National Institute for Agro-Environmental Sciences

Although research on human-mediated exchanges of species has substantially intensified during the last centuries, we know surprisingly little about temporal dynamics of alien species accumulations across regions and taxa. Using a novel database of 45,813 first records of 16,926 established alien species, we show that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970-2014). Inter-continental and inter-taxonomic variation can be largely attributed to the diaspora of European settlers in the nineteenth century and to the acceleration in trade in the twentieth century. For all taxonomic groups, the increase in numbers of alien species does not show any sign of saturation and most taxa even show increases in the rate of first records over time. This highlights that past efforts to mitigate invasions have not been effective enough to keep up with increasing globalization.

Development of insecticide resistance has been a serious concern worldwide, whose mechanisms have been attributed to evolutionary changes in pest insect genomes such as alteration of drug target sites, up-regulation of degrading enzymes, and enhancement of drug excretion. Here, we report a previously unknown mechanism of insecticide resistance: Infection with an insecticide-degrading bacterial symbiont immediately establishes insecticide resistance in pest insects. The bean bug Riptortus pedestris and allied stinkbugs harbor mutualistic gut symbiotic bacteria of the genus Burkholderia, which are acquired by nymphal insects from environmental soil every generation. In agricultural fields, fenitrothion-degrading Burkolderia strains are present at very low densities. We demonstrated that the fenitrothion-degrading Burkholderia strains establish a specific and beneficial symbiosis with the stinkbugs and confer a resistance of the host insects against fenitrothion. Experimental applications of fenitrothion to field soils drastically enriched fenitrothion-degrading bacteria from undetectable levels to >80% of total culturable bacterial counts in the field soils, and >90% of stinkbugs reared with the enriched soil established symbiosis with fenitrothion-degrading Burkholderia. In a Japanese island where fenitrothion has been constantly applied to sugarcane fields, we identified a stinkbug population wherein the insects live on sugarcane and ≈8% of them host fenitrothion-degrading Burkholderia. Our finding suggests the possibility that the symbiont-mediated insecticide resistance may develop even in the absence of pest insects, quickly establish within a single insect generation, and potentially move around horizontally between different pest insects and other organisms.

Abstract Agricultural fields are an important anthropogenic source of atmospheric nitrous oxide (N 2 O) and nitric oxide (NO). Although many field studies have tested the effectiveness of possible mitigation options on N 2 O and NO emissions, the effectiveness of each option varies across sites due to environmental factors and field management. To combine these results and evaluate the overall effectiveness of enhanced‐efficiency fertilizers [i.e., nitrification inhibitors (NIs), polymer‐coated fertilizers (PCFs), and urease inhibitors (UIs)] on N 2 O and NO emissions, we performed a meta‐analysis using field experiment data (113 datasets from 35 studies) published in peer‐reviewed journals through 2008. The results indicated that NIs significantly reduced N 2 O emissions (mean: −38%, 95% confidential interval: −44% to −31%) compared with those of conventional fertilizers. PCFs also significantly reduced N 2 O emissions (−35%, −58% to −14%), whereas UIs were not effective in reducing N 2 O. NIs and PCFs also significantly reduced NO (−46%, −65% to −35%; −40%, −76% to −10%, respectively). The effectiveness of NIs was relatively consistent across the various types of inhibitors and land uses. However, the effect of PCFs showed contrasting results across soil and land‐use type: they were significantly effective for imperfectly drained Gleysol grassland (−77%, −88% to −58%), but were ineffective for well‐drained Andosol upland fields. Because available data for PCFs were dominated by certain regions and soil types, additional data are needed to evaluate their effectiveness more reliably. NIs were effective in reducing N 2 O emission from both chemical and organic fertilizers. Moreover, the consistent effect of NIs indicates that they are potent mitigation options for N 2 O and NO emissions.

Abstract Microorganisms play important roles in the nitrogen cycles of various ecosystems. Research has revealed that a greater diversity of microorganisms is involved in the nitrogen cycle than previously understood. It is becoming clear that denitrifying fungi, nitrifying archaea, anammox bacteria, aerobic denitrifying bacteria and heterotrophic nitrifying microorganisms are key players in the nitrogen cycle. Studies have revealed a major contribution by fungi in the production of N2O and N2 in grasslands, semiarid regions and forest soils. Some fungi can grow under various O2 conditions by using three types of energy-yielding metabolism: O2 respiration, denitrification (nitrite respiration) and ammonia fermentation. The amoA-like gene copies of Crenarchaeota were shown to be more abundant in soils than in autotrophic ammonia-oxidizing bacteria, and the gene was expressed at higher levels in soil to which ammonia was added. There are some contradictory findings, however, regarding archaeal and bacterial nitrification. Anammox bacteria have been shown to be widely distributed and to play an important role in both artificial and natural environments. The contribution of heterotrophic microorganisms to nitrification has been recognized in soil, and the biochemical mechanisms of several bacteria are becoming clear. A wide variety of bacteria have been found to be able to carry out aerobic denitrification and to be distributed across diverse environments. Using molecular biological techniques for soil bacteria, Nitrosospira species of clusters 2, 3 and 4 have been shown to be the dominant group in soils. Genome analyses of autotrophic nitrifying bacteria are providing new insights into their ecology and functions in soils.

Physiological properties involved in divergent cadmium (Cd) accumulation among rice genotypes were characterized using the indica cultivar 'Habataki' (high Cd in grains) and the japonica cultivar 'Sasanishiki' (low Cd in grains). Time-dependence and concentration-dependence of symplastic Cd absorption in roots were revealed not to be responsible for the different Cd accumulation between the two cultivars because root Cd uptake was not greater in the Cd-accumulating cultivar 'Habataki' compared with 'Sasanishiki'. On the other hand, rapid and greater root-to-shoot Cd translocation was observed in 'Habataki', which could be mediated by higher abilities in xylem loading of Cd and transpiration rate as a driving force. To verify whether different abilities in xylem-mediated shoot-to-root translocation generally account for the genotypic variation in shoot Cd accumulation in rice, the world rice core collection, consisting of 69 accessions which covers the genetic diversity of almost 32,000 accessions of cultivated rice, was used. The results showed strong correlation between Cd levels in xylem sap and shoots and grains among the 69 rice accessions. Overall, the results presented in this study revealed that the root-to-shoot Cd translocation via the xylem is the major and common physiological process determining the Cd accumulation level in shoots and grains of rice plants.

Abstract Emission rates of CH4 from four Japanese paddy fields were measured throughout the cultivation period in 1988 by using the closed chamber method. Large seasonal variations of the CH4 flux were observed. The emission was closely related to the decrease of the redox potential (Eh) in paddy soils. Drainage and supplementary application of mineral fertilizer substantially reduced the CH4 emission. Emission rates of CH4 differed markedly with the soil types. The highest rate was observed in a paddy field consisting of Peat soil (44.8 g-CH4/m2 during a cultivation period), followed by Gley soil (8.0-27.0). The emission rates in the Andosols were significantly lower (0.6-12.6). Application of rice straw at a rate of 6-9 t/ha to the paddy fields increased the CH4 emission rates 1.8- to 3.5-fold. Application of compost slightly increased the CH4 emission. Annual emission rates of CH4 from individual plots were positively correlated with the contents of readily mineralizable carbon (RMC) in paddy soils collected before flooding, suggesting that RMC is one of the main factors affecting CH4 emission from flooded soils.

Arsenic (As) and cadmium (Cd) concentrations in rice grains are a human health concern. We conducted field experiments to investigate optimal conditions of Eh and pH in soil for simultaneously decreasing As and Cd accumulation in rice. Water managements in the experiments, which included continuous flooding and intermittent irrigation with different intervals after midseason drainage, exerted striking effects on the dissolved As and Cd concentrations in soil through changes in Eh, pH, and dissolved Fe(II) concentrations in the soil. Intermittent irrigation with three-day flooding and five-day drainage was found to be effective for simultaneously decreasing the accumulation of As and Cd in grain. The grain As and Cd concentrations were, respectively, linearly related to the average dissolved As and Cd concentrations during the 3 weeks after heading. We propose a new indicator for expressing the degree to which a decrease in the dissolved As or Cd concentration is compromised by the increase in the other. For minimizing the trade-off relationship between As and Cd in rice grains in the field investigated, water management strategies should target the realization of optimal soil Eh of -73 mV and pH of 6.2 during the 3 weeks after heading.

Cadmium (Cd) is a heavy metal toxic to humans and the accumulation of Cd in the rice grain is a major agricultural problem, particularly in Asia. The role of the iron transporter OsNRAMP1 in Cd uptake and transport in rice was investigated here. An OsNRAMP1:GFP fusion protein was localized to the plasma membrane in onion epidermal cells. The growth of yeast expressing OsNRAMP1 was impaired in the presence of Cd compared with yeast transformed with an empty vector. Moreover, the Cd content of OsNRAMP1-expressing yeast exceeded that of the vector control. The expression of OsNRAMP1 in the roots was higher in a high Cd-accumulating cultivar (Habataki) than a low Cd-accumulating cultivar (Sasanishiki) regardless of the presence of Cd, and the amino acid sequence of OsNRAMP1 showed 100% identity between Sasanishiki and Habataki. Over-expression of OsNRAMP1 in rice increased Cd accumulation in the leaves. These results suggest that OsNRAMP1 participates in cellular Cd uptake and Cd transport within plants, and the higher expression of OsNRAMP1 in the roots could lead to an increase in Cd accumulation in the shoots. Our results indicated that OsNRAMP1 is an important protein in high-level Cd accumulation in rice.

When output ( x ) of a mechanistic model is compared with measurement ( y ), it is common practice to calculate the correlation coefficient between x and y , and to regress y on x . There are, however, problems in this approach. The assumption of the regression, that y is linearly related to x , is not guaranteed and is unnecessary for the x – y comparison. The correlation and regression coefficients are not explicitly related to other commonly used statistics [e.g., root mean squared deviation (RMSD)]. We present an approach based on the mean squared deviation (MSD = RMSD 2 ) and show that it is better suited to the x – y comparison than regression. Mean squared deviation is the sum of three components: squared bias (SB), squared difference between standard deviations (SDSD), and lack of correlation weighted by the standard deviations (LCS). To show examples, the MSD‐based analysis was applied to simulation vs. measurement comparisons in literature, and the results were compared with those from regression analysis. The analysis of MSD clearly identified the simulation vs. measurement contrasts with larger deviation than others; the correlation–regression approach tended to focus on the contrasts with lower correlation and regression line far from the equality line. It was also shown that results of the MSD‐based analysis were easier to interpret than those of regression analysis. This is because the three MSD components are simply additive and all constituents of the MSD components are explicit. This approach will be useful to quantify the deviation of calculated values obtained with this model from measurements.

The behavior of As in paddy fields is of great interest considering high As contents of groundwater in several Asian countries where rice is the main staple. We determined the concentrations of Fe, Mn, and As in soil, soil water, and groundwater samples collected at different depths down to 2 m in an experimental paddy field in Japan during the cycle of flooded and non-flooded periods. In addition, we measured the oxidation states of Fe, Mn, and As in situ in soil samples using X-ray absorption near-edge structure (XANES) and conducted sequential extraction of the soil samples. The results show that Fe (hydr)oxide hosts As in soil. Arsenic in irrigation waters is incorporated in Fe (hydr)oxide in soil during the non-flooded period, and the As is quickly released from soil to water during the flooded period because of reductive dissolution of the Fe (hydr)oxide phase and reduction of As from As(V) to As(III). The enhancement of As dissolution by the reduction of As is supported by high As/Fe ratios of soil water during the flooded period and our laboratory experiments where As(III) concentrations and As(III)/As(V) ratios in submerged soil were monitored. Our work, primarily based on data from an actual paddy field, suggests that rice plants are enriched in As because the rice grows in flooded paddy fields when mobile As(III) is released to soil water.

Rice consumption is a major source of cadmium and arsenic for the population of Asia. We investigated the effects of water management in rice paddy on levels of cadmium and arsenic in Japanese rice grains. Flooding increased arsenic concentrations in rice grains, whereas aerobic treatment increased the concentration of cadmium. Flooding for 3 weeks before and after heading was most effective in reducing grain cadmium concentrations, but this treatment increased the arsenic concentration considerably, whereas aerobic treatment during the same period was effective in reducing arsenic concentrations but increased the cadmium concentration markedly. Flooding treatment after heading was found to be more effective than flooding treatment before heading in reducing rice grain cadmium without a concomitant increase in total arsenic levels, although it increased inorganic arsenic levels. Concentrations of dimethylarsinic acid (DMA) in grain were very low under aerobic conditions but increased under flooded conditions. DMA accounted for 3-52% of the total arsenic concentration in grain grown in soil with a lower arsenic concentration and 10-80% in soil with a higher arsenic concentration. A possible explanation for the accumulation of DMA in rice grains is that DMA translocates from shoots/roots to the grains more readily than does inorganic arsenic.

Metals like manganese (Mn) and iron (Fe) are essential for metabolism, while cadmium (Cd) is toxic for virtually all living organisms. Understanding the transport of these metals is important for breeding better crops. We have identified that OsNRAMP5 contributes to Mn, Fe and Cd transport in rice. OsNRAMP5 expression was restricted to roots epidermis, exodermis, and outer layers of the cortex as well as in tissues around the xylem. OsNRAMP5 localized to the plasma membrane, and complemented the growth of yeast strains defective in Mn, Fe, and Cd transport. OsNRAMP5 RNAi (OsNRAMP5i) plants accumulated less Mn in the roots, and less Mn and Fe in shoots, and xylem sap. The suppression of OsNRAMP5 promoted Cd translocation to shoots, highlighting the importance of this gene for Cd phytoremediation. These data reveal that OsNRAMP5 contributes to Mn, Cd, and Fe transport in rice and is important for plant growth and development.

Accumulation of cadmium (Cd) in rice (Oryza sativa L.) grains poses a potential health problem, especially in Asia. Most Cd in rice grains accumulates through phloem transport, but the molecular mechanism of this transport has not been revealed. In this study, we identified a rice Cd transporter, OsLCT1, involved in Cd transport to the grains. OsLCT1-GFP was localized at the plasma membrane in plant cells, and OsLCT1 showed Cd efflux activity in yeast. In rice plants, strong OsLCT1 expression was observed in leaf blades and nodes during the reproductive stage. In the uppermost node, OsLCT1 transcripts were detected around large vascular bundles and in diffuse vascular bundles. RNAi-mediated knockdown of OsLCT1 did not affect xylem-mediated Cd transport but reduced phloem-mediated Cd transport. The knockdown plants of OsLCT1 accumulated approximately half as much Cd in the grains as did the control plants. The content of other metals in rice grains and plant growth were not negatively affected by OsLCT1 suppression. These results suggest that OsLCT1 functions at the nodes in Cd transport into grains and that in a standard japonica cultivar, the regulation of OsLCT1 enables the generation of "low-Cd rice" without negative effects on agronomical traits. These findings identify a transporter gene for phloem Cd transport in plants.

Rice (Oryza sativa L.) grain is a major dietary source of cadmium (Cd), which is toxic to humans, but no practical technique exists to substantially reduce Cd contamination. Carbon ion-beam irradiation produced three rice mutants with <0.05 mg Cd⋅kg(-1) in the grain compared with a mean of 1.73 mg Cd⋅kg(-1) in the parent, Koshihikari. We identified the gene responsible for reduced Cd uptake and developed a strategy for marker-assisted selection of low-Cd cultivars. Sequence analysis revealed that these mutants have different mutations of the same gene (OsNRAMP5), which encodes a natural resistance-associated macrophage protein. Functional analysis revealed that the defective transporter protein encoded by the mutant osnramp5 greatly decreases Cd uptake by roots, resulting in decreased Cd in the straw and grain. In addition, we developed DNA markers to facilitate marker-assisted selection of cultivars carrying osnramp5. When grown in Cd-contaminated paddy fields, the mutants have nearly undetectable Cd in their grains and exhibit no agriculturally or economically adverse traits. Because mutants produced by ion-beam radiation are not transgenic plants, they are likely to be accepted by consumers and thus represent a practical choice for rice production worldwide.

The Intergovernmental Panel on Climate Change (IPCC) regularly publishes guidelines for national greenhouse gas inventories and methane emission (CH 4 ) from rice paddies has been an important component of these guidelines. While there have been many estimates of global CH 4 emissions from rice fields, none of them have been obtained using the IPCC guidelines. Therefore, we used the Tier 1 method described in the 2006 IPCC guidelines to estimate the global CH 4 emissions from rice fields. To accomplish this, we used country‐specific statistical data regarding rice harvest areas and expert estimates of relevant agricultural activities. The estimated global emission for 2000 was 25.6 Tg a −1 , which is at the lower end of earlier estimates and close to the total emission summarized by individual national communications. Monte Carlo simulation revealed a 95% uncertainty range of 14.8–41.7 Tg a −1 ; however, the estimation uncertainty was found to depend on the reliability of the information available regarding the amount of organic amendments and the area of rice fields that were under continuous flooding. We estimated that if all of the continuously flooded rice fields were drained at least once during the growing season, the CH 4 emissions would be reduced by 4.1 Tg a −1 . Furthermore, we estimated that applying rice straw off season wherever and whenever possible would result in a further reduction in emissions of 4.1 Tg a −1 globally. Finally, if both of these mitigation options were adopted, the global CH 4 emission from rice paddies could be reduced by 7.6 Tg a −1 . Although draining continuously flooded rice fields may lead to an increase in nitrous oxide (N 2 O) emission, the global warming potential resulting from this increase is negligible when compared to the reduction in global warming potential that would result from the CH 4 reduction associated with draining the fields.

Abstract. The Intergovernmental Technical Panel on Soils has completed the first State of the World's Soil Resources Report. Globally soil erosion was identified as the gravest threat, leading to deteriorating water quality in developed regions and to lowering of crop yields in many developing regions. We need to increase nitrogen and phosphorus fertilizer use in infertile tropical and semi-tropical soils – the regions where the most food insecurity among us are found – while reducing global use of these products overall. Stores of soil organic carbon are critical in the global carbon balance, and national governments must set specific targets to stabilize or ideally increase soil organic carbon stores. Finally the quality of soil information available for policy formulation must be improved – the regional assessments in the State of the World's Soil Resources Report frequently base their evaluations on studies from the 1990s based on observations made in the 1980s or earlier.

Predicting rice (Oryza sativa) productivity under future climates is important for global food security. Ecophysiological crop models in combination with climate model outputs are commonly used in yield prediction, but uncertainties associated with crop models remain largely unquantified. We evaluated 13 rice models against multi-year experimental yield data at four sites with diverse climatic conditions in Asia and examined whether different modeling approaches on major physiological processes attribute to the uncertainties of prediction to field measured yields and to the uncertainties of sensitivity to changes in temperature and CO2 concentration [CO2 ]. We also examined whether a use of an ensemble of crop models can reduce the uncertainties. Individual models did not consistently reproduce both experimental and regional yields well, and uncertainty was larger at the warmest and coolest sites. The variation in yield projections was larger among crop models than variation resulting from 16 global climate model-based scenarios. However, the mean of predictions of all crop models reproduced experimental data, with an uncertainty of less than 10% of measured yields. Using an ensemble of eight models calibrated only for phenology or five models calibrated in detail resulted in the uncertainty equivalent to that of the measured yield in well-controlled agronomic field experiments. Sensitivity analysis indicates the necessity to improve the accuracy in predicting both biomass and harvest index in response to increasing [CO2 ] and temperature.

Most studies of the influence of weather and climate on food production have examined the influence on crop yields. However, climate influences all components of crop production, includes cropping area (area planted or harvested) and cropping intensity (number of crops grown within a year). Although yield increases have predominantly contributed to increased crop production over the recent decades, increased cropping area as well as increases in cropping intensity, especially in the tropics, have played a substantial role. Therefore, we need to consider these important aspects of production to get a more complete understanding of the future impacts of climate change. This article reviews available evidence on how climate might influence these under-studied components of crop production. We also discuss how farmer decision making and technology might modulate the production response to climate. We conclude by discussing important knowledge gaps that need to be addressed in future research and potential ways for moving forward.

To clarify the mechanisms of methane transport from the rhi- zosphere into the atmosphere through rice plants (Oryza sativa

Abstract. The terrestrial carbon (C) cycle has received increasing interest over the past few decades, however, there is still a lack of understanding of the fate of newly assimilated C allocated within plants and to the soil, stored within ecosystems and lost to the atmosphere. Stable carbon isotope studies can give novel insights into these issues. In this review we provide an overview of an emerging picture of plant-soil-atmosphere C fluxes, as based on C isotope studies, and identify processes determining related C isotope signatures. The first part of the review focuses on isotopic fractionation processes within plants during and after photosynthesis. The second major part elaborates on plant-internal and plant-rhizosphere C allocation patterns at different time scales (diel, seasonal, interannual), including the speed of C transfer and time lags in the coupling of assimilation and respiration, as well as the magnitude and controls of plant-soil C allocation and respiratory fluxes. Plant responses to changing environmental conditions, the functional relationship between the physiological and phenological status of plants and C transfer, and interactions between C, water and nutrient dynamics are discussed. The role of the C counterflow from the rhizosphere to the aboveground parts of the plants, e.g. via CO2 dissolved in the xylem water or as xylem-transported sugars, is highlighted. The third part is centered around belowground C turnover, focusing especially on above- and belowground litter inputs, soil organic matter formation and turnover, production and loss of dissolved organic C, soil respiration and CO2 fixation by soil microbes. Furthermore, plant controls on microbial communities and activity via exudates and litter production as well as microbial community effects on C mineralization are reviewed. A further part of the paper is dedicated to physical interactions between soil CO2 and the soil matrix, such as CO2 diffusion and dissolution processes within the soil profile. Finally, we highlight state-of-the-art stable isotope methodologies and their latest developments. From the presented evidence we conclude that there exists a tight coupling of physical, chemical and biological processes involved in C cycling and C isotope fluxes in the plant-soil-atmosphere system. Generally, research using information from C isotopes allows an integrated view of the different processes involved. However, complex interactions among the range of processes complicate or currently impede the interpretation of isotopic signals in CO2 or organic compounds at the plant and ecosystem level. This review tries to identify present knowledge gaps in correctly interpreting carbon stable isotope signals in the plant-soil-atmosphere system and how future research approaches could contribute to closing these gaps.