Removal of water‐surface reflection effects with a temporal minimum filter for UAV‐based shallow‐water photogrammetry

The recent development of structure‐from‐motion (SfM) and multi‐view stereo (MVS) photogrammetry techniques has enabled semi‐automatic high‐resolution bathymetry using aerial images taken by consumer‐grade digital cameras mounted on unmanned aerial vehicles (UAVs). However, the applicability of these techniques is sometimes limited by sun and sky reflections at the water surface, which render the point‐cloud density and accuracy insufficient. In this research, we present a new imaging technique to suppress the effect of these water‐surface reflections. In this technique, we order a drone to take a short video instead of a still picture at each waypoint. We then apply a temporal minimum filter to the video. This filter extracts the smallest RGB values in all the video frames for each pixel, and composes an image with greatly reduced reflection effects. To assess the performance of this technique, we applied it at three small shallow‐water sites. Specifically, we evaluated the effect of the technique on the point cloud density and the accuracy and precision of the photogrammetry. The results showed that the proposed technique achieved a far denser point cloud than the case in which a randomly chosen frame was used for each waypoint, and also showed better overall accuracy and precision in estimating water‐bottom elevation. The effectiveness of this new technique should depend on the surface wave state and sky radiance distribution, and this dependence, as well as the applicability to large areas, should be investigated in future research. Copyright © 2018 John Wiley & Sons, Ltd.     

Vertical distribution of smaller macrobenthos and larger meiobenthos in the sediment profile in the deep-sea system of Suruga Bay (central Japan)

The vertical distribution of benthic organisms in the sediment profile was studied using horizontally sliced sediments collected at five stations at depths from 115 to 472 m in Suruga Bay, central Japan. Using sieves of 1.0 and 0.5 mm mesh, benthic organisms were divided into two size classes, smaller macrobenthos (>1mm, <1g wet weight) and larger meiobenthos (1.0 mm0.5 mm). The maximum depth of vertical distribution of organisms in the sediment profile was expressed by the 95 % intercept of the cumulative % curve of the number of individuals drawn with respect to depth in the sediment. It has long been supposed that benthic animals are concentrated in the surface centimeters of sediment in the deep-sea system, and the present study clearly substantiated this. Most benthic organisms of both of these two size classes were concentrated in the upper 5 cm of sediment. The vertical distribution was almost always deeper in the case of smaller macrobenthos than for larger meiobenthos. However the difference could not be substantiated statistically since the number of samples was insufficient. The maximum depth indices of polychaetes were found to be significantly larger than those of crustaceans in the case of macrobenthos, while in the case of meiobenthos, the difference was not significant. The maximum depth index of all benthic organisms was positively and significantly correlated with water-depth and the possible cause for this relationship is discussed.     

Active spreading and hydrothermalism in North Fiji Basin (SW Pacific). Results of Japanese French Cruise Kaiyo 87

The aim of the Japanese-French Kaiyo 87 cruise was the study of the spreading axis in the North Fiji Basin (SW Pacific). A Seabeam and geophysical survey allowed us to define the detailed structure of the active NS spreading axis between 16° and 22° S and its relationships with the left lateral motion of the North Fiji Fracture Zone. Between 21° S and 18°10′ S, the spreading axis trends NS. From 18°10 S to 16°40 S the orientation of the spreading axis changes from NS to 015°. North of 16°40′ S the spreading axis trends 160°. These two 015° and 160° branches converge with the left lateral North Fiji fracture zone around 16°40′ S to define an RRFZ triple junction. Water sampling, dredging and photo TV deep towing give new information concerning the hydrothermal activity along the spreading axis. The discovery of hydrothermal deposits associated with living communities confirms this activity.     

Estimating Co2 Source/Sink Distributions Within A Rice Canopy Using Higher-Order Closure Model

Source/sink strengths and vertical fluxdistributions of carbon dioxide within and above arice canopy were modelled using measured meanconcentration profiles collected during aninternational rice experiment in Okayama, Japan (IREX96). The model utilizes an Eulerian higher-orderclosure approach that permits coupling of scalar andmomentum transport within vegetation to infer sourcesand sinks from mean scalar concentration profiles; theso-called `inverse problem'. To compute the requiredvelocity statistics, a Eulerian second-order closuremodel was considered. The model well reproducedmeasured first and second moment velocity statisticsinside the canopy. Using these modelled velocitystatistics, scalar fluxes within and above the canopywere computed and compared with CO<sub>2</sub>eddy-correlation measurements above the canopy. Goodagreement was obtained between model calculations offluxes at the top of the canopy and measurements. Close to the ground, the model predicted higherrespiratory fluxes when the paddy was drained comparedto when it was flooded. This is consistent with thefloodwater providing a barrier to diffusion ofCO<sub>2</sub> from the soil to the atmosphere. TheEulerian sources and flux calculations were alsocompared to source and flux distributions estimatedindependently using a Lagrangian Localized Near Fieldtheory, the first study to make such a comparison.Some differences in source distributions werepredicted by these analyses. Despite this, thecalculated fluxes by the two approaches compared wellprovided a closure constant, accounting for theinfluence of `near-field' sources in the Eulerian fluxtransport term, was given a value of 1.5 instead ofthe value of 8 found in laboratory studies.     

Comparisons of deep-sea sediments and overlying water collected using Multiple Corer and Box Corer

Sediments and overlying water collected using Multiple Corer (MC) and Box Corer (BC) at three stations in Suruga Bay were compared from the view points of meiobenthic and chemical characteristics. Dissolved oxygen, pH, ammonium and nitrite concentrations of the overlying waters were lower, whereas nitrate and phosphate concentrations were higher constantly in the samples collected by MC than those by BC, suggesting contamination of surface seawater in the BC samples. Sediments were sliced into 0–1, 1–2 and 2–3 cm layers, and water content and Eh, and abundance of meiofauna were analyzed. Water content in MC samples was always higher than BC ones. For the whole meiobenthos, MC collected significantly more individuals than BC at only one out of three stations, whereas for harpacticoid copepods, which aggregated to the surface layer of the sediment, MC constantly collected significantly more individuals than BC. In the vertical profiles of both water content and meiofaunal density, data of 0–1, and 1–2 cm layers in the BC samples were similar to those of 1–2 and 2–3 cm layers in the MC samples, respectively. These results suggested only MC can collect the real sediment surface (so called fluffy layer), which was lost due to bow wave effects in the BC samples.     

N2 fixation variability in the oligotrophic Sulu Sea, western equatorial Pacific region over the past 83 kyr

N₂ fixation is an important biological process that adds new nitrogen to oceans and plays a key role in modulating the oceanic nitrate inventory. However, it is not known how, when, and where N₂ fixation rates have varied in response to past climate changes. This study presents a new record of nitrogen isotopic composition (δ¹⁵N) over the last 83 kyr from a sediment core (KH02-4 SUP8) taken in the Sulu Sea in the western equatorial Pacific region; data allow the N₂ fixation variability in the sea to be reconstructed. Sediments, sinking, and suspended particulate organic matter (POM) all have lighter isotopic values compared to the δ¹⁵N values of substrate nitrate (av. 5.8‰) in North Pacific Intermediate Water. These lighter δ¹⁵N values are regarded as reflecting N₂ fixation in the Sulu Sea surface water. A δ¹⁵N mass balance model shows that N₂ fixation rates were significantly enhanced during 54–34 kyr in MIS-3 and MIS-2. It has been speculated that higher interglacial denitrification rates in the Arabian Sea and the eastern tropical Pacific would have markedly decreased the global oceanic N inventory and contributed to the increase in N₂ fixation in oligotrophic regions, but such a model was not revealed by our study. It is possible that changes in N₂ fixation rates in the Sulu Sea were regional response, and accumulation of phosphate in the surface waters due to enhanced monsoon-driven mixing is thought to have stimulated enhancements of N₂ fixation during MIS-3 and MIS-2.     

Cross-Validation of Open-Path and Closed-Path Eddy-Covariance Techniques for Observing Methane Fluxes

Methane ( ${\mathrm {CH}}_{4}$ ) fluxes observed with the eddy-covariance technique using an open-path ${\mathrm {CH}}_{4}$ analyzer and a closed-path ${\mathrm {CH}}_{4}$ analyzer in a rice paddy field were evaluated with an emphasis on the flux correction methodology. A comparison of the fluxes obtained by the analyzers revealed that both the open-path and closed-path techniques were reliable, provided that appropriate corrections were applied. For the open-path approach, the influence of fluctuations in air density and the line shape variation in laser absorption spectroscopy (hereafter, spectroscopic effect) was significant, and the relative importance of these corrections would increase when observing small ${\mathrm {CH}}_{4}$ fluxes. A new procedure proposed by Li-Cor Inc. enabled us to accurately adjust for these effects. The high-frequency loss of the open-path ${\mathrm {CH}}_{4}$ analyzer was relatively large (11 % of the uncorrected covariance) at an observation height of 2.5 m above the canopy owing to its longer physical path length, and this correction should be carefully applied before correcting for the influence of fluctuations in air density and the spectroscopic effect. Uncorrected ${\mathrm {CH}}_{4}$ fluxes observed with the closed-path analyzer were substantially underestimated (37 %) due to high-frequency loss because an undersized pump was used in the observation. Both the bandpass and transfer function approaches successfully corrected this flux loss. Careful determination of the bandpass frequency range or the transfer function and the cospectral model is required for the accurate calculation of ${\mathrm {CH}}_{4}$ fluxes with the closed-path technique.     

Factors regulating the distribution of elements in marine sediments predicted by a simulation model

The contents of oxyanionic elements (V, Se and Mo) and cationic transition metals (Mn, Fe, Co, Ni, Cu and Zn) in sediments from near-shore to deep-sea environments were measured to clarify factors regulating the distribution of these elements in marine sediments. For cationic transition metals of which contents increase from near-shore to deep-sea environments, the chemical composition of pelagic clays is modeled by a mixture of aluminosilicates having the chemical composition of average shale and Fe–Mn oxides having the chemical composition of associated manganese nodules. The content of V is fairly constant in sediments from near-shore to deep-sea areas. The mixture model of average shale and manganese nodules holds also for V, although most of the V is located in the aluminosilicate lattices. The content of Se in the near-shore sediments is higher and that in the deep-sea sediments is lower than that in average shale. The high content in the near-shore sediments is interpreted as the addition of biogenic materials to aluminosilicates with average shale composition and the low content in deep-sea sediments is explained by oxidative release of Se from aluminosilicates. The content of Mo in sediments increases from near-shore to deep-sea environments. The general distribution of Mo in marine sediments is expressed by the mixture model. An anomalously high content of Mo in a near-shore sediment is attributed to adsorption of molybdate on manganese oxides.     

Apparent downward CO2 flux observed with open-path eddy covariance over a non-vegetated surface

Summary The open-path eddy covariance (EC) method often shows unlikely downward CO₂ fluxes in late winter and early spring over drained paddy fields with few active plants. To understand why, we carried out intensive measurements in a bare paddy field from 9 to 11 April 2003, simultaneously using open- and closed-path EC methods; aerodynamic and dynamic closed-chamber methods were also used. During this period, the open-path EC method showed downward daytime CO₂ fluxes ranging from 0 to −5.9 μmol m⁻² s⁻¹, even after application of the WPL correction (density correction) and ordinary quality control tests. Because the closed-path EC and aerodynamic methods showed upward CO₂ fluxes, the downward CO₂ fluxes observed with open-path EC appear not to represent true CO₂ transport. Diurnal variations in the downward daytime CO₂ fluxes appeared to be correlated with increases in solar radiation during the day, and also with increases in sensible heat flux in weak winds but not under strongly windy conditions. The daytime 10-Hz time series data of vertical wind and CO₂ mixing ratio demonstrated that updrafts were CO₂ depleted in the open-path system, whereas the same updrafts were CO₂ enriched in the closed-path system. Careful examination of the discrepancies between the open- and the closed-path EC measurements revealed that the amplitudes of the 10-Hz temperature signals from the sonic anemometer and the resultant sensible heat fluxes were too small to compensate for the discrepancies observed during the daytime. The open-path EC method with the conventional application of the WPL correction is not necessarily appropriate for measuring small magnitudes of CO₂ flux (≤5 μmol m⁻² s⁻¹) under such surface and atmospheric conditions that the magnitude of the WPL correction is as great as that of the uncorrected CO₂ flux itself. Author’s addresses: Keisuke Ono, 3-1-3 Kannondai, Tsukuba, Ibaraki 305-8604, Japan; Akira Miyata, Tomoyasu Yamada, National Institute for Agro-Environmental Sciences, Tsukuba, Japan