Yukiko Nagai’s research while affiliated with Japan Agency for Marine-Earth Science Technology and other places

Floating materials of both natural and anthropogenic origin affect marine ecosystems and human economic activities. Although the tracking of floating materials is important to manage the economic risks, it is difficult to trace them back to the events of origin, such as tsunamis and underwater volcanic eruptions. The gooseneck barnacle Lepas anserifera, a rapid colonizer in pelagic environments, is a potential “natural logger” of floating materials. In this study, we performed temperature-controlled culture experiments and growth line staining in the laboratory to quantify the growth increments of shells (scutum and tergum) consisting the capitulum of L. anserifera separately, and to examine the effects of the temperature on their growth. Following calcein staining, the growth lines of L. anserifera were visualized under a fluorescent microscope, and gross (capitular length and width) and individual (scutum and tergum) shell growth were compared. Shells grew in twice as much in the capitular length direction than in the capitular width direction owing to the larger growth increases in the scutum than in the tergum. Growth increments were unaffected by temperatures in the range from 20°C to 30°C, although the growth appeared to slow down in September and October compared with August. The stable oxygen isotope composition (δ¹⁸O) of the shells represented the water temperature as previously known, and the present results showed that ¹⁸O enriched in scutum than tergum in most cases. Further understanding for the biomineralization process of barnacles is required for the precise application of environmental proxies in barnacle shells.

Foraminifera encompass vastly differing morphologies, ecological preferences, and elemental/isotopic test compositions. The calcification mechanism is completely unknown for some wall-type taxa and might be different from that of well-studied groups. This study aims to understand the test growth and determine the calcification rate of Spirillina vivipara Ehrenberg, 1843 (order Spirillinida) and to compare them to other foraminiferal species. Spirillinids have a closely coiled spiral chamber like a tube, yet their calcitic microstructure is unique amongst foraminifera. Calcification observations in S. vivipara facilitate the estimation of carbonate precipitation rates during active test growth, which are revealed to be independent of the individual's size. Spirillina vivipara grows its test in response to food availability, suggesting that calcification directly corresponds to cell growth. Time-lapse observations of S. vivipara indicate continuous growth, suggesting active growth phases interspersed with resting periods, hinting at potential biological rhythms in the growth and calcification process. We also implemented a 24 h observation period using calcein staining, showing calcite precipitation rates of 8.08 µm h-1, which corresponds to approximately 364 nmol cm-2 min-1 (i.e., 36.4 mg cm-2 min-1). These rates are higher than those of other foraminiferal species and those in most inorganic precipitation experiments. Such high rates in spirillinid foraminifera may explain their distinctive morphology, elemental composition, unusual reproduction, and ecological distribution.

Floating materials of both natural and anthropogenic origin can affect marine ecosystems and human economic activities. Although the tracking and forecasting of floating materials are important, these processes are difficult to trace back after the events of origins, such as tsunamis and underwater volcanic eruptions. The goose barnacle Lepas anserifera , a rapid colonizer in pelagic environments, is a potential “natural logger” of floating materials. In this study, we performed temperature-controlled culture experiments and growth line identification in the laboratory to quantify the growth increments of individual shells consisting of the capitulum of L. anserifera and to examine the effects of the temperature on their growth. Following calcein staining, the growth line of L. anserifera was visualized under a fluorescent microscope, and gross (capitular length and width) and individual (scutum and tergum) shell growth were compared. Shells grew in twice as much in the CL direction than in the CW direction owing to the larger growth increases in the scutum than in the tergum. Growth increments were unaffected by temperatures from 20°C to 30°C, although growth appeared somewhat limited after August. The stable oxygen isotope composition (δ ¹⁸ O) of the shells represented the water temperature as previously known, and the present results showed that the scutum had heavier δ ¹⁸ O than the tergum in most cases. Further understanding for the biomineralization process of barnacles is required for the precise application of environmental proxies in barnacle shells.

Foraminiferal groups encompass vastly differing morphologies, ecological preferences and elemental/ isotopic test compositions. For some of these groups, the calcification mechanism is completely unknown, but is likely differing from that of well-studied groups. This study aimed to understand the test growth and calcification rate of Spirillina vivipara Ehrenberg, 1843 (Order Spirillinida), and to compare them to other foraminifera species. Spirillinids have a closely coiled spiral chamber like a tube, yet their calcitic microstructure is unique amongst foraminifera. Calcification observations in S. vivipara facilitate the estimation of carbonate precipitation rates during active test elongation, which are revealed to be independent of the individual’s size. We found that S. vivipara grows its test in response to food availability, suggesting that calcification directly corresponds to cell growth. Timelapse observations of S. vivipara indicate continuous growth, suggesting active growth phases and interspersed rest periods, hinting at potential biological rhythms in the growth and calcification process. We also implemented a 24-hour observation period using Calcein staining, showing calcite precipitation rates of 8.08 µm/hour in S. vivipara, which correspond to approximately 364 nmol/cm2/min i.e. 36.4mg/cm2/min. These rates are higher than those published for other foraminifera and those in most inorganic precipitation experiments. Such high rates in spirillinid foraminifera may explain their distinctive morphology, elemental composition, unusual reproduction and ecological distribution.

Foraminifera, the most ancient known calcium carbonate-producing eukaryotes, are crucial players in global biogeochemical cycles and well-used environmental indicators in biogeosciences. However, little is known about their calcification mechanisms. This impedes understanding the organismal responses to ocean acidifi-cation, which alters marine calcium carbonate production, potentially leading to biogeochemical cycle changes. We conducted comparative single-cell transcriptomics and fluorescent microscopy and identified calcium ion (Ca 2+) transport/secretion genes and α-carbonic anhydrases that control calcification in a foraminifer. They actively take up Ca 2+ to boost mitochondrial adenosine triphosphate synthesis during calcification but need to pump excess intracellular Ca 2+ to the calcification site to prevent cell death. Unique α-carbonic anhydrase genes induce the generation of bicarbonate and proton from multiple CO 2 sources. These control mechanisms have evolved independently since the Precambrian to enable the development of large cells and calcification despite decreasing Ca 2+ concentrations and pH in seawater. The present findings provide previously unknown insights into the calcification mechanisms and their subsequent function in enduring ocean acidification.

Alvinocaridid shrimps are endemic and globally widespread in chemosynthetic ecosystems such as hydrothermal vents and hydrocarbon seeps. Though the biology of Atlantic alvinocaridid species have received considerable attention, little is known about their Pacific relatives. Here we described population structures and reproductive biology of three Pacific alvinocaridid species—Shinkaicaris leurokolos, Opaepele loihi, Alvinocaris longirostris—with notes on a fourth species—A. dissimilis—from several chemosynthetic ecosystems around Japan and compared their size frequency distributions and reproductive outputs. We showed that population demographics differ among these species, including a significantly larger proportion of juveniles in O. loihi and spatial variation of sex ratio in S. leurokolos, but all shared sex ratios biased toward females. The three shrimp species were characterized by relatively small sizes at onset of maturity, although this varied among sites for A. longirostris. Overall, size-specific fecundities and egg volumes of A. longirostris, O. loihi and S. leurokolos were in a similar range to Atlantic alvinocaridids. In addition, we performed egg incubation experiments of O. loihi under different temperature conditions to characterize thermal physiology during its brooding period. This confirmed a strong influence of temperature on both brooding duration and hatching rate, with a thermal preference that differs from previously published data for A. longirostris and S. leurokolos. Finally, our results indicated that these alvinocaridid species from the northwestern Pacific likely differ in reproductive timing, either through distinct brooding durations and/or distinct brooding periodicity, although further investigations are required to confirm these patterns.

We have developed a method to combine morphological and chemical information for the accurate identification of different particle types using optical measurement techniques that require no sample preparation. A combined holographic imaging and Raman spectroscopy setup is used to gather data from six different types of marine particles suspended in a large volume of seawater. Unsupervised feature learning is performed on the images and the spectral data using convolutional and single-layer autoencoders. The learned features are combined, where we demonstrate that non-linear dimensional reduction of the combined multimodal features can achieve a high clustering macro F1 score of 0.88, compared to a maximum of 0.61 when only image or spectral features are used. The method can be applied to long-term monitoring of particles in the ocean without the need for sample collection. In addition, it can be applied to data from different types of sensor measurements without significant modifications.

Large Benthic Foraminifera are a crucial component of coral-reef ecosystems, which are currently threatened by ocean acidification. We conducted culture experiments to evaluate the impact of low pH on survival and test dissolution of the symbiont-bearing species Peneroplis spp., and to observe potential calcification recovery when specimens are placed back under reference pH value (7.9). We found that Peneroplis spp. displayed living activity up to 3 days at pH 6.9 (Ω cal < 1) or up to 1 month at pH 7.4 (Ω cal > 1), despite the dark and unfed conditions. Dissolution features were observed under low Ω cal values, such as changes in test density, peeled extrados layers, and decalcified tests with exposed organic linings. A new calcification phase started when specimens were placed back at reference pH. This calcification’s resumption was an addition of new chambers without reparation of the dissolved parts, which is consistent with the porcelaneous calcification pathway of Peneroplis spp. The most decalcified specimens displayed a strong survival response by adding up to 8 new chambers, and the contribution of food supply in this process was highlighted. These results suggest that porcelaneous LBF species have some recovery abilities to short exposure (e.g., 3 days to 1 month) to acidified conditions. However, the geochemical signature of trace elements in the new calcite was impacted, and the majority of the new chambers were distorted and resulted in abnormal tests, which might hinder the specimens’ reproduction and thus their survival on the long term.