1. 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.2. 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 2013-2015.3. 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.4. 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 | 1971 Journal of Applied Ecology KATAYAMA eT Al. Additional supporting information may be found online in the Supporting Information section at the end of the article. How to cite this article: Katayama N, Osada Y, Mashiko M, et al. Organic farming and associated management practices benefit multiple wildlife taxa: A large-scale field study in rice paddy landscapes.

Understanding the mechanisms of habitat selection is fundamental to the construction of proper conservation and management plans for many avian species. Habitat changes caused by human beings increase the landscape complexity and thus the complexity of data available for explaining species distribution. New techniques that assume no linearity and capable to extrapolate the response variables across landscapes are needed for dealing with difficult relationships between habitat variables and distribution data. We used a random forest algorithm to study breeding‐site selection of herons and egrets in a human‐influenced landscape by analyzing land use around their colonies. We analyzed the importance of each land‐use variable for different scales and its relationship to the probability of colony presence. We found that there exist two main spatial scales on which herons and egrets select their colony sites: medium scale (4 km) and large scale (10–15 km). Colonies were attracted to areas with large amounts of evergreen forests at the medium scale, whereas avoidance of high‐density urban areas was important at the large scale. Previous studies used attractive factors, mainly foraging areas, to explain bird‐colony distributions, but our study is the first to show the major importance of repellent factors at large scales. We believe that the newest non‐linear methods, such as random forests, are needed when modelling complex variable interactions when organisms are distributed in complex landscapes. These methods could help to improve the conservation plans of those species threatened by the advance of highly human‐influenced landscapes.

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Habitat selection in avian species is a hierarchical process driven by different factors acting at multiple scales. Habitat preferences and site fidelity are two main factors affecting how colonial birds choose their breeding locations. Although these two factors affect how colonial species choose their habitats, previous studies have only focused on one factor at a time to explain the distribution of species at regional scales. Here we used 28 yr of colony location data of herons and egrets around Ibaraki prefecture in Japan in order to analyze the relative importance of habitat preferences and colony site fidelity for selecting breeding locations. We used Landsat satellite images together with a ground survey-based map to create land-use maps for past years and determine the habitats surrounding the herons and egrets colonies. Combining the estimated colony site fidelity with the habitat data, we used a random forest algorithm to create habitat selection models, which allowed us to analyze the changes in the importance of those factors over the years. We found high levels of colony site fidelity for each year of study, with its relative importance as a predictor for explaining colony distribution increasing drastically in the most recent five years. The increase in collective site fidelity could have been caused by recent changes in the population size of grey herons Ardea cinerea, a key species for colony establishment. We observed a balance between habitat preferences and colony site fidelity: habitat preferences were a more powerful predictor of colony distribution until 2008, when colony site fidelity levels were lower. Considering changes in the relative importance of these factors can lead to a better understanding of the habitat selection process and help to analyze bird species' responses to environmental changes.

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To investigate the effect of organic farming on food intake and abundance of three egret and heron species (Great Egret Ardea alba, Intermediate Egret Egretta intermedia, Grey Heron A. cinerea), field surveys were conducted in conventional and organic rice fields in five cities in Ibaraki and Tochigi prefectures, Japan, from May to July 2013 and 2014. Direct observation of prey captures revealed that fish (mainly Oriental Weather Loach Misgurnus anguillicaudatus) and frogs Rana spp. are the primary food sources, although their compositions differed among bird species; proportion of fish biomass was higher in the order of Great Egret, Intermediate Egret and Grey Heron. In addition, for all three species, composition of fish mass in organic fields was higher than that in conventional ones. Generalized linear models showed that organic farming had a positive effect on food intake rates (g/min) although the effect seemed to be clear only for Great Egret. Organic farming also had a positive effect on the abundance of foraging Great Egrets and Grey Herons. Therefore, we concluded that the benefit of organic farming was consistently shown for Great Egret, but not for Intermediate Egret and Grey Heron, possibly due to differential effects of rice pesticides on prey species (e.g., fish and frogs) and the small area of organic rice fields in Japan (only 0.28% of rice fields are managed for organic farming in Japan amounting to 18-68% of census plots in this study).