Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.

甘蔗（甘蔗spp.) 作为食品和可持续能源的相关来源在世界范围内生产。然而，不断提高作物产量的需求导致在植物培养中过度使用合成农用化学品投入物，例如无机肥料、除草剂和杀虫剂。众所周知，这些传统做法会对健康和环境造成有害影响。有机农业成为传统系统的可持续替代品；然而，农场管理对植物相关微生物群的影响仍不清楚。在这里，目的是确定耕作系统对甘蔗微生物群的影响。为了解决这个问题，我们从巴西两个农田的有机和传统农业中的土壤和植物中采样了微生物群。然后，我们评估了它们的成分、结构、通过扩增和测序细菌（16S rRNA 基因，V3-V4 区域）和真菌（内部转录间隔区 - ITS2）的系统发育标记物和功能特征。DADA2 管道的数据处理和分析揭示了 12,839 个细菌和 3,222 个真菌序列变体。此外，考虑到不同的耕作系统，检测到类似生态位之间的差异，来自传统系统的样本显示微生物的丰富度和多样性略高。农业系统之间的组成也不同，分别有 389 和 401 个不同丰富的细菌和真菌类群，包括能够促进植物生长的类群。微生物共生网络显示微生物群落的结构变化，有机网络更具凝聚力，因为它们具有更紧密的分类群和更少的生态位模块化。最后，功能预测揭示了丰富的代谢途径，包括传统农业系统中抗菌素耐药性的增加。综上所述，根据农业管理，我们的研究结果揭示了与田间甘蔗植物相关的微生物群落的功能、结构和组成适应性。有了这个，我们指出需要解开驱动这些适应的机制。根据农业管理，与田间甘蔗植物相关的微生物群落的组成适应性。有了这个，我们指出需要解开驱动这些适应的机制。根据农业管理，与田间甘蔗植物相关的微生物群落的组成适应性。有了这个，我们指出需要解开驱动这些适应的机制。