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A large-scale ecological restoration project was initiated in the 1990s in southwest China, which is one of the largest areas of rocky desertification globally. However, the influence and potential mechanisms of vegetation restoration on soil carbon(C) sequestration in karst and non-karst regions remains unclear. Based on field investigation and multi-source data synthesis, the mechanisms of soil C sequestration were investigated to determine the most important variables affecting the rate of soil C change (Rs) in southwest China. Our results show significant differences in soil C sequestration between karst and non-karst regions with faster and longer C sequestration occurring in karst regions. In these areas, Rs was approximately 31% higher than in non-karst soils. The Rs of shrubland, grassland and cropland sites in karst areas was significantly higher than that observed in non-karst areas. We found that temperatures were the primary factor inhibiting soil C sequestration instead of precipitation. The total effect of nitrogen (N) on Rs was positive in both karst and non-karst regions. Phosphorus was the dominant factor limiting the use of N by vegetation in karst regions and then resulting in limitation of C sequestration. The results indicated that soil C storage may increase intermittently due to combination of karst environment and climate change in southwest China in future.

Liaodong oak (Quercus liaotungensis Koidz.) dominated forests contribute to the few natural forest ecosystems in the semiarid Loess Plateau region in China. This study investigated the influence of soil nutrients and stand structure on aboveground net primary productivity (ANPP) in the oak communities. We aimed to understand the major factors and their possible pathways that determine the ecosystem productivity. The biomass and the ANPP were estimated using plot surveys and litterfall collection in fixed plots. Linear regressions and structural equation models were used to evaluate the relationships among soil nutrients, stand structure (including vertical and horizontal structure), and ANPP. The results showed that the effect sizes of soil nutrients on ANPP and leaf production were near 60% and 70%, respectively. More than 70% of the variation in woody production was explained by stand structure, while litterfall production was largely dependent on stand vertical structure with effect size of 64%. The effect of soil nutrients on stand structural indices was detected only in the case of the vertical structure. The results suggested that soil nutrients could affect forest productivity both directly and indirectly in coordination with stand vertical structure, and that the effect of stand structure was limited in these communities.

There is little knowledge about microbial functional community structures and the relationships between microbial communities and nitrogen transformation processes. Here, we investigated the relationships between soil microbial communities and nitrogen mineralisation potentials in a cool temperate forest throughout the growing season. Microbial communities were assessed by quantification of the total bacterial, archaeal, and fungal gene abundances and the bacterial and archaeal amoA gene abundances, functional predictions of bacteria and fungi, and analysis of the bacterial-fungal co-occurrence network. In mid-summer, ectomycorrhizal fungal abundance was significantly higher, whereas the total bacterial abundance was significantly lower. Bacterial and archaeal amoA gene abundances were also significantly higher in mid-summer. However, regardless of the seasonal fluctuation of microbial gene abundances, the net nitrification and nitrogen mineralisation potential did not show clear seasonality. In the network analysis, the microbial community was divided into 13 modules, which were subgroups assumed to have similar niches. Furthermore, two modules that mainly consisted of microbial species of Proteobacteria and Bacteroidetes were significantly and positively correlated with the net nitrification and mineralisation potentials. Our results indicated that microbial subgroups sharing similar niches, instead of total microbial abundances and functional gene abundances, could be important factors affecting the net nitrogen mineralisation potential.

To investigate the effect of reduced snow cover on fine root dynamics in a cool-temperate forest in northern Japan because of decreases in snowfall at high latitudes due to global warming, we monitored root length, production, and mortality before and after snow removal with an in-ground root scanner. We measured root dynamics of both overstory deciduous oak (Quercus crispula) and understory evergreen dwarf bamboo (Sasa nipponica), the two major species in the forest. Snow removal advanced the timing of peak root production by a month both in total and in Sasa, but not in oak. There was a significant interaction between snow removal and plant form on root production; this indicates that enhanced Sasa root production following snow removal might increase its ability to compete with oak. In contrast, snow removal did not enhance root mor-tality, suggesting that the roots of these species tolerate soil freezing. The earlier snow disappearance in the snow removal plot expanded the growing season in Sasa. We speculate that this change in the understory environment would advance the timing of root production by Sasa by extending the photosynthetic period in spring. We propose that different responses of root production to reduced snow cover between the two species would change the competitive interactions of overstory and understory vegetation, influencing net primary production and biogeochemistry (e.g., carbon and nitrogen cycles) in the forest ecosystem.

Topographic positions within a natural forest can considerably influence litter traits, soil microbial characteristics, and nitrogen (N) mineralization, causing plant–soil feedbacks. Despite the high abundance of coarse litter (woody debris and coarse roots) in forest ecosystems, most studies have focused on linkages between fine litter (leaves and fine roots) and N dynamics and/or the soil microbial community. We investigated the association of fine and coarse litter with soil microbial biomass, community structure, and N mineralization at upper and lower slope positions on sedimentary rocks in a temperate forest dominated by Fagus crenata. Greater coarse litter abundance and litter C-to-N ratio, and lower soil microbial biomass, bacterial abundance, and N mineralization potential were found in upper positions than in lower positions. Among litter traits, coarse litter abundance and litter C-to-N ratio were the best predictors of the microbial biomass and fungal-to-bacterial dominance, possibly due to differences in climatic stress among plant communities. Microbial traits were the best predictors of N mineralization potential. Fine litter traits and coarse litter abundance are likely linked to soil microbial characteristics and N mineralization in natural forests with variable topography.

Fine root is a significant component in carbon (C) and nitrogen (N) dynamics in temperate forests. Winter processes affect plant growth and nutrient concentration, however, the effect of reduced sn...

Understory dwarf bamboo mitigated soil N competition with co-existing canopy oak trees by foraging in deeper soils and increasing dependence on N forms that differ from those used by canopy trees. Nitrogen (N) competition among co-existing plant species utilizing different mycorrhiza types was explored through the investigation of N sources of oak trees and dwarf bamboo. Vertical distribution of fine roots, soil N pools, δ15N of leaves, and possible soil N sources and nitrate reductase activity (NRA) were all quantified. The fine roots of canopy trees were more concentrated in the surface soils than roots of the understory dwarf bamboo. Soil NH4+ and extractable organic N (EON) content (based on unit weight) decreased from the organic horizon (O horizon) to the deep soils, the size of the NH4+ pool per unit volume increased with soil depth, and the EON was approximately constant. Soil NO3− was not detected at any soil depth or was not significant in value, while NO3− captured by ion-exchange resin (IER) buried at a 10 cm soil depth and net nitrification were observed via laboratory incubation at all soil depths. The δ15N of the NH4+ and EON pools increased with soil depth and the δ15N of NO3− of IER was lower than that of other N forms, except for the δ15N of NH4+ in the O horizon. Furthermore, root NRA tended to be lower in canopy trees than in the understory, implying lower dependency on NO3− by canopy trees. The pattern of root distribution and mycorrhizal fungi association of the understory vegetation (as well as the high root NRA) suggested that dependence on N in deeper soils was higher in understory plants than in canopy trees. These findings indicate that understory vegetation mitigates soil N competition against co-existing canopy trees via the use of alternative N sources.

The use of heavy forestry machines for clear-cutting and site preparation causes soil compaction, which can decrease forest productivity. This process becomes complicated in forests with high levels of precipitation due to the erosion and deposition of surface soil. Here, we investigated how soil compaction and slash dispersal on compacted soil affect soil nitrogen (N) mineralization in a high precipitation area with erodible volcanic soil in southern Japan. The physical and chemical properties of the soil were measured inside and outside the ruts of work roads in the presence and absence of dispersed slash in three Cryptomeria japonica plantations 9–10 months after clear-cutting and site preparation. We found that the soil N mineralization rate, particularly the soil nitrification rate, was lower in compacted soil, but the dispersal of slash after soil compaction enhanced the soil N mineralization and nitrification rates. Soil compaction also led to a low soil water permeability and high volumetric soil water content and was associated with the erosion and deposition of surface soil, with soil deposition including organic matter, being observed under dispersed slash. Additionally, the soil carbon (C) and N concentrations were lower in compacted soil but improved under dispersed slash. Principal component analysis showed that soil compaction and the soil C and N concentrations were closely related to each other on the first principal component (PC1), while the soil C/N ratio was separated from other factors on PC2. Furthermore, the scores of both PC1 and PC2 were related to soil N mineralization. These results suggest that soil compaction by forestry machines has a negative impact on soil N mineralization under high precipitation, but slash dispersal on the compacted soil is an effective approach for maintaining the soil N mineralization. The soil C/N ratio is likely related with N mineralization in the impacted soils, but the negative relationship between soil compaction and soil C and N concentrations through the movement of surface soil containing these elements should also be considered to fully understand the changes in soil N mineralization that occurs in forests under high precipitation.

PurposePlant roots alter nutrient cycling within the soil surrounding them (rhizosphere). Recent studies have focused on nutrient uptake by plants in low-temperature seasons. This study aimed to reveal the nutrient dynamics in rhizosphere during low-temperature seasons in a northern hardwood forest in Japan.MethodsThe 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.ResultsThe abundance of fungi and the activity of nitrogen- and phosphorus-degrading enzymes were higher in the rhizosphere than in non-rhizosphere bulk soil regardless of the season. The concentration of extractable organic and inorganic N was higher in the rhizosphere than in the non-rhizosphere bulk soil at the beginning and end of the dormant season, but this trend was not observed in the middle of the growing season. ConclusionSince 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.

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.

Tree species influence the chemical properties of the organic horizon and mineral soil. Microbial communities, including fungi and bacteria, which are the main drivers of nutrient cycles in forest soils, may be affected by tree species via litter chemical properties and root exudation. Therefore, conversion from natural forest to plantation could affect the microbial communities. Here, we aimed to reveal the effects of conversion from natural forest to coniferous plantation on soil microbial community structure, biodiversity, and co-occurrence networks, as well as soil chemical properties. For this purpose, we investigated chemical and microbial properties of the organic horizon and mineral topsoil (0–10 cm depth) in three forest types (a natural forest dominated by broad-leaved deciduous trees, and two types of plantations). Forest type had significant effects on chemical properties, including the C/N ratio, pH, and dissolved inorganic N of the organic horizon, while it had no significant effect on the chemical properties of topsoil, except for microbial biomass N and C. Microbial community structures in both the organic horizon and topsoil differed significantly among forest types and with changes in soil properties such as pH and C/N ratio. Microbial diversity indices did not significantly differ among forest types in either layer, while the microbial co-occurrence networks in the mineral soil of the natural forest were more complex and robust than the networks of plantations. Therefore, our results showed that conversion from natural forest to coniferous plantation could affect soil chemical properties and microbial community structure in the organic horizon, and the microbial co-occurrence network in the mineral topsoil; these impacts may vary according to the planted tree species.

Rainfall patterns are predicted to change dramatically in many terrestrial landscapes, including drylands. The most limiting resources for plant growth in arid regions is nitrogen (N) as well as water. A natural aridity gradient provides appropriate candidate conditions for predicting the impacts of changes in rainfall on soil N dynamics. To comprehensively and mechanistically examine soil N dynamics, we focused on the steps of N transformation, their microbial drivers, and the determining soil properties. We divided the N transformation process into three steps: (i) organic matter degradation, (ii) N mineralization, and (iii) nitrification, which are driven primarily by fungi, prokaryotes, and ammonia oxidizers, respectively. Soil samples were collected from three black locust forests with mean annual precipitations ranging from 449 to 606 mm. Along the aridity gradient, all three steps changed while maintaining a balance. The degradation and mineralization steps varied with changes in the soil fungal and prokaryotic communities, respectively. The compositions of these communities were determined by soil substrate quality and quantity; saprotrophs and copiotrophs decreased along the aridity gradient. On the other hand, the abundance of ammonia-oxidizing bacteria, which correlated with the rate of nitrification, was likely determined by soil moisture. Therefore, if precipitation were to decrease, changes in the nitrification step might be the first mechanism to limit plant productivity in semi-arid forests. This limitation would extend to the other steps in the N cycling process via plant–soil feedback. Thus, N cycling dynamics are predicted to achieve new stable states suited to the changed precipitation regime.

In this study, we investigated the effects of reduced snow depth on plant phenology, productivity, nitrogen (N) cycling, and N use in canopy and understory vegetation. We hypothesized that decreased snow depth would hasten the timing of leaf flushing and N uptake in understory vegetation, increasing its N competitive advantage over canopy trees. Snow removal did not directly affect the phenology of either canopy or understory vegetation. Understory vegetation took up more N in the snow removal plots than in the control plots, particularly in the mid- to late-growing season. Leaf production and N uptake in canopy trees also did not differ between the control and snow removal plots, but N resorption efficiency in the snow removal plots (57.6%) was significantly higher than those in control plots (50.0%). Increased N uptake by understory plants may induce N limitation in canopy trees, which in turn may cause canopy trees to increase their N use efficiency. Such competitive advantage of understory vegetation over canopy trees against snow reduction may affect N cycling via litter quality and quantity not only just after the growing season but also in subsequent seasons.

Recent global warming models project a significant change in winter climate over the next few decades. The decrease in snowpack in the winter will decrease the heat insulation function of the snowpack, resulting in increased soil freeze–thaw cycles. Here, we examined the impact of winter freeze–thaw cycles on year-round dissolved nitrogen (N) and carbon (C) dynamics and their relationship with dissolved organic matter and microbial biomass in soil by conducting an in situ experimental reduction in snowpack. We investigated dissolved inorganic N (NH4+ and NO3−), dissolved organic N (DON), dissolved organic carbon (DOC), inorganic N leaching, soil microbial biomass, and microbial activities (mineralization and nitrification) in the surface soil of a northern hardwood forest located in Japan. Experimental snowpack reduction significantly increased the number of soil freeze–thaw cycles and soil frost depth. The NH4+ content of the surface soil was significantly increased by the amplified soil freeze–thaw cycles due to decreased snowpack, while the soil NO3– content was unchanged or decreased slightly. The gravimetric soil moisture, DON and DOC contents in soil and soil microbial biomass significantly increased by the snowpack removal in winter. Our results suggest that the amplified freeze–thaw cycles in soil increase the availability of DON and DOC for soil microbes due to an increase in soil freezing. The increases in both DON and DOC in winter contributed to the enhanced growth of soil microbes, resulting in the increased availability of NH4+ in winter from net mineralization following an increase in soil freeze–thaw cycles. Our study clearly indicated that snow reduction significantly increased the availability of dissolved nitrogen and carbon during winter, caused by increased soil water content due to freeze–thaw cycles in winter.

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.

Backgrounds A large-scale ecological restoration project has been initiated since 1990s in southwest China, which is one of the largest areas of rocky desertification globally. However, the different influences and potential mechanisms of vegetation restoration on soil carbon(C) sequestration in karst and non-karst regions are still unclear. Methods Based on field investigation and multi-source data synthesis, the mechanisms of soil C sequestration were investigated to determine the most important variables affecting the rate of soil C change (Rs) in southwest China. Results Our results show significant differences in soil C sequestration between karst and non-karst regions with faster and longer C sequestration in karst regions, where Rs was approximately 31 % higher than in non-karst soils. And temperatures could be the primary factor inhibiting soil C sequestration without precipitation. The total effect of nitrogen (N) on Rs was positive in both karst and non-karst regions. Conclusions Phosphorus was the dominant factor limiting the use of N in karst regions and then resulting in limitation of C sequestration. The results indicated that soil C storage could be led to intensify uneven increases due to combination of karst environment and climate change in southwest China in future.

In order to examine the hypothesis that the soil microbial community in a nitrogen-limited forest responds to moderately elevated nitrogen deposition (< 10kg N ha-1 yr-1), correlations between nitrogen deposition and soil microbial properties were analyzed in a cool temperate forest surrounded by normally fertilized pasture grasslands in northern Japan. Three experimental plots were established in forest edges adjacent to the grasslands and the other three plots were in forest interiors at least 700 m away from the grasslands. Nitrogen deposition in each plot was measured from May to November 2018. In August 2018, litter and surface soil samples were collected from all plots to measure net nitrogen mineralization and nitrification rates as indicators of microbial activity, and microbial biomass and various gene abundances (i.e., bacterial 16S rRNA, fungal ITS, and bacterial and archaeal amoA genes) as indicators of microbial abundance. Nitrogen deposition in forest edges was 1.4-fold greater than that in forest interiors, whereas maximum deposition was 3.7 kg N ha−1. Nitrogen deposition was significantly correlated with net nitrogen mineralization and nitrification rates and 16S rRNA and bacterial amoA gene abundances. Microbial community structures analyzed for bacterial 16S rRNA and fungal ITS gene amplicons were different between litter and soil samples, but were similar between the forest edge and interior. Nitrogen deposition was also correlated with the soil carbon-to-nitrogen ratio and nitrate and ammonium contents. Thus, it was suggested that some soil microbial activities and abundances in a nitrogen-limited forest likely responded to moderately elevated nitrogen deposition. These findings provide primary information on soil microbial response to moderately elevated nitrogen deposition.

Little is known of the earliest stages of soil biota development of volcanic ash, and how rapidly it can proceed. We investigated the potential for soil biota development during the first 3 years, using outdoor mesocosms of sterile, freshly fallen volcanic ash from the Sakurajima volcano, Japan. Mesocosms were positioned in a range of climates across Japan and compared over 3 years, against the developed soils of surrounding natural ecosystems. DNA was extracted from mesocosms and community composition assessed using 16S rRNA gene sequences. Metagenome sequences were obtained using shotgun metagenome sequencing. While at 12 months there was insufficient DNA for sequencing, by 24 months and 36 months, the ash-soil metagenomes already showed a similar diversity of functional genes to the developed soils, with a similar range of functions. In a surprising contrast with our hypotheses, we found that the developing ash-soil community already showed a similar gene function diversity, phylum diversity and overall relative abundances of kingdoms of life when compared to developed forest soils. The ash mesocosms also did not show any increased relative abundance of genes associated with autotrophy (rbc, coxL), nor increased relative abundance of genes that are associated with acquisition of nutrients from abiotic sources (nifH). Although gene identities and taxonomic affinities in the developing ash-soils are to some extent distinct from the natural vegetation soils, it is surprising that so many of the key components of a soil community develop already by the 24-month stage. In this system, however, rapid development may be facilitated by the relatively moderate pH of the Sakurajima ash, proximity of our mesocosms to propagule sources, and the rapid establishment of a productive bryophyte and lichen layer on the surface. Ash from other volcanoes richer in acids or more distant from propagule sources could show a different pattern and slower soil biota development.

The soil microbial community actively drives biogeochemical cycling even in the plant-dormant season of winter in temperate forests. The northern ecosystems are experiencing considerable winter climate change, which causes the snowpack to become thinner and the soil freeze-thaw cycles to occur more frequently in winter. These climatic and edaphic changes may affect the microbial community function. This study aimed to characterize the soil microbial community's response to winter climate change and its consequences in nitrogen (N) cycling. We conducted a large-scale snow removal experiment in a cool-temperate forest in northern Japan to simulate a winter climate change and assessed the abundance of total bacteria and fungi and ammonia oxidizers and the bacterial community composition throughout a year. This experiment indicated that snowpack decline prolonged the soil freeze-thaw period, which increased the carbon (C) availability to soil microbes in winter. The soil microbial community then sensitively responded by increasing the abundance and shifting the composition based on each taxon's absolute and relative abundances in the way that was phylogenetically patterned, which further activated microbial N cycling. However, the soil microbial community's high resilience driven by the C availability prevented the functional and compositional responses to winter climate change from persisting into the plant-growing season, which left no apparent cascading effect on the soil microbial community and N content during the plant-growing season. This study highlights the sensitive and phylogenetically patterned response of the soil microbial community to the change in soil nutrient availability and its high resilience under winter climate change in a forest.

We analyzed relationships between nitrogen deposition (deposition of nitrate and ammonium ions) and soil microbial properties, which were spatially varied in a cool temperate forest surrounded by normally fertilized pasture grasslands in northern Japan. The aim of the present study was to gain the primary information on soil microbial response to moderately elevated nitrogen deposition (< 10 kg N ha−1 y−1). We established three experimental plots in the forest edge adjacent to the grasslands and other three plots in the forest interior at least 700 m away from the grasslands. During May to November 2018, nitrogen deposition in each plot was measured. In August 2018, litter and soil (0−5 cm depth) samples were collected from all plots to measure net nitrogen mineralization and nitrification rates as indicators of microbial activity, and microbial biomass carbon and nitrogen and various gene abundances (i.e. bacterial 16S rRNA, fungal ITS, bacterial amoA, and archaeal amoA genes) as indicators of microbial abundance. Nitrogen deposition in the forest edge was 1.4-fold greater than that in the forest interior, even while the maximum deposition was 3.7 kg N ha−1. Nitrogen deposition was significantly correlated to the net nitrogen mineralization and nitrification rates and the 16S rRNA and bacterial amoA gene abundances. Microbial community structures in litter and soil samples were also analyzed using a high throughput DNA sequencer for the bacterial 16S rRNA and fungal ITS gene amplicons. Microbial community structures were different between litter and soil samples but were similar between the forest edge and interior. Significant correlations of nitrogen deposition to the soil carbon-to-nitrogen ratio, and the nitrate and ammonium contents were also observed. Thus, our results show that moderately elevated nitrogen deposition in nitrogen-limited forest edges likely stimulate microbial activities and abundances in soils.

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., Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.4853145.

The effects of elevated atmospheric nitrogen (N) deposition on N cycling in Japanese forest ecosystems are reviewed here to assess the sensitivity of nitrate (NO3−) leaching from forests to streams...

The soil microbial community plays essential roles in bioavailable nitrogen (N) cycling, and microbial dynamics during the plant dormant season could affect N cycling in the subsequent growing season. Despite frequent observations of seasonal shifts in microbial community composition in forests, the biogeochemical consequences for bioavailable N cycling have not been well characterized. Here we examine the relationship between microbial community dynamics and bioavailable N dynamics throughout a year in a cool-temperate deciduous forest, with a focus on the dormant season. Specifically, we analyzed temporal changes in abundances of N-cycling microbial populations and N concentrations and transformations in soils. We also assessed temporal changes in bacterial community composition by deep sequencing of 16S rRNA genes. Even though the bacterial community composition was stable throughout the year, we found a drastic increase in abundances of total bacterial and fungal populations in the mid-winter, followed by a subsequent decrease during the snowmelt period in the early spring. We also found a temporary increase in abundances of NH3-oxidizing bacterial population in the mid-winter and of denitrifying bacterial and fungal populations during the snowmelt period. Correspondingly, soil NH4+, NO3−, and dissolved organic N concentrations sequentially peaked in the winter and early spring. These results suggest that successive growth of litter degraders, ammonifiers, nitrifiers, and denitrifiers in the dormant season drives the subsequent bioavailable N transformations. High microbial N metabolic activities during the dormant season could also support plant growth during the growing season and increase the efficiency of annual N cycling in the forest via the seasonal partitioning of N between plants and microbial communities.

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 of ECM fungi or by the influence of neighboring conspecific and/or heterospecific hosts. In the present study, we aimed to evaluate the effects of host species on the ECM community compositions in a forest landscape (~ 10 km) where monodominant forest stands of six ECM host species belonging to three families were patchily distributed. The ECM communities were identified with DNA metabarcoding. A total of 180 ECM operational taxonomic units (OTUs) were detected. 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 detected from particular host tree species. Furthermore, the neighboring plots harbored 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 of ECM fungi is a primary determinant of ECM fungal compositions in the forest landscape.

The quantity of root exudate carbon produced by Quercus crispula Blume was strongly influenced by the amount of solar radiation 1 day before collection. We aimed to investigate seasonality in the quantity of root exudate produced, and the factors affecting exudate quantity, in mature Quercus crispula Blume trees throughout the growing season. We also aimed to understand the timespan of exudation, from production of photosynthate to release as exudate. We measured the amount of root exudate C produced by Q. crispula, as well as environmental factors including solar radiation and soil and air temperature throughout the growing season. The model best explaining the amount of exudate C, based on the lowest Akaike’s information criterion, was selected to determine the environmental factors that affect exudation. The quantity of exudates did not show clear seasonality, and instead varied widely among sampling dates. A regression model with daily solar radiation for 1 day before sample collection as the sole factor affecting the quantity of exudates was selected as the best model. Solar radiation, which fluctuated greatly among days, more strongly affected the quantity of exudates produced than factors that fluctuated seasonally, such as average temperature. Furthermore, most root exudates from Q. crispula are released within 1 day of being generated by photosynthesis, rather than over several days.

The 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., Special Feature: Radiocesium dynamics in forest ecosystems after the Fukushima Nuclear Power Plant accident: Experiences during the initial five years

Soil respiration is a dynamic and fundamental process across all terrestrial ecosystems. However, how physical and biogeochemical factors control seasonal variation and annual rates of soil respiration remains poorly understood. A topographical gradient in a semiarid forest was chosen as the study site to assess how both biogeochemical and physical factors control respiration rates. Parameters measured include soil respiration, litterfall, fine root biomass, soil physical and chemical properties, soil bacteria and archaea gene abundance, ectomycorrhizal fungi abundance and richness, and soil carbon isotope signatures. The results showed that increases in soil temperature and moisture exponentially and linearly promoted root activity, driving seasonal variation of total soil respiration. Seasonal variation of heterotrophic respiration was driven by soil moisture in a second-order polynomial pattern. Autotrophic respiration only contributed to 20% of the total soil respiration, and seasonal variation in the soil respiration rate was driven by heterotrophic respiration. Utilizing soil moisture as a scalar, the values of Q 10 and R 10 in different poisons on the slope indicated soil respiration was controlled by interaction of soil temperature and moisture, and a new transformation of the R 10 function inducing soil moisture was proposed. Along the topographical gradient, the long-term average soil temperature and moisture significantly varied from the top to the bottom of a slope. This variation in physical processes induced differences in plant productivity and biomass accumulation, leading to varying organic matter accumulation across the gradient. The topographical position also induced differences in the size of the soil organic matter aggregates, archaea and bacteria gene abundances, and ectomycorrhizal fungi abundance and richness. The aforementioned parameters are interrelated due to their association with the long-term average soil temperature and moisture, and the interrelation of these parameters ultimately affects annual rates of soil respiration.

Extreme soil freeze–thaw regimes caused by winter climate change can alter nitrogen (N) transformations through plant root mortality. In this study, we conducted a snow removal experiment to simulate extreme soil freeze–thaw to understand the effect of soil freeze–thaw on N transformations in soils under two northern temperate forests (oak and larch) in northern Japan. We also investigated the effect of root input on microbial biomass and transformations of dissolved organic carbon (DOC) and N by experimentally adding root litter to obtain mechanistic insight. Snow removal significantly reduced net nitrification and N mineralization, while it increased net ammonification in both soils. Root litter addition provided contrasting effects of vegetation type on net DOC change; it significantly decreased net DOC production in the oak soil, while it was increased in the larch soil. The contrasting responses of DOC change with vegetation were possibly related to specific microbial composition and physiology of the vegetation. Further, root addition eliminated the differences in net N mineralization and microbial biomass between the two vegetation types in the snow removal plots. Our results indicated that soil freeze–thaw could reduce the differences in vegetation type on soil N dynamics through root litter input.

Native tree species are frequently unable to effectively grow in non-native tree cultivation scenarios. In the Loess Plateau, China, it is difficult to find native oak (Quercus liaotungensis) seedlings in non-native black locust forests. Black locust is an arbuscular mycorrhizal (AM) tree, but oak is an ectomycorrhizal (ECM) tree. Plants highly depend on their symbiotic mycorrhizal fungi to take up water, nitrogen (N) and other nutrients. We hypothesized that black locust forests would not provide ECM inoculum to oak seedlings, limiting their water and nutrient uptake, which would be improved by ECM inoculum. Here, we (1) sowed seeds, with or without oak forest soils, (2) transplanted seedlings collected in oak forests, with or without oak forest soils, and (3) planted seedlings germinated in autoclaved or unautoclaved oak forest soils. We measured the survival and growth rate for all three experiments, along with chemical properties, and root ECM colonization. Oak seeds sowed with oak forest soils had higher mycorrhizal colonization, leaf N concentrations and survival rate, and lower root δ13C than the seeds sowed without oak forest soils. Planting with oak forest soils also increased the survival rate of the germinated seedlings, but not the transplanted seedlings. Overall, our study suggested that the use of oak forest soils in the black locust forest to improve the water and N uptake of oak seedlings by providing the ECM inoculum, resulting in a high survival rate. Our study also implies that the method of sowing seeds was effortless and effectively compared to transplanting wild/nursery seedlings.

The objective of this study was to investigate how plants maintain productivity under a limited supply of water and N along the topographical soil water and N gradients in semi-arid forests. We investigated forest structure and productivity, N cycling, and water and N use by plants at three different slope positions in a forested area near an arid boundary on a loess plateau in China. Net primary production (NPP) and aboveground N uptake decreased as soil water and/or N availability decreased on upper slopes; however, NPP and aboveground N uptake were only slightly lower than those of more humid forest ecosystems. Water use efficiency (WUE), N use efficiency (NUE), and fine root biomass increased as soil water and/or N supply decreased with altitude. High NUE was linked to higher N mean residence time, caused by higher N resorption efficiency rather than increasing N productivity. Our results suggest that NPP and N uptake can be maintained by increasing WUE and NUE and increasing fine root biomass in water and N co-limited semi-arid forest ecosystems near arid boundaries. Such changes in resource use and acquisition strategy can affect production and N cycling via plant-soil feedback systems.

We tested the potential of estimating in-field (in situ) nitrogen (N) transformation rates based on soil temperature data and N transformation parameters (Q10 and N transformation rates at standard temperature) obtained through laboratory incubations at three constant temperatures for 4 weeks. This test was conducted based on a comparison between in situ measurements and estimates using soils from 16 sites across 9 regions within the Japanese archipelago. The actual in situ N mineralization and nitrification rates measured using the buried-bag method at 0–50-cm-soil depth were 111 ± 34 and 106 ± 45 kg N ha−1 year−1, respectively, and estimates of both the rate and the amount were largely accurate. For rate alone, estimates were accurate in the 0–10-cm soil layer for annual and seasonal averages (except for spring–summer) whereas for amount alone, estimates were accurate to depths of 50 and 30 cm for N mineralization and nitrification, respectively. Thus, estimates of the rates and amounts were approximately equal to the actual in situ rate/amount, given the wide range of prediction intervals of the field measurement data. The differences between the estimates of N transformation rates derived from hourly measured and monthly average soil temperatures were negligible. Therefore, in situ soil N transformations, which are laborious to measure in the field, have the potential to be estimated from a combination of monthly average soil temperatures and N transformation parameters, which are relatively straightforward to obtain through laboratory incubation.

Mycorrhizal fungi have considerable effects on soil carbon (C) storage, as they control the decomposition of soil organic matter (SOM), by modifying the amount of soil nitrogen (N) available for free-living microbes. Through their access to organic N, ectomycorrhizal (ECM) fungi compete with free-living soil microbes; this competition is thought to slow down SOM decomposition. However, arbuscular mycorrhizal (AM) fungi cannot decompose SOM, and therefore must wait for N to first be processed by free-living microbes. It is unclear what form of N the ECM fungi and free-living microbes compete for, or which microbial groups compete for N with ECM fungi. To investigate this, we focused on the N transformation steps (i.e., the degradation of high-molecular-weight organic matter, mineralization, and nitrification) and the microbes driving each step. Simple comparisons between AM forests and ECM forests are not sufficient to assert that mycorrhizal types would determine the N transformation steps in soil, because soil physiochemistry, which strongly affects N transformation steps, differs between the forests. We used an aridity gradient with large differences in soil moisture, pH, and SOM quantity and quality, to distinguish the mycorrhizal and physicochemical effects on N transformation. Soil samples (0-10 cm depth) were collected from AM-symbiotic black locust forests under three aridity levels, and from ECM-symbiotic oak forests under two aridity levels. Soil physicochemical properties, extractable N dynamics and abundance, composition, and function of soil microbial communities were measured. In ECM forests, the ammonia-oxidizing prokaryotic abundance was low, whereas that of ECM fungi was high, resulting in lower nitrate N content than in AM forests. Since ECM forests did not have lower saprotrophic fungal abundance and prokaryotic decompositional activity than the AM forests, the hypothesis that ECM fungi could reduce SOM decay and ammonification by free-living microbes, might not hold in ECM forests. However, the limitation of ECM fungi on nitrate N production would result in a feedback that will accelerate plant dependence on these fungi, thereby raising soil C storage through an increase in the ECM biomass and plant C investment in soils.

We tested the ecosystem functions of microbial diversity with a focus on ammonification (involving diverse microbial taxa) and nitrification (involving only specialized microbial taxa) in forest nitrogen cycling. This study was conducted on a forest slope, in which the soil environment and plant growth gradually changed. We measured the gross and net rates of ammonification and nitrification, the abundance of predicted ammonifiers and nitrifiers, and their community compositions in the soils. The abundance of predicted ammonifiers did not change along the soil environmental gradient, leading to no significant change in the gross ammonification rate. On the other hand, the abundance of nitrifiers and the gross nitrification rate gradually changed. These accordingly determined the spatial distribution of net accumulation of ammonium and nitrate available to plants. The community composition of predicted ammonifiers gradually changed along the slope, implying that diverse ammonifiers were more likely to include taxa that were acclimated to the soil environment and performed ammonification at different slope locations than specialized nitrifiers. Our findings suggest that the abundance of ammonifiers and nitrifiers directly affects the corresponding nitrogen transformation rates, and that their diversity affects the stability of the rates against environmental changes. This study highlights the role of microbial diversity in biogeochemical processes under changing environments and plant growth.

Nitrogen (N) is the primary limiting nutrient for forest production. Therefore, understanding how environmental factors affect N transformation rates is essential for the provision of sustainable ecosystem services. Because these factors are interlinked, it is important to consider direct and indirect structural relationships to better understand the factors contributing to N transformations. In this study, we analyzed the structural cause–effect relationships surrounding N transformations by structural equation modeling using a database containing net and gross N transformation rates and related soil chemical properties from 38 sites across the Japanese archipelago. The average net N mineralization and nitrification rates in the Japanese forest soils were 0.62 ± 0.68 and 0.59 ± 0.65 mg N kg−1 d−1, respectively, and gross N mineralization and nitrification rates were 4.22 ± 3.59 and 0.98 ± 0.68 mg N kg−1 d−1, respectively. Compared with previous large scale studies, net and gross N transformation rates in Japanese forest soils were considerably diverse despite their relatively small land area and were representative of temperate forest ecosystems. Structural equation modeling analysis showed that net N transformations were directly affected by gross N transformations, which in turn were significantly and directly affected by soil organic matter contents. Soil organic matter was significantly affected by organic layer amount, tree species and soil group. The effect of soil group was the greatest among these factors, suggesting that soil organic matter contents in Japanese forest soils were mainly influenced by soil parent materials. This was especially evident for Andosols, which are derived from volcanic sediments and contain large amounts of soil organic matter leading to high N transformation rates in the Japanese forest soils. Among the factors related to organic layers and mineral soil layers, soil organic matter content and organic layer amount, which represent substrate availability, had significant effects on gross and net N transformation rates. However, by refining the scale of the dataset using soil groups/soil parent materials, the influence of substrate quality and soil chemical properties on N transformations was suggested. From the current dataset, it was indicated that soil parent materials were the most important factor controlling the pattern of N transformations in the soil of Japanese forest ecosystems. This conclusion should be repeatedly refined considering the spatial distribution of factors such as climatic conditions and forest types with additional site datasets obtained from future surveys.

Soil microbial communities, which play important roles in biogeochemical cycling, are affected by plants in many ways. To understand how plants affect soil microbes, we compared soils under halophytic shrubs and herbs, whose effects on soil salinity (one of the strongest determining factors for soil microbes in saline grasslands) were different. We measured soil physicochemical properties, as well as prokaryotic abundance, community structure, diversity, and the quantified and predicted abundances of functional genes for nitrogen (N) cycling. As we intended, we found the soil salinity to be the highest in barren areas (BA), intermediate under a tamarisk crown (UC), and the lowest in herbaceous patches (HP), whereas other plant-related properties, e.g. soil organic matter content, differed between vegetated areas (UC and HP) and BA. Prokaryotic community structure and diversity changed along the soil salinity gradient, but not as a function of plant presence or absence. However, N transformation rate and N availability were not affected by the salinity gradient alone. The dominant prokaryotic groups that contributed the most to changes in prokaryotic community structure and diversity were likely not those primarily responsible for N mineralization.

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.