Conventional agricultural practices, such as rice plantations, often contaminate the soil and water with xenobiotics. Here we evaluated the microbiota composition in experimental rice planting with a record of prolonged pesticide use, using 16S and 18S rRNA amplicon sequencing. We investigated four components of a complete agricultural system: affluent water (A), rice rhizosphere soil (R), sediment from a storage pond (S), and effluent (E) water (drained from the storage pond). Despite the short spatial distance between our sites, the beta diversity analysis of bacterial communities showed two well-defined clusters, separating the water and sediment/rhizosphere samples; rhizosphere and sediment were richer while the effluent was less diverse. Overall, the site with the highest evenness was the rhizosphere. Unlike the bacterial communities, Shannon diversity of microeukaryotes was significantly different between A and E. The effluent presented the lowest values for all ecological indexes tested and differed significantly from all sampled sites, except on evenness. When mapped the metabolic pathways, genes corresponding to the degradation of aromatic compounds, including genes related to pesticide degradation, were identified. The most abundant genes were related to the degradation of benzoate. Our results indicate that the effluent is a selective environment for fungi. Interestingly, the overall fungal diversity was higher in the affluent, the water that reached the system before pesticide application, and where the prokaryotic diversity was the lowest. The affluent and effluent seem to have the lowest environmental quality, given the presence of bacteria genera previously recorded in environments with high concentrations of pesticide residues. The microbiota, environmental characteristics, and pesticide residues should be further studied and try to elucidate the potential for pesticide degradation by natural consortia. Thus, extensive comparative studies are needed to clarify the microbial composition, diversity, and functioning of rice cultivation environments, and how pesticide use changes may reflect differences in microbial structure.

中文翻译：

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长期使用农药的水稻种植园中的原核和微真核生物群落。

常规的农业实践，例如水稻种植园，经常被异种生物污染土壤和水。在这里，我们使用16S和18S rRNA扩增子测序技术评估了水稻实验种植中的微生物群组成，并记录了长期使用农药的情况。我们调查了完整农业系统的四个组成部分：富裕水（A），水稻根际土壤（R），储水塘（S）的沉积物和出水（E）（储水塘的排水）。尽管我们站点之间的空间距离很短，但是细菌群落的β多样性分析显示出两个明确定义的簇，它们将水和沉积物/根际样品分隔开来。根际和沉积物较丰富，而流出物的多样性较差。总体而言，均匀度最高的位置是根际。与细菌群落不同，微型真核生物的香农多样性在A和E之间有显着差异。废水的所有生态指标值最低，除均匀度外，所有采样点均存在显着差异。在绘制代谢途径图时，鉴定出了与芳香族化合物降解相对应的基因，包括与农药降解有关的基因。最丰富的基因与苯甲酸酯的降解有关。我们的结果表明，废水是真菌的选择性环境。有趣的是，富裕度，使用农药之前到达系统的水，以及原核生物多样性最低的地方的总体真菌多样性更高。富裕者和流出者似乎具有最低的环境质量，考虑到以前在高农药残留浓度的环境中记录的细菌属的存在。微生物群，环境特征和农药残留应进一步研究，并试图阐明自然财团对农药降解的潜力。因此，需要进行广泛的比较研究来阐明水稻种植环境的微生物组成，多样性和功能，以及农药使用变化如何反映微生物结构的差异。