cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22008/fk2/yemdis/lypqlo
title: Reduktionmap_Sc1g_Corr.asc

description: :unav
DOI: 10.22008/fk2/yemdis/m6pgik
title: Reduktionmap_Sc33_Corr.asc

description: :unav
DOI: 10.22008/fk2/yemdis/nmhxea
title: Reduktionmap_Sc31_Corr.asc

description: :unav
DOI: 10.22008/fk2/yemdis/df4pzo
title: Reduktionmap_Sc1q_Corr.asc

description: :unav
DOI: 10.22008/fk2/yemdis/y888dy
title: Reduktionmap_Sc1k_Corr.asc

description: :unav
DOI: 10.22008/fk2/yemdis/kclvxz
title: Reduktionmap_Sc44_Corr.asc

description: :unav
DOI: 10.22008/fk2/yemdis/g70jwp
title: Reduktionmap_Sc1c_Corr.asc

description: :unav
DOI: 10.22008/fk2/yemdis/i2qwkn
title: Reduktionmap_Sc4_Corr.asc

description: :unav
DOI: 10.22008/fk2/yemdis/46gp9r
title: Reduktionmap_Sc1r_Corr.asc

description: :unav
DOI: 10.22008/fk2/yemdis/ea2ml0
title: Reduktionmap_Sc1e_Corr.asc

description: :unav
DOI: 10.6084/m9.figshare.16837324.v1
title: Dfluo_carto_200825.zip

description: Raw data : cartography of fluorescence emissionInstrument : LIF spectrofluorimeter (conception: EDYTEM laboratory)Settings : Excitation 266 nm, grating 300 lines, central wavelength 620 nm, acquisition time 100 ms, entrance slit width 0.05 mm, resolution 100 µm x 100 µmSample : S-ECA-05 (Points cave, France)Data: <i>carto_pts_eca1705_07.dat</i>+ 1 file : wavelengths <i>carto_pts_eca1705_07.wl</i>+ 1 file : measures steps <i>carto_pts_eca1705_07.xsc</i>+ 1 file : instrument correction <i>qeccd.txt</i><br>+ 1 file : sample photograph under UV light <i>seca_05_lum_uv2.jpg</i><br>
DOI: 10.6084/m9.figshare.12961549
title: Susceptibility and resilience of the soil ciliate community to high temperatures

description: Ciliates play important ecological roles as microbial predators in soil. Although arable soils can experience a wide range of temperatures caused by agricultural land management, the effect of temperature on soil ciliates has been poorly documented, particularly for high temperatures over 30°C. Here, we studied the response of the soil ciliate community to different temperatures in comparison with that of the bacterial and fungal communities. Soils collected from a greenhouse were supplemented with organic fertilizer and incubated at different temperatures (10–60°C). Ciliate trophozoites were detected in the pore water of the soils incubated at 20°C and 10°C, while no trophozoites were observed at temperatures of 30°C and higher. The diversity of the ciliate community represented by fingerprints of denaturing gradient gel electrophoresis (DGGE) also decreased at temperatures higher than 20°C. A few DGGE bands were exclusively dominated at 40°C. The ciliate community composition in the soil incubated at 40°C recovered after subsequent incubation at 20°C, suggesting the resilience of the ciliate community to heat stress. Such recovery was not observed in the soil incubated at 60°C, probably because of the lethal effect on most soil ciliates. The responses of the ciliate community to temperature were similar to those of the fungal community, while the bacterial community showed higher resistance and resilience than the ciliate and fungal communities. The results suggested that temperature is an important factor controlling the ciliate community and affects the structure and functions of the soil microbial food web.
DOI: 10.6084/m9.figshare.12961549.v1
title: Susceptibility and resilience of the soil ciliate community to high temperatures

description: Ciliates play important ecological roles as microbial predators in soil. Although arable soils can experience a wide range of temperatures caused by agricultural land management, the effect of temperature on soil ciliates has been poorly documented, particularly for high temperatures over 30°C. Here, we studied the response of the soil ciliate community to different temperatures in comparison with that of the bacterial and fungal communities. Soils collected from a greenhouse were supplemented with organic fertilizer and incubated at different temperatures (10–60°C). Ciliate trophozoites were detected in the pore water of the soils incubated at 20°C and 10°C, while no trophozoites were observed at temperatures of 30°C and higher. The diversity of the ciliate community represented by fingerprints of denaturing gradient gel electrophoresis (DGGE) also decreased at temperatures higher than 20°C. A few DGGE bands were exclusively dominated at 40°C. The ciliate community composition in the soil incubated at 40°C recovered after subsequent incubation at 20°C, suggesting the resilience of the ciliate community to heat stress. Such recovery was not observed in the soil incubated at 60°C, probably because of the lethal effect on most soil ciliates. The responses of the ciliate community to temperature were similar to those of the fungal community, while the bacterial community showed higher resistance and resilience than the ciliate and fungal communities. The results suggested that temperature is an important factor controlling the ciliate community and affects the structure and functions of the soil microbial food web.
DOI: 10.6084/m9.figshare.13204861.v1
title: Effects of rhizosphere sulfur concentration on sulfur content and sulfate transporter gene expression in Japanese heirloom vegetables of the Brassicaceae family

description: Several region-specific vegetable varieties in Japan have an extensive cultivation history. Distinct tastes and aromas make them suitable for use in spices and pickles, and varieties with a high content of functional sulfur-containing compounds have been preferentially selected over the years. In the present study, we investigated the effects of different rhizosphere sulfate concentrations (0, 0.2, 0.4, and 0.8 mM) on the dry weight and sulfur content of 40 varieties of Brassicaceae heirloom vegetables. We also analyzed the expression levels of sulfate transporter genes, such as <i>SULTR1s</i> (sum of <i>SULTR1;1, SULTR1;2</i>, and <i>SULTR1;3</i>) and <i>SULTR2;1</i>, in 20 vegetable varieties. At 0 mM sulfate, plants have small leaves, as well as thin and scarce roots, whereas the mean shoot sulfur content per plant was 10% of that in control. Sulfur content increased by 29% at 0.4 mM and by 66% at 0.8 mM sulfate compared with that in control (0.2 mM sulfate); however, dry weight was not significantly affected. Mean shoot sulfur concentration was 0.12% at 0 mM, 0.52% at 0.2 mM, 0.65% at 4 mM, and 0.86% at 0.8 mM of sulfate. Shoot sulfur concentration exceeded 1% at 0.4 mM sulfate in several varieties. Shoot sulfur content and dry weight were positively correlated, suggesting that the capacity for sulfate ion absorption had a strong effect on biomass production in plants of the Brassicaceae family. Sulfur content and <i>SULTR1s</i> and <i>SULTR2;1</i> expression were poorly correlated regardless of rhizosphere sulfur concentration. These genes did not respond to shoot sulfur content but responded to sulfate levels in the rhizosphere. Overall, our data indicated that sulfate absorption response to sulfate concentration in the rhizosphere by sulfate transporters in Brassicaceae plants depends on the inherent characteristics of the variety.
DOI: 10.6084/m9.figshare.12980592
title: Changes in paddy soil fertility in Thailand due to the Green Revolution during the last 50 years

description: Understanding of the long-term soil fertility trends is the basis for rational and sustainable management of the soil resources in agricultural fields. In tropical Asia, the Green Revolution initiated in the late 1960s contributed to a drastic increase in both food production and human population. Among the tropical Asian countries, Thailand is known as a rice-exporting country, but the country’s rice yield is still relatively low. Therefore, this research aimed to investigate the effect of the Green Revolution on the changes in paddy soil fertility status in Thailand over the last 50 years. In total, 65 surface soil samples were collected in 2015 and 2016 from paddy fields in the northeast, north, central plain, and Bangkok Plain of Thailand. To compare the fertility-related data of the samples with those of soils collected from 1964 to 1972, the sampling sites in the 2010s were placed at or near the same locations of the original sites. Over the last 50 years, the mean pH, total C, total N, available N, available P, and exchangeable K values increased significantly (p &lt; 0.01). In particular, the available P content dramatically increased from 3.19 to 42.8 mg kg<sup>–1</sup>, reflecting the rapid increase in fertilizer application. Contrarily, the mean exchangeable Mg and clay content values decreased significantly (p &lt; 0.05). Regionally, the total C and total N contents of the soils in the northeast were significantly lower than those in the other regions (p &lt; 0.05), and the available P, exchangeable K, and available Si contents were often evaluated as deficient, reflecting the very sandy texture of the soils. In conclusion, the fertility status of the paddy soil in Thailand has improved considerably over the last 50 years, and the increase in total C suggests the potential of paddy soil for C sequestration, even in the tropics. These trends should be considered to achieve more sustainable food production and environmental conservation in Thailand.
DOI: 10.6084/m9.figshare.13204861
title: Effects of rhizosphere sulfur concentration on sulfur content and sulfate transporter gene expression in Japanese heirloom vegetables of the Brassicaceae family

description: Several region-specific vegetable varieties in Japan have an extensive cultivation history. Distinct tastes and aromas make them suitable for use in spices and pickles, and varieties with a high content of functional sulfur-containing compounds have been preferentially selected over the years. In the present study, we investigated the effects of different rhizosphere sulfate concentrations (0, 0.2, 0.4, and 0.8 mM) on the dry weight and sulfur content of 40 varieties of Brassicaceae heirloom vegetables. We also analyzed the expression levels of sulfate transporter genes, such as <i>SULTR1s</i> (sum of <i>SULTR1;1, SULTR1;2</i>, and <i>SULTR1;3</i>) and <i>SULTR2;1</i>, in 20 vegetable varieties. At 0 mM sulfate, plants have small leaves, as well as thin and scarce roots, whereas the mean shoot sulfur content per plant was 10% of that in control. Sulfur content increased by 29% at 0.4 mM and by 66% at 0.8 mM sulfate compared with that in control (0.2 mM sulfate); however, dry weight was not significantly affected. Mean shoot sulfur concentration was 0.12% at 0 mM, 0.52% at 0.2 mM, 0.65% at 4 mM, and 0.86% at 0.8 mM of sulfate. Shoot sulfur concentration exceeded 1% at 0.4 mM sulfate in several varieties. Shoot sulfur content and dry weight were positively correlated, suggesting that the capacity for sulfate ion absorption had a strong effect on biomass production in plants of the Brassicaceae family. Sulfur content and <i>SULTR1s</i> and <i>SULTR2;1</i> expression were poorly correlated regardless of rhizosphere sulfur concentration. These genes did not respond to shoot sulfur content but responded to sulfate levels in the rhizosphere. Overall, our data indicated that sulfate absorption response to sulfate concentration in the rhizosphere by sulfate transporters in Brassicaceae plants depends on the inherent characteristics of the variety.
DOI: 10.6084/m9.figshare.12980592.v2
title: Changes in paddy soil fertility in Thailand due to the Green Revolution during the last 50 years

description: Understanding of the long-term soil fertility trends is the basis for rational and sustainable management of the soil resources in agricultural fields. In tropical Asia, the Green Revolution initiated in the late 1960s contributed to a drastic increase in both food production and human population. Among the tropical Asian countries, Thailand is known as a rice-exporting country, but the country’s rice yield is still relatively low. Therefore, this research aimed to investigate the effect of the Green Revolution on the changes in paddy soil fertility status in Thailand over the last 50 years. In total, 65 surface soil samples were collected in 2015 and 2016 from paddy fields in the northeast, north, central plain, and Bangkok Plain of Thailand. To compare the fertility-related data of the samples with those of soils collected from 1964 to 1972, the sampling sites in the 2010s were placed at or near the same locations of the original sites. Over the last 50 years, the mean pH, total C, total N, available N, available P, and exchangeable K values increased significantly (p &lt; 0.01). In particular, the available P content dramatically increased from 3.19 to 42.8 mg kg<sup>–1</sup>, reflecting the rapid increase in fertilizer application. Contrarily, the mean exchangeable Mg and clay content values decreased significantly (p &lt; 0.05). Regionally, the total C and total N contents of the soils in the northeast were significantly lower than those in the other regions (p &lt; 0.05), and the available P, exchangeable K, and available Si contents were often evaluated as deficient, reflecting the very sandy texture of the soils. In conclusion, the fertility status of the paddy soil in Thailand has improved considerably over the last 50 years, and the increase in total C suggests the potential of paddy soil for C sequestration, even in the tropics. These trends should be considered to achieve more sustainable food production and environmental conservation in Thailand.
DOI: 10.6084/m9.figshare.13110806
title: Catchment topography and the distribution of electron donors for denitrification control the nitrate concentration in headwater streams of the Lake Hachiro watershed

description: We examined the linkages between topography and electron donors for denitrification on in-stream NO<sub>3</sub><sup>−</sup> concentration in headwater catchments in the Lake Hachiro watershed having marine sedimentary rock, Japan. In 35 headwater catchments (0.07–16.9 km<sup>2</sup>), we sampled stream water every season in 2 years. The water samples were analyzed for NO<sub>3</sub><sup>–</sup>, dissolved nitrous oxide (dN<sub>2</sub>O), and SO<sub>4</sub><sup>2 –</sup> concentrations. Stream sediment was sampled once for the measurement of denitrification potential (DP). Water-extractable soil organic carbon (WESOC) and easily oxidizable sulfide (EOS) in the sediment, which can be considered the principal potential electron donors for denitrification, were measured. The topographical features of each catchment were calculated using a digital elevation model with 10-m grid cells. Stream NO<sub>3</sub> <sup>–</sup> concentrations displayed large spatial variation among catchments, ranging from 0.06 to 0.52 mg N L<sup>–1</sup>, and were negatively correlated with topographic wetness index (TWI) (<i>P</i> P 3 <sup>–</sup> concentrations decreased in wetter and gentle slope catchments. Sediment DP and the WESOC content in sediments were positively correlated with TWI, significantly. These results suggested denitrification was likely to occur in higher TWI catchments. Generalized linear model showed that TWI, slope aspect, and sediment DP significantly affected in-stream NO<sub>3</sub> <sup>–</sup> concentration and WESOC was a significant explanatory variable for sediment DP. EOS content in riverbed sediments was not selected as a significant explanatory variable for either in-stream NO<sub>3</sub><sup>−</sup> concentrations or sediment DP. But higher soil DP with higher EOS was detected in the stream bank subsoil at the catchment where the higher EOS content in the riverbed sediment was observed, which suggested EOS in riverbed sediments can contain site-specific information about denitrification hotspot driven by sulfides. We conclude that catchment topography and the distribution of electron donors in riverbed sediment can be important factors to explain the spatial variation in in-stream NO<sub>3</sub> <sup>–</sup> concentration and sediment DP.
DOI: 10.6084/m9.figshare.13110806.v1
title: Catchment topography and the distribution of electron donors for denitrification control the nitrate concentration in headwater streams of the Lake Hachiro watershed

description: We examined the linkages between topography and electron donors for denitrification on in-stream NO<sub>3</sub><sup>−</sup> concentration in headwater catchments in the Lake Hachiro watershed having marine sedimentary rock, Japan. In 35 headwater catchments (0.07–16.9 km<sup>2</sup>), we sampled stream water every season in 2 years. The water samples were analyzed for NO<sub>3</sub><sup>–</sup>, dissolved nitrous oxide (dN<sub>2</sub>O), and SO<sub>4</sub><sup>2 –</sup> concentrations. Stream sediment was sampled once for the measurement of denitrification potential (DP). Water-extractable soil organic carbon (WESOC) and easily oxidizable sulfide (EOS) in the sediment, which can be considered the principal potential electron donors for denitrification, were measured. The topographical features of each catchment were calculated using a digital elevation model with 10-m grid cells. Stream NO<sub>3</sub> <sup>–</sup> concentrations displayed large spatial variation among catchments, ranging from 0.06 to 0.52 mg N L<sup>–1</sup>, and were negatively correlated with topographic wetness index (TWI) (<i>P</i> P 3 <sup>–</sup> concentrations decreased in wetter and gentle slope catchments. Sediment DP and the WESOC content in sediments were positively correlated with TWI, significantly. These results suggested denitrification was likely to occur in higher TWI catchments. Generalized linear model showed that TWI, slope aspect, and sediment DP significantly affected in-stream NO<sub>3</sub> <sup>–</sup> concentration and WESOC was a significant explanatory variable for sediment DP. EOS content in riverbed sediments was not selected as a significant explanatory variable for either in-stream NO<sub>3</sub><sup>−</sup> concentrations or sediment DP. But higher soil DP with higher EOS was detected in the stream bank subsoil at the catchment where the higher EOS content in the riverbed sediment was observed, which suggested EOS in riverbed sediments can contain site-specific information about denitrification hotspot driven by sulfides. We conclude that catchment topography and the distribution of electron donors in riverbed sediment can be important factors to explain the spatial variation in in-stream NO<sub>3</sub> <sup>–</sup> concentration and sediment DP.
DOI: 10.6084/m9.figshare.12980592.v1
title: Changes in paddy soil fertility in Thailand due to the Green Revolution during the last 50 years

description: Understanding of the long-term soil fertility trends is the basis for rational and sustainable management of the soil resources in agricultural fields. In tropical Asia, the Green Revolution initiated in the late 1960s contributed to a drastic increase in both food production and human population. Among the tropical Asian countries, Thailand is known as a rice-exporting country, but the country’s rice yield is still relatively low. Therefore, this research aimed to investigate the effect of the Green Revolution on the changes in paddy soil fertility status in Thailand over the last 50 years. In total, 65 surface soil samples were collected in 2015 and 2016 from paddy fields in the northeast, north, central plain, and Bangkok Plain of Thailand. To compare the fertility-related data of the samples with those of soils collected from 1964 to 1972, the sampling sites in the 2010s were placed at or near the same locations of the original sites. Over the last 50 years, the mean pH, total C, total N, available N, available P, and exchangeable K values increased significantly (p &lt; 0.01). In particular, the available P content dramatically increased from 3.19 to 42.8 mg kg<sup>–1</sup>, reflecting the rapid increase in fertilizer application. Contrarily, the mean exchangeable Mg and clay content values decreased significantly (p &lt; 0.05). Regionally, the total C and total N contents of the soils in the northeast were significantly lower than those in the other regions (p &lt; 0.05), and the available P, exchangeable K, and available Si contents were often evaluated as deficient, reflecting the very sandy texture of the soils. In conclusion, the fertility status of the paddy soil in Thailand has improved considerably over the last 50 years, and the increase in total C suggests the potential of paddy soil for C sequestration, even in the tropics. These trends should be considered to achieve more sustainable food production and environmental conservation in Thailand.
DOI: 10.6084/m9.figshare.12853501.v1
title: Effect of phytochrome-mediated red light signaling on phosphorus uptake and accumulation in rice

description: Phosphorus (P) is a macronutrient essential for plant growth and productivity. Plants uptake P as inorganic phosphate (Pi); however, in the natural ecosystem, Pi availability is frequently a severe limiting factor for plant growth. Thus, plants have evolved several mechanisms, such as the expression of Pi starvation-responsive genes, to adapt to Pi deficient conditions. Although we recently reported that phytochrome (Phy)-mediated red light signaling promotes Pi uptake by increasing expression levels of such genes in the model plant Arabidopsis, it remains elusive whether a similar mechanism exists in agricultural crops. In the present study, we analyzed the effects of red light signaling on Pi uptake in rice (<i>Oryza sativa</i> L.) using <i>osphyA</i> and <i>osphyB</i> single mutants, and the <i>osphyA osphyB</i> double mutant. Unlike <i>osphyA</i> seedlings, <i>osphyB</i> seedlings showed a reduction in Pi uptake and Pi content. Furthermore, illumination of wild-type seedlings with red light significantly promoted Pi uptake, whereas illumination with blue or far-red light did not. The <i>osphyB</i> mutant showed reduced expression levels of several Pi starvation-responsive genes including Pi transporter genes. Additionally, these phenotypes of <i>osphyB</i> knockout mutants were much more evident under Pi deficient conditions than under Pi sufficient conditions. Moreover, red light promoted Pi uptake in seedlings of other plant species including broccoli (<i>Brassica oleracea</i> L. var. <i>italica</i>) and lettuce (<i>Latuca sativa</i> L.). These results suggest that OsPhyB-mediated red light signaling promotes Pi uptake in rice by up-regulating the expression of Pi starvation response-associated genes, and this phenomenon may be conserved in a wide range of plant species.