To estimate the impact of aggregate mining on a marine ecosystem, fish assemblages and phytoplankton communities were analyzed using environmental DNA metabarcoding. Metabarcoding analysis revealed 152 fish amplicon sequence variants (ASVs) (88 in September and 118 in February), which were assigned to 29 orders, 62 families, 104 genera, and 114 species (73 in September and 89 in February). Heatmap analysis showed that the fish assemblages in the mining area clearly differed from those in the surrounding area and that Pagrus major, Lateolabrax japonicus, Zeus faber, and Eopsetta grigorjewi were significantly more abundant there than in the surrounding area. In the phytoplankton community in September, the phyla Cyanobacteria and Haptophyta differed significantly between the mining area and its surroundings. By contrast, no such significant differences were identified in February, presumably due to the low temperature impeding phytoplankton growth. Taking these findings together, mining activities clearly affect fish and phytoplankton communities, but further long-term study is required to assess their impacts on marine ecosystems.

Although spatiotemporal analysis of the cephalopod larvae provides the useful information for the effective management of their resources, it has been difficult mainly due to their low numbers in the mixed zooplankton net samples and difficulty in morphological identification. In order to analyze the planktonic cephalopods using next-generation sequencing (NGS), we have designed a cephalopod-specific universal (CPD) primer set targeting a region covering mitochondrial cytochrome b and ND6 genes based on the currently identified 36 complete cephalopod mitochondrial genome sequences in the GenBank database. The expected amplicon sizes by CPD primers were between 465 and 471 bp, which was applicable to the MiSeq system (Illumina, San Diego, CA, USA). NGS results of pooled DNAs from 8 months (including 739 zooplankton net samples) collected from Korean waters in 2016 showed the exclusive cephalopod sequences with little contaminant sequences supporting the specificity of CPD primer set. Total 47 representative cephalopod haplotypes (seven families and 10 genera) were obtained from 1,439,414 merged reads. Among the total analyzed haplotypes, Watasenia scintillans, Todarodes pacificus, and Sepiola birostrata were the most abundant species in Korean waters. Two “unidentified” clades in order Oegopsida were identified, which was showed less than 90% sequence identity but closely related to Enoploteuthidae and Idiosepiidae, respectively. Monthly changes in proportions of each haplotype were also identified, which may reflect its reproduction and spawning period. The larvae of W. scintillans was dominant from February to June, while high proportions of other cephalopod taxa were also identified from August to November. Only single haplotype was dominant in W. scintillans (Type 2) throughout the year, while two distinct haplotypes showed seasonal differences in T. pacificus.

The Japanese sea lion, Zalophus japonicus, is an extinct pinniped species, which had inhabited along the coast of the Japanese archipelago and Korean peninsula. Its mitochondrial genome was determined by the assembly of PCR amplicons from the skeletal remains excavated from the Ulleungdo, South Korea. The whole mitogenome was 16,698 bp in length, which encoded 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA), 2 ribosomal RNAs (rRNA), an origin of light-strand replication (OL), and a control region (D-loop). Unusual start codons were identified in ND2 (ATA), ND3 (ATA), and ND5 (ATC), while COIII, ND3, and ND4 were terminated with an incomplete stop codon (T-/TA-). Phylogenetic analysis showed that Z. japonicus was a sister species to Z. californianus with 98.61% nucleotide sequence identity among 11 pinniped species in the infraorder Pinnipedia, which supported the previous results. The complete mitochondrial genome sequence of Z. japonicus would be valuable information for its restoration and the evolutional understandings of pinniped species in the Pacific Ocean.

As one of efforts to conserve a genetic resource of the endemic cobitid species in the Korean peninsula, the complete mitogenome of Cobitis hankugensis (Kim, Park, Son & Nalbant, 2003) was determined using Illumina MiSeq system. The circular mitogenome was 16,557 bp length and encoded 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 tRNA genes, and a control region. Only the COX1 gene was identified with an aberrant initiation codon GTG, and an incomplete termination codon (T—/TA–) was identified in six PCGs including COX2, COX3, ND2, ND3, ND4, and Cytb genes. Phylogenetic analysis using 30 mitochondrial genomes belonging to Cobitidae, Botiidae, and Gyrinocheilidae showed that the highest identity (92.38%) with Kichulchoia brevifasciata (NC_027166). The complete mitogenome of C. hankugensis , an endemic species in Korea, will provide fundamental data on the evolutionary relationship of Cobitidae species.