The recent climate changes are largely affecting agricultural activity and production in Japan. Yield and quality losses are already reported for many cereals, fruits, and livestock. On the other hand, agriculture has contributed to accelerate the global warming through ongoing greenhouse gas emissions. The crop canopy temperature, which is determined through energy exchanges such as evapotranspiration, is one of the most important environmental factors that control crop growth and production. Climate near and within a crop canopy is generally unique compared with the climate well above the canopy. Greenhouse gases such as carbon dioxide, methane, and nitrous oxide are also exchanged through crop canopies. Quantification of those fluxes is necessary for planning the strategy to mitigate global warming. Therefore, many efforts have been made for understanding the phenomena and their underlying principles of crop micrometeorology and fluxes, and new findings have been reported in the Journal of Agricultural Meteorology. A turning point in this research field in recent decades is the release of commercial models of open-path gas analyzer and laser spectroscopic gas analyzer, which allowed researchers to carry out long-term and continuous observations of fluxes at both plot and ecosystem levels. Accumulation of new data and findings have been accelerated since then. Another progress in this research field includes the advancement of canopy micrometeorology and gas exchange models. With the recent rapid growth of machine learning techniques, new statistical model approaches, which do not assume the processes explicitly, are also emerging. As part of the activity of JapanFlux, this special collection, entitled “Gas fluxes and micrometeorology of agricultural ecosystems in Japan”, compiles original articles from a wide range of agricultural ecosystems and methodologies aiming at summarizing the advancement over the last 20 years in this research field. And it will provide a foundation towards robust and sustainable agriculture under future climate change in Japan.

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　Grasslands provide a globally essential ecosystem service by storing carbon (C). Management practices affect the net C balance in grasslands positively and negatively. In Japan, farmyard manure (FYM) application and grassland renovation are common and essential grassland management practices; however, the long-term effects of these practices on C balance are not known. We conducted a field experiment in a managed grassland for 11 years (2004-2015) to investigate the effects of FYM application and grassland renovation on net ecosystem C balance (NECB), estimated from eddy covariance measurements. Two experimental plots were used: One received only chemical fertilizer (CF plot), and the other received FYM and supplementary chemical fertilizer (CM plot). Grassland renovation with full inversion tillage was conducted twice during the study period. The C annually removed from the grassland through harvest always exceeded the annual net ecosystem production, resulting in a net C loss (NECB = -1.32 Mg C ha^-1 y^-1) in the CF plot. In contrast, the CM plot gained net C (NECB = 1.79 Mg C ha^-1 y^-1) due to FYM application. The difference in ecosystem respiration between the plots suggested that 45% of C in annually applied FYM remained in the soil. The FYM application-mediated C input necessary to avoid net C loss was 3.67 Mg C ha^-1 y^-1. Grassland renovation conducted twice showed a mixed but relatively minor effect. Grassland renovation had little impact on annual NECB when the degree of sward/soil disturbance was low. In contrast, renovation with a high degree of sward/soil disturbance led to negative NECB in the year of renovation even in the CM plot. Overall, FYM application contributed to a net C gain, and the effect of grassland renovation on annual NECB was likely limited to the years of renovation.

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　To investigate the reasons for irregular and severe decreases in net ecosystem production (NEP) in a sod-cultured apple orchard for better understanding orchard carbon dynamics, CO₂ flux observation was conducted from April to November (2013 and 2014) using two sets of eddy covariance equipment on different towers that were 15 m apart. Special attention was paid to the effect of grass mowing, which was conducted ten times during the observation period. In the latter half of, or just after the grass mowing period, gross primary production (GPP) on fine (sunny) days decreased to 50%-73% of the level before the grass mowing nine out of ten times, whereas ecosystem respiration (RE) did not decrease or slightly increased. As a result, NEP (=GPP－RE) on fine days drastically diminished after every grass mowing event. Moreover, three other moderate NEP decreases were observed, in addition to mowing events. Two of these events, which occurred 9-10 days before apple flowering, were possibly caused by a temporal increase in the respiration of apple tree. The remaining event, which occurred immediately after the drought period, was possibly caused by the recovery of microorganism and root respirations. Moreover, in comparing the daily GPP trend in 2013 and 2014, it was apparent that meteorological conditions, such as low temperature from April to May or severe soil water deficiency and low solar radiation in the vigorous growth stage, also negatively affected the population photosynthesis of the orchard.

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　Dew formation in the rice canopy was directly observed to assess its actual nature and was simulated using a multilayer microclimate model to understand the relationship between the dew amount and atmospheric conditions. Observations were made on four nights during August and October in a paddy field in Kumamoto, Japan under warm temperate climate. The vertical profile of the dew amount in the canopy was measured every 2 h at 0.2 m intervals. The maximum dew amount was recorded in the early morning on all observation days. The total dew amount for the whole canopy at 6:00 on August 19, 21, and 24, and on October 1 was 0.10, 0.07, 0.15, and 0.23 mm, respectively. The dew amount determined from the simulation showed a good agreement with the actual observations. The dew amount per unit leaf area was larger in the upper layers than in the lower layers of the canopy on all days. This vertical difference in the dew amount was explained by the difference in effective radiation (net longwave radiation). The vertical gradient of the dew amount was steep on August 19 and October 1, whereas it was gentle on August 21 and 24. This difference in gradient was explained by the difference in paddy water temperature. When the water temperature was higher than the air temperature, the vertical gradient of the effective radiation and dew amount became steeper. The total amount and source of dew also varied with water temperature. The dominant source of dew was dewfall (water flux from the atmosphere) at lower water temperature, whereas it was distillation (water flux from the ground surface) at higher water temperature. From these results, we conclude that water temperature plays an important role in dew formation in the rice canopy.

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　The emission and absorption of trace gases in the biosphere affect atmospheric chemistry and influence the potential indirect effects on the carbon and nitrogen cycles, air pollution, and climate. Ozone (O₃) and nitrogen oxides are important for the atmosphere and have adverse effects on plant growth and human health. In this review, the observed fluxes and deposition velocities of O₃, NO, and NO₂ in various forest ecosystems and the commonly used measurement methodologies were summarized and compared. Canopy O₃ fluxes have been reported in evergreen coniferous and deciduous broadleaf forests. O₃ deposition was observed in the forest ecosystems during daytime and nighttime, because O₃ is absorbed through stomata, deposited on the surface of the plant and the ground, and lost through forest chemical reactions. There were no significant differences in O₃ fluxes and deposition velocities in broadleaf and coniferous forests during the summer. The O₃ flux in the forest at night were 15±8% and 22±7% of those at daytime for broadleaf and coniferous forests, respectively.

　The observed NO flux was both negative (deposition) and positive (emission), whereas that of NO₂ was only positive during the daytime in summer- autumn. NO₂ emissions mechanisms have been discussed in terms of NO emissions from forest soil, NO₂ absorption and emission by plant leaves through stomata, and NO and NO₂ concentration gradients caused by photochemical reactions according to the differences in sunlight intensity inside and outside the forest. Nitrates attached to leaves are possible sources of NO₂.

　Simultaneous measurements of O₃, NO, and NO₂ fluxes are important in different vegetation types for investigating the differences between vegetation types and for developing a global forest inventory of NO and NO₂ fluxes, and O₃ deposition because of their closely related exchange mechanisms.

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　Atmospheric CO₂ concentration ([CO₂]) would double by the end of this century. Although the short-term elevated [CO₂] substantially accelerates photosynthesis in C₃ plants, the photosynthetic response under long-term elevated [CO₂] varies depending on the plant size and sink capacity and is still unclear. In addition, only a few studies have been performed on mature fruit tree species under field conditions. Therefore, this study aimed to examine whether, to what extent, and why long-term (throughout the growing seasons from 2019 to 2021) elevated [CO₂] down-regulates photosynthetic performance in mature field-grown apple trees. Measured leaves were selected in greenhouses with ambient (400 ppm) and elevated (600 ppm) [CO₂]. The temperature of the greenhouses was maintained at 3°C higher than outside, anticipating a warmer climate. The number of bearing fruits was adjusted to 8.3 and 16.7 m^-2 by 2020 and 2021, respectively. Photosynthetic light- or CO₂-response curves, along with photosynthesis parameters, were measured in June, August, and October in both years. Our results revealed that photosynthesis down-regulation occurred clearly only under low fruit load conditions. Namely, the photosynthetic rate of leaves measured at 600 ppm [CO₂] in the elevated greenhouse was 6% lower in the elevated greenhouse compare to the ambient greenhouse, when averaging all measurements. This down-regulation was not associated with stomatal limitation; however, it was a consequence of the reduction in Rubisco carboxylation activity and RuBP regeneration efficiency. In high fruit load conditions, the reduction in photosynthetic rate in the elevated greenhouse was 4%, without showing significant differences in the biochemical parameters of photosynthesis. As a whole, photosynthesis downregulation was not clearly detected in high fruit load condition. In spite of the down-regulation, the leaf photosynthetic rate measured under the prospected future climate condition increased by 25% and 33% under low and high fruit load respectively, compared with current condition.

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