cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8192198.v1
title: Microbial community structure and relationship with physicochemical properties of soil stockpiles in selected South African opencast coal mines

description: At present, there is no comprehensive soil quality assessment practice for soil stockpiles in the South African coal mining industry. Soil microorganisms and enzymes are suitable indicators for soil quality monitoring. Therefore, this study investigated the microbial community and enzyme (beta-glucosidase and urease) activities in soil stockpiles of opencast coal mines in the coal-rich region of South Africa. Soil stockpiles of three opencast coal mines were sampled at depths of 0–20 cm (‘topsoil’) and &gt;20 cm (‘subsoil’) across three seasons. Beta-glucosidase and urease activities were mostly higher in soil stockpiles than in unmined soils and were significantly influenced (<i>P</i> &lt; 0.05) by the interaction of site and seasonal factors. However, analyses of PCR-denaturing gradient gel electrophoresis (PCR-DGGE) profiles of partial 16S rRNA gene and internally transcribed spacer 2 (ITS2) sequences revealed higher microbial diversity in unmined (reference) soils compared to soil stockpiles across all seasons. Redundancy analysis further revealed that microbial communities of topsoil were not significantly (<i>P</i> &gt; 0.05) influenced by soil properties, whereas microbial communities of subsoils were significantly (<i>P</i> &lt; 0.05) influenced by pH, organic carbon, total nitrogen and phosphorus contents. Furthermore, operational taxonomic units (OTUs) belonging to genera of known phytobeneficial species such as <i>Azomonas, Aureobasidium, Phialocephala, Phoma</i> and <i>Sordariomycetes</i> were detected in these soils. Overall, results suggest that the microbial community structure and diversity observed in stockpiles is impaired (compared to the unmined site), although variations in the microbial community structure of soil stockpiles across seasons are site-specific. The impaired microbial community of stockpiles may have negative implications on soil biological processes driven by microbes; especially those that are critical for nutrient cycling and ecosystem sustainability. More importantly, such alteration in soil biodiversity may impair post-mining land use capability of stockpile soils.
DOI: 10.6084/m9.figshare.8300216
title: Short-term changes in chemical and microbial characteristics of paddy soil in response to consecutive addition of organic ameliorants in a rice–rice–vegetable rotation system

description: With regard of the problems of soil acidification and soil degradation caused by high intensive planting in south China, a 2-year pot experiment consisting of six harvests under a rice–rice–vegetable rotation cropping system was conducted to assess the effects of NPK+ rice straw (RS) and combined application of RS with peanut bran, biochar, and organic fertilizer on soil chemical and microbial characteristics in paddy soil. The control treatment received chemical fertilizer alone. Results showed that RS and the combination of RS with organic ameliorants, especially NPK+ rice straw + biochar (RSBC) treatment led to the greatest improvement of soil pH, soil organic carbon, microbial biomass carbon, and total nitrogen (TN) content, and urease (UE), acid phosphatase (ACP) and catalase (CAT) activities concurrently without yield sacrificing, which inferred that RSBC treatment could be an effective measure to alleviate soil acidification, boost carbon sequestration and nutrients content as well as soil enzyme activities in rice-rice-vegetable rotation system. Besides, Pearson’s correlation analysis showed that soil mineral nitrogen (N<sub>min</sub>) content was negatively related to pH, and the available potassium (AK) content was positively related to UE and CAT activity but negatively related to ACP activity. Canonical correspondence analysis demonstrated the N<sub>min</sub> and AK explained 27.2% and 13.7% of the variation in microbial species, respectively. Therefore, it is believed that soil N<sub>min</sub> and AK content could be the primary factors of soil microbial properties under the rice-rice-vegetable rotation system.
DOI: 10.6084/m9.figshare.8300216.v1
title: Short-term changes in chemical and microbial characteristics of paddy soil in response to consecutive addition of organic ameliorants in a rice–rice–vegetable rotation system

description: With regard of the problems of soil acidification and soil degradation caused by high intensive planting in south China, a 2-year pot experiment consisting of six harvests under a rice–rice–vegetable rotation cropping system was conducted to assess the effects of NPK+ rice straw (RS) and combined application of RS with peanut bran, biochar, and organic fertilizer on soil chemical and microbial characteristics in paddy soil. The control treatment received chemical fertilizer alone. Results showed that RS and the combination of RS with organic ameliorants, especially NPK+ rice straw + biochar (RSBC) treatment led to the greatest improvement of soil pH, soil organic carbon, microbial biomass carbon, and total nitrogen (TN) content, and urease (UE), acid phosphatase (ACP) and catalase (CAT) activities concurrently without yield sacrificing, which inferred that RSBC treatment could be an effective measure to alleviate soil acidification, boost carbon sequestration and nutrients content as well as soil enzyme activities in rice-rice-vegetable rotation system. Besides, Pearson’s correlation analysis showed that soil mineral nitrogen (N<sub>min</sub>) content was negatively related to pH, and the available potassium (AK) content was positively related to UE and CAT activity but negatively related to ACP activity. Canonical correspondence analysis demonstrated the N<sub>min</sub> and AK explained 27.2% and 13.7% of the variation in microbial species, respectively. Therefore, it is believed that soil N<sub>min</sub> and AK content could be the primary factors of soil microbial properties under the rice-rice-vegetable rotation system.
DOI: 10.6084/m9.figshare.10011461
title: Evidence for rice Heading date 16 contribution to yield increase under low-nutrient conditions

description: Breeding new rice cultivars that are tolerant to low-nutrient condition is a solution to saving the usage of commercial fertilizer. We isolated Hitomebore EMS mutant, 520-6. Seedling growth of 520-6 is tolerant to low-nutrient supply, especially to low phosphorus (low P) supply and genetic mapping revealed the existence of nonsynonymous substitution within <i>Os03g0793500</i> 9th exon in 520-6. <i>Os03g0793500</i> is reported as <i>Heading date 16</i> (<i>Hd16</i>)/<i>Early flowering1</i> (<i>EL1</i>), which is related with the rice flowering pathway. <i>Hd16/EL1</i> encodes a casein kinase-I protein, and phosphorylates the floral repressor Ghd7 and the rice DELLA protein Slender rice 1 (SLR1). 520-6 carries the same nonfunctional <i>Hd16</i> allele to that of Koshihikari, and the parental cultivar, Hitomebore, carries the functional <i>Hd16</i> allele, as with Nipponbare. mRNA accumulation of GA-biosynthesis-related gene, <i>OsGA2ox3</i> was enhanced in 520-6 compared with Hitomebore, indicating that Hd16 takes a part in feedback regulation of the GA biosynthetic gene. 520-6 and near-isogenic line (NIL) with nonfunctional <i>Hd16</i> allele showed heavy straw weight and panicle weight in paddy fields with low nitrogen input and no fertilizer application in Kashimadai at Miyagi prefecture and Hikone at Shiga prefecture, respectively. In addition, plants with nonfunctional <i>Hd16</i> allele showed late flowering phenotype in all tested fields. These results imply that disruption of Hd16 contributes to the improvement of rice growth by positively regulating GA signaling and late flowering, which resulted in increased rice yield under low-nutrient conditions.
DOI: 10.6084/m9.figshare.10011461.v1
title: Evidence for rice Heading date 16 contribution to yield increase under low-nutrient conditions

description: Breeding new rice cultivars that are tolerant to low-nutrient condition is a solution to saving the usage of commercial fertilizer. We isolated Hitomebore EMS mutant, 520-6. Seedling growth of 520-6 is tolerant to low-nutrient supply, especially to low phosphorus (low P) supply and genetic mapping revealed the existence of nonsynonymous substitution within <i>Os03g0793500</i> 9th exon in 520-6. <i>Os03g0793500</i> is reported as <i>Heading date 16</i> (<i>Hd16</i>)/<i>Early flowering1</i> (<i>EL1</i>), which is related with the rice flowering pathway. <i>Hd16/EL1</i> encodes a casein kinase-I protein, and phosphorylates the floral repressor Ghd7 and the rice DELLA protein Slender rice 1 (SLR1). 520-6 carries the same nonfunctional <i>Hd16</i> allele to that of Koshihikari, and the parental cultivar, Hitomebore, carries the functional <i>Hd16</i> allele, as with Nipponbare. mRNA accumulation of GA-biosynthesis-related gene, <i>OsGA2ox3</i> was enhanced in 520-6 compared with Hitomebore, indicating that Hd16 takes a part in feedback regulation of the GA biosynthetic gene. 520-6 and near-isogenic line (NIL) with nonfunctional <i>Hd16</i> allele showed heavy straw weight and panicle weight in paddy fields with low nitrogen input and no fertilizer application in Kashimadai at Miyagi prefecture and Hikone at Shiga prefecture, respectively. In addition, plants with nonfunctional <i>Hd16</i> allele showed late flowering phenotype in all tested fields. These results imply that disruption of Hd16 contributes to the improvement of rice growth by positively regulating GA signaling and late flowering, which resulted in increased rice yield under low-nutrient conditions.
DOI: 10.6084/m9.figshare.10192421.v1
title: Spatial variability of vertical profiles of radiocesium in a paddy field measured by conventional core sampling

description: Our analyses revealed the spatial variability of the vertical distribution of fallout radiocesium measured in small cylindrical soil cores taken in a non-disturbed paddy field contaminated by the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident in 2011. The field is in Iitate Village 40km northwest of FDNPP and had been designated as an off-limit area. In December 2012, soil samples were taken along a longitudinal and transverse line in the field at intervals of 1 or 2 m. In May 2013, 36 additional soil samples were taken from a 1m<sup>2</sup> plot at 20cm intervals, where the ground undulated considerably. The core samples were carefully cut into slices, dried, and subjected to measurement of the radiocesium concentration. The coefficient of variation in the total radiocesium inventory (i.e. the radioactivity of total radiocesium in the unit area of the soil profile) and the averaged radiocesium concentration at 0～10 cm were 47.8 % and 53.5 %, respectively, demonstrating that the mean of a few representative points in a paddy lot provides huge uncertainty. Our analysis of semivariograms for the mean radiocesium concentration revealed no spatial correlation even between the shortest lag distance (2 m). It should thus be noted that the mean concentration determined from a small core sample cannot represent the tendency around the sampled point. However, the result of the 20 cm<sup>2</sup> grid samplings suggested that undulations on a 10-cm scale can cause radiocesium to migrate to a concave spot. Among the 82 sampling points, 50 % of the vertical profiles of the radiocesium concentration had a concentration peak at the ground surface, but the other points had an s-shape or bell shape, suggesting variation in the water flow regime among the sampled profiles. The apparent convective velocity of the radiocesium ranged widely from 0.00 to 3.38 cmy<sup>-1</sup> with a mean of 0.75 cm y<sup>-1</sup>.
DOI: 10.6084/m9.figshare.10192421
title: Spatial variability of vertical profiles of radiocesium in a paddy field measured by conventional core sampling

description: Our analyses revealed the spatial variability of the vertical distribution of fallout radiocesium measured in small cylindrical soil cores taken in a non-disturbed paddy field contaminated by the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident in 2011. The field is in Iitate Village 40km northwest of FDNPP and had been designated as an off-limit area. In December 2012, soil samples were taken along a longitudinal and transverse line in the field at intervals of 1 or 2 m. In May 2013, 36 additional soil samples were taken from a 1m<sup>2</sup> plot at 20cm intervals, where the ground undulated considerably. The core samples were carefully cut into slices, dried, and subjected to measurement of the radiocesium concentration. The coefficient of variation in the total radiocesium inventory (i.e. the radioactivity of total radiocesium in the unit area of the soil profile) and the averaged radiocesium concentration at 0～10 cm were 47.8 % and 53.5 %, respectively, demonstrating that the mean of a few representative points in a paddy lot provides huge uncertainty. Our analysis of semivariograms for the mean radiocesium concentration revealed no spatial correlation even between the shortest lag distance (2 m). It should thus be noted that the mean concentration determined from a small core sample cannot represent the tendency around the sampled point. However, the result of the 20 cm<sup>2</sup> grid samplings suggested that undulations on a 10-cm scale can cause radiocesium to migrate to a concave spot. Among the 82 sampling points, 50 % of the vertical profiles of the radiocesium concentration had a concentration peak at the ground surface, but the other points had an s-shape or bell shape, suggesting variation in the water flow regime among the sampled profiles. The apparent convective velocity of the radiocesium ranged widely from 0.00 to 3.38 cmy<sup>-1</sup> with a mean of 0.75 cm y<sup>-1</sup>.
DOI: 10.6084/m9.figshare.11733204
title: Genome-wide responses to shoot nitrate satiety are attenuated by external ammonium in <i>Arabidopsis thaliana</i>

description: The supply of exogenous nitrate to nitrate-depleted plants transiently changes the expression of nitrate-responsive genes within minutes. In addition to this so-called primary nitrate response, nitrate is suspected to play a long-term regulatory role, acting as a nitrogen (N) status signal for the entire plant. In our recent study using <i>Arabidopsis thaliana</i>, the manipulation of the internal nitrate levels independently of internal organic N without external N indicated that nitrate accumulation in the shoot alone causes genome-wide responses systemically, including the induction of nitrate assimilation genes and repression of N starvation-inducible genes. These responses mimic high nitrate growth situations for plants, suggesting that shoot nitrate acts as a N satiety signal. On the other hand, it is widely known that external supply of ammonium as another major N source also triggers N-rich responses, which led us to hypothesize that the existence of external ammonium may interfere with the genome-wide responses regarding shoot nitrate satiety. To clarify this, we compared transcriptional responses to shoot nitrate satiety with and without external ammonium both in Arabidopsis shoots and roots. Further, in order to determine the major role of nitrate satiety signaling, we extracted those genes regulated by shoot nitrate level regardless of the presence or absence of external ammonium and annotated them by two independent enrichment analyses. Here, we show that genome-wide transcriptional responses to shoot nitrate satiety are significantly lowered in the presence of external ammonium especially in the shoot. A major component for the ammonium-dependent attenuation of the nitrate satiety responses comprised a set of genes encoding the machinery for translation, glucosinolate biosynthesis, and photosynthesis. On the other hand, the nitrate satiety responses commonly observed irrespective of the presence/absence of ammonium included the components for translation and nitrate assimilation, whose transcriptional responses could be mediated partly via NIN-LIKE PROTEIN (NLP), NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1), and cytokinin signaling on the basis of our transcriptional profiling and cytokinin determination.
DOI: 10.6084/m9.figshare.11733204.v1
title: Genome-wide responses to shoot nitrate satiety are attenuated by external ammonium in <i>Arabidopsis thaliana</i>

description: The supply of exogenous nitrate to nitrate-depleted plants transiently changes the expression of nitrate-responsive genes within minutes. In addition to this so-called primary nitrate response, nitrate is suspected to play a long-term regulatory role, acting as a nitrogen (N) status signal for the entire plant. In our recent study using <i>Arabidopsis thaliana</i>, the manipulation of the internal nitrate levels independently of internal organic N without external N indicated that nitrate accumulation in the shoot alone causes genome-wide responses systemically, including the induction of nitrate assimilation genes and repression of N starvation-inducible genes. These responses mimic high nitrate growth situations for plants, suggesting that shoot nitrate acts as a N satiety signal. On the other hand, it is widely known that external supply of ammonium as another major N source also triggers N-rich responses, which led us to hypothesize that the existence of external ammonium may interfere with the genome-wide responses regarding shoot nitrate satiety. To clarify this, we compared transcriptional responses to shoot nitrate satiety with and without external ammonium both in Arabidopsis shoots and roots. Further, in order to determine the major role of nitrate satiety signaling, we extracted those genes regulated by shoot nitrate level regardless of the presence or absence of external ammonium and annotated them by two independent enrichment analyses. Here, we show that genome-wide transcriptional responses to shoot nitrate satiety are significantly lowered in the presence of external ammonium especially in the shoot. A major component for the ammonium-dependent attenuation of the nitrate satiety responses comprised a set of genes encoding the machinery for translation, glucosinolate biosynthesis, and photosynthesis. On the other hand, the nitrate satiety responses commonly observed irrespective of the presence/absence of ammonium included the components for translation and nitrate assimilation, whose transcriptional responses could be mediated partly via NIN-LIKE PROTEIN (NLP), NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1), and cytokinin signaling on the basis of our transcriptional profiling and cytokinin determination.
DOI: 10.6084/m9.figshare.12089175
title: Multiphase characterization of wild <i>Vigna</i> associated root nodule bacteria from Japanese subtropical islands unveiled novel high temperature resistant <i>Bradyrhizobium</i> strains having high symbiotic compatibility with soybean and mungbean

description: <i>Vigna riukiuensis</i> plant – a rare type of vigna, found only in Taiwan and the islands of Okinawa prefecture, Japan – possesses intrinsic property of high level of salt and heat tolerance. To understand the diversity and identify suitable rhizobia, multiphase characterization of root nodule bacteria associated with <i>V. riukiuensis</i> grown in Ishigaki and Iriomote Islands of Okinawa prefecture was performed. Multigene phylogenetic analysis of housekeeping genes based on 16S rRNA gene sequences, 16S-23S rRNA gene internal transcribed spacer (ITS) and 23S rRNA gene sequences identified three main groups closely similar to <i>Bradyrhizobium japonicum, B. elkanii</i> and <i>B</i>. <i>jicamae</i> family. However, analysis of symbiotic <i>nifH</i> and <i>nodD1</i> genes and their phylogenetic trees showed similar topology, having only few discrepancies in comparison to the housekeeping gene phylogeny. Interestingly, for some of the isolates having similarity with <i>B. elkanii</i>, growth was observed at 40°C, which exceed the highest record for <i>B. elkanii</i> to the best of our knowledge. All the isolates were observed to have the capability of forming root nodules and fix nitrogen in their original host plant <i>V. riukiuensis</i> and two other crops: soybean and mungbean. Most of the isolates showed similar or higher nitrogen-fixing capability in comparison with <i>B</i>. <i>diazoefficiens</i> USDA110 in <i>V. riukiuensis</i> and <i>V. radiata</i> (mungbean), and Iri 5/6 in <i>V. riukiuensis</i>, Iri 5/12 in soybean and Ishi 7/2 in mungbean showed highest acetylene reduction assay (in µmol/h/gm nodule dry weight) activity, which was significantly higher than <i>B. diazoefficiens</i> USDA110. In addition, six isolates attained higher soybean biomass production compared with <i>B. diazoefficiens</i> USDA110, suggesting high symbiotic compatibility with soybean. Among them, Iri 5/7 of <i>B. elkanii</i> group contributed 29% higher soybean biomass production than <i>B. diazoefficiens</i> USDA110 and could grow at 40°C, hence it could be a promising soybean inoculant in the tropics. ARA: acetylene reduction assay, ISR: intergenic spacer regions, ITS: internal transcribed spacer
DOI: 10.6084/m9.figshare.12089175.v1
title: Multiphase characterization of wild <i>Vigna</i> associated root nodule bacteria from Japanese subtropical islands unveiled novel high temperature resistant <i>Bradyrhizobium</i> strains having high symbiotic compatibility with soybean and mungbean

description: <i>Vigna riukiuensis</i> plant – a rare type of vigna, found only in Taiwan and the islands of Okinawa prefecture, Japan – possesses intrinsic property of high level of salt and heat tolerance. To understand the diversity and identify suitable rhizobia, multiphase characterization of root nodule bacteria associated with <i>V. riukiuensis</i> grown in Ishigaki and Iriomote Islands of Okinawa prefecture was performed. Multigene phylogenetic analysis of housekeeping genes based on 16S rRNA gene sequences, 16S-23S rRNA gene internal transcribed spacer (ITS) and 23S rRNA gene sequences identified three main groups closely similar to <i>Bradyrhizobium japonicum, B. elkanii</i> and <i>B</i>. <i>jicamae</i> family. However, analysis of symbiotic <i>nifH</i> and <i>nodD1</i> genes and their phylogenetic trees showed similar topology, having only few discrepancies in comparison to the housekeeping gene phylogeny. Interestingly, for some of the isolates having similarity with <i>B. elkanii</i>, growth was observed at 40°C, which exceed the highest record for <i>B. elkanii</i> to the best of our knowledge. All the isolates were observed to have the capability of forming root nodules and fix nitrogen in their original host plant <i>V. riukiuensis</i> and two other crops: soybean and mungbean. Most of the isolates showed similar or higher nitrogen-fixing capability in comparison with <i>B</i>. <i>diazoefficiens</i> USDA110 in <i>V. riukiuensis</i> and <i>V. radiata</i> (mungbean), and Iri 5/6 in <i>V. riukiuensis</i>, Iri 5/12 in soybean and Ishi 7/2 in mungbean showed highest acetylene reduction assay (in µmol/h/gm nodule dry weight) activity, which was significantly higher than <i>B. diazoefficiens</i> USDA110. In addition, six isolates attained higher soybean biomass production compared with <i>B. diazoefficiens</i> USDA110, suggesting high symbiotic compatibility with soybean. Among them, Iri 5/7 of <i>B. elkanii</i> group contributed 29% higher soybean biomass production than <i>B. diazoefficiens</i> USDA110 and could grow at 40°C, hence it could be a promising soybean inoculant in the tropics. ARA: acetylene reduction assay, ISR: intergenic spacer regions, ITS: internal transcribed spacer
DOI: 10.17630/057e6e1d-cd0d-4f5c-b062-53a71f62d619
title: High silica zeolites are widely used catalysts; those with different structural topologies being used for different applications. This protocol describes the Assembly-Disassembly-Organization-Reassembly (ADOR) process for preparing new zeolites. (dataset)