Shu-ichi Sugiyama

Comparison of molecular fingerprinting methods for analysis of soil microbial community structure

Denaturing gradient gel electrophoresis (DGGE), terminal-restriction fragment length polymorphism (T-RFLP) analysis, and automated ribosomal intergenic spacer analysis (ARISA) have been widely used as molecular fingerprinting methods for analysis of microbial communities. To find suitable methods, we compared the three fingerprinting methods by analyzing soil fungal communities in four differing land-use types: bare ground, crop fields, grasslands, and forests. We also examined optimal primer pairs for DGGE analysis by comparing single and mixed DNA samples of cultured fungal populations. Principal coordinate analysis (PCO), nonmetric multidimensional scaling method (NMDS), and analysis of similarities (ANOSIM), which are major multivariate statistical analyses for quantifying fingerprint patterns, were compared. All three fingerprinting methods yielded clear discrimination of soil fungal communities among the four land-use types, irrespective of statistical methods. The advantages and disadvantages of the three fingerprinting methods were discussed.

Differentiation in competitive ability and cold tolerance between diploid and tetraploid cultivars in Lolium perenne

In a diploid grass, perennial ryegrass (Lolium perenne L.), many autotetraploid cultivars have been released and widely used in many cool temperate countries. In this study, competitive ability and cold tolerance, which seem to be important factors in determining geographical distribution and persistency of this species, were compared between six diploid and five autotetraploid cultivars. The tetraploid cultivars had significantly higher competitive ability and lower cold tolerance than the diploid cultivars. Furthermore, there was no overlap in the two traits between them. These results suggest that chromosome doubling has a larger effect on competitive ability and cold tolerance than does the genetic difference between the populations within a single ploidy level.

Geographical distribution and phenotypic differentiation in populations of Dactylis glomerata L. in Japan

Although the perennial grass Dactylis glomerata L. has established dominant populations in Japan since its introduction in the 1870s, there have been marked reductions in its abundance in southern and northeastern regions. In order to examine the effects of climatic factors on distribution and differentiation of the naturalized populations of D. glomerata, abundance of 26 populations over a distance of 1500 km along a latitudinal gradient was recorded at each site, and life-history traits of each population were measured in a common garden. It was found that the reduction in abundance was related to the mean summer temperature in southern regions and to the lowest temperature before snow cover in northeastern regions. Recent climatic records in Japan show an increase in the mean summer temperature but no apparent changes in the lowest temperature before snow cover. These data suggest that, assuming the recent trend in climatic changes continues, the population abundance will decrease in southern regions and will change little in the northeastern regions. Germination speed, leaf width and reproductive allocations showed clinal variation over a geographical range, and the southern populations had more rapid germination, narrower leaves and lower reproductive allocation than did the northern populations. On the other hand, seed size and germination date showed margin-center differentiation. Marginal populations in both distributional borders had smaller seeds and lower germination rates than did the central populations.

Microbial community composition controls the effects of climate change on methane emission from rice paddies

Rice paddies are one of the most important sources of CH4 emission from the terrestrial ecosystem. A Free-air CO2 Enrichment (FACE) experiment, which included a soil warming treatment, was conducted in a rice paddy at Shizukuishi, Japan. In this study, the changes in CH4 emission from a rice paddy, caused by global climate change, were explored in relation to the structural changes that have occurred in the methanogenic archaeal communities found in the soil and roots. The composition of the archaeal community was examined by terminal restriction fragment length polymorphism (T-RFLP) using the 16S rRNA gene, while its abundance was measured by real-time PCR using the methyl coenzyme M reductase (mcrA) gene. The archaeal community in the roots showed considerable change, characterized by the dominance of hydrogenotrophic methanogens and a corresponding decrease in acetoclastic methanogens. Seasonal changes in CH4 flux were closely related to the changes in methanogen abundance in the roots. Elevated CO2 caused an increase in root mass, which increased the abundance of methanogens leading to a rise in CH4 emissions. However, soil warming stimulated CH4 emissions by increasing CH4 production per individual methanogen. These results demonstrated that climate warming stimulates CH4 emission in a rice paddy by altering the abundance and activity of methanogenic archaea in the roots.

How meristem plasticity in response to soil nutrients and light affects plant growth in four Festuca grass species

Investigation of responses of meristems to environmental conditions is important for understanding the mechanisms and consequences of plant phenotypic plasticity. Here, we examined how meristem plasticity to light and soil nutrients affected leaf growth and relative growth rate (RGR) in fast- and slow-growing Festuca grass species. Activity in shoot apical meristems was measured by leaf appearance rate, and that in leaf meristems by the duration and rate of cell production, which was further divided into single cell cycle time and the number of dividing cells. Light and soil nutrients affected activity in shoot apical meristems similarly. The high nutrient supply increased the number of dividing cells, which was responsible for enhancement of cell production rate; shaded conditions extended the duration of cell production. As a result, leaf length increased under high nutrient and shaded conditions. The RGR was correlated positively with the total meristem size of the shoot under a low nutrient supply, implying inhibition of RGR by cell production under nutrient-limited conditions. Fast-growing species were more plastic for cell production rate and specific leaf area (SLA) but less plastic for RGR than slow-growing species. This study demonstrates that meristem plasticity plays key roles in characterizing environmental responses of plant species.

Intraspecific phenotypic variation associated with nuclear DNA content in Lolium perenne L.

The variation in nuclear DNA content and its association with phenotypic traits were examined in 15 cultivated populations of perennial ryegrass (Lolium perenne L.), including herbage and turf populations. Nuclear DNA contents of 15 populations were measured by a flow cytometric method using DAPI (4′-6-diamidino-2-phenylindole) as a fluorochrome. DNA contents were also measured using PI (propidium iodide) for six populations that showed large differences in DAPI values to confirm the difference. There were significant differences in nuclear DNA contents among the populations for both dyes. Of the total variation in nuclear DNA content measured with DAPI, 29% was ascribed to the inter-population variation, 46% was ascribed to the intra-population variation, 24% was ascribed to the random error variation. Herbage populations tended to have larger DNA content than did turf populations. 2C DNA content was positively correlated with cell size, seed size and single leaf size, although significant correlations were mainly due to a small number of populations with large and small DNA contents. These results suggest that intraspecific variation in nuclear DNA content plays important roles in determining phenotypic differences between cultivated populations of L. perenne.

Impacts of root symbiotic associations on interspecific variation in sugar exudation rates and rhizosphere microbial communities: a comparison among four plant families

Background and aimsSymbiotic associations between rhizobia and arbuscular mycorrhyzal fungi (AMF) influence changes in carbon allocation to plant roots and alter the exudation of signal molecules in their host plants. In this study, we examined the impacts of bacterial and fungal symbiotic associations on the variation in sugar exudation rates from plant roots, and in rhizosphere microbial community structure, by comparing four plant families (e.g., Asteraceae, Brassicaceae, Fabaceae, and Poaceae) with different bacterial and fungal symbiotic associations.Methods and resultsWe determined sugar exudation rates of 23 plant species by regressions of exuded sugars against root mass through periodic samplings of plants grown in pots. Banding patterns from PCR-DGGE analyses of 28 plant species were evaluated by ordination scores relative to their rhizosphere bacterial and fungal community structures. Plant family was the most important source of variation in sugar exudation rates and microbial community structure between plant species. Brassicaceae, which lacks a root symbiotic association, had the lowest sugar exudation rate, the lowest rhizosphere microbial mass, and a distinct fungal community structure relative to the other plant families. Fabaceae had a different bacterial community structure relative to the other plant families.ConclusionsThese results demonstrate that root symbiotic associations have great impacts on the rate of sugar exudation and free-living microbial communities that inhabit the rhizosphere.

Dynamics of Microbial Community in Japanese Andisol of Apple Orchard Production Systems

Abstract In this study, two fields of temperate Andisols from high‐input and low‐input (zero‐input) management practices of an apple orchard were selected to assess microbial community dynamics based on environmental variables. Soils from an Ap horizon were sampled in five consecutive months from May to September and assessed for phospholipid fatty acids as a biomarker of soil microbial community, soil hardness, bulk density, porosity, pH, electrical conductivity (EC), organic carbon (C), available nitrogen (N) and phosphorus (P), and exchangeable cations as soil environmental variables. For all sample dates, total phospholipid fatty acids (PLFAs), total bacterial PLFAs, fungal PLFA, mycorrhizal PLFA, PLFA for actinomycetes, and earthworm were higher in low‐input management than high‐input management. Total PLFAs showed a high degree of seasonality, having August maxima and May minima. Significant effect on the relationships among soil environmental variables and microbiological attributes were observed. Soil management practices also showed a remarkable effect on the relationships among microbiological traits, indicating that some mechanism regulated soil microbial dynamics under two soil management practices. Comparatively higher correlations among the microbiological attributes were observed in low‐input management than high‐input management. Irrespective of soil management practices, bacterial and fungal lipid biomarkers were negatively correlated, suggesting that these subsets of fatty acids are contrasting components of the microbial biomass. Bulk density has negative influence on all soil microbial communities except fungi. On the other hand, linoleic acid and organic C were positively correlated, referring to the distribution of soil organic C implying an upper layer of soils. Microbial community composition and structure were greatly affected by sampling date and to a lesser extent by long‐term management practice. In this study, both ecosystems were characterized by a very diverse microbial community.

Increased Cell-Wall Mass and Resistance to Freezing and Snow Mold during Cold Acclimation of Winter Wheat under Field Conditions

Abstract Accumulation of soluble carbohydrates plays an important role in enhancement of resistance to freezing and snow mold of plants during cold acclimation. Nevertheless, few studies have examined whether changes in cell wall properties are involved in enhancement of resistance during cold acclimation. In this study, four winter wheat cultivars were sown in a field on six different dates during August–October, and their resistance to freezing and snow mold were compared in relation to soluble carbohydrate content and cell-wall mass in leaves. Resistance to freezing and snow mold was much higher in the plants sown on 23 September than in those sown on 9 September. The percentage of cell-wall mass in leaf to total dry mass (%CW) and water-soluble carbohydrate content also increased considerably during 9–23 September. Multiple regression analyses revealed that %CW contributed significantly to freezing resistance, whereas total water-soluble carbohydrate content contributed significantly to snow mold resistance. These results suggest that increased %CW enhances freezing resistance during cold acclimation.

Microbial community composition controls the effects of climate change on methane emission from rice paddies: CH4emission and methanogenic archaea

Rice paddies are one of the most important sources of CH4 emission from the terrestrial ecosystem. A Free-air CO2 Enrichment (FACE) experiment, which included a soil warming treatment, was conducted in a rice paddy at Shizukuishi, Japan. In this study, the changes in CH4 emission from a rice paddy, caused by global climate change, were explored in relation to the structural changes that have occurred in the methanogenic archaeal communities found in the soil and roots. The composition of the archaeal community was examined by terminal restriction fragment length polymorphism (T-RFLP) using the 16S rRNA gene, while its abundance was measured by real-time PCR using the methyl coenzyme M reductase (mcrA) gene. The archaeal community in the roots showed considerable change, characterized by the dominance of hydrogenotrophic methanogens and a corresponding decrease in acetoclastic methanogens. Seasonal changes in CH4 flux were closely related to the changes in methanogen abundance in the roots. Elevated CO2 caused an increase in root mass, which increased the abundance of methanogens leading to a rise in CH4 emissions. However, soil warming stimulated CH4 emissions by increasing CH4 production per individual methanogen. These results demonstrated that climate warming stimulates CH4 emission in a rice paddy by altering the abundance and activity of methanogenic archaea in the roots.