cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29118323
title: Soil plant available silicon from a bamboo forest on karst mountain in southwest China differs between wet and dry seasons

description: The distribution and its controlling factors of soil plant available silicon (PASi) are the basis for understanding the terrestrial silicon cycle and are poorly understood in karst mountainous areas. In this study, soil PASi concentrations of <i>Dendrocalamus ronganensis</i> bamboo forest topsoil using the citric acid extraction method (citric-Si) and cave drip water Si concentrations were measured during the wet and dry seasons with the aim of understanding the relationship between available silicon and climatic variables. The citric-Si content of soils and drip water Si was in the range of 24.6–164 mg·kg<sup>−1</sup> and 3.63–13.6 mg·kg<sup>−1</sup>, respectively, and decreased in the following order: A and AB horizon, O horizon, and drip water. Drip water Si was very low compared with soil citric-Si and water-soluble Si. The soil water-soluble Si and organic matter showed no significant difference between wet and dry seasons. The soil pH (KCl) and pH (H<sub>2</sub>O) showed higher values during the wet season, and pH (H<sub>2</sub>O) was correlated with the soil citric-Si content. The citric-Si content of soils showed variations between wet and dry seasons and was correlated positively with monthly precipitation. Drip water Si, which contributes to the loss of soil citric-Si, had no control on the soil citric-Si variation between dry and wet season. Phytoliths had a high proportion of soil dry weight, and they might be the main contributors to the DSi (soluble silicon) pool in this bamboo forest. The wet/dry seasonal difference of PASi in soils was probably linked to the dissolution of soil biogenic silicon, and precipitation altered soil water content and pH and promoted the dissolution of phytolith. This study is informative for ecological restoration and improving our understanding of silicon cycling in the karst mountain region.
DOI: 10.6084/m9.figshare.29118323.v1
title: Soil plant available silicon from a bamboo forest on karst mountain in southwest China differs between wet and dry seasons

description: The distribution and its controlling factors of soil plant available silicon (PASi) are the basis for understanding the terrestrial silicon cycle and are poorly understood in karst mountainous areas. In this study, soil PASi concentrations of <i>Dendrocalamus ronganensis</i> bamboo forest topsoil using the citric acid extraction method (citric-Si) and cave drip water Si concentrations were measured during the wet and dry seasons with the aim of understanding the relationship between available silicon and climatic variables. The citric-Si content of soils and drip water Si was in the range of 24.6–164 mg·kg<sup>−1</sup> and 3.63–13.6 mg·kg<sup>−1</sup>, respectively, and decreased in the following order: A and AB horizon, O horizon, and drip water. Drip water Si was very low compared with soil citric-Si and water-soluble Si. The soil water-soluble Si and organic matter showed no significant difference between wet and dry seasons. The soil pH (KCl) and pH (H<sub>2</sub>O) showed higher values during the wet season, and pH (H<sub>2</sub>O) was correlated with the soil citric-Si content. The citric-Si content of soils showed variations between wet and dry seasons and was correlated positively with monthly precipitation. Drip water Si, which contributes to the loss of soil citric-Si, had no control on the soil citric-Si variation between dry and wet season. Phytoliths had a high proportion of soil dry weight, and they might be the main contributors to the DSi (soluble silicon) pool in this bamboo forest. The wet/dry seasonal difference of PASi in soils was probably linked to the dissolution of soil biogenic silicon, and precipitation altered soil water content and pH and promoted the dissolution of phytolith. This study is informative for ecological restoration and improving our understanding of silicon cycling in the karst mountain region.
DOI: 10.6084/m9.figshare.29320292.v3
title: Paddy-upland rotation makes distinct impacts on the abundance of methane-oxidizing and ammonia-oxidizing microbial communities in paddy field soil

description: Paddy-upland rotation systems have been used as a major land management of paddy fields in Japan. In the paddy-upland rotational fields, upland crops are cultivated under drained conditions in summer for one year to several years, followed by paddy rice cropping for one year to several years. The soil conditions are kept oxic during the upland periods in these fields. Microbial communities in paddy field soil are greatly affected by these managements. In the present study, effect of paddy-upland rotation on the abundance of methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) and archaea (AOA) was investigated. Soil samples were collected from the rotational plots and consecutive paddy (control) plots at the experimental fields, where paddy rice under flooded conditions was rotated with soybean under upland conditions at different rotation histories. Abundance of MOB, AOB, and AOA communities was estimated by the quantitative PCR analyses of <i>pmoA</i> and <i>amoA</i> genes for DNAs extracted from the soil samples. The gene abundance of <i>pmoA</i> of MOB was an order of magnitude greater in the consecutive paddy plots (10<sup>6</sup> copies g<sup>−1</sup> dry soil) than in the rotational plots (10<sup>5</sup> copies g<sup>−1</sup> dry soil). In contrast, the gene abundance of <i>amoA</i> of AOB was an order of magnitude greater in the rotational plots (10<sup>8</sup> copies g<sup>−1</sup> dry soil) than in the consecutive paddy plots (10<sup>7</sup> copies g<sup>−1</sup> dry soil). The gene abundance of <i>amoA</i> of AOA was on the order of 10<sup>9</sup> copies g<sup>−1</sup> dry soil both in the rotational and consecutive paddy plots and showed very small differences between the plots. These results indicated that the factors affecting fluctuation in the community abundance caused by the paddy-upland rotation could be different among MOB, AOB, and AOA in the paddy field soil.
DOI: 10.6084/m9.figshare.29154694
title: Soil texture affects the nitrogen fate in the methane fermentation digestate applied to paddy soil

description: Waste fluid (digestate) from methane fermentation (MFW) is increasingly used as a fertilizer in paddy fields to reduce greenhouse gas emissions and mitigate climate change. However, the influence of soil texture on the fate of nitrogen (N) following MFW application remains unclear. This study aimed to elucidate the effects of MFW application rates on rice growth and N pathways in soils with contrasting textures to minimize environmental N loss during rice cultivation. Two-year pot experiments were conducted using sandy loam (SL) and clayey loam (CL) soils. Five treatments were applied, each with four replicates: a chemical fertilizer (NH<sub>4</sub>Cl, 200 mg N pot<sup>−1</sup>), three MFW rates of total N (100, 200, and 400 mg N pot<sup>−1</sup>), and a no-fertilizer control. To trace N derived from the inorganic fertilizer (Ndfif), <sup>15</sup>NH<sub>4</sub>Cl was added to account for 20% of the inorganic N in each treatment, while maintaining total N input constant. Increasing MFW application rates significantly enhanced the rice growth and yield, with a more pronounced effect in CL soil compared to SL soil. Higher MFW application rates further increased Ndfif uptake by plant, soil N retention, and NH<sub>3</sub> volatilization in CL soil, whereas SL soil showed more significant Ndfif leaching. Chemical fertilizers showed significantly higher Ndfif recovery but were more prone to leaching in SL soil compared to MFW-derived N. Based on normalized comparisons of rice yield and N loss, optimal MFW application rates were estimated at approximately 180 mg N-MFW pot<sup>−1</sup> for both soils, beyond which further yield increases were accompanied by substantial N leaching and emissions. Soil texture critically affects the fate of N following MFW application, especially regarding NH₃ volatilization in CL soils and N leaching in SL soils. Optimizing MFW application rates is crucial for achieving enhanced rice yields with minimal environmental N loss, thereby facilitating sustainable rice production. These findings emphasize the importance of soil texture in determining optimal nutrient management for sustainable rice production.
DOI: 10.6084/m9.figshare.29320292.v2
title: Paddy-upland rotation makes distinct impacts on the abundance of methane-oxidizing and ammonia-oxidizing microbial communities in paddy field soil

description: Paddy-upland rotation systems have been used as a major land management of paddy fields in Japan. In the paddy-upland rotational fields, upland crops are cultivated under drained conditions in summer for one year to several years, followed by paddy rice cropping for one year to several years. The soil conditions are kept oxic during the upland periods in these fields. Microbial communities in paddy field soil are greatly affected by these managements. In the present study, effect of paddy-upland rotation on the abundance of methane-oxidizing bacteria (MOB) and ammonia-oxidizing bacteria (AOB) and archaea (AOA) was investigated. Soil samples were collected from the rotational plots and consecutive paddy (control) plots at the experimental fields, where paddy rice under flooded conditions was rotated with soybean under upland conditions at different rotation histories. Abundance of MOB, AOB, and AOA communities was estimated by the quantitative PCR analyses of <i>pmoA</i> and <i>amoA</i> genes for DNAs extracted from the soil samples. The gene abundance of <i>pmoA</i> of MOB was an order of magnitude greater in the consecutive paddy plots (10<sup>6</sup> copies g<sup>−1</sup> dry soil) than in the rotational plots (10<sup>5</sup> copies g<sup>−1</sup> dry soil). In contrast, the gene abundance of <i>amoA</i> of AOB was an order of magnitude greater in the rotational plots (10<sup>8</sup> copies g<sup>−1</sup> dry soil) than in the consecutive paddy plots (10<sup>7</sup> copies g<sup>−1</sup> dry soil). The gene abundance of <i>amoA</i> of AOA was on the order of 10<sup>9</sup> copies g<sup>−1</sup> dry soil both in the rotational and consecutive paddy plots and showed very small differences between the plots. These results indicated that the factors affecting fluctuation in the community abundance caused by the paddy-upland rotation could be different among MOB, AOB, and AOA in the paddy field soil.
DOI: 10.6084/m9.figshare.29154694.v2
title: Soil texture affects the nitrogen fate in the methane fermentation digestate applied to paddy soil

description: Waste fluid (digestate) from methane fermentation (MFW) is increasingly used as a fertilizer in paddy fields to reduce greenhouse gas emissions and mitigate climate change. However, the influence of soil texture on the fate of nitrogen (N) following MFW application remains unclear. This study aimed to elucidate the effects of MFW application rates on rice growth and N pathways in soils with contrasting textures to minimize environmental N loss during rice cultivation. Two-year pot experiments were conducted using sandy loam (SL) and clayey loam (CL) soils. Five treatments were applied, each with four replicates: a chemical fertilizer (NH<sub>4</sub>Cl, 200 mg N pot<sup>−1</sup>), three MFW rates of total N (100, 200, and 400 mg N pot<sup>−1</sup>), and a no-fertilizer control. To trace N derived from the inorganic fertilizer (Ndfif), <sup>15</sup>NH<sub>4</sub>Cl was added to account for 20% of the inorganic N in each treatment, while maintaining total N input constant. Increasing MFW application rates significantly enhanced the rice growth and yield, with a more pronounced effect in CL soil compared to SL soil. Higher MFW application rates further increased Ndfif uptake by plant, soil N retention, and NH<sub>3</sub> volatilization in CL soil, whereas SL soil showed more significant Ndfif leaching. Chemical fertilizers showed significantly higher Ndfif recovery but were more prone to leaching in SL soil compared to MFW-derived N. Based on normalized comparisons of rice yield and N loss, optimal MFW application rates were estimated at approximately 180 mg N-MFW pot<sup>−1</sup> for both soils, beyond which further yield increases were accompanied by substantial N leaching and emissions. Soil texture critically affects the fate of N following MFW application, especially regarding NH₃ volatilization in CL soils and N leaching in SL soils. Optimizing MFW application rates is crucial for achieving enhanced rice yields with minimal environmental N loss, thereby facilitating sustainable rice production. These findings emphasize the importance of soil texture in determining optimal nutrient management for sustainable rice production.
DOI: 10.6084/m9.figshare.29270841
title: Peri-urban agricultural management impacts the soil nutrient status of Nitisols in the central highlands of Kenya

description: In sub-Saharan Africa, urban and peri-urban agriculture (UPA) plays an important role in improving food and nutrition security amid rapid urbanization in the region. Poor soil fertility has been suggested as the primary reason for low crop productivity in the region, however UPA is often associated with soil nutrient accumulation in other developed or recently developed nations. There is still a lack of evidence regarding soil nutrient status of UPA in this region. To understand the current soil fertility status and the impacts of soil nutrient management, an evaluation of soil profiles, surface soil conditions, and current nutrient management was conducted in Kiambu County, which is a part of the Greater Nairobi Metropolitan Region of Kenya. Soil samples were collected from both the Tigoni experimental station and 26 surrounding small-scale peri-urban farms. All three soil profiles were classified as Eutric Nitisols with well-developed soil structure, adequate cation exchange capacity, relatively high phosphate retention, and high base saturation. The surface soil nutrient status between the Tigoni experimental station and the surrounding farms showed significant differences except for exchangeable K, which is likely derived from the parent materials. Available phosphate (Truog-P) levels were excessively high, exceeding 1000 mg‑P<sub>2</sub>O<sub>5</sub> kg<sup>−1</sup> in three commercial farms, and nearly half of the farms were in the excessive range, contrary to the past findings in other counties in Kenya. In contrast, phosphate levels at the experimental station were mostly deficient. Exchangeable Ca levels followed a similar trend to Truog-P, while Mg was deficient relative to K at the experimental station and relative to both K and Ca in the commercial farm fields. The use of animal manure is considered a major factor contributing to the high P and Ca levels observed in the peri-urban farm fields. Future studies are needed to explore the relationship between the current variable soil fertility status and vegetable productivity. Additionally, the introduction of a low-cost soil testing method is necessary to establish a system for optimizing the soil conditions.
DOI: 10.6084/m9.figshare.29270841.v1
title: Peri-urban agricultural management impacts the soil nutrient status of Nitisols in the central highlands of Kenya

description: In sub-Saharan Africa, urban and peri-urban agriculture (UPA) plays an important role in improving food and nutrition security amid rapid urbanization in the region. Poor soil fertility has been suggested as the primary reason for low crop productivity in the region, however UPA is often associated with soil nutrient accumulation in other developed or recently developed nations. There is still a lack of evidence regarding soil nutrient status of UPA in this region. To understand the current soil fertility status and the impacts of soil nutrient management, an evaluation of soil profiles, surface soil conditions, and current nutrient management was conducted in Kiambu County, which is a part of the Greater Nairobi Metropolitan Region of Kenya. Soil samples were collected from both the Tigoni experimental station and 26 surrounding small-scale peri-urban farms. All three soil profiles were classified as Eutric Nitisols with well-developed soil structure, adequate cation exchange capacity, relatively high phosphate retention, and high base saturation. The surface soil nutrient status between the Tigoni experimental station and the surrounding farms showed significant differences except for exchangeable K, which is likely derived from the parent materials. Available phosphate (Truog-P) levels were excessively high, exceeding 1000 mg‑P<sub>2</sub>O<sub>5</sub> kg<sup>−1</sup> in three commercial farms, and nearly half of the farms were in the excessive range, contrary to the past findings in other counties in Kenya. In contrast, phosphate levels at the experimental station were mostly deficient. Exchangeable Ca levels followed a similar trend to Truog-P, while Mg was deficient relative to K at the experimental station and relative to both K and Ca in the commercial farm fields. The use of animal manure is considered a major factor contributing to the high P and Ca levels observed in the peri-urban farm fields. Future studies are needed to explore the relationship between the current variable soil fertility status and vegetable productivity. Additionally, the introduction of a low-cost soil testing method is necessary to establish a system for optimizing the soil conditions.
DOI: 10.6084/m9.figshare.29098117.v1
title: Insights into microbial removal of ammonia and nitrous oxide from biological air purification reactors used for livestock farming: a review

description: A large portion of ammonia (NH<sub>3</sub>) originates from the agricultural sector, and intensive livestock farming is one of the fundamental causes of the airborne nitrogen (N) load. Treatment of NH<sub>3</sub> is therefore crucial for the better management of livestock farming. Biological air purification technology is one of the best options for mitigating NH<sub>3</sub> emissions from livestock farms. Inorganic nitrogen often accumulates in the filtering material and water inside the air purification reactor if they are not washed out because of requirements for wastewater reduction. They usually need to be removed and subsequently treated elsewhere to avoid inhibition of nitrification of free ammonia and free nitrous acid in drain water. Furthermore, nitrous oxide (N<sub>2</sub>O) is emitted from the air purification reactor as a result of microbial N transformations. Because these concerns are all related to N cycles driven by microorganisms in the purification reactor, proper operations require informed understanding of microbiology related to NH<sub>3</sub> removal. The relationship between key operational parameters and the dynamics of microbial communities relative to nitrification, denitrification, and N<sub>2</sub>O emissions from a biological air purification system have not been updated. Current knowledge of the mechanisms of NH<sub>3</sub> removal, the N cycle, and the complex network of microbes involved in N transformations that are affected by operational conditions in such a system is reviewed, with special emphasis on practices at livestock farms. Biodegradation might be a limiting factor, even if the load is lower than the critical inlet load at full-scale operation. Although biological air purification reactors are constantly aerated, a certain amount of N could be lost because of denitrification. After treatment of livestock air, up to 40% of the input NH<sub>3</sub>-N can be transferred to N<sub>2</sub>O. The operational parameters affecting N<sub>2</sub>O emissions are packing material moisture content, pH, and nitrite concentration. The functional microbial community might change if it adapts to the surrounding environment in full-scale operation. Apart from water control, the effects of different properties of the packing material on the growth and activities of microbes have to be clearly elucidated to provide optimum conditions for microorganisms to both remove NH<sub>3</sub> and reduce N<sub>2</sub>O emissions.
DOI: 10.6084/m9.figshare.29154694.v1
title: Soil texture affects the nitrogen fate in the methane fermentation digestate applied to paddy soil

description: Waste fluid (digestate) from methane fermentation (MFW) is increasingly used as a fertilizer in paddy fields to reduce greenhouse gas emissions and mitigate climate change. However, the influence of soil texture on the fate of nitrogen (N) following MFW application remains unclear. This study aimed to elucidate the effects of MFW application rates on rice growth and N pathways in soils with contrasting textures to minimize environmental N loss during rice cultivation. Two-year pot experiments were conducted using sandy loam (SL) and clayey loam (CL) soils. Five treatments were applied, each with four replicates: a chemical fertilizer (NH<sub>4</sub>Cl, 200 mg N pot<sup>−1</sup>), three MFW rates of total N (100, 200, and 400 mg N pot<sup>−1</sup>), and a no-fertilizer control. To trace N derived from the inorganic fertilizer (Ndfif), <sup>15</sup>NH<sub>4</sub>Cl was added to account for 20% of the inorganic N in each treatment, while maintaining total N input constant. Increasing MFW application rates significantly enhanced the rice growth and yield, with a more pronounced effect in CL soil compared to SL soil. Higher MFW application rates further increased Ndfif uptake by plant, soil N retention, and NH<sub>3</sub> volatilization in CL soil, whereas SL soil showed more significant Ndfif leaching. Chemical fertilizers showed significantly higher Ndfif recovery but were more prone to leaching in SL soil compared to MFW-derived N. Based on normalized comparisons of rice yield and N loss, optimal MFW application rates were estimated at approximately 180 mg N-MFW pot<sup>−1</sup> for both soils, beyond which further yield increases were accompanied by substantial N leaching and emissions. Soil texture critically affects the fate of N following MFW application, especially regarding NH₃ volatilization in CL soils and N leaching in SL soils. Optimizing MFW application rates is crucial for achieving enhanced rice yields with minimal environmental N loss, thereby facilitating sustainable rice production. These findings emphasize the importance of soil texture in determining optimal nutrient management for sustainable rice production.
DOI: 10.5065/d6dv1h4n
title: Navigation, State Parameter, and Microphysics HRT Data in GENPROI format. Version 1.0

description: This data set includes airborne measurements obtained from the L-188 Electra aircraft (Tail Number N595KR) during the BLD project. This dataset contains high rate navigation, state parameter, and microphysics flight-level data in GENPRO-I format.