Toward ecosystem-scale biodiversity monitoring: Metabarcoding of microbial and environmental DNA from identical water samples
1Department of Biological Sciences, the University of Tokyo, 2Department of Computational Biology, the University of Tokyo, 3Atmosphere and Ocean Research Institute, the University of Tokyo, 4Department of Zoology, Natural History Museum and Institute, 5Tohoku Medical Megabank Organization, Tohoku University, 6Okinawa Churashima Research Center, 7Kobe University, 8Faculty of Science and Technology, Ryukoku University, 9Research Faculty of Agriculture, Hokkaido University
In addition to microbial cells, environmental samples also contain environmental DNA (eDNA), which are DNA molecules shed by any organism into the environment and can be targeted by a combination of PCR amplification and next-generation sequencing. Recently, we developed a set of universal PCR primers (MiFish-U/E) for metabarcoding fish eDNA, by analyzing whole mitochondrial genome (mitogenome) sequences from 880 fish species and partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163_185_bp) and successfully detected 93.3% of fish species distributed across 59 families and 123 genera, when applied to water tanks of the Okinawa Churaumi Aquarium with known species compositions. We subsequently applied the MiFish-U/E primers to 48 seawater samples collected for marine microbial community analysis off the coast of the Tohoku area from October 2012 to March 2014. The amplicon-seq analysis using the MiFish-U/E primers detected several fish species that are typically found in northern Japanese coastal areas, proving that simultaneous metabarcoding of microbial and environmental DNA from identical water samples is possible. We argue that, by taking advantage of the fact that environmental samples contain abundant information about compositions of not only microbial but also diverse organisms in the ecosystems, biodiversity monitoring can enter the next stage.
keywords:bioinformatics,metabarcoding,environmental DNA,PCR primers,biodiversity monitoring