upon the introduction of said substrate, although seasonal variation could be a confounding factor. More importantly, this study demonstrates a useful level of temporal resolution of eDNA metabarcoding and establishes a baseline for fish species richness in an understudied tropical mangrove coastal zone in Demak, Java, Indonesia. Our results are valuable for informing future restoration efforts and other (metabarcoding) biodiversity studies in the region.