Soil nitrogen dynamics during stand development after clear-cutting of Japanese cedar (Cryptomeria japonica) plantations

We examined soil N dynamics, including inorganic N concentration, net N transformation rates, and estimated plant N uptake (EPNU) from soil N budgets, and litterfall inputs, in five Japanese cedar plantation stands of different ages (5, 16, 31, 42, and 89 years) in the Mt Gomadan Experimental Forest (GEF). Net soil N mineralization and nitrification rates did not differ significantly between the youngest and oldest stands; soil moisture and inorganic N concentration were higher in the youngest stand. The EPNU was highest in the 16-year-old stand and lowest in the 31-year-old stand, and had a significant negative correlation with litter C:N ratio. The oldest (89-year-old) stand had a higher soil C:N ratio, lower proportion of nitrification rate to mineralization rate (%NIT), and higher estimated plant NH4 + uptake than did the other stands, indicating that changes of soil organic matter quality can alter soil N dynamics. These results suggest that as a Japanese cedar plantation develops, soil N dynamics can be altered by the quantity and quality of input litter and soil organic matter, and can generate the imbalance between N supply from soil and N demand by plant

Temperature effects on the first three years of soil ecosystem development on volcanic ash

Little is known of the earliest stages of soil ecosystem development on volcanic ash, and how this process is affected by temperature. We studied the first three years of soil development in a field-based mesocosm experiment, situated in different climates across Japan. Newly fallen, sterilized volcanic ash from the Sakurajima volcano (Kyushu, Japan) was placed into pots and positioned at six locations with mean annual temperatures ranging from - 1.6 °C to 18.6 °C. At 24 months into the experiment, C and N accumulation showed only a weak linear correlation with temperature, but by 36 months there was a clear exponential relationship. This applied only to the top 2 cm of the developing soil, and was not apparent in the lower part of the ash. We suggest that this acceleration in warmer climates relates to a positive feedback involving bryophyte cover, which had become much denser by the third year in the warmer sites. Surprisingly, the abundance of 16S rRNA gene copies of bacteria, fungi, archaea - as well as ammonia oxidizers – did not increase from 12 months to 36 months, and did not show any relationship to temperature, suggesting that input from plants is the major factor in increasing C and N buildup in the soil. Overall it appears that temperature effects on bryophyte cover buildup may be important in controlling the temperature relationship in soil development on volcanic ash

Evaluation of host effects on ectomycorrhizal fungal community compositions in a forested landscape in northern Japan

Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.4853145.Community compositions of ectomycorrhizal (ECM) fungi are similar within the same host taxa. However, careful interpretation is required to determine whether the combination of ECM fungi and plants is explained by the host preference for ECM fungi, or by the influence of neighbouring heterospecific hosts. In the present study, we aimed to evaluate the effects of host species on the ECM community compositions in a forested landscape (approx. 10 km) where monodominant forest stands of six ECM host species belonging to three families were patchily distributed. A total of 180 ECM operational taxonomic units (OTUs) were detected with DNA metabarcoding. Quantitative multivariate analyses revealed that the ECM community compositions were primarily structured by host species and families, regardless of the soil environments and spatial arrangements of the sampling plots. In addition, 38 ECM OTUs were only detected from particular host tree species. Furthermore, the neighbouring plots harboured similar fungal compositions, although the host species were different. The relative effect of the spatial factors on the ECM compositions was weaker than that of host species. Our results suggest that the host preference for ECM fungi is the primary determinant of ECM fungal compositions in the forested landscape

Soil pH and biome are both key determinants of soil archaeal community structure

The mechanisms underlying community composition and diversity of soil archaea are poorly understood. We compared both total archaea and ammonia oxidizing archaea (AOA) using 16S rRNA and amoA genes pyrosequencing respectively, in two different biomes: tropics (Malaysia), and temperate (Korea and Japan). Despite differences in characteristics of these biomes, we found that at the broad taxonomic level the dominant archaeal lineages are the same, except in certain instances (16S rRNA gene: group 1.1a Thaumarchaeota; amoA gene: Nitrososphaera and Nitrosotalea lineages). However, at the OTU level, both total archaea and AOA communities showed biome-specific patterns, indicating that at lower taxonomic levels biome differences are also important. In both biomes, total archaeal diversity showed a negative correlation with pH, but a hump-shaped curve for AOA diversity, peaking at ∼pH 6.0. Within each biome, pH also emerged as the delimiting factor determining variation in community composition of both total archaea and AOA. Communities from each biome clustered separately, even at analogous pH levels. At the OTU level, certain shared OTUs did occur at approximately the same pH range in both biomes. We found that closely related OTUs of both total archaea and AOA respectively tended to co-occur, suggesting that in evolutionary terms these closely related lineages have conserved very similar ecological requirements. This predictability also strongly suggests that soil archaeal community assembly has strongly deterministic aspect. Overall, our findings emphasize that soil archaeal communities are to large extent predictable and structured by both biome and by soil chemical environment, especially pH

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

シンリン コウゾウ ニ ソッタ チッソ ト ヒカリ ノ ソウタイテキナ シゲンリョウ ニ タイスル ジュモク ノ チッソ リヨウ コウリツ

京都大学0048新制・課程博士博士(農学)甲第10270号農博第1342号新制||農||868(附属図書館)学位論文||H15||N3791(農学部図書室)UT51-2003-H691京都大学大学院農学研究科地域環境科学専攻(主査)教授 武田 博清, 教授 東 順一, 教授 谷 誠学位規則第4条第1項該当Doctor of Agricultural ScienceKyoto UniversityDA

Nitrogen resorption efficiency of 13 tree species of a cool temperate deciduous forest in Central Japan

Special Feature: Radiocesium dynamics in forest ecosystems after the Fukushima Nuclear Power Plant accident: Experiences during the initial five yearsThe nitrogen (N) concentration of green and senescent leaves, and the N resorption efficiency of 13 dominant species from three distribution patterns along a slope (Ridge, Valley, and Uniform types) and two types of leaf emergence pattern (determinate and indeterminate flush types) were examined in a cool temperate natural forest in central Japan. Ridge species tended to have lower N concentrations of green and senescent leaves and higher N resorption efficiency than those of Valley species, and those of Uniform species were intermediate to other types with some exceptions. Furthermore, indeterminate flush species tended to have higher N concentrations in green and senescent leaves and lower N resorption efficiency than those of the determinate type. The N concentration of senescent leaves, which is an index of leaf-level N use efficiency (NUE), was significantly correlated with N concentrations in green leaves and with N resorption efficiency. The concentration in green leaves was not correlated with N resorption efficiency, suggesting that interspecific variation in the N concentration was not a major determinate of the N resorption efficiency at this study site. Rather N resorption efficiency was positively correlated with the start date of leaf fall, suggesting that early leaf fall species, which tended to have intermediate leaf flush types (with some exceptions), were not proficient in N resorption. Thus, the patterns in NUE and N resorption efficiencies were affected not only by the distribution pattern along the slope but also by leaf phenology in this cool temperate deciduous forest

In-situ measurement of the effect of canopy tree fine roots on nitrogen availability in forest soil

Plant fine roots affect the amount of soil inorganic nitrogen (N) via their N uptake and their effects on organic matter decomposition and N mineralization. However, the effects of the fine roots of canopy trees on N availability in forest soil remain largely unknown owing to the limitations of in-situ measurements. Therefore, to reveal the effects of the fine roots of canopy trees on forest soil N availability, we developed a novel in-situ method that combines a modified in-situ resin-core method, using live fine roots, with a tree N demand estimation, using the N-balance method. Furthermore, we measured soil extracellular enzyme activities in the rhizosphere and bulk soils to determine whether fine roots stimulate soil enzyme activities. The results showed that soil enzyme activities were stimulated by the fine roots of canopy trees, especially in the rhizosphere, and this indicates that fine roots stimulate organic matter decomposition and N mineralization. However, fine roots had no significant effect on either the pool size or leaching of inorganic N. The estimated amount of potential N uptake by fine roots was greater than the amount of inorganic N released via fine root-induced N mineralization. Overall, our results indicate that almost all of the fine root-induced increment of mineralized inorganic N is taken up by the fine roots; thus, the fine roots of canopy trees did not affect N availability in forest soil. This study was limited by the fact that the fine roots in the resin cores were less dense than natural roots, and the fact that the actual root N uptake can differ from the estimated N uptake; these limitations should be resolved in future studies. Nevertheless, the proposed method can be used to investigate the effects of fine roots on the N cycle in forest soil under field conditions considering N uptake and priming

Rhizosphere effects on soil extracellular enzymatic activity and microbial abundance during the low-temperature dormant season in a northern hardwood forest

Plant roots alter nutrient cycling, including nitrogen (N) and phosphorus (P) cycling, within the soil surrounding them (rhizosphere) by affecting microbes and enzyme activities. Recent studies have focused on nutrient uptake by plants in low-temperature seasons. This study aimed to reveal the nutrient dynamics in the rhizosphere during low-temperature seasons in a northern hardwood forest in Japan. For this purpose, the potential extracellular enzymatic activity, bacterial, fungal, and archaeal abundances, and soil chemical properties in the rhizosphere of canopy trees and understory vegetation and non-rhizosphere bulk soil were measured at the beginning of the dormant season (November), end of the dormant season (April and May), and middle of the growing season (August) in a northern hardwood forest in Japan. The abundance of fungi was 1.1–1.7 times higher in the rhizosphere than in non-rhizosphere bulk soil regardless of the season. The activity of enzymes involved in N- and P- cycles in the rhizospheres was also 1.4 to 4.0 and 1.3 to 1.9 times higher than that in bulk soil, respectively. The concentration of extractable organic N was 1.5–2.0 times higher in the rhizosphere than in the non-rhizosphere bulk soil at the beginning and end of the dormant season, respectively, but this trend was not observed in the middle of the growing season for organic N. Since the concentration of nutrients in the rhizosphere is determined by the balance between nutrient uptake by fine roots and root-induced acceleration of decomposition, our results suggest that plant roots would accelerate N and P cycles during the dormant season, even though the amount of nutrient uptake by plants was lower during the season