Coastal shallow water, particularly tidal flats, provide essential ecosystem services, with bivalves playing a key role in material cycling. This study assesses the impact of bivalves on material cycling processes in the Hichirippu Lagoon, Hokkaido, and the Midorikawa River tidal flats, the Ariake Bay, Kyusyu, Japan, to clarify the systems supporting their populations. Carbon and nitrogen stable isotope analyses of the Hichirippu Lagoon revealed that the dense clam (Ruditapes philippinarum) population mainly feeds on microphytobenthos, with daily feeding rates comparable to the standing stocks of primary producers such as microphytobenthos and phytoplankton. Long-term observations indicated that during summer, clam excretions support microphytobenthos productivity, thereby sustaining an internal nutrient cycle. Conversely, during winter, oceanic nitrate supports system productivity. In the Midorikawa River tidal flats, the maintenance of Asian mussel (Arcuatula senhousia) populations necessitates external food inputs, given that their feeding rate can reach ≤ 22-fold the primary production. The accumulation of mussel feces in sediments corresponded with the secondary production scale, highlighting feces, alongside feeding and the secondary production, as integral to material cycling. This study explores bivalve population dynamics by examining nutrient cycling, primary production, and organic matter flows, aiming to illuminate the broader ecological roles bivalves play within these ecosystems.

The family Smeagolidae (Mollusca: Gastropoda: Pulmonata) typically inhabits the undersides of boulders buried in gravel bottoms and crevices on beaches. These snails have a colourless, translucent, tiny slug-like body that is approximately 2–10 mm in length, and notably lack shells, eyes, and tentacles. Smeagolidae is an exceptionally rare taxon globally, with only five described species known from Australia and New Zealand in the Southern Hemisphere and only four islands of Japan in the Northern Hemisphere. The taxonomic position of this family remains uncertain owing to its unique morphology and distribution patterns. This study presents the first record of Smeagolidae in Honshu from Wakayama Prefecture, Japan. Over an 11-year period (2014–2025), distribution surveys across 88 sites in the prefecture revealed the presence of Smeagolidae, specifically in Cape Shionomisaki, Kushimoto-cho. Cape Shionomisaki became the fifth locality in the Northern Hemisphere after Narugashima Island in the Hyogo Prefecture, thereby extending the easternmost boundary of its distribution in the Northern Hemisphere. The survey documented a substantial population of Smeagolidae, totalling 582 individuals over a 2-year period, making it the largest population discovered worldwide. Despite the restricted habitat, observations throughout the study period at Cape Shionomisaki suggest that this family may have completed its life cycle in the area. Further investigations using both morphological and molecular analyses are needed to determine whether the Smeagolidae discovered in Wakayama Prefecture belong to the same species found at other sites in Japan.

To analyze length-frequency data obtained simultaneously from multiple sites, we developed a new R function for estimating parameters of Gaussian mixture models that can be applied concurrently to multiple datasets with varying mixing ratios. The new function, “GMM_EM”, estimates parameters (means, standard deviations, and mixing ratios) by maximizing the log-likelihood of the Gaussian mixture model using the Expectation-Maximization (EM) algorism. The number of Gaussian components must be specified prior to running the function. To evaluate the performance of the new function, two datasets were analyzed: artificially generated length-frequency data and empirical length-frequency data for Ruditapes philippinarum obtained from 20 sites during a field survey at Yokohama-Umi-no-Koen (Marine Park). Results were compared with those obtained using the existing function “normalmixEM”.

Macrobenthic fauna were investigated at nine sites in shallow coastal habitats, including bare flats, seagrass beds, reed marshes, and hard substrate reefs, along the coast of Nanao Bay, Noto Peninsula (Japan). In the 2017 and 2018 surveys, we identified 296 taxa, including 40 Red List species. The actiniarians Paracondylactis hertwigi and Paranthus sociatus are the first records, and the gastropod Cerithium coralium is the northernmost records along the Japan Sea coast of Honshu Island. Of the 296 taxa, 166 occurred only at one site, indicating high β-diversity in the bay. Cluster analysis revealed that the macrozoobenthic assemblage structure differed significantly among the sites and/or years. Randomized block design sampling conducted in 2018 showed that macrozoobenthic structures differed significantly between bare flats and Zostera marina beds at the Wakura and Ninzaki sites. Several taxa, including the gastropod Alaba picta and the polychaetes Scoletoma nipponica and Prionospio krusadensis occurred more densely in Z. marina beds, indicating the contribution of seagrass to spatial heterogeneity in the macrozoobenthic assemblage structure. The macrozoobenthic diversity is comparable with that reported for major tidal flats along the Pacific Coast of central to southwestern Japan, indicating that the shallow coastal zones of Nanao Bay act as important habitats for macrozoobenthos, including endangered intertidal species. Habitat variability such as bare soft bottoms, hard substrates, seagrass beds, and reed marshes would contribute significantly to the α-, β-, and γ-diversity of macrozoobenthos in the bay system.

A columbellid gastropod, Mitrella martensi (Lischke, 1871), known from the temperate Asian intertidal coasts, is now considered endangered in Japan. In this study, we have reported its occurrence in the seagrass meadow of Akkeshi-ko Estuary, Hokkaido, northeastern Japan, as the northernmost record of this species. The observed population was considered part of the native Japanese population based on historical occurrence records from Akkeshi-ko Estuary and northern Honshu Island during the early 1900s, as evidenced by museum specimens and the literature, together with a morphological examination. M. martensi occurred in the seagrass bed and at an oyster farm adjacent to the bed. However, individuals with mature shells were only found at the oyster farm. The field survey in seagrass beds and a generalized linear modeling approach suggested a significant but marginal association between the abundance of M. martensi and the algal dry weight, but not with the seagrass density or the seagrass dry weight. This result is consistent with a previous study suggesting this species inhabits tidal flats and seagrass or algal beds with pebbles. Macroalgae attached to cobbles and pebbles were associated with M. martensi abundance. Meanwhile, seagrass with belowground roots was not. The findings show that M. martensi is distributed in subarctic northeastern Japan. Hard substrates, such as pebbles, oyster shells, and artificial substrates, in seagrass beds may play a crucial role for the species.

We investigated the invasion history and geographic distribution of marine nonnative species anthropogenically introduced to or within Japan using a questionnaire survey that was distributed to experts in such academic fields in 2022–2023. A total of 7,458 records on their occurrence in the field or at aquaculture facilities, including published and unpublished records, were reported by 36 respondents. According to the criteria for determining nonnative species by Iwasaki (2004a), we found 112 nonnative species that were introduced from abroad to Japanese waters (nonnative species with foreign origin), 63 native species introduced from abroad (nonnative populations with foreign origin), 46 native species introduced within Japan (nonnative species with domestic origin), and 60 cryptogenic species whose native areas have been unclear. Of the 112 nonnative species with foreign origin, 77 were unintentionally introduced with ballast water, ship fouling, or imported live fish and shellfish for aquaculture, and remaining 35 were introduced intentionally for aquaculture, fish baits, or as ornamental aquatic plants. For the taxonomic groups of the nonnative species, 16 species were pathogens (four viruses, six bacteria, three platyhelminths, etc.), and 95 others were non-pathogens (five cnidarians, 25 mollusks, 10 annelids, 33 arthropods, eight ascidians, 10 fishes, etc.). The rate of introduction per decade, as revealed by the first year of relevant data collection in Japan, increased after the 1950s to 1990s with a maximum of 26 species per decade and thereafter decreased. Understanding the import and domestic transport of live fish and shellfish needs more effort, and reinforcing legislative management is essential for controlling marine nonnative organisms.