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Organic farming has potential for the conservation of global biodiversity and associated ecosystem services. Despite this, knowledge of the effects of organic farming systems on farmland biodiversity is limited in Asia, the worldwide leader in rice production. We conducted the first national‐scale study to investigate the effects of three different rice farming systems (conventional, low‐input and organic) and specific management practices (e.g. herbicide and insecticide applications, crop rotation and levee‐vegetation management) on species richness and abundance of multiple taxonomic groups (plants, invertebrates, Pelophylax and Hyla japonica frogs, cobitid loaches and birds) in Japan during 2013–2015. Organic fields supported the highest richness and abundance of several taxonomic groups (native/Red List plants, Tetragnatha spiders, Sympetrum dragonflies and Pelophylax frogs), followed by low‐input and conventional fields. We also found taxon‐specific responses to specific management practices. For instance, plant richness and Tetragnatha and Sympetrum abundance increased with reduced herbicide and/or insecticide applications. Sympetrum and cobitid loach abundance increased in the absence of crop rotation, whereas H. japonica abundance increased with crop rotation. Pelophylax abundance increased with an increased height of levee vegetation. At spatial scales larger than single fields, waterbird richness and abundance were positively correlated with the proportion of organic rice fields, presumably due to increased prey abundance. Meanwhile, landbird richness and abundance were positively associated with annual precipitation and annual mean temperature, suggesting that such climate increases food availability. Synthesis and applications. We highlight the positive effects of organic and low‐input farming for biodiversity relative to conventional farming in rice paddies. We also provide the scientific basis of the current agri‐environmental schemes in Japan, subsidising organic and low‐input farming for biodiversity. The taxon‐specific associations with management practices indicate that avoiding crop rotation, maintaining levee vegetation and organic farming at large spatial scales can also be wildlife friendly. These practices may thus be incorporated into agri‐environment schemes for effective biodiversity conservation. 要旨 有機農業は、生物多様性と、それに関連する生態系サービスの保全に重要な役割を果たすと考えられている。しかし、有機農業が農地の生物多様性にもたらす影響は十分にわかっておらず、特に水稲の主要な生産地であるアジアにおいて知見が非常に少ない。 私たちは、日本の水田では初となる全国規模の野外調査を2013–2015年に行い、慣行、減農薬および有機栽培の3つの農法の違い、および、除草剤・殺虫剤の施用、輪作の有無、畦畔の植生管理等の管理手法の違いが複数の生物種群（植物、無脊椎動物、トノサマガエル属、ニホンアマガエル、ドジョウ科および鳥類）に与える影響を評価した。 在来／レッドリスト植物種数、アシナガグモ属、アカネ属およびトノサマガエル属の個体数は有機栽培の水田で最も多く、次いで減農薬栽培田、慣行栽培田となった。また、管理手法の違いに対する応答は分類群毎に異なることが明らかとなった。具体的には、植物種数、およびアシナガグモ属とアカネ属の個体数は除草剤もしくは殺虫剤施用の少ない水田に多かった。アカネ属とドジョウ科の個体数は輪作を実施しない水田に多かったが、一方でニホンアマガエルの個体数は輪作を実施する水田に多かった。トノサマガエル属の個体数は畦畔の植生高に比例して増加した。 水田団地のスケールでみると、水鳥類の種数・個体数は有機栽培田の面積率と正の相関を示しており、これは食物量の増加によるものと考えられた。一方、陸鳥類の種数・個体数は年降水量および年平均気温と正に相関しており、こうした気候が食物量を増加させる結果と示唆された。 総括および応用　慣行栽培と比較して、有機栽培および減農薬栽培が農地の生物多様性に正の影響をもたらすことが明らかになった。これにより、現在、日本で実施される農業環境政策（有機・減農薬栽培等に対する交付金制度）の効果について科学的な評価基盤を提供することができた。さらに、輪作を回避すること、畦畔植生を適当な高さに維持すること、および有機栽培を行う水田を空間的にまとめることも、特定の分類群の保全に有効であることがわかり、こうした取組の推進が望まれる。 We highlight the positive effects of organic and low‐input farming for biodiversity relative to conventional farming in rice paddies. We also provide the scientific basis of the current agri‐environmental schemes in Japan, subsidising organic and low‐input farming for biodiversity. The taxon‐specific associations with management practices indicate that avoiding crop rotation, maintaining levee vegetation and organic farming at large spatial scales can also be wildlife friendly. These practices may thus be incorporated into agri‐environment schemes for effective biodiversity conservation.

ABSTRACT Microbial communities associated with plants are greatly influenced by water availability in soil. In flooded crops, such as rice, the impact of water management on microbial dynamics is not fully understood. Here, we present a comprehensive study of the rice microbiota investigated in an experimental field located in one of the most productive areas of northern Italy. The microbiota associated with paddy soil and root was investigated using 454 pyrosequencing of 16S, ITS and 18S rRNA gene amplicons under two different water managements, upland (non-flooded, aerobic) and lowland (traditional flooding, anaerobic), at three plant development stages. Results highlighted a major role of the soil water status in shaping microbial communities, while phenological stage had low impacts. Compositional shifts in prokaryotic and fungal communities upon water management consisted in significant abundance changes of Firmicutes, Methanobacteria, Chloroflexi, Sordariomycetes, Dothideomycetes and Glomeromycotina. A vicariance in plant beneficial microbes and between saprotrophs and pathotrophs was observed between lowland and upland. Moreover, through network analysis, we demonstrated different co-abundance dynamics between lowland and upland conditions with a major impact on microbial hubs (strongly interconnected microbes) that fully shifted to aerobic microbes in the absence of flooding. Rice water management deeply shapes root/soil microbiota assembly, structure and microbial hubs at three growth stages with consistent shifts in pathogens, saprotrophs and beneficial microbes.

Spiders are important bio-control agents of rice insect pests such as plant- and leafhoppers. To investigate temporal changes in spider prey and variations in prey due to landscape structure around rice fields, carbon and nitrogen stable isotopes of rice field arthropods were analysed over three consecutive sampling dates during the rice cropping season. Initial isotope composition of gnats and midges emerging from submersed rice fields indicates a larval algae diet, while later values suggest a switch to rice-derived carbon. Initial δ¹³C values of plant-and leafhoppers were higher in fields of rice-heterogeneous landscapes, indicating migration from source populations feeding on C4 grasses into rice fields; later, their δ¹³C values approached those of rice. Isotope values of web-building and cursorial spiders in the earliest samples indicate aquatic gnat and midge prey. The later shift toward terrestrial herbivore prey was more pronounced for small than for larger species and in rice paddies near permanent vegetation, indicating use of prey from the surrounding landscape. The results suggest that rice field spiders are supported by three different carbon pools: (1) aquatic carbon originating from algae and (2) legacy carbon from previous growing cycles, both incorporated via between-season predation on gnats and midges, and (3) carbon from the current rice season incorporated via herbivore prey. In conclusion, fostering aquatic midge and gnat larvae, e.g. via mulching, and integrating rice fields into rice-heterogeneous landscapes likely strengthens biological control of pest species in rice paddies by supporting high populations of spiders between cropping seasons.

Indonesia, through the Regulation of the Minister of ATR/BPN Number 12 of 2020, designates Protected Rice Fields (LSD) to secure productive rice lands. This policy supports the food estate program and national food security. In Semarang Regency, the establishment of LSD has been reinforced by the Semarang Regency Spatial Plan (RTRW). This study aims to examine whether the determination of LSD in Semarang Regency has supported rice production as part of the food estate program. The methods used in this study include rice production mapping, map overlay, and calculation of rice availability needs. The analysis results show that in 2023, Semarang Regency experienced a rice production surplus. However, by 2043, the regency is projected to be unable to maintain its rice self-sufficiency. Three sub-districts will shift from surplus to deficit between 2023 and 2043, namely Tuntang, Banyubiru, and Bawen Districts. The findings of this study can serve as a basis for developing agricultural and rice field management strategies.

In Japan, abandonment of rice fields has rapidly increased, resulting in biodiversity loss. Fallow field biotopes are attractive measures for compensating wetland species habitats in paddy environments. However, effective management practices of fallow field biotopes for biodiversity conservation are largely unknown, especially for lentic aquatic insects (Odonata, Hemiptera, and Coleoptera). We conducted field experiments in abandoned rice terraces in western Hyogo Prefecture, central Japan. We plowed and flooded nine abandoned paddy fields and divided them into three types: paddy fields, biotopes, and mixed fields. We also surveyed irrigation ponds. To assess the function of the four habitat types, we examined how species richness, abundance, and community composition of aquatic insects differed among habitat types. Aquatic insect assemblages in biotopes differed from paddy fields and ponds and resembled that in a mixed field. The effects of environmental factors on the abundance and species richness of aquatic insects differ according to their order or life stages. The abundance of aquatic insects increased with surface area. The abundance of Odonata nymphs increased with water depth, whereas that of Hemiptera nymphs and Coleoptera larvae decreased. The abundance of Odonata nymphs and Hemiptera adults increased with increasing vegetation cover, whereas the species richness of aquatic insects decreased. Thus, it is important to prevent high vegetation cover by plowing and create a water depth gradient for creating habitats for multiple taxa. We suggest that creating or maintaining mosaic habitats, including paddy fields, biotopes, and ponds could enhance aquatic insect diversity in abandoned rice terraces.

Weedy rice (Oryza sativa f. spontanea or O. sativa complex) has become a severe threat to Malaysian rice (Oryza sativa L.) granaries after the direct-seeding method of rice cultivation was introduced in the late 1980s. Since then, researchers have studied the biology and ecology of weedy rice and espoused the evolutionary theory of the origin of Malaysian weedy rice. This review paper aimed to synthesize the body of knowledge about weedy rice and the evolution of herbicide-resistant (HR) weedy rice in Malaysia. The imidazolinone (IMI) herbicide component of the Clearfield® Production System (CPS) rice package is among the most effective tools for weedy rice control. However, dependence solely on this technology and farmers’ ignorance about the appropriate use of IMI herbicides with the CPS rice package have resulted in the evolution of IMI-resistant (IMI-R) weedy rice. This has reduced the efficacy of IMI herbicides on weedy rice, ultimately nullifying the benefit of CPS rice in affected fields. At present, it is assumed that IMI-R weedy rice populations are widely distributed across the rice granaries in Malaysia. Therefore, it is important that integrated management measures be adopted comprehensively by Malaysian rice growers to curb the spread of IMI-R weedy rice problem in Malaysia, especially in fields planted with CPS rice. This review focuses on the biology of Malaysian weedy rice, the history of the establishment of weedy rice in Malaysian rice fields, the impact of HR rice technology on the evolution of IMI-R weedy rice in Malaysia, the distribution of resistant weedy rice populations across Peninsular Malaysia rice granaries, the weedy rice resistance mechanisms, and weedy rice management. The synthesis of all this information is helpful to researchers, policy makers, the private agricultural industry, advisers to farmers, and proactive farmers themselves with the goal of working toward sustainable rice production.

Purple nutsedge (Cyperus rotundus L.) is one of the world's resilient upland weeds, primarily spreading through its tubers. Its emergence in rice (Oryza sativa L.) fields has been increasing, likely due to changing paddy-farming practices. This study aimed to investigate how C. rotundus, an upland weed, can withstand soil flooding and become a problematic weed in rice fields. The first comparative analysis focused on the survival and recovery characteristics of growing and mature tubers of C. rotundus exposed to soil-flooding conditions. Notably, mature tubers exhibited significant survival and recovery abilities in these environments. Based on this observation, further investigation was carried out to explore the morphological structure, nonstructural carbohydrates, and respiratory mechanisms of mature tubers in response to prolonged soil flooding. Over time, the mature tubers did not form aerenchyma but instead gradually accumulated lignified sclerenchymal fibers, with lignin content also increasing. After 90 d, the lignified sclerenchymal fibers and lignin contents were 4.0 and 1.1 times higher than those in the no soil-flooding treatment. Concurrently, soluble sugar content decreased while starch content increased, providing energy storage, and alcohol dehydrogenase activity rose to support anaerobic respiration via alcohol fermentation. These results indicated that mature tubers survived in soil-flooding conditions by adopting a low-oxygen quiescence strategy, which involves morphological adaptations through the development of lignified sclerenchymal fibers, increased starch reserves for energy storage, and enhanced anaerobic respiration. This mechanism likely underpins the flooding tolerance of mature C. rotundus tubers, allowing them to endure unfavorable conditions and subsequently germinate and grow once flooding subsides. This study provides a preliminary explanation of the mechanism by which mature tubers of C. rotundus from the upland areas confer flooding tolerance, shedding light on the reasons behind this weed's increasing presence in rice fields.

This study analyzed long-term fluctuations of groundwater levels in six shallow observation wells in the Nasunogahara alluvial fan, Japan’s second largest source of agricultural irrigation groundwater, and presented a simple method for predicting groundwater levels in April prior to the annual planting of paddy rice. The 22-year time-series of groundwater levels (1998–2019) clearly showed seasonal periodicity, with higher levels in summer than in winter. In particular, groundwater levels were lowest in April when groundwater demand was greatest. Groundwater levels in two wells at the beginning of the April irrigation period showed long-term declining trends that can be attributed more to changes in land use than to changes in precipitation or air temperature. A simple linear regression of mean groundwater level in April to antecedent precipitation provided reasonable predictions of April groundwater levels, which were significantly influenced by precipitation in the preceding 3–5 months. Further modeling after subtraction of long-term seasonal trends (detrending) improved these estimates. The performance of the linear regression model for prediction of April groundwater levels is comparable to that of the statistical benchmark model. Using long-term monthly or seasonal weather forecasts, the modeling presented here can be applied to inform appropriate changes of water use practices, such as decreasing groundwater extraction by implementing rotational water supply, changing rice-cropping seasons, or targeting deeper aquifers. The identification of the critical period of antecedent precipitation that affected April groundwater levels in the Nasunogahara alluvial fan is also important for understanding appropriate precipitation periods to be targeted in modeling for future drought risk assessments under climate change.

Cloud cover hinders the effective use of vegetation indices from optical satellite-acquired imagery in cloudy agricultural production areas, such as Guangdong, a subtropical province in southern China which supports two-season rice production. The number of cloud-free observations for the earth-orbiting optical satellite sensors must be determined to verify how much their observations are affected by clouds. This study determines the quantified wide-ranging impact of clouds on optical satellite observations by mapping the annual total observations (ATOs), annual cloud-free observations (ACFOs), monthly cloud-free observations (MCFOs) maps, and acquisition probability (AP) of ACFOs for the Sentinel 2 (2017–2019) and Landsat 8 (2014–2019) for all the paddy rice fields in Guangdong province (APRFG), China. The ATOs of Landsat 8 showed relatively stable observations compared to the Sentinel 2, and the per-field ACFOs of Sentinel 2 and Landsat 8 were unevenly distributed. The MCFOs varied on a monthly basis, but in general, the MCFOs were greater between August and December than between January and July. Additionally, the AP of usable ACFOs with 52.1% (Landsat 8) and 47.7% (Sentinel 2) indicated that these two satellite sensors provided markedly restricted observation capability for rice in the study area. Our findings are particularly important and useful in the tropics and subtropics, and the analysis has described cloud cover frequency and pervasiveness throughout different portions of the rice growing season, providing insight into how rice monitoring activities by using Sentinel 2 and Landsat 8 imagery in Guangdong would be impacted by cloud cover.

Fisheries of the Mekong Basin are crucial to regional food security. They rely on seasonal monsoon rains that inundate rice fields and reconnect water bodies. Species assemblages vary over time and space, but infrastructure developments and climate change are negatively impacting the timing and magnitude of the flood pulse as well as fish migration routes and populations. In lowland rice field landscapes of Cambodia, community fish refuges (CFRs) are used to maintain fish abundance and biodiversity, with varying success. There is little knowledge of the drivers of this variation to guide management interventions. We used beta diversity to explore the effectiveness of 40 CFRs in maintaining species abundance and diversity during the dry seasons from 2012 to 2015. Results show CFR connectivity to the floodplain is important and suggest the type of inlet/outlet influences fish retention. CFRs connected to a large area of rice fields during the wet season had lower losses in species abundance through the dry season. However, large CFRs, or those part of a larger body of water, had higher losses in species abundance. Key design features of CFRs must be coupled with strong management capacity to guide the conservation and fisheries strategy in the Mekong Basin.