Hidetaka Nomaki

Evidence of Global Chlorophyll d

Although analyses of chlorophyll d (Chl d)‐dominated oxygenic photosystems have been conducted since their discovery 12 years ago, Chl d distribution in the environment and quantitative importance for aquatic photosynthesis remain to be investigated. We analyzed the pigment compositions of surface sediments and detected Chl d and its derivatives from diverse aquatic environments. Our data show that the viable habitat for Chl d‐producing phototrophs extends across salinities of 0 to 50 practical salinity units and temperatures of 1� to 40�C, suggesting that Chl d production can be ubiquitously observed in aquatic environments that receive near-infrared light. The relative abundances of Chl d derivatives over that of Chl a derivatives in the studied samples are up to 4%, further suggesting that Chl d‐based photosynthesis plays a quantitatively important role in the aquatic photosynthesis.

Modern deep-sea benthic foraminifera: a brief review of their morphology-based biodiversity and trophic diversity

Abstract Most fossil deep-sea foraminifera are multichambered and have relatively robust, calcareous or agglutinated shells. Modern assemblages, on the other hand, include many fragile monothalamous (single-chambered) forms and komokiaceans (a superfamily of protist currently placed within the foraminifera) with soft test walls. These groups are poorly known and most of the hundreds of morphospecies recognized in deep-sea samples are undescribed. The relative abundance of robust and fragile taxa varies with water depth and food supply. Calcareous and other hard-shelled species tend to predominate in relatively eutrophic areas, particularly on continental margins, but decrease as a proportion of the ‘entire’ live fauna (i.e. including soft-shelled species) with increasing water depth, even above the CCD (carbonate compensation depth). Most of the species on which the foraminiferal proxies used in palaeoceanography are based live in these bathyal regions. At abyssal depths, and particularly below the CCD, faunas are largely agglutinated and dominated by monothalamous forms. These assemblages have a much lower fossilization potential than those found on continental margins. In addition to carbonate dissolution, these patterns probably reflect adaptations to increasingly oligotrophic conditions on the ocean floor with increasing depth and distance from land. Bathyal species include herbivores and opportunistic deposit feeders (omnivores) that consume labile organic material, in addition to deep-infaunal deposit feeders, and must contribute significantly to carbon cycling. Many abyssal monothalamous foraminifera, in constrast, accumulate stercomata (waste pellets composed of fine sediment particles) and probably ingest sediment, associated bacteria and more refractory organic matter. Some monothalamous species without stercomata may be bacteriovores. Although they probably process organic carbon at a slower rate than calcareous species, the shear abundance of monothalamous taxa at abyssal depths suggests that they are important in carbon cycling on a global scale. The loss of a substantial proportion of foraminiferal biomass and biodiversity from the fossil record should be considered when using foraminifera to reconstruct palaeoproductivity, for example, by using the Benthic Foraminiferal Accummulation Rate (BFAR). Different dietary preferences among calcareous species have implications for the stable carbon isotope signal preserved in their shells.

Proton pumping accompanies calcification in foraminifera

Ongoing ocean acidification is widely reported to reduce the ability of calcifying marine organisms to produce their shells and skeletons. Whereas increased dissolution due to acidification is a largely inorganic process, strong organismal control over biomineralization influences calcification and hence complicates predicting the response of marine calcifyers. Here we show that calcification is driven by rapid transformation of bicarbonate into carbonate inside the cytoplasm, achieved by active outward proton pumping. Moreover, this proton flux is maintained over a wide range of pCO2 levels. We furthermore show that a V-type H+ ATPase is responsible for the proton flux and thereby calcification. External transformation of bicarbonate into CO2 due to the proton pumping implies that biomineralization does not rely on availability of carbonate ions, but total dissolved CO2 may not reduce calcification, thereby potentially maintaining the current global marine carbonate production.

Intracellular Isotope Localization in Ammonia sp. (Foraminifera) of Oxygen-Depleted Environments: Results of Nitrate and Sulfate Labeling Experiments

Some benthic foraminiferal species are reportedly capable of nitrate storage and denitrification, however, little is known about nitrate incorporation and subsequent utilization of nitrate within their cell. In this study, we investigated where and how much 15N or 34S were assimilated into foraminiferal cells or possible endobionts after incubation with isotopically labeled nitrate and sulfate in dysoxic or anoxic conditions. After 2 weeks of incubation, foraminiferal specimens were fixed and prepared for Transmission Electron Microscopy (TEM) and correlative nanometer-scale secondary ion mass spectrometry (NanoSIMS) analyses. TEM observations revealed that there were characteristic ultrastructural features typically near the cell periphery in the youngest two or three chambers of the foraminifera exposed to anoxic conditions. These structures, which are electron dense and ~200–500 nm in diameter and co-occurred with possible endobionts, were labeled with 15N originated from 15N-labeled nitrate under anoxia and were labeled with both 15N and 34S under dysoxia. The labeling with 15N was more apparent in specimens from the dysoxic incubation, suggesting higher foraminiferal activity or increased availability of the label during exposure to oxygen depletion than to anoxia. Our results suggest that the electron dense bodies in Ammonia sp. play a significant role in nitrate incorporation and/or subsequent nitrogen assimilation during exposure to dysoxic to anoxic conditions.

Sex Ratio and Gut Contents of the Deep-sea Harpacticoid Neocervinia itoi and Other Cerviniids: A Possibility of Reduced Foraging among Males

Abstract We investigated the sex differences in the spatiotemporal distribution, body length, and gut contents of adult Neocervinia itoi, the most abundant cerviniid harpacticoid in Sagami Bay, Japan. Two other cerviniid species, Cerviniopsis sp. A and Cervinia bradyi, were also examined for comparison. The density of N. itoi tended to be higher at stations in or below sea bights with steep slopes in the bay, although there was no correlation between their distribution and chloroplastic pigment equivalent (CPE) in the sediment. In general, the sex ratio was strongly biased toward females in this species; the overall mean percentage of males was approximately 23% of adults. The sex ratio seemed to fluctuate temporally, even at the same site, although this fluctuation was not statistically significant. Comparisons of body size and sex ratio between the three species suggest that sampling bias was not the only cause for the observed skewed sex ratio. Distinct sex differences were observed in gut contents of N. itoi. Detritus-like gut contents were clearly observed in the urosomes of almost all females, whereas few males had gut contents. This result suggests that males do not forage during the adult stage. This non-feeding habit of males may result in a shorter lifespan than that of females and may be one cause of the skewed sex ratio. It remains unknown, however, whether this is a general trend among cerviniid species.

Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan

Previous studies on marine environmental virology have primarily focused on double-stranded DNA (dsDNA) viruses; however, it has recently been suggested that single-stranded DNA (ssDNA) viruses are more abundant in marine ecosystems. In this study, we performed a quantitative viral community DNA analysis to estimate the relative abundance and composition of both ssDNA and dsDNA viruses in offshore upper bathyal sediment from Tohoku, Japan (water depth = 500 m). The estimated dsDNA viral abundance ranged from 3 × 106 to 5 × 106 genome copies per cm3 sediment, showing values similar to the range of fluorescence-based direct virus counts. In contrast, the estimated ssDNA viral abundance ranged from 1 × 108 to 3 × 109 genome copies per cm3 sediment, thus providing an estimation that the ssDNA viral populations represent 96.3–99.8% of the benthic total DNA viral assemblages. In the ssDNA viral metagenome, most of the identified viral sequences were associated with ssDNA viral families such as Circoviridae and Microviridae. The principle components analysis of the ssDNA viral sequence components from the sedimentary ssDNA viral metagenomic libraries found that the different depth viral communities at the study site all exhibited similar profiles compared with deep-sea sediment ones at other reference sites. Our results suggested that deep-sea benthic ssDNA viruses have been significantly underestimated by conventional direct virus counts and that their contributions to deep-sea benthic microbial mortality and geochemical cycles should be further addressed by such a new quantitative approach.

In situ measurement of time-series two dimensional O2 distributions at sediment-water interface using a planar O2 optode system connected with a submarine cable

The first long time monitoring of O2 dynamics at sediment-water interface (SWI) was conducted using with a newly developed planar O2 optode system for in situ measurement. The monitoring was carried out connecting the optode system with Hatsushima permanent station with a 100 meter-long extension cable under supporting by the operation of ROV Hyper-dolphin. The monitoring was successfully carried out for 113.3 hours. During the experiment, 3,141 two dimensional O2 profiles and the corresponding pseudo-grayscale images across SWI were obtained, respectively. From the results, further understanding of new insights on dynamic interactions between fauna activities and environmental changes are expected.

Compound-specific isotope analysis of benthic foraminifer amino acids suggests microhabitat variability in rocky-shore environments

Abstract The abundance and biomass of benthic foraminifera are high in intertidal rocky‐shore habitats. However, the availability of food to support their high biomass has been poorly studied in these habitats compared to those at seafloor covered by sediments. Previous field and laboratory observations have suggested that there is diversity in the food preferences and modes of life among rocky‐shore benthic foraminifera. In this study, we used the stable nitrogen isotopic composition of amino acids to estimate the trophic position, trophic niche, and feeding strategy of individual foraminifera species. We also characterized the configuration and structure of the endobiotic microalgae in foraminifera using transmission electron microscopy, and we identified the origin of endobionts based on nucleotide sequences. Our results demonstrated a large variation in the trophic positions of different foraminifera from the same habitat, a reflection of endobiotic features and the different modes of life and food preferences of the foraminifera. Foraminifera did not rely solely on exogenous food sources. Some species effectively used organic matter derived from endobionts in the cell cytoplasm. The high biomass and species density of benthic foraminifera found in intertidal rocky‐shore habitats are thus probably maintained by the use of multiple nitrogen resources and by microhabitat segregation among species as a consequence.