Two tropical sea cucumber species, Holothuria (Thymiosycia) impatiens and H. (Cystipus) inhabilis, collected from Kushimoto, Wakayama, are reported here for the first time from Japan’s Honshu Island, extending the geographical range of these species northward. Here we describe their external, internal and ossicle morphologies along with the phylogenetic position of the two species. We present DNA sequence data on three Japanese Holothuria species, H. (T.) impatiens, H. (C.) dura and H. (C.) inhabilis, including two from the Cystipus subgenus for the first time. Phylogenetic analysis was performed using two mitochondrial gene markers in combination with sequence data from other Holothuria species. Our phylogenetic tree showed (1) Japanese H. (T.) impatiens formed a monophyletic clade with specimens from other waters, and (2) the two Cystipus species were divided into polyphyletic positions topologically.

Microphytobenthos (MPB) are important primary producers in tidal flats that supply various ecosystem services. However, high turbidity water can limit the amount of photosynthetically active radiation (PAR) that reaches the seafloor in estuaries. Most studies assessing MPB production have been conducted using culture bottles placed in situ for short periods (e.g., one day). However, the in situ method does not take into account changes in weather conditions and/or tidal cycles, and errors may occur when obtaining representative values over a longer period (monthly to yearly). Here, we measured, with high resolution, primary production (PP) of MPB in the Midori River tidal flat facing the Ariake Bay, Japan, by combining photosynthesis–irradiance curves from laboratory experiments and continuous PAR measurements from a mooring system above the seafloor. We compared the median PP and in situ PP (PP_{in situ}, assumed to be PP during the spring tides) for each season. We found that the PP_{in situ} values were 0.887 to 1.92 times the values obtained from the laboratory experiment and the mooring system. The PP_{in situ} values, which varied greatly and were uniformly distributed, had maximum values that were 2.8 times higher than the representative values, except in the spring (1.29 times higher); and the minimum values ranged from 0.00994 to 0.654 times the representative values. Our results suggest that the monthly PP values obtained from the in situ slurry method are erroneous.

Prey often share predation risk with their neighbors. The presence of neighbors can dilute the probability of attack on any given individual, thereby decreasing predation risk. If the identity of a neighboring prey species affects predation risk, prey individuals might alter their antipredator response accordingly. This study tested the hypothesis that the intertidal gastropod Nassarius hypolius responds differently to the carnivorous whelk Neptunea arthritica in the presence of neighboring conspecifics, Gigahomalopoma sangarense, or Cantharidus japonicus. Both Na. hypolius and G. sangarense are preferred over C. japonicus by the whelk, but the handling time for G. sangarense is approximately 10 times longer than that of the other two species. This suggests that the predation risk to Na. hypolius is more strongly reduced by the presence of neighboring G. sangarense than by conspecifics, but less strongly reduced by neighboring C. japonicus. The frequency of antipredator response (i.e., burrowing in the sand) before and after exposure to a predator stimulus were compared among three groups in which a focal Na. hypolius was placed among five (1) conspecifics, (2) G. sangarense, or (3) C. japonicus. A significant increase in the frequency of antipredator response was observed in groups 2 and 3 following the predator stimulus, but not in group 1. Although this suggests that the antipredator response of Na. hypolius is influenced by the identity of neighboring prey species, the direction of response did not align with our initial hypothesis. Alternatively, Na. hypolius may tailor its antipredator response to the density of nearby conspecifics.

We investigated the benthic fauna in central Sagami Bay, Japan, using dredge sampling from 2006 to 2019. When we rechecked all the samples, two lingulid brachiopod individuals were discovered in those collected in 2009. The shell shape and pedicle features of these lingulids were similar to those of Lingula reevei. However, some distinct morphological characteristics, including the separation of the anterior and median internal oblique muscles from the perimial line, were also observed in these individuals. In genetic analyses using the DNA sequences of nuclear 28S rRNA and H3, as well as mitochondrial 16S rRNA and COI, one lingulid individual, from which we successfully extracted total DNA, differed by only one base pair in the COI from a known member of the L. reevei complex from the waters adjacent to Japan. The genetic distance between this individual and L. reevei collected from the type locality in Hawaii was substantial. Therefore, L. aff. reevei and the known member of the L. reevei complex from the waters adjacent to Japan are the same species but should not be identified as L. reevei.

The golden mussel, Limnoperna fortunei (Dunker), is small freshwater bivalve species native to China and Korea that is invasive in Japan. To establish efficient control of the mussel by drainage of reservoirs, I investigated its survival time under dry conditions in field experiments during fall and winter, and examined the effects of temperature, rainfall, and body size on survival. Following drainage, complete mortality took 7 to 15 days. Drainage for at least 15 days is recommended to ensure mortality. The main factors affecting survival were drying time, temperature, and body size, but the effect of drying time varied with temperature. Complete mortality was fastest during the coldest months, and therefore drainage during this period may be effective in achieving mortality quickly.

The massive outbreaks of the giant jellyfish Nemopilema nomurai have caused serious problems in fisheries, and monitoring its distribution is necessary to predict its occurrence around Japan. In this study, we designed a primer/probe set of mitochondrial 16S for species-specific qPCR to detect N. nomurai. The utility of qPCR using environmental DNA (eDNA) was compared with conventional approaches (sight survey and net collection) in the Sea of Japan and the East China Sea in 2021–2023. The newly developed qPCR method showed an average 98.9% PCR efficiency (r²=0.9992). In the East China Sea, the highest copy numbers of the species were observed at stations using conventional methods to detect the maximum number of N. nomurai. The qPCR method also detected N. nomurai at stations that reported no observations using conventional methods in both sampling areas. Possible DNA degradation was observed in eDNA samples from the Sea of Japan in 2021, and the qPCR method detected N. nomurai at only a subset of the stations that reported the species using conventional methods. These results indicate that qPCR using eDNA can be an effective monitoring tool for N. nomurai; however, eDNA should be properly preserved and analyzed immediately to prevent its underestimation.