Machine learning highlights the importance of primary and secondary production in determining habitat for marine fish and macroinvertebrates

1. Species distribution models for marine organisms are increasingly used for a range of applications, including spatial planning, conservation, and fisheries management. These models have been constructed using a variety of mathematical forms and drawing on both physical and biological independent variables; however, what might be called first-generation models have mainly followed the form of linear models, or smoothing splines, informed by data collected in the context of fish surveys.
2. The performance of different classes of variables were tested in a series of species occurrence models built with machine learning methods, specifically evaluating the potential contribution of lower trophic level data. Random forest models were fitted based on the classification of the absence/presence for fish and macroinvertebrates surveyed on the US Northeast Continental Shelf.
3. The potential variables included physical, primary production, secondary production, and terrain variables. For accepted model fits, six variable importance measures were computed, which collectively showed that physical and secondary production variables make the greatest contribution across all models. In contrast, terrain variables made the least contribution to these models.
4. Multivariable analyses that account for all performance measures reinforce the role of water depth and temperature in defining species presence and absence; however, chlorophyll concentration and some specific zooplankton taxa, such as Metridia lucens and Paracalanus parvus, also make important contributions with strong seasonal variations.
5. Our results suggest that lower trophic level variables, if available, are valuable in the creation of species distribution models for marine organisms.

     

Spatial-uniform application method of methane fermentation digested slurry with irrigation water in the rice paddy field

Promoting biomass utilization, the objectives of this study were to clarify the spatial distribution of nitrogen, one of the most important fertilizer components in the methane fermentation digested slurry (i.e., the digested slurry), and to establish an effective method to apply spatial-uniformly digested slurry with irrigation water in the rice paddy field. A numerical model describing the unsteady two-dimensional flow and solution transport of paddy irrigation water was introduced. The accuracy of this model was verified with a field observation. The tendencies of the TN simulated in inlet and outlet portions had good agreement with the measured data and the accuracy of the numerical model could be verified. Using the numerical model, scenario analyses were conducted to determine the method for spatial-uniform application of the digested slurry with irrigation water. The simulated results indicated that drainage of the surface water and trenches at the soil surface were effective for spatial-uniform application of the digested slurry with irrigation water in the rice paddy fields. The effect of the trenches was maximized when the surface water of the rice paddy field was drained adequately.     

Ionomic Profiling of Rice Genotypes and Identification of Varieties with Elemental Covariation Effects

Ionomic profiles are primarily influenced by genetic and environmental factors. Identifying ionomic responses to varietal effects is necessary to understand the ionomic variations among species or subspecies and to potentially understand genetic effects on ionomic profiles. We cultivated 120 rice (Oryza sativa) varieties to seedling stage in identical hydroponic conditions and determined the concentrations of 26 elements (including 3 anions) in the shoots and roots of rice. Although the subspecies effects were limited by the genus Oryza pre-framework and its elemental chemical properties, we found significant differences in ionomic variations in most elements among the aus, indica and japonica subspecies. Principal component analysis of the correlations indicated that variations in the root-to-shoot ionomic transport mechanisms were the main causes of ionomic differences among the subspecies. Furthermore, the correlations were primarily associated with the screening of varieties for elemental covariation effects that can facilitate breeding biofortified rice varieties with safe concentrations of otherwise toxic elements. The japonica subspecies exhibited the strongest elemental correlations and elemental covariation effects, therefore, they showed greater advantages for biofortification than the indica and aus subspecies, whereas indica and aus subspecies were likely safer in metal(loid) polluted soils. We also found that geographical and historical distribution significantly defined the ionomic profiles. Overall, the results of this study provided a reference for further association studies to improve the nutritional status and minimize toxicity risks in rice production.     

Diluted rotifer, Brachionus plicatilis (Muller), extract as culture medium stimulates hatching of red sea bream, Pagrus major (Temminck & Schlegel)

Hatching rates and hatching times (50% hatch) of red sea bream, Pagrus major (Temminck & Schlegel), eggs in culture media that were prepared to dilute rotifer Brachionus plicatilis Muller extract at 4000-, 6000-. 8000- and 10 000-fold with artificial sea water (σ₁₅, = 24.0) were investigated. Although differences in hatching rate between the culture media and control artificial sea water were negligible, hatching time was significantly shorter in media at 4000- and 6000-fold dilutions than in media at 8000- and 10 000-fold dilutions and in the control artificial sea water, when the eggs immediately post spawning were incubated. The hatching rates of eggs at three developmental stages, immediately post-spawning, gastrula stage and heart-beat initiation stage, incubated respectively in the medium at 6000-fold dilution and the control, did not differ either, yet the hatching times at each egg stage in the medium were significantly shorter than that in the control. These results suggest that hatching enzyme secretion from the hatching glands is promoted to perceive chemical stimuli in the water-soluble fraction of rotifer extract via the embryo's chemoreceptors, from the heart-beat initiation stage to immediately before hatching, thus shortening the hatching time.     

Limited but specific variations of seed storage proteins in Japanese common wheat (Triticum aestivum L.)

The electrophoretic banding patterns ofgliadin in common wheat lines derived fromJapan were determined byacid-polyacrylamide gel electrophoresis. For the 107 wheat lines used in our study,27 different patterns were identified, 13corresponding to the -gliadin, 8 tothe , -gliadin and 6 to the-gliadin. The gliadin patterns ofJapanese wheat cultivars and landracesgreatly differed from the patterns of wheatlines from other countries, and thevariation seen in wheat lines from Japanwas limited to 46 patterns. Sevencollection or breeding areas in Japanshowed different frequencies in theirgliadin patterns. Combining the gliadinpatterns with high molecular weightglutenin subunit compositions, 67combinations were observed. One gliadinpattern consisting of -gliadinpattern F, , -gliadinpattern H and -gliadin pattern Dwas frequently found in many Japanese wheatlines, though the other patterns werelimited to only one or two wheat lines.     

Studies on absorption and hydrolysis of ethyl alpha-D-glucoside in rat intestine

Ethyl alpha-D-glucoside (alpha-EG) is normally contained in Sake, which has been taken by Japanese people since ancient times. In this study, the intestinal absorption of alpha-EG was investigated using rat everted intestinal sac. Furthermore, the alpha-EG hydrolytic activity in rat intestine was compared with disaccharides hydrolytic activities, and the effects of alpha-EG on disaccharides hydrolysis were examined using crude enzyme preparation from rat intestinal acetone powder. Glucose liberated from alpha-EG was detected in a serosal solution of everted rat intestinal sac, but it was only less than 4% of absorbed intact alpha-EG. alpha-EG absorption into small intestinal tissue was reduced by elimination of sodium ion from the mucosal solution or under the presence of phlorizin. The hydrolytic activity for alpha-EG was detected in crude enzyme preparation from rat intestinal acetone powder, but it showed a low value as compared to those for disaccharides. alpha-EG showed mixed type inhibition for maltose and sucrose hydrolysis, but inhibitory concentrations of alpha-EG required for 50% inhibition for the maltose and sucrose hydrolysis were higher than those of arabinose and acarbose. In conclusion, a small amount of alpha-EG was hydrolyzed and most of it was absorbed via SGLT1 as an intact form in the rat small intestine, and the inhibitory effect of alpha-EG on disaccharides hydrolysis was weak.     

Influences of Forest Decline on Various Properties of Soils at Mt. Hirugatake, Tanzawa Mountains, Kanto District, Japan

At Mt. Hirugatake in the Tanzawa Mountains, Kanto district, Japan, the deciduous broadleaved forests have rapidly declined. In our previous studies, we reported that the amount of soil organic matter had significantly decreased at the early and final stages of forest decline, and that the soil microbial biomass also showed a large decrease at these stages, suggesting that the composition of soil organic matter might have also changed with forest decline. To clarify the influences of forest decline on the composition of soil organic matter, the amount of humic substances, optical properties of humic acid, and the amount of soil carbohydrates in surface soils at different stages of forest decline were investigated. The amounts of humic acid and fulvic acid decreased to a lesser extent at the early and middle stages of forest decline, and showed a significant decrease at the final stage. As the amount of humin significantly decreased at the early stage, it was plausible that the distinct decrease in the total carbon content of the soil surface horizons at the early stage of forest decline was induced by the decrease in the amount of humin, and at the final stage, by the decrease in the amounts of humic acid and fulvic acid. The amount of soil carbohydrates did not change appreciably with forest decline although the soil organic matter content markedly decreased. It was suggested that most of the carbohydrates in the soil surface horizons were in a stabilized form consisting of complexes with humic substances, metals, and minerals, and would not be affected by the environmental changes associated with forest decline.     

Experimental studies on sulfur dioxide injuries in higher plants

Photosynthesis is reversibly inhibited by exposing plants to SO₂. The formation of α-hydroxy sulfonate in the exposed plants is suggested as one of the effects, because this compound inhibits glycolic oxidase which is necessary in the glycolic acid pathway. The suppression of the glycolic acid path should affect various aspects of metabolism in plants, particularly the reduction of the biosynthesis of glycine and serine. In this paper, the biosynthesis of these amino acids in plants exposed to SO₂ was investigated to estimate the significance of the formation of α-hydroxy sulfonate in the plants. The results show that photosynthetic formation of serine was reduced in the exposed plants, and that α-hydroxy sulfonate was formed.